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Štrancar U, D’Ercole C, Cikatricisová L, Nakić M, De March M, de Marco A. A Practical Guide for the Quality Evaluation of Fluobodies/Chromobodies. Biomolecules 2024; 14:587. [PMID: 38785994 PMCID: PMC11117837 DOI: 10.3390/biom14050587] [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: 04/09/2024] [Revised: 05/07/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND Fluorescent proteins (FPs) are pivotal reagents for flow cytometry analysis or fluorescent microscopy. A new generation of immunoreagents (fluobodies/chromobodies) has been developed by fusing recombinant nanobodies to FPs. METHODS We analyzed the quality of such biomolecules by a combination of gel filtration and SDS-PAGE to identify artefacts due to aggregation or material degradation. RESULTS In the SDS-PAGE run, unexpected bands corresponding to separate fluobodies were evidenced and characterized as either degradation products or artefacts that systematically resulted in the presence of specific FPs and some experimental conditions. The elimination of N-terminal methionine from FPs did not impair the appearance of FP fragments, whereas the stability and migration characteristics of some FP constructs were strongly affected by heating in loading buffer, which is a step samples undergo before electrophoretic separation. CONCLUSIONS In this work, we provide explanations for some odd results observed during the quality control of fluobodies and summarize practical suggestions for the choice of the most convenient FPs to fuse to antibody fragments.
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Affiliation(s)
| | | | | | | | | | - Ario de Marco
- Laboratory of Environmental and Life Sciences, University of Nova Gorica, Vipavska cesta 13, Rožna Dolina, 5000 Nova Gorica, Slovenia; (U.Š.); (C.D.); (L.C.); (M.N.); (M.D.M.)
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Cong Y, Devoogdt N, Lambin P, Dubois LJ, Yaromina A. Promising Diagnostic and Therapeutic Approaches Based on VHHs for Cancer Management. Cancers (Basel) 2024; 16:371. [PMID: 38254860 PMCID: PMC10814765 DOI: 10.3390/cancers16020371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/04/2024] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
The discovery of the distinctive structure of heavy chain-only antibodies in species belonging to the Camelidae family has elicited significant interest in their variable antigen binding domain (VHH) and gained attention for various applications, such as cancer diagnosis and treatment. This article presents an overview of the characteristics, advantages, and disadvantages of VHHs as compared to conventional antibodies, and their usage in diverse applications. The singular properties of VHHs are explained, and several strategies that can augment their utility are outlined. The preclinical studies illustrating the diagnostic and therapeutic efficacy of distinct VHHs in diverse formats against solid cancers are summarized, and an overview of the clinical trials assessing VHH-based agents in oncology is provided. These investigations demonstrate the enormous potential of VHHs for medical research and healthcare.
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Affiliation(s)
- Ying Cong
- The M-Lab, Department of Precision Medicine, GROW—School for Oncology and Reproduction, Maastricht University, 6211 LK Maastricht, The Netherlands; (Y.C.); (P.L.)
| | - Nick Devoogdt
- Molecular Imaging and Therapy Research Group (MITH), Vrije Universiteit Brussel, 1090 Brussels, Belgium;
| | - Philippe Lambin
- The M-Lab, Department of Precision Medicine, GROW—School for Oncology and Reproduction, Maastricht University, 6211 LK Maastricht, The Netherlands; (Y.C.); (P.L.)
- Department of Radiology and Nuclear Medicine, Maastricht University Medical Centre+, 6229 HX Maastricht, The Netherlands
| | - Ludwig J. Dubois
- The M-Lab, Department of Precision Medicine, GROW—School for Oncology and Reproduction, Maastricht University, 6211 LK Maastricht, The Netherlands; (Y.C.); (P.L.)
| | - Ala Yaromina
- The M-Lab, Department of Precision Medicine, GROW—School for Oncology and Reproduction, Maastricht University, 6211 LK Maastricht, The Netherlands; (Y.C.); (P.L.)
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D’Ercole C, De March M, Veggiani G, Oloketuyi S, Svigelj R, de Marco A. Biological Applications of Synthetic Binders Isolated from a Conceptually New Adhiron Library. Biomolecules 2023; 13:1533. [PMID: 37892215 PMCID: PMC10605594 DOI: 10.3390/biom13101533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/24/2023] [Accepted: 09/25/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND Adhirons are small (10 kDa) synthetic ligands that might represent an alternative to antibody fragments and to alternative scaffolds such as DARPins or affibodies. METHODS We prepared a conceptionally new adhiron phage display library that allows the presence of cysteines in the hypervariable loops and successfully panned it against antigens possessing different characteristics. RESULTS We recovered binders specific for membrane epitopes of plant cells by panning the library directly against pea protoplasts and against soluble C-Reactive Protein and SpyCatcher, a small protein domain for which we failed to isolate binders using pre-immune nanobody libraries. The best binders had a binding constant in the low nM range, were produced easily in bacteria (average yields of 15 mg/L of culture) in combination with different tags, were stable, and had minimal aggregation propensity, independent of the presence or absence of cysteine residues in their loops. DISCUSSION The isolated adhirons were significantly stronger than those isolated previously from other libraries and as good as nanobodies recovered from a naïve library of comparable theoretical diversity. Moreover, they proved to be suitable reagents for ELISA, flow cytometry, the western blot, and also as capture elements in electrochemical biosensors.
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Affiliation(s)
- Claudia D’Ercole
- Lab of Environmental and Life Sciences, University of Nova Gorica, Vipavska cesta 13, Rožna Dolina, 5000 Nova Gorica, Slovenia; (C.D.); (M.D.M.); (S.O.)
| | - Matteo De March
- Lab of Environmental and Life Sciences, University of Nova Gorica, Vipavska cesta 13, Rožna Dolina, 5000 Nova Gorica, Slovenia; (C.D.); (M.D.M.); (S.O.)
| | - Gianluca Veggiani
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA;
| | - Sandra Oloketuyi
- Lab of Environmental and Life Sciences, University of Nova Gorica, Vipavska cesta 13, Rožna Dolina, 5000 Nova Gorica, Slovenia; (C.D.); (M.D.M.); (S.O.)
| | - Rossella Svigelj
- Department of Agrifood, Environmental and Animal Science, University of Udine, via Cotonificio 108, 33100 Udine, Italy;
| | - Ario de Marco
- Lab of Environmental and Life Sciences, University of Nova Gorica, Vipavska cesta 13, Rožna Dolina, 5000 Nova Gorica, Slovenia; (C.D.); (M.D.M.); (S.O.)
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D’Ercole C, de Marco A. Native Agarose Gels and Contact Blotting as Means to Optimize the Protocols for the Formation of Antigen-Ligand Complexes. Bioengineering (Basel) 2023; 10:1111. [PMID: 37892841 PMCID: PMC10604731 DOI: 10.3390/bioengineering10101111] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/08/2023] [Accepted: 09/12/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND Protein complexes provide valuable biological information, but can be difficult to handle. Therefore, technical advancements designed to improve their manipulation are always useful. METHODS We investigated the opportunity to exploit native agarose gels and the contact blot method for the transfer of native proteins to membranes as means for optimizing the conditions for obtaining stable complexes. As a simple model of protein-protein interactions, an antigen-ligand complex was used in which both proteins were fused to reporters. RESULTS At each step, it was possible to visualize both the antigen, fused to a fluorescent protein, and the ligand, fused to a monomeric ascorbate peroxidase (APEX) and, as such, a way to tune the protocol. The conditions for the complex formation were adapted by modifying the buffer conditions, the concentration of the proteins and of the cross-linkers. CONCLUSIONS The procedure is rapid, inexpensive, and the several detection opportunities allow for both the monitoring of complex stability and the preservation of the functionality of its components, which is critical for understanding their biomedical implications and supporting drug discovery. The overall protocol represents a handy alternative to gel filtration, uses very standard and ubiquitous equipment, and can be implemented rapidly and without specific training.
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Affiliation(s)
| | - Ario de Marco
- Laboratory of Environmental and Life Sciences, University of Nova Gorica, Vipavska Cesta 13, P.O. Box 301, SI-5000 Nova Gorica, Slovenia;
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Zelenovic N, Filipovic L, Popovic M. Recent Developments in Bioprocessing of Recombinant Antibody Fragments. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:1191-1204. [PMID: 37770388 DOI: 10.1134/s0006297923090018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 07/12/2023] [Accepted: 08/18/2023] [Indexed: 09/30/2023]
Abstract
Biotechnological and biomedical applications of antibodies have been on a steady rise since the 1980s. As unique and highly specific bioreagents, monoclonal antibodies (mAbs) have been widely exploited and approved as therapeutic agents. However, the use of mAbs has limitations for therapeutic applications. Antibody fragments (AbFs) with preserved antigen-binding sites have a significant potential to overcome the disadvantages of conventional mAbs, such as heterogeneous tissue distribution after systemic administration, especially in solid tumors, and Fc-mediated bystander activation of the immune system. AbFs possess better biodistribution coefficient due to lower molecular weight. They preserve the functional features of mAbs, such as antigen specificity and binding, while at the same time, ensuring much better tissue penetration. An additional benefit of AbFs is the possibility of their production in bacterial and yeast cells due to the small size, more robust structure, and lack of posttranslational modifications. In this review, we described current approaches to the AbF production with recent examples of AbF synthesis in bacterial and yeast expression systems and methods for the production optimization.
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Affiliation(s)
- Nevena Zelenovic
- Center for Chemistry, Institute for Chemistry, Technology, and Metallurgy, National Institute of Republic of Serbia, University of Belgrade, Belgrade, 11000, Serbia
| | - Lidija Filipovic
- Innovative Centre, Faculty of Chemistry, University of Belgrade, Belgrade, 11000, Serbia
| | - Milica Popovic
- Department of Biochemistry, Faculty of Chemistry, University of Belgrade, Belgrade, 11000, Serbia.
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de Marco A. Mechanisms underlying the efficacy and safety of IgG, antibody fragments, and design immune biologics. J Allergy Clin Immunol 2023:S0091-6749(23)00082-9. [PMID: 36669622 DOI: 10.1016/j.jaci.2023.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/10/2023] [Accepted: 01/12/2023] [Indexed: 01/19/2023]
Affiliation(s)
- Ario de Marco
- Laboratory for Environmental and Life Sciences, University of Nova Gorica, Nova Gorica, Slovenia.
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7
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Alsadig A, Abbasgholi-NA B, Vondracek H, Medagli B, Fortuna S, Posocco P, Parisse P, Cabrera H, Casalis L. DNA-Directed Protein Anchoring on Oligo/Alkanethiol-Coated Gold Nanoparticles: A Versatile Platform for Biosensing Applications. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 13:nano13010078. [PMID: 36615988 PMCID: PMC9823620 DOI: 10.3390/nano13010078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 12/12/2022] [Accepted: 12/22/2022] [Indexed: 05/27/2023]
Abstract
Herein, we report on a smart biosensing platform that exploits gold nanoparticles (AuNPs) functionalized through ssDNA self-assembled monolayers (SAM) and the DNA-directed immobilization (DDI) of DNA-protein conjugates; a novel, high-sensitivity optical characterization technique based on a miniaturized gel electrophoresis chip integrated with online thermal lens spectrometry (MGEC-TLS), for the high-sensitivity detection of antigen binding events. Specifically, we characterized the physicochemical properties of 20 nm AuNPs covered with mixed SAMs of thiolated single-stranded DNA and bio-repellent molecules, referred to as top-terminated oligo-ethylene glycol (TOEG6), demonstrating high colloidal stability, optimal binder surface density, and proper hybridization capacity. Further, to explore the design in the frame of cancer-associated antigen detection, complementary ssDNA fragments conjugated with a nanobody, called C8, were loaded on the particles and employed to detect the presence of the HER2-ECD antigen in liquid. At variance with conventional surface plasmon resonance detection, MGEC-TLS characterization confirmed the capability of the assay to titrate the HER2-ECD antigen down to concentrations of 440 ng/mL. The high versatility of the directed protein-DNA conjugates immobilization through DNA hybridization on plasmonic scaffolds and coupled with the high sensitivity of the MGEC-TLS detection qualifies the proposed assay as a potential, easily operated biosensing strategy for the fast and label-free detection of disease-relevant antigens.
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Affiliation(s)
- Ahmed Alsadig
- Department of Physics, University of Trieste, 34127 Trieste, Italy
- NanoInnovation Lab, Elettra-Sincrotrone Trieste S.C.p.A., 34149 Trieste, Italy
| | - Behnaz Abbasgholi-NA
- NanoInnovation Lab, Elettra-Sincrotrone Trieste S.C.p.A., 34149 Trieste, Italy
- Optics Lab, STI Unit, The Abdus Salam International Centre for Theoretical Physics, 34151 Trieste, Italy
| | - Hendrik Vondracek
- NanoInnovation Lab, Elettra-Sincrotrone Trieste S.C.p.A., 34149 Trieste, Italy
| | - Barbara Medagli
- Department of Medicine, Surgery and Health Sciences at the University of Trieste, 34149 Trieste, Italy
| | - Sara Fortuna
- Italian Institute of Technology (IIT), Via Melen–83, B Block, 16152 Genova, Italy
| | - Paola Posocco
- Department of Engineering and Architecture, University of Trieste, 34127 Trieste, Italy
| | - Pietro Parisse
- NanoInnovation Lab, Elettra-Sincrotrone Trieste S.C.p.A., 34149 Trieste, Italy
- Institute of Materials (IOM-CNR), Area Science Park, 34149 Trieste, Italy
| | - Humberto Cabrera
- Optics Lab, STI Unit, The Abdus Salam International Centre for Theoretical Physics, 34151 Trieste, Italy
| | - Loredana Casalis
- NanoInnovation Lab, Elettra-Sincrotrone Trieste S.C.p.A., 34149 Trieste, Italy
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Mei Y, Chen Y, Sivaccumar JP, An Z, Xia N, Luo W. Research progress and applications of nanobody in human infectious diseases. Front Pharmacol 2022; 13:963978. [PMID: 36034845 PMCID: PMC9411660 DOI: 10.3389/fphar.2022.963978] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 07/04/2022] [Indexed: 01/18/2023] Open
Abstract
Infectious diseases, caused by pathogenic microorganisms, are capable of affecting crises. In addition to persistent infectious diseases such as malaria and dengue fever, the vicious outbreaks of infectious diseases such as Neocon, Ebola and SARS-CoV-2 in recent years have prompted the search for more efficient and convenient means for better diagnosis and treatment. Antibodies have attracted a lot of attention due to their good structural characteristics and applications. Nanobodies are the smallest functional single-domain antibodies known to be able to bind stably to antigens, with the advantages of high stability, high hydrophilicity, and easy expression and modification. They can directly target antigen epitopes or be constructed as multivalent nanobodies or nanobody fusion proteins to exert therapeutic effects. This paper focuses on the construction methods and potential functions of nanobodies, outlines the progress of their research, and highlights their various applications in human infectious diseases.
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Affiliation(s)
- Yaxian Mei
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Science, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, China
| | - Yuanzhi Chen
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Science, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, China
| | - Jwala P. Sivaccumar
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, TX, United States
| | - Zhiqiang An
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, TX, United States
| | - Ningshao Xia
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Science, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, China
| | - Wenxin Luo
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Science, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, China
- *Correspondence: Wenxin Luo,
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9
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Filipović L, Spasojević M, Prodanović R, Korać A, Matijaševic S, Brajušković G, de Marco A, Popović M. Affinity-based isolation of extracellular vesicles by means of single-domain antibodies bound to macroporous methacrylate-based copolymer. N Biotechnol 2022; 69:36-48. [PMID: 35301156 DOI: 10.1016/j.nbt.2022.03.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 02/11/2022] [Accepted: 03/06/2022] [Indexed: 01/30/2023]
Abstract
Correct elucidation of physiological and pathological processes mediated by extracellular vesicles (EV) is highly dependent on the reliability of the method used for their purification. Currently available chemical/physical protocols for sample fractionation are time-consuming, often scarcely reproducible and their yields are low. Immuno-capture based approaches could represent an effective purification alternative to obtain homogeneous EV samples. An easy-to-operate chromatography system was set-up for the purification of intact EVs based on a single domain (VHH) antibodies-copolymer matrix suitable for biological samples as different as conditioned cell culture medium and human plasma. Methacrylate-based copolymer is a porous solid support, the chemical versatility of which enables its efficient functionalization with VHHs. The combined analyses of morphological features and biomarker (CD9, CD63 and CD81) presence indicated that the recovered EVs were exosomes. The lipoprotein markers APO-A1 and APO-B were both negative in tested samples. This is the first report demonstrating the successful application of spherical porous methacrylate-based copolymer coupled with VHHs for the exosome isolation from biological fluids. This inexpensive immunoaffinity method has the potential to be applied for the isolation of EVs belonging to different morphological and physiological classes.
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Affiliation(s)
| | | | | | | | | | | | - Ario de Marco
- Laboratory for Environmental and Life Sciences, University of Nova Gorica, Nova Gorica, Slovenia
| | - Milica Popović
- University of Belgrade-Faculty of Chemistry, Belgrade, Serbia.
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Barakat S, Berksöz M, Zahedimaram P, Piepoli S, Erman B. Nanobodies as molecular imaging probes. Free Radic Biol Med 2022; 182:260-275. [PMID: 35240292 DOI: 10.1016/j.freeradbiomed.2022.02.031] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/08/2022] [Accepted: 02/14/2022] [Indexed: 12/12/2022]
Abstract
Camelidae derived single-domain antibodies (sdAbs), commonly known as nanobodies (Nbs), are the smallest antibody fragments with full antigen-binding capacity. Owing to their desirable properties such as small size, high specificity, strong affinity, excellent stability, and modularity, nanobodies are on their way to overtake conventional antibodies in terms of popularity. To date, a broad range of nanobodies have been generated against different molecular targets with applications spanning basic research, diagnostics, and therapeutics. In the field of molecular imaging, nanobody-based probes have emerged as a powerful tool. Radioactive or fluorescently labeled nanobodies are now used to detect and track many targets in different biological systems using imaging techniques. In this review, we provide an overview of the use of nanobodies as molecular probes. Additionally, we discuss current techniques for the generation, conjugation, and intracellular delivery of nanobodies.
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Affiliation(s)
- Sarah Barakat
- Faculty of Engineering and Natural Sciences, Sabanci University, 34956, Tuzla, Istanbul, Turkey.
| | - Melike Berksöz
- Faculty of Engineering and Natural Sciences, Sabanci University, 34956, Tuzla, Istanbul, Turkey.
| | - Pegah Zahedimaram
- Faculty of Engineering and Natural Sciences, Sabanci University, 34956, Tuzla, Istanbul, Turkey.
| | - Sofia Piepoli
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Bogazici University, 34342, Bebek, Istanbul, Turkey.
| | - Batu Erman
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Bogazici University, 34342, Bebek, Istanbul, Turkey.
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Cytoplasmic Production of Nanobodies and Nanobody-Based Reagents by Co-Expression of Sulfhydryl Oxidase and DsbC Isomerase. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2446:145-157. [PMID: 35157272 DOI: 10.1007/978-1-0716-2075-5_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Nanobodies are stable molecules that can often fold correctly even in the absence of the disulfide bond(s) that stabilize their three-dimensional conformation. Nevertheless, some nanobodies require the formation of disulfide bonds, and therefore they are commonly expressed from vectors that promote their secretion into the oxidizing environment of the Escherichia coli periplasm. As an alternative, the bacterial cytoplasm can be an effective compartment for producing correctly folded nanobodies when sulfhydryl oxidase and disulfide-bond isomerase activities are co-expressed from a recombinant vector. The larger volume and wider chaperone/foldase availability of the cytoplasm enable the achievement of high yields of both nanobodies and nanobody-tag fusions, independently of their redox requirements. Among other examples, the protocol described here was used to successfully produce nanobody fusions with fluorescent proteins that do not fold correctly in the periplasm, nanobodies with Fc domains, and nanobodies containing free cysteine tags.
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12
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Wang J, Kang G, Yuan H, Cao X, Huang H, de Marco A. Research Progress and Applications of Multivalent, Multispecific and Modified Nanobodies for Disease Treatment. Front Immunol 2022; 12:838082. [PMID: 35116045 PMCID: PMC8804282 DOI: 10.3389/fimmu.2021.838082] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 12/30/2021] [Indexed: 12/22/2022] Open
Abstract
Recombinant antibodies such as nanobodies are progressively demonstrating to be a valid alternative to conventional monoclonal antibodies also for clinical applications. Furthermore, they do not solely represent a substitute for monoclonal antibodies but their unique features allow expanding the applications of biotherapeutics and changes the pattern of disease treatment. Nanobodies possess the double advantage of being small and simple to engineer. This combination has promoted extremely diversified approaches to design nanobody-based constructs suitable for particular applications. Both the format geometry possibilities and the functionalization strategies have been widely explored to provide macromolecules with better efficacy with respect to single nanobodies or their combination. Nanobody multimers and nanobody-derived reagents were developed to image and contrast several cancer diseases and have shown their effectiveness in animal models. Their capacity to block more independent signaling pathways simultaneously is considered a critical advantage to avoid tumor resistance, whereas the mass of these multimeric compounds still remains significantly smaller than that of an IgG, enabling deeper penetration in solid tumors. When applied to CAR-T cell therapy, nanobodies can effectively improve the specificity by targeting multiple epitopes and consequently reduce the side effects. This represents a great potential in treating malignant lymphomas, acute myeloid leukemia, acute lymphoblastic leukemia, multiple myeloma and solid tumors. Apart from cancer treatment, multispecific drugs and imaging reagents built with nanobody blocks have demonstrated their value also for detecting and tackling neurodegenerative, autoimmune, metabolic, and infectious diseases and as antidotes for toxins. In particular, multi-paratopic nanobody-based constructs have been developed recently as drugs for passive immunization against SARS-CoV-2 with the goal of impairing variant survival due to resistance to antibodies targeting single epitopes. Given the enormous research activity in the field, it can be expected that more and more multimeric nanobody molecules will undergo late clinical trials in the next future. Systematic Review Registration.
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Affiliation(s)
- Jiewen Wang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
- Institute of Shaoxing, Tianjin University, Zhejiang, China
| | - Guangbo Kang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
- Institute of Shaoxing, Tianjin University, Zhejiang, China
| | - Haibin Yuan
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
- Institute of Shaoxing, Tianjin University, Zhejiang, China
| | - Xiaocang Cao
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China
| | - He Huang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
- Institute of Shaoxing, Tianjin University, Zhejiang, China
| | - Ario de Marco
- Laboratory for Environmental and Life Sciences, University of Nova Gorica, Nova Gorica, Slovenia
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13
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D'Agostino S, Mazzega E, Praček K, Piccinin S, Pivetta F, Armellin M, Fortuna S, Maestro R, de Marco A. Interference of p53:Twist1 interaction through competing nanobodies. Int J Biol Macromol 2022; 194:24-31. [PMID: 34863830 DOI: 10.1016/j.ijbiomac.2021.11.160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 10/25/2021] [Accepted: 11/22/2021] [Indexed: 12/16/2022]
Abstract
Twist1 promote the bypass of p53 response by interacting with p53 and facilitating its MDM2-mediated degradation. We reasoned that reagents able to interfere with the p53:Twist1 complex might alleviate Twist1 inhibitory effect over p53, thus representing potential therapeutic tools in p53 wild type tumors. From a pre-immune library of llama nanobodies (VHH), we isolated binders targeting the p53 C-terminal region (p53-CTD) involved in the interaction with Twist1 by using recombinant Twist1 as an epitope-specific competitor during elution. Positive hits were validated by proving their capacity to immunoprecipitate p53 and to inhibit Twist1:p53 binding in vitro. Molecular modeling confirmed a preferential docking of positive hits with p53-CTD. D11 VHH activity was validated in human cell models, succeeded in immunoprecipitating endogenous p53 and, similarly to Twist1 knock-down, interfered with p53 turnover, p53 phosphorylation at Serine 392 and affected cell viability. Despite the limited functional effect determined by D11 expression in target cells, our results provide the proof of principle that nanobodies ectopically expressed within a cell, have the capacity to target the assembly of the pro-tumorigenic Twist1:p53 complex. These results disclose novel tools for dissecting p53 biology and lay down the grounds for the development of innovative targeted therapeutic approaches.
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Affiliation(s)
- Serena D'Agostino
- Unit of Oncogenetics and Functional Oncogenomics, Centro di Riferimento Oncologico di Aviano (CRO Aviano) IRCCS, National Cancer Institute, Via Gallini 2, 33081 Aviano, PN, Italy
| | - Elisa Mazzega
- Lab of Environmental and Life Sciences, University of Nova Gorica, Vipavska cesta 13, 5000 Rožna Dolina, Nova Gorica, Slovenia
| | - Katja Praček
- Lab of Environmental and Life Sciences, University of Nova Gorica, Vipavska cesta 13, 5000 Rožna Dolina, Nova Gorica, Slovenia; Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri 1, 34127 Trieste, Italy
| | - Sara Piccinin
- Unit of Oncogenetics and Functional Oncogenomics, Centro di Riferimento Oncologico di Aviano (CRO Aviano) IRCCS, National Cancer Institute, Via Gallini 2, 33081 Aviano, PN, Italy
| | - Flavia Pivetta
- Unit of Oncogenetics and Functional Oncogenomics, Centro di Riferimento Oncologico di Aviano (CRO Aviano) IRCCS, National Cancer Institute, Via Gallini 2, 33081 Aviano, PN, Italy
| | - Michela Armellin
- Unit of Oncogenetics and Functional Oncogenomics, Centro di Riferimento Oncologico di Aviano (CRO Aviano) IRCCS, National Cancer Institute, Via Gallini 2, 33081 Aviano, PN, Italy
| | - Sara Fortuna
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri 1, 34127 Trieste, Italy
| | - Roberta Maestro
- Unit of Oncogenetics and Functional Oncogenomics, Centro di Riferimento Oncologico di Aviano (CRO Aviano) IRCCS, National Cancer Institute, Via Gallini 2, 33081 Aviano, PN, Italy
| | - Ario de Marco
- Lab of Environmental and Life Sciences, University of Nova Gorica, Vipavska cesta 13, 5000 Rožna Dolina, Nova Gorica, Slovenia.
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Li D, Peng Q, Huang C, Zang B, Ren J, Ji F, Muyldermans S, Jia L. Cytoplasmic Expression of Nanobodies with Formylglycine Generating Enzyme Tag and Conversion to a Bio-Orthogonal Aldehyde Group. Methods Mol Biol 2022; 2446:357-371. [PMID: 35157283 DOI: 10.1007/978-1-0716-2075-5_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Nanobodies (Nbs) can be successfully retrieved following phage, bacterial, yeast, or ribosome display of immune, synthetic, or naïve libraries. However, after panning, multiple individual Nb clones need to be screened and assessed for solubility, antigen specificity, affinity, and potential biological function. Therefore, it is highly desirable to have a convenient expression strategy to obtain sufficient protein for in-depth characterization of the Nbs. The presence of a purification and detection tag, as well as a chemically reactive group to enable simple generation of Nb derivatives, would be of great help in this regard. Here, we provide a general protocol for high yield cytoplasmic expression and purification of formylglycine generating enzyme (FGE)-tagged Nbs. The cysteine within the FGE tag is easily converted to formylglycine by passing the FGE-tag containing Nb over a continuous-flow bio-catalysis system. The aldehyde group within the formylglycine side chain at the C-terminal end of the Nb is suitably located for subsequent bio-orthogonal reactions to fluorescent dyes, biotin, polyethylene glycol, or chromatography resins. We also include methods for production of high yield recombinant FGE, as well as conditions for its immobilization on Sepharose to produce the continuous-flow bio-catalysis system.
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Affiliation(s)
- Da Li
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, China
| | - Qiang Peng
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, China
| | - Chungdong Huang
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, China
| | - Berlin Zang
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, China
| | - Jun Ren
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, China
| | - Fangling Ji
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, China
| | - Serge Muyldermans
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, China.
- Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium.
| | - Lingyun Jia
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, China
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Oloketuyi S, Bernedo R, Christmann A, Borkowska J, Cazzaniga G, Schuchmann HW, Niedziółka-Jönsson J, Szot-Karpińska K, Kolmar H, de Marco A. Native llama Nanobody Library Panning Performed by Phage and Yeast Display Provides Binders Suitable for C-Reactive Protein Detection. BIOSENSORS 2021; 11:bios11120496. [PMID: 34940253 PMCID: PMC8699515 DOI: 10.3390/bios11120496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/22/2021] [Accepted: 12/02/2021] [Indexed: 06/14/2023]
Abstract
C-reactive protein (CRP) is an inflammation biomarker that should be quantified accurately during infections and healing processes. Nanobodies are good candidates to replace conventional antibodies in immunodiagnostics due to their inexpensive production, simple engineering, and the possibility to obtain higher binder density on capture surfaces. Starting from the same pre-immune library, we compared the selection output resulting from two independent panning strategies, one exclusively exploiting the phage display and another in which a first round of phage display was followed by a second round of yeast display. There was a partial output convergence between the two methods, since two clones were identified using both panning protocols but the first provided several further different sequences, whereas the second favored the recovery of many copies of few clones. The isolated anti-CRP nanobodies had affinity in the low nanomolar range and were suitable for ELISA and immunoprecipitation. One of them was fused to SpyTag and exploited in combination with SpyCatcher as the immunocapture element to quantify CRP using electrochemical impedance spectroscopy. The sensitivity of the biosensor was calculated as low as 0.21 μg/mL.
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Affiliation(s)
- Sandra Oloketuyi
- Laboratory for Environmental and Life Sciences, University of Nova Gorica, 5000 Nova Gorica, Slovenia; (S.O.); (R.B.); (G.C.)
| | - Robert Bernedo
- Laboratory for Environmental and Life Sciences, University of Nova Gorica, 5000 Nova Gorica, Slovenia; (S.O.); (R.B.); (G.C.)
| | - Andreas Christmann
- Applied Biochemistry, Technical University of Darmstadt, 64200 Darmstadt, Germany; (A.C.); (H.W.S.); (H.K.)
| | - Justyna Borkowska
- Institute of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland; (J.B.); (J.N.-J.); (K.S.-K.)
| | - Giulia Cazzaniga
- Laboratory for Environmental and Life Sciences, University of Nova Gorica, 5000 Nova Gorica, Slovenia; (S.O.); (R.B.); (G.C.)
| | - Horst Wilhelm Schuchmann
- Applied Biochemistry, Technical University of Darmstadt, 64200 Darmstadt, Germany; (A.C.); (H.W.S.); (H.K.)
| | - Joanna Niedziółka-Jönsson
- Institute of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland; (J.B.); (J.N.-J.); (K.S.-K.)
| | - Katarzyna Szot-Karpińska
- Institute of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland; (J.B.); (J.N.-J.); (K.S.-K.)
| | - Harald Kolmar
- Applied Biochemistry, Technical University of Darmstadt, 64200 Darmstadt, Germany; (A.C.); (H.W.S.); (H.K.)
| | - Ario de Marco
- Laboratory for Environmental and Life Sciences, University of Nova Gorica, 5000 Nova Gorica, Slovenia; (S.O.); (R.B.); (G.C.)
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Orlando M, Fortuna S, Oloketuyi S, Bajc G, Goldenzweig A, de Marco A. CDR1 Composition Can Affect Nanobody Recombinant Expression Yields. Biomolecules 2021; 11:biom11091362. [PMID: 34572576 PMCID: PMC8465892 DOI: 10.3390/biom11091362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 01/03/2023] Open
Abstract
The isolation of nanobodies from pre-immune libraries by means of biopanning is a straightforward process. Nevertheless, the recovered candidates often require optimization to improve some of their biophysical characteristics. In principle, CDRs are not mutated because they are likely to be part of the antibody paratope, but in this work, we describe a mutagenesis strategy that specifically addresses CDR1. Its sequence was identified as an instability hot spot by the PROSS program, and the available structural information indicated that four CDR1 residues bound directly to the antigen. We therefore modified the loop flexibility with the addition of an extra glycine rather than by mutating single amino acids. This approach significantly increased the nanobody yields but traded-off with moderate affinity loss. Accurate modeling coupled with atomistic molecular dynamics simulations enabled the modifications induced by the glycine insertion and the rationale behind the engineering design to be described in detail.
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Affiliation(s)
- Marco Orlando
- Department of Biotechnology and Life Sciences, University of Insubria, Via J. H. Dunant 3, 21100 Varese, Italy;
| | - Sara Fortuna
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri 1, 34127 Trieste, Italy;
| | - Sandra Oloketuyi
- Lab of Environmental and Life Sciences, University of Nova Gorica, Vipavska cesta 13, Rožna Dolina, 5000 Nova Gorica, Slovenia;
| | - Gregor Bajc
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, 1000 Ljubljana, Slovenia;
| | - Adi Goldenzweig
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel;
| | - Ario de Marco
- Lab of Environmental and Life Sciences, University of Nova Gorica, Vipavska cesta 13, Rožna Dolina, 5000 Nova Gorica, Slovenia;
- Correspondence: ; Tel.: +386-(05)-3315295
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Khaleghi S, Rahbarizadeh F, Nikkhoi SK. Anti-HER2 VHH Targeted Fluorescent Liposome as Bimodal Nanoparticle for Drug Delivery and Optical Imaging. Recent Pat Anticancer Drug Discov 2021; 16:552-562. [PMID: 34365930 DOI: 10.2174/1574892816666210806150929] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 04/07/2021] [Accepted: 04/14/2021] [Indexed: 11/22/2022]
Abstract
OBJECTIVE The aim of this study was to formulate fluorescent-labeled targeted immunoliposome to visualize the delivery and distribution of drugs in real-time. METHODS In this study, fluorescent-labeled liposomes were decorated with anti-HER2 VHH or Herceptin to improve the monitoring of intracellular drug delivery and tumor cell tracking with minimal side effects. The conjugation efficiency of antibodies was analyzed by SDS-PAGE silver staining. In addition, the physicochemical characterization of liposomes was performed using DLS and TEM. Finally, confocal microscopy visualized nanoparticles in the target cells. RESULTS Quantitative and qualitative methods characterized the intracellular uptake of 110±10 nm particles with near 70% conjugation efficiency. In addition, live-cell trafficking during hours of incubation was monitored by wide-field microscopy imaging. The results show that the fluorescent-labeled nanoparticles can specifically bind to HER2-positive breast cancer with minimal off-target delivery. CONCLUSION This kind of nanoparticles can have several applications in personalized medicine, especially drug delivery and real-time visualization of cancer therapy. Moreover, this method also can be applied in the targeted delivery of contrast agents in imaging and thermotherapy.
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Affiliation(s)
- Sepideh Khaleghi
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran. Iran
| | - Fatemeh Rahbarizadeh
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran. Iran
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Drozd M, Karoń S, Malinowska E. Recent Advancements in Receptor Layer Engineering for Applications in SPR-Based Immunodiagnostics. SENSORS (BASEL, SWITZERLAND) 2021; 21:3781. [PMID: 34072572 PMCID: PMC8198293 DOI: 10.3390/s21113781] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 05/23/2021] [Accepted: 05/26/2021] [Indexed: 12/12/2022]
Abstract
The rapid progress in the development of surface plasmon resonance-based immunosensing platforms offers wide application possibilities in medical diagnostics as a label-free alternative to enzyme immunoassays. The early diagnosis of diseases or metabolic changes through the detection of biomarkers in body fluids requires methods characterized by a very good sensitivity and selectivity. In the case of the SPR technique, as well as other surface-sensitive detection strategies, the quality of the transducer-immunoreceptor interphase is crucial for maintaining the analytical reliability of an assay. In this work, an overview of general approaches to the design of functional SPR-immunoassays is presented. It covers both immunosensors, the design of which utilizes well-known and often commercially available substrates, as well as the latest solutions developed in-house. Various approaches employing chemical and passive binding, affinity-based antibody immobilization, and the introduction of nanomaterial-based surfaces are discussed. The essence of their influence on the improvement of the main analytical parameters of a given immunosensor is explained. Particular attention is paid to solutions compatible with the latest trends in the development of label-free immunosensors, such as platforms dedicated to real-time monitoring in a quasi-continuous mode, the use of in situ-generated receptor layers (elimination of the regeneration step), and biosensors using recombinant and labelled protein receptors.
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Affiliation(s)
- Marcin Drozd
- Faculty of Chemistry, The Chair of Medical Biotechnology, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland;
- Center for Advanced Materials and Technologies, Warsaw University of Technology, Poleczki 19, 02-822 Warsaw, Poland
| | - Sylwia Karoń
- Faculty of Chemistry, The Chair of Medical Biotechnology, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland;
- Center for Advanced Materials and Technologies, Warsaw University of Technology, Poleczki 19, 02-822 Warsaw, Poland
| | - Elżbieta Malinowska
- Faculty of Chemistry, The Chair of Medical Biotechnology, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland;
- Center for Advanced Materials and Technologies, Warsaw University of Technology, Poleczki 19, 02-822 Warsaw, Poland
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19
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Nanobody-Dependent Detection of Microcystis aeruginosa by ELISA and Thermal Lens Spectrometry. Appl Biochem Biotechnol 2021; 193:2729-2741. [PMID: 33871768 DOI: 10.1007/s12010-021-03552-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 03/22/2021] [Indexed: 12/26/2022]
Abstract
Nanobodies against cell surface antigens of toxic cyanobacteria Microcystis aeruginosa were recovered by whole-cell biopanning of a naïve phage display library of nanobodies. Six unique sequences were identified and three sub-cloned and purified as fusion immunoreagents together with either green fluorescent protein or AviTag to be used for diagnostics. The yields of nanobody constructs were in the range of 5-10 mg/l and their specificity and sensitivity was initially evaluated by immunofluorescence and by fluorescent enzyme-linked immunosorbent assay (ELISA) using fluorescent nanobodies. The ELISA data confirmed the nanobody specificity but showed that the saturation of the fluorescence signal already in the presence of few hundreds of cells limited the dynamic range of the method. As an alternative, Avi-tagged nanobodies were used in combination with streptavidin-linked horseradish peroxidase for developing a diagnostic colorimetric cell ELISA, the limit-of-detection of which was 3.2 and 4.5 cells/ml for the two tested cyanobacteria strains, whereas the linear range of the assay was expanded from 10 to 10,000 cells. The fluorescent nanobodies were finally exploited for quantifying cyanobacteria by thermal lens spectrometry (TLS) that enabled to reach a limit-of-detection of 1.2 cells/ml and provided a linear range of measurement between 0 and 10,000 cells. No cross-reactivity with unrelated microalgae was detected and both colorimetric ELISA and TLS provided a linear range of detection of few logs. The data indicate that nanobodies are suitable capture reagents and that both TLS and colorimetric ELISA are reliable to monitor variations of cyanobacteria populations.
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20
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Ubbiali D, Orlando M, Kovačič M, Iacobucci C, Semrau MS, Bajc G, Fortuna S, Ilc G, Medagli B, Oloketuyi S, Storici P, Sinz A, Grandori R, de Marco A. An anti-HER2 nanobody binds to its antigen HER2 via two independent paratopes. Int J Biol Macromol 2021; 182:502-511. [PMID: 33848543 DOI: 10.1016/j.ijbiomac.2021.04.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 03/10/2021] [Accepted: 04/05/2021] [Indexed: 01/02/2023]
Abstract
High-resolution structural data of complexes between antibodies and membrane receptors still represent a demanding task. In this study, we used complementary sets of experimental data to obtain a structural model of the complex formed by the human epidermal growth factor receptor 2 (HER2) and its specific nanobody A10. First we identified by NMR the residues that bind or rearrange as a consequence of the complex formation. In parallel, the complex was cross-linked, digested and the resulting peptides were characterized by mass-spectrometry to define maximal distance restraints between HER2 and A10 amino acids in their complex. These independent datasets guided a docking process, refined by molecular dynamics simulations, to develop a model of the complex and estimate per-residue free-energy contributions. Such a model explains the experimental data and identifies a second, non-canonical paratope, located in the region opposite to the conventional nanobody paratope, formed by the hypervariable loop regions LH1 and LH3. Both paratopes contributed substantially to the overall affinity by binding to independent HER2 epitopes. Nanobody mutants with substitution of key interaction residues, as indicated by the model, possess significantly lower affinity for HER2. This is the first described case of a "natural" biparatopic nanobody, directly selected by in-vitro panning.
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Affiliation(s)
- Daniele Ubbiali
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Marco Orlando
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy; Department of Biotechnology and Life Sciences, University of Insubria, Via J. H. Dunant 3, 21100 Varese, Italy
| | - Matic Kovačič
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia
| | - Claudio Iacobucci
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Marta S Semrau
- Structural Biology Lab, Elettra Sincrotrone Trieste S.C.p.A., 34149, Basovizza, Trieste, Italy; CIBIO, Centre for Integrative Biology, University of Trento, via Sommarive 9, Povo 38123, Italy
| | - Gregor Bajc
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Sara Fortuna
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri 1, 34127 Trieste, Italy
| | - Gregor Ilc
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia
| | - Barbara Medagli
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri 1, 34127 Trieste, Italy
| | - Sandra Oloketuyi
- Lab of Environmental and Life Sciences, University of Nova Gorica, Vipavska cesta 13, 5000 Rožna Dolina, Nova Gorica, Slovenia
| | - Paola Storici
- Structural Biology Lab, Elettra Sincrotrone Trieste S.C.p.A., 34149, Basovizza, Trieste, Italy
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Rita Grandori
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy
| | - Ario de Marco
- Lab of Environmental and Life Sciences, University of Nova Gorica, Vipavska cesta 13, 5000 Rožna Dolina, Nova Gorica, Slovenia.
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21
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Peleg Y, Vincentelli R, Collins BM, Chen KE, Livingstone EK, Weeratunga S, Leneva N, Guo Q, Remans K, Perez K, Bjerga GEK, Larsen Ø, Vaněk O, Skořepa O, Jacquemin S, Poterszman A, Kjær S, Christodoulou E, Albeck S, Dym O, Ainbinder E, Unger T, Schuetz A, Matthes S, Bader M, de Marco A, Storici P, Semrau MS, Stolt-Bergner P, Aigner C, Suppmann S, Goldenzweig A, Fleishman SJ. Community-Wide Experimental Evaluation of the PROSS Stability-Design Method. J Mol Biol 2021; 433:166964. [PMID: 33781758 DOI: 10.1016/j.jmb.2021.166964] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 03/08/2021] [Accepted: 03/22/2021] [Indexed: 10/21/2022]
Abstract
Recent years have seen a dramatic improvement in protein-design methodology. Nevertheless, most methods demand expert intervention, limiting their widespread adoption. By contrast, the PROSS algorithm for improving protein stability and heterologous expression levels has been successfully applied to a range of challenging enzymes and binding proteins. Here, we benchmark the application of PROSS as a stand-alone tool for protein scientists with no or limited experience in modeling. Twelve laboratories from the Protein Production and Purification Partnership in Europe (P4EU) challenged the PROSS algorithm with 14 unrelated protein targets without support from the PROSS developers. For each target, up to six designs were evaluated for expression levels and in some cases, for thermal stability and activity. In nine targets, designs exhibited increased heterologous expression levels either in prokaryotic and/or eukaryotic expression systems under experimental conditions that were tailored for each target protein. Furthermore, we observed increased thermal stability in nine of ten tested targets. In two prime examples, the human Stem Cell Factor (hSCF) and human Cadherin-Like Domain (CLD12) from the RET receptor, the wild type proteins were not expressible as soluble proteins in E. coli, yet the PROSS designs exhibited high expression levels in E. coli and HEK293 cells, respectively, and improved thermal stability. We conclude that PROSS may improve stability and expressibility in diverse cases, and that improvement typically requires target-specific expression conditions. This study demonstrates the strengths of community-wide efforts to probe the generality of new methods and recommends areas for future research to advance practically useful algorithms for protein science.
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Affiliation(s)
- Yoav Peleg
- Department of Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Renaud Vincentelli
- Unité Mixte de Recherche (UMR) 7257, Centre National de la Recherche Scientifique (CNRS) Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques (AFMB), Marseille, France
| | - Brett M Collins
- The University of Queensland, Institute for Molecular Bioscience, St. Lucia, Queensland 4072, Australia
| | - Kai-En Chen
- The University of Queensland, Institute for Molecular Bioscience, St. Lucia, Queensland 4072, Australia
| | - Emma K Livingstone
- The University of Queensland, Institute for Molecular Bioscience, St. Lucia, Queensland 4072, Australia
| | - Saroja Weeratunga
- The University of Queensland, Institute for Molecular Bioscience, St. Lucia, Queensland 4072, Australia
| | - Natalya Leneva
- The University of Queensland, Institute for Molecular Bioscience, St. Lucia, Queensland 4072, Australia
| | - Qian Guo
- The University of Queensland, Institute for Molecular Bioscience, St. Lucia, Queensland 4072, Australia
| | - Kim Remans
- European Molecular Biology Laboratory (EMBL), Protein Expression and Purification Core Facility, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Kathryn Perez
- European Molecular Biology Laboratory (EMBL), Protein Expression and Purification Core Facility, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Gro E K Bjerga
- NORCE Norwegian Research Centre, Postboks 22 Nygårdstangen, 5038 Bergen, Norway
| | - Øivind Larsen
- NORCE Norwegian Research Centre, Postboks 22 Nygårdstangen, 5038 Bergen, Norway
| | - Ondřej Vaněk
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12840 Prague, Czech Republic
| | - Ondřej Skořepa
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12840 Prague, Czech Republic
| | - Sophie Jacquemin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique (CNRS), UMR 7104, Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Université de Strasbourg, France
| | - Arnaud Poterszman
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique (CNRS), UMR 7104, Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Université de Strasbourg, France
| | - Svend Kjær
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Evangelos Christodoulou
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Shira Albeck
- Department of Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Orly Dym
- Department of Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Elena Ainbinder
- Department of Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tamar Unger
- Department of Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Anja Schuetz
- Max-Delbrück Center for Molecular Medicine (MDC), Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany
| | - Susann Matthes
- Max-Delbrück Center for Molecular Medicine (MDC), Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany
| | - Michael Bader
- Max-Delbrück Center for Molecular Medicine (MDC), Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany; University of Lübeck, Institute for Biology, Ratzeburger Allee 160, 23562 Lübeck, Germany; Charité University Medicine, Charitéplatz 1, 10117 Berlin, Germany; German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany
| | - Ario de Marco
- Laboratory for Environmental and Life Sciences, University of Nova Gorica, Slovenia
| | - Paola Storici
- Elettra Sincrotrone Trieste - SS 14 - km 163, 5 in Area Science Park, 34149 Basovizza, Trieste, Italy
| | - Marta S Semrau
- Elettra Sincrotrone Trieste - SS 14 - km 163, 5 in Area Science Park, 34149 Basovizza, Trieste, Italy
| | - Peggy Stolt-Bergner
- Vienna Biocenter Core Facilities GmbH, Dr. Bohr-gasse 3, 1030 Vienna, Austria
| | - Christian Aigner
- Vienna Biocenter Core Facilities GmbH, Dr. Bohr-gasse 3, 1030 Vienna, Austria
| | - Sabine Suppmann
- Max-Planck Institute of Biochemistry, Biochemistry Core Facility, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Adi Goldenzweig
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sarel J Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel.
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Soler MA, Medagli B, Wang J, Oloketuyi S, Bajc G, Huang H, Fortuna S, de Marco A. Effect of Humanizing Mutations on the Stability of the Llama Single-Domain Variable Region. Biomolecules 2021; 11:biom11020163. [PMID: 33530572 PMCID: PMC7911018 DOI: 10.3390/biom11020163] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/21/2021] [Accepted: 01/24/2021] [Indexed: 11/24/2022] Open
Abstract
In vivo clinical applications of nanobodies (VHHs) require molecules that induce minimal immunoresponse and therefore possess sequences as similar as possible to the human VH domain. Although the relative sequence variability in llama nanobodies has been used to identify scaffolds with partially humanized signature, the transformation of the Camelidae hallmarks in the framework2 still represents a major problem. We assessed a set of mutants in silico and experimentally to elucidate what is the contribution of single residues to the VHH stability and how their combinations affect the mutant nanobody stability. We described at molecular level how the interaction among residues belonging to different structural elements enabled a model llama nanobody (C8WT, isolated from a naïve library) to be functional and maintain its stability, despite the analysis of its primary sequence would classify it as aggregation-prone. Five chimeras formed by grafting CDRs isolated from different nanobodies into C8WT scaffold were successfully expressed as soluble proteins and both tested clones preserved their antigen binding specificity. We identified a nanobody with human hallmarks that seems suitable for humanizing selected camelid VHHs by grafting heterologous CDRs in its scaffold and could serve for the preparation of a synthetic library of human-like single domains.
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Affiliation(s)
- Miguel A. Soler
- CONCEPT Lab, Italian Institute of Technology (IIT), 16152 Genova, Italy
- Correspondence: (M.A.S.); (A.d.M.); Tel.: +386-05-3315295 (A.d.M.); Fax: +386-05-90-99-722 (A.d.M.)
| | - Barbara Medagli
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, 34127 Trieste, Italy; (B.M.); (S.F.)
| | - Jiewen Wang
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, China; (J.W.); (H.H.)
| | - Sandra Oloketuyi
- Lab of Environmental and Life Sciences, University of Nova Gorica, 5000 Rožna Dolina-Nova Gorica, Slovenia;
| | - Gregor Bajc
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia;
| | - He Huang
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, China; (J.W.); (H.H.)
| | - Sara Fortuna
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, 34127 Trieste, Italy; (B.M.); (S.F.)
| | - Ario de Marco
- Lab of Environmental and Life Sciences, University of Nova Gorica, 5000 Rožna Dolina-Nova Gorica, Slovenia;
- Correspondence: (M.A.S.); (A.d.M.); Tel.: +386-05-3315295 (A.d.M.); Fax: +386-05-90-99-722 (A.d.M.)
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23
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Tang Y, Zhou Y, Li HJ. Advances in mesenchymal stem cell exosomes: a review. Stem Cell Res Ther 2021; 12:71. [PMID: 33468232 PMCID: PMC7814175 DOI: 10.1186/s13287-021-02138-7] [Citation(s) in RCA: 131] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 01/04/2021] [Indexed: 12/14/2022] Open
Abstract
Stem cells can be used for regenerative medicine and as treatments for disease. The application of tissue engineering-related transplantation, stem cells, and local changes in the microenvironment is expected to solve major medical problems. Currently, most studies focus on tissue repair and regeneration, and mesenchymal stem cells (MSCs) are among the most common research topics. MSCs are applicable as seed cells, and they represent one of the current hot topics in regenerative medicine research. However, due to storage limitations and because cell senescence occurs during in vitro expansion, their clinical application is challenging. Exosomes, which are secreted by MSCs through paracrine signalling, not only have the same effects as MSCs, but they also have the advantages of targeted delivery, low immunogenicity, and high repairability. This article reviews the acquisition methods, characteristics, biological functions, and clinical applications of exosomes.
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Affiliation(s)
- Yaya Tang
- Key Laboratory of Vaccine Research and Development for Major Infectious Diseases of Yunnan Province, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650118 People’s Republic of China
- Kunming Medical University, Kunming, 650500 People’s Republic of China
| | - Yan Zhou
- Key Laboratory of Vaccine Research and Development for Major Infectious Diseases of Yunnan Province, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650118 People’s Republic of China
| | - Hong-Jun Li
- Key Laboratory of Vaccine Research and Development for Major Infectious Diseases of Yunnan Province, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650118 People’s Republic of China
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24
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Abstract
Recombinant antibodies in single-domain format (VHHs) have been recently used for stabilizing antigens during their purification and crystallization. VHHs are also known for their structural stability and a significant part of them share the characteristic of remaining functionally folded also in the absence of the internal disulfide bond. Therefore, they can be expressed as intrabodies in the cell cytoplasm as well as in the bacterial periplasm. This evidence means that, in theory, VHHs can be co-expressed with their antigens independently on the redox constrains. It has also suggested the idea of using co-expression and co-purification of antigen-antibody complexes for maximizing the stabilizing effect of the antibody on its antigen during all the production steps for both cytoplasmic and periplasmic expression strategies.
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25
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Abstract
Unique, functional, homodimeric heavy chain-only antibodies, devoid of light chains, are circulating in the blood of Camelidae. These antibodies recognize their cognate antigen via one single domain, known as VHH or Nanobody. This serendipitous discovery made three decades ago has stimulated a growing number of researchers to generate highly specific Nanobodies against a myriad of targets. The small size, strict monomeric state, robustness, and easy tailoring of these Nanobodies have inspired many groups to design innovative Nanobody-based multi-domain constructs to explore novel applications. As such, Nanobodies have been employed as an exquisite research tool in structural, cell, and developmental biology. Furthermore, Nanobodies have demonstrated their benefit for more sensitive diagnostic tests. Finally, several Nanobody-based constructs have been designed to develop new therapeutic products.
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Affiliation(s)
- Serge Muyldermans
- Cellular and Molecular Immunology, Vrije Universiteit Brussel, 1050 Brussels, Belgium; .,Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian 116023, Liaoning, People's Republic of China
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26
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Ban B, Sharma M, Shetty J. Optimization of Methods for the Production and Refolding of Biologically Active Disulfide Bond-Rich Antibody Fragments in Microbial Hosts. Antibodies (Basel) 2020; 9:E39. [PMID: 32764309 PMCID: PMC7551518 DOI: 10.3390/antib9030039] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/24/2020] [Accepted: 07/28/2020] [Indexed: 11/17/2022] Open
Abstract
Antibodies have been used for basic research, clinical diagnostics, and therapeutic applications. Escherichia coli is one of the organisms of choice for the production of recombinant antibodies. Variable antibody genes have canonical and non-canonical disulfide bonds that are formed by the oxidation of a pair of cysteines. However, the high-level expression of an antibody is an inherent problem to the process of disulfide bond formation, ultimately leading to mispairing of cysteines which can cause misfolding and aggregation as inclusion bodies (IBs). This study demonstrated that fragment antibodies are either secreted to the periplasm as soluble proteins or expressed in the cytoplasm as insoluble inclusion bodies when expressed using engineered bacterial host strains with optimal culture conditions. It was observed that moderate-solubilization and an in vitro matrix that associated refolding strategies with redox pairing more correctly folded, structured, and yielded functionally active antibody fragments than the one achieved by a direct dilution method in the absence of a redox pair. However, natural antibodies have canonical and non-canonical disulfide bonds that need a more elaborate refolding process in the presence of optimal concentrations of chaotropic denaturants and redox agents to obtain correctly folded disulfide bonds and high yield antibodies that retain biological activity.
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Affiliation(s)
- Bhupal Ban
- Antibody Engineering and Technology Core, University of Virginia, Charlottesville, VA 22904, USA
- Department of Cell Biology, University of Virginia, Charlottesville, VA 22904, USA
- Pharmaceutical Biotechnology Center, Indiana Biosciences Research Institutes (IBRI), Indianapolis, IN 46202, USA
| | - Maya Sharma
- Department of Data Science, School of Informatics and Computing Indiana University–Purdue University Indianapolis (IUPUI), Indianapolis, IN 46202, USA;
| | - Jagathpala Shetty
- Antibody Engineering and Technology Core, University of Virginia, Charlottesville, VA 22904, USA
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22904, USA
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27
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de Marco A. Recombinant expression of nanobodies and nanobody-derived immunoreagents. Protein Expr Purif 2020; 172:105645. [PMID: 32289357 PMCID: PMC7151424 DOI: 10.1016/j.pep.2020.105645] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 04/06/2020] [Accepted: 04/09/2020] [Indexed: 12/12/2022]
Abstract
Antibody fragments for which the sequence is available are suitable for straightforward engineering and expression in both eukaryotic and prokaryotic systems. When produced as fusions with convenient tags, they become reagents which pair their selective binding capacity to an orthogonal function. Several kinds of immunoreagents composed by nanobodies and either large proteins or short sequences have been designed for providing inexpensive ready-to-use biological tools. The possibility to choose among alternative expression strategies is critical because the fusion moieties might require specific conditions for correct folding or post-translational modifications. In the case of nanobody production, the trend is towards simpler but reliable (bacterial) methods that can substitute for more cumbersome processes requiring the use of eukaryotic systems. The use of these will not disappear, but will be restricted to those cases in which the final immunoconstructs must have features that cannot be obtained in prokaryotic cells. At the same time, bacterial expression has evolved from the conventional procedure which considered exclusively the nanobody and nanobody-fusion accumulation in the periplasm. Several reports show the advantage of cytoplasmic expression, surface-display and secretion for at least some applications. Finally, there is an increasing interest to use as a model the short nanobody sequence for the development of in silico methodologies aimed at optimizing the yields, stability and affinity of recombinant antibodies. There is an increasing request for immunoreagents based on nanobodies. The multiplicity of their applications requires constructs with different structural complexity. Alternative expression methods are necessary to achieve such structural requirements. In silico optimization of nanobody biophysical characteristics becomes more and more reliable.
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Affiliation(s)
- Ario de Marco
- Laboratory for Environmental and Life Sciences, University of Nova Gorica, Vipavska cesta 13, S-5000, Nova Gorica, Slovenia.
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28
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Li X, Wang M, Zhang X, Liu C, Xiang H, Huang M, Ma Y, Gao X, Jiang L, Liu X, Li B, Hou Y, Zhang X, Yang S, Yang N. The novel llama-human chimeric antibody has potent effect in lowering LDL-c levels in hPCSK9 transgenic rats. Clin Transl Med 2020; 9:16. [PMID: 32056048 PMCID: PMC7018876 DOI: 10.1186/s40169-020-0265-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 01/21/2020] [Indexed: 01/12/2023] Open
Abstract
Background The advent of proprotein convertase subtilisin/kexin type 9 (PCSK9)–inhibiting drugs have provided an effective, but extremely expensive treatment for the management of low density lipoprotein (LDL). Our aim was to explore a cost-effective application of camelid anti-PCSK9 single domain antibodies (sdAbs), which are high variable regions of the camelid heavy chain antibodies (VHHs), as a human PCSK9 (hPCSK9) inhibitor. One female llama was immunized with hPCSK9. Screening of high affinity anti-PCSK9 VHHs was carried out based on surface plasmon resonance (SPR) technology. We reported a lysate kinetic analysis method improving the screening efficiency. To increase the serum half-life and targeting properties, the constant region fragment of the human immunoglobulin gamma sub-type 4 (IgG4 Fc) was incorporated to form a novel llama-human chimeric molecule (VHH-hFc). Results The PCSK9 inhibiting effects of the VHH proteins were analyzed in two human liver hepatocellular cells (HepG2 and Huh7) and in the hPCSK9 transgenic Sprague–Dawley (SD) rat model. The hPCSK9 antagonistic potency of the bivalent VHH-hFc exceeded the monovalent VHH (P < 0.001) in hepatocarcinoma cells. Furthermore, the llama-human chimeric VHH-Fc protein had a similar reduction (~ 40%) of the LDL-c and total cholesterol when compared to the approved evolocumab in transgenic SD rat model, but with low cost. More surprisingly, the chimeric heavy chain antibodies could be persevered for 3 months at room temperature with little loss of the affinity. Conclusions Due to the high yield and low cost of Pichia pastoris, lipid-lowering effect and strong stability, the llama-human chimeric antibody (VHH-Fc) offers a potent therapeutic candidate for the control of the serum lipid level.
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Affiliation(s)
- Xinyang Li
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China.,BGI-Shenzhen, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Meiniang Wang
- BGI-Shenzhen, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Xinhua Zhang
- BGI-Shenzhen, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Chuxin Liu
- BGI-Shenzhen, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Haitao Xiang
- BGI-Shenzhen, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Mi Huang
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China.,BGI-Hubei, BGI-Shenzhen, Wuhan, 430074, China
| | - Yingying Ma
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China.,BGI-Hubei, BGI-Shenzhen, Wuhan, 430074, China
| | - Xiaoyan Gao
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China.,BGI-Hubei, BGI-Shenzhen, Wuhan, 430074, China
| | - Lin Jiang
- BGI-Shenzhen, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Xiaopan Liu
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China.,BGI-Shenzhen, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Bo Li
- BGI-Shenzhen, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Yong Hou
- BGI-Shenzhen, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Xiuqing Zhang
- BGI-Shenzhen, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Shuang Yang
- BGI-Shenzhen, Shenzhen, 518083, China. .,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China.
| | - Naibo Yang
- BGI-Shenzhen, Shenzhen, 518083, China. .,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China. .,Complete Genomics, Inc., 2904 Orchard Parkway, San Jose, CA, 95134, USA.
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29
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Oloketuyi S, Mazzega E, Zavašnik J, Pungjunun K, Kalcher K, de Marco A, Mehmeti E. Electrochemical immunosensor functionalized with nanobodies for the detection of the toxic microalgae Alexandrium minutum using glassy carbon electrode modified with gold nanoparticles. Biosens Bioelectron 2020; 154:112052. [PMID: 32056958 DOI: 10.1016/j.bios.2020.112052] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 01/22/2020] [Accepted: 01/24/2020] [Indexed: 12/28/2022]
Abstract
In this work an electrochemical immunosensor for the toxic microalgae Alexandrium minutum (A. minutum AL9T) detection is described. A glassy carbon electrode (GCE) was modified by depositing gold nanoparticles followed by L-cysteine for obtaining a self-assembled monolayer. The SpyTagged nanobody C1, specific for the A. minutum toxic strain AL9T, was then covalently immobilized via SpyCatcher on the surface of the modified electrode and used for the selective capture of such microalgae strain. Electrochemical impedance spectroscopy (EIS) was used for the quantification of A. minutum cells present in water samples by measuring the charge-transfer resistance changes of the electrode with a hexacyanoferrate probe. Each electrode modification step was accompanied by cyclic voltammetry (CV) and scanning electron microscopy (SEM). The immunosensor provided highly reproducible data, was simple to fabricate at low cost, exhibited higher sensitivity than previously described alternative diagnostic methods and showed a broad linear range between 103 and 109 cells L-1 with detection limit of 3 × 103 cells L-1 of A. minutum AL9T. The immunosensor was successfully applied to quantify A. minutum AL9T in seawater and brackish water samples proving that it can be used for early detection of harmful microalgae without the necessity of pre-concentration or dialysis steps.
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Affiliation(s)
- Sandra Oloketuyi
- Laboratory of Environmental and Life Sciences, University of Nova Gorica, Vipavska cesta 13, SI-5000, Rožna Dolina (Nova Gorica), Slovenia
| | - Elisa Mazzega
- Laboratory of Environmental and Life Sciences, University of Nova Gorica, Vipavska cesta 13, SI-5000, Rožna Dolina (Nova Gorica), Slovenia
| | - Janez Zavašnik
- Department for Nanostructured Materials, Jožef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia
| | - Kingkan Pungjunun
- Electrochemistry and Optical Spectroscopy Center of Excellence (EOSCE), Department of Chemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Pathumwan, Bangkok, 10330, Thailand
| | - Kurt Kalcher
- Institute of Chemistry, Analytical Chemistry, Karl-Franzens University, Universitätsplatz 1, Graz, A-8010, Austria
| | - Ario de Marco
- Laboratory of Environmental and Life Sciences, University of Nova Gorica, Vipavska cesta 13, SI-5000, Rožna Dolina (Nova Gorica), Slovenia.
| | - Eda Mehmeti
- Institute of Chemistry, Analytical Chemistry, Karl-Franzens University, Universitätsplatz 1, Graz, A-8010, Austria.
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30
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Veggiani G, Giabbai B, Semrau MS, Medagli B, Riccio V, Bajc G, Storici P, de Marco A. Comparative analysis of fusion tags used to functionalize recombinant antibodies. Protein Expr Purif 2020; 166:105505. [DOI: 10.1016/j.pep.2019.105505] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 09/20/2019] [Accepted: 09/25/2019] [Indexed: 02/06/2023]
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31
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Applications of catalyzed cytoplasmic disulfide bond formation. Biochem Soc Trans 2019; 47:1223-1231. [DOI: 10.1042/bst20190088] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 09/09/2019] [Accepted: 09/20/2019] [Indexed: 12/14/2022]
Abstract
Abstract
Disulfide bond formation is an essential post-translational modification required for many proteins to attain their native, functional structure. The formation of disulfide bonds, otherwise known as oxidative protein folding, occurs in the endoplasmic reticulum and mitochondrial inter-membrane space in eukaryotes and the periplasm of prokaryotes. While there are differences in the molecular mechanisms of oxidative folding in different compartments, it can essentially be broken down into two steps, disulfide formation and disulfide isomerization. For both steps, catalysts exist in all compartments where native disulfide bond formation occurs. Due to the importance of disulfide bonds for a plethora of proteins, considerable effort has been made to generate cell factories which can make them more efficiently and cheaper. Recently synthetic biology has been used to transfer catalysts of native disulfide bond formation into the cytoplasm of prokaryotes such as Escherichia coli. While these engineered systems cannot yet rival natural systems in the range and complexity of disulfide-bonded proteins that can be made, a growing range of proteins have been made successfully and yields of homogenously folded eukaryotic proteins exceeding g/l yields have been obtained. This review will briefly give an overview of such systems, the uses reported to date and areas of future potential development, including combining with engineered systems for cytoplasmic glycosylation.
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32
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Non-affinity purification of a nanobody by void-exclusion anion exchange chromatography and multimodal weak cation exchange chromatography. Sep Purif Technol 2019. [DOI: 10.1016/j.seppur.2019.05.068] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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33
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Oloketuyi S, Dilkaute C, Mazzega E, Jose J, de Marco A. Purification-independent immunoreagents obtained by displaying nanobodies on bacteria surface. Appl Microbiol Biotechnol 2019; 103:4443-4453. [PMID: 30989251 DOI: 10.1007/s00253-019-09823-x] [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: 12/14/2018] [Revised: 03/29/2019] [Accepted: 04/01/2019] [Indexed: 12/27/2022]
Abstract
The availability of preimmune libraries of antibody fragments allows for the fast generation of binders which can be expressed in both eukaryotic and prokaryotic systems. We exploited the recombinant nature of antibody fragments to demonstrate the possibility of expressing them as functional proteins displayed on the surface of Escherichia coli and by such a way to generate living reagents ready-to-use for diagnostics. Such immunoreagents were effectively exploited without the necessity of any purification step to prepare immunocapture surfaces suitable for the diagnostic of both cancer cells and toxic microalgae. The same nanobody-displaying bacteria were also engineered to coexpress GFP in their cytoplasm. Suspensions of such living fluorescent immunoreagents effectively bound to eukaryotic cells making them visible and quantifiable by flow cytometry analysis and using 96-well plate readers. The collected data showed the suitability of such living immunoreagents for reproducible and inexpensive diagnostic applications.
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Affiliation(s)
- Sandra Oloketuyi
- Laboratory of Environmental and Life Sciences, University of Nova Gorica, Vipavska cesta 13, SI-5000, Rožna Dolina, Nova Gorica, Slovenia
| | - Carina Dilkaute
- Institut für Pharmazeutische und Medizinische Chemie, PharmaCampus, Westfälische Wilhelms-Universität Münster, Corrensstr. 48, 48149, Münster, Germany
| | - Elisa Mazzega
- Laboratory of Environmental and Life Sciences, University of Nova Gorica, Vipavska cesta 13, SI-5000, Rožna Dolina, Nova Gorica, Slovenia
| | - Joachim Jose
- Institut für Pharmazeutische und Medizinische Chemie, PharmaCampus, Westfälische Wilhelms-Universität Münster, Corrensstr. 48, 48149, Münster, Germany
| | - Ario de Marco
- Laboratory of Environmental and Life Sciences, University of Nova Gorica, Vipavska cesta 13, SI-5000, Rožna Dolina, Nova Gorica, Slovenia.
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34
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Mazzega E, Beran A, Cabrini M, de Marco A. In vitro isolation of nanobodies for selective Alexandrium minutum recognition: A model for convenient development of dedicated immuno-reagents to study and diagnostic toxic unicellular algae. HARMFUL ALGAE 2019; 82:44-51. [PMID: 30928010 DOI: 10.1016/j.hal.2019.01.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 01/03/2019] [Accepted: 01/03/2019] [Indexed: 06/09/2023]
Abstract
At the present, the identification of planktonic species in coastal water is still a time intensive process performed by highly trained personnel that relies either on qPCR or on light microscopy observation and in vitro culturing. Furthermore, the increasing danger represented by Harmful Algal Blooms (HABs) inside phytoplankton community and the recent implementation of the legislation on ballast water management to prevent the introduction of HABs and NIS (Non Indigenous Species) urge the development of faster and reliable diagnostic methods. Immuno-based approaches could fulfil this need provided that the costs for antibody selection and production will be reduced. In this work it is demonstrated for the first time the feasibility to recover nanobodies (VHHs) selective for native surface epitopes of Alexandrium minutum by direct whole cell bio-panning using a pre-immune phage display library. The recombinant nature of VHHs enabled their rapid engineering into eGFP fluorescent reagents (fluobodies) that were produced recombinantly in bacteria and are directly suitable for fluorescence microscopy and flow cytometry. Immune-detection identified also cysts and anti-Alexandrium fluobodies showed no cross-reactivity with indigenous not-toxic phytoplankton microalgae belonging to different geni. The fluobodies were able to bind selectively to the target cells in both fixed and fresh samples with minimal processing.
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Affiliation(s)
- Elisa Mazzega
- Laboratory for Environmental and Life Sciences, University of Nova Gorica, Slovenia
| | - Alfred Beran
- Istituto Nazionale di Oceanografia e di Geofisica Sperimentale (OGS), Trieste, Italy
| | - Marina Cabrini
- Istituto Nazionale di Oceanografia e di Geofisica Sperimentale (OGS), Trieste, Italy
| | - Ario de Marco
- Laboratory for Environmental and Life Sciences, University of Nova Gorica, Slovenia.
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35
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Anderson GP, Shriver-Lake LC, Walper SA, Ashford L, Zabetakis D, Liu JL, Breger JC, Brozozog Lee PA, Goldman ER. Genetic Fusion of an Anti-BclA Single-Domain Antibody with Beta Galactosidase. Antibodies (Basel) 2018; 7:antib7040036. [PMID: 31544886 PMCID: PMC6698959 DOI: 10.3390/antib7040036] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 09/26/2018] [Accepted: 09/27/2018] [Indexed: 02/06/2023] Open
Abstract
The Bacillus collagen-like protein of anthracis (BclA), found in Bacillus anthracis spores, is an attractive target for immunoassays. Previously, using phage display we had selected llama-derived single-domain antibodies that bound to B. anthracis spore proteins including BclA. Single-domain antibodies (sdAbs), the recombinantly expressed heavy domains from the unique heavy-chain-only antibodies found in camelids, provide stable and well-expressed binding elements with excellent affinity. In addition, sdAbs offer the important advantage that they can be tailored for specific applications through protein engineering. A fusion of a BclA targeting sdAb with the enzyme Beta galactosidase (β-gal) would enable highly sensitive immunoassays with no need for a secondary reagent. First, we evaluated five anti-BclA sdAbs, including four that had been previously identified but not characterized. Each was tested to determine its binding affinity, melting temperature, producibility, and ability to function as both capture and reporter in sandwich assays for BclA. The sdAb with the best combination of properties was constructed as a fusion with β-gal and shown to enable sensitive detection. This fusion has the potential to be incorporated into highly sensitive assays for the detection of anthrax spores.
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Affiliation(s)
- George P Anderson
- Naval Research Laboratory, Center for Biomolecular Science and Engineering, Washington, DC 20375, USA.
| | - Lisa C Shriver-Lake
- Naval Research Laboratory, Center for Biomolecular Science and Engineering, Washington, DC 20375, USA.
| | - Scott A Walper
- Naval Research Laboratory, Center for Biomolecular Science and Engineering, Washington, DC 20375, USA.
| | - Lauryn Ashford
- The Washington Center for Internships and Academic Seminars, 1333 16th Street N.W., Washington, DC 20036, USA.
| | - Dan Zabetakis
- Naval Research Laboratory, Center for Biomolecular Science and Engineering, Washington, DC 20375, USA.
| | - Jinny L Liu
- Naval Research Laboratory, Center for Biomolecular Science and Engineering, Washington, DC 20375, USA.
| | - Joyce C Breger
- Naval Research Laboratory, Center for Biomolecular Science and Engineering, Washington, DC 20375, USA.
| | | | - Ellen R Goldman
- Naval Research Laboratory, Center for Biomolecular Science and Engineering, Washington, DC 20375, USA.
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Khoshtinat Nikkhoi S, Rahbarizadeh F, Ahmadvand D, Moghimi SM. Multivalent targeting and killing of HER2 overexpressing breast carcinoma cells with methotrexate-encapsulated tetra-specific non-overlapping variable domain heavy chain anti-HER2 antibody-PEG-liposomes: In vitro proof-of-concept. Eur J Pharm Sci 2018; 122:42-50. [DOI: 10.1016/j.ejps.2018.06.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 06/09/2018] [Accepted: 06/18/2018] [Indexed: 12/17/2022]
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37
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Li Q, Miao Z, Luo XG, Zhao J, Song YJ, Li ZY, Zhou H, Zhang TC, Mao LS. Expression and bioactivity analysis of TNF30, a TNFα nanobody, in Escherichia coli. BIOTECHNOL BIOTEC EQ 2018. [DOI: 10.1080/13102818.2018.1480422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
Affiliation(s)
- Qian Li
- Key Laboratory of Industrial Fermentation Microbiology, Tianjin University of Science and Technology, Ministry of Education, Tianjin, P.R. China
- Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, P.R. China
| | - Zhi Miao
- Key Laboratory of Industrial Fermentation Microbiology, Tianjin University of Science and Technology, Ministry of Education, Tianjin, P.R. China
- Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, P.R. China
| | - Xue-Gang Luo
- Key Laboratory of Industrial Fermentation Microbiology, Tianjin University of Science and Technology, Ministry of Education, Tianjin, P.R. China
- Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, P.R. China
| | - Jian Zhao
- Lidzix Biotechnology Tianjin Co., Ltd, Tianjin, P.R. China
| | - Ya-Jian Song
- Key Laboratory of Industrial Fermentation Microbiology, Tianjin University of Science and Technology, Ministry of Education, Tianjin, P.R. China
- Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, P.R. China
| | - Zhong-Yuan Li
- Key Laboratory of Industrial Fermentation Microbiology, Tianjin University of Science and Technology, Ministry of Education, Tianjin, P.R. China
- Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, P.R. China
| | - Hao Zhou
- Key Laboratory of Industrial Fermentation Microbiology, Tianjin University of Science and Technology, Ministry of Education, Tianjin, P.R. China
- Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, P.R. China
| | - Tong-Cun Zhang
- Key Laboratory of Industrial Fermentation Microbiology, Tianjin University of Science and Technology, Ministry of Education, Tianjin, P.R. China
- Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, P.R. China
| | - Li-Song Mao
- Lidzix Biotechnology Tianjin Co., Ltd, Tianjin, P.R. China
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38
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Farasat A, Rahbarizadeh F, Ahmadvand D, Ranjbar S, Khoshtinat Nikkhoi S. Effective suppression of tumour cells by oligoclonal HER2-targeted delivery of liposomal doxorubicin. J Liposome Res 2018; 29:53-65. [DOI: 10.1080/08982104.2018.1430829] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Alireza Farasat
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Fatemeh Rahbarizadeh
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Davoud Ahmadvand
- School of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Saeed Ranjbar
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
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39
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Soler MA, Fortuna S, de Marco A, Laio A. Binding affinity prediction of nanobody-protein complexes by scoring of molecular dynamics trajectories. Phys Chem Chem Phys 2018; 20:3438-3444. [PMID: 29328338 DOI: 10.1039/c7cp08116b] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Nanobodies offer a viable alternative to antibodies for engineering high affinity binders. Their small size has an additional advantage: it allows exploiting computational protocols for optimizing their biophysical features, such as the binding affinity. The efficient prediction of this quantity is still considered a daunting task especially for modelled complexes. We show how molecular dynamics can successfully assist in the binding affinity prediction of modelled nanobody-protein complexes. The approximate initial configurations obtained by in silico design must undergo large rearrangements before achieving a stable conformation, in which the binding affinity can be meaningfully estimated. The scoring functions developed for the affinity evaluation of crystal structures will provide accurate estimates for modelled binding complexes if the scores are averaged over long finite temperature molecular dynamics simulations.
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40
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Popovic M, Mazzega E, Toffoletto B, de Marco A. Isolation of anti-extra-cellular vesicle single-domain antibodies by direct panning on vesicle-enriched fractions. Microb Cell Fact 2018; 17:6. [PMID: 29331148 PMCID: PMC5766977 DOI: 10.1186/s12934-017-0856-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 12/29/2017] [Indexed: 01/08/2023] Open
Abstract
Background The thorough understanding of the physiological and pathological processes mediated by extracellular vesicles (EVs) is challenged by purification methods which are cumbersome, not reproducible, or insufficient to yield homogeneous material. Chromatography based on both ion-exchange and immune-capture can represent an effective method to improve EV purification and successive analysis. Methods Cell culture supernatant was used as a model sample for assessing the capacity of anion-exchange chromatography to separate distinct EV fractions and to isolate nanobodies by direct panning on whole EVs to recover binders specific for the native conformation of EV-surface epitopes and suitable to develop EV immune-capture reagents. Results Anion-exchange chromatography of cell culture supernatant separated distinct protein-containing fractions and all of them were positive for CD9, a biomarker associated to some EVs. This suggested the existence of several EV fractions but did not help in separating EVs from other contaminants. We further isolated several nanobodies instrumental for implementing immune-affinity protocols. These were able to immobilize EVs from both cell culture supernatant and biological samples, to be used in ELISA, flow-cytometry, and immune-purification. Conclusions Here we report the first successful isolation of anti-EV nanobodies for the use in immunoaffinity-based EV capture by panning a phage library directly on partially purified EVs. This achievement paves the way for the application of direct EV panning for the discovery of novel antibody-vesicle surface biomarker pairs and represents the preliminary requirement for the development of selective immune-capture that, in combination with anion-exchange chromatography, can simplify the systematic stratification of EV sub-populations and their individual characterization. Electronic supplementary material The online version of this article (10.1186/s12934-017-0856-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Milica Popovic
- Faculty of Chemistry, Department of Biochemistry, University of Belgrade, Studentski trg 12-16, 11000, Belgrade, Serbia.
| | - Elisa Mazzega
- Laboratory for Environmental and Life Sciences, University of Nova Gorica, Glavni Trg 8-SI-5271, Vipava, Slovenia
| | - Barbara Toffoletto
- Azienda Sanitaria Universitaria Integrata di Udine-Istituto di Anatomia Patologica, Udine, Italy
| | - Ario de Marco
- Laboratory for Environmental and Life Sciences, University of Nova Gorica, Glavni Trg 8-SI-5271, Vipava, Slovenia.
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41
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Goldman ER, Broussard A, Anderson GP, Liu JL. Bglbrick strategy for the construction of single domain antibody fusions. Heliyon 2017; 3:e00474. [PMID: 29322100 PMCID: PMC5753753 DOI: 10.1016/j.heliyon.2017.e00474] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 11/07/2017] [Accepted: 11/27/2017] [Indexed: 11/30/2022] Open
Abstract
Single domain antibodies, recombinantly expressed variable domains derived from camelid heavy chain antibodies, are often expressed as multimers for detection and therapeutic applications. Constructs in which several single domain antibodies are genetically fused serially, as well as those in which single domain antibodies are genetically linked with domains that naturally form multimers, yield improvement in apparent binding affinity due to avidity. Here, using a single domain antibody that binds envelope protein from the Dengue virus, we demonstrated the construction of single domain antibody dimers using the Bglbrick cloning strategy. Constructing single domain antibodies and multimerization domains as Bglbrick parts enables the easy mixing and matching of parts. The dimeric constructs provided enhanced fluorescent signal in assays for detection of Dengue virus like particles over the monomeric single domain antibody.
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Affiliation(s)
- Ellen R Goldman
- US Naval Research Laboratory, Center for Biomolecular Science and Engineering, 4555 Overlook Ave SW, Washington DC 20375, USA
| | - Aeris Broussard
- US Naval Research Laboratory, Historically Black Colleges and Universities/Minority Institutions Summer Internship Program, 4555 Overlook Ave SW, Washington, DC 20375, USA
| | - George P Anderson
- US Naval Research Laboratory, Center for Biomolecular Science and Engineering, 4555 Overlook Ave SW, Washington DC 20375, USA
| | - Jinny L Liu
- US Naval Research Laboratory, Center for Biomolecular Science and Engineering, 4555 Overlook Ave SW, Washington DC 20375, USA
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42
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Liu Y, Huang H. Expression of single-domain antibody in different systems. Appl Microbiol Biotechnol 2017; 102:539-551. [DOI: 10.1007/s00253-017-8644-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 11/09/2017] [Accepted: 11/12/2017] [Indexed: 10/18/2022]
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43
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Mazzega E, de Marco A. Engineered cross-reacting nanobodies simplify comparative oncology between humans and dogs. Vet Comp Oncol 2017; 16:E202-E206. [DOI: 10.1111/vco.12359] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 09/22/2017] [Indexed: 11/30/2022]
Affiliation(s)
- E. Mazzega
- Laboratory for Environmental and Life Sciences; University of Nova Gorica; Vipava Slovenia
| | - A. de Marco
- Laboratory for Environmental and Life Sciences; University of Nova Gorica; Vipava Slovenia
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44
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Crepin R, Veggiani G, Djender S, Beugnet A, Planeix F, Pichon C, Moutel S, Amigorena S, Perez F, Ghinea N, de Marco A. Whole-cell biopanning with a synthetic phage display library of nanobodies enabled the recovery of follicle-stimulating hormone receptor inhibitors. Biochem Biophys Res Commun 2017; 493:1567-1572. [PMID: 29017919 DOI: 10.1016/j.bbrc.2017.10.036] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 10/06/2017] [Indexed: 10/18/2022]
Abstract
Antibodies are essential reagents that are increasingly used in diagnostics and therapy. Their specificity and capacity to recognize their native antigen are critical characteristics for their in vivo application. Follicle-stimulating hormone receptor is a GPCR protein regulating ovarian follicular maturation and spermatogenesis. Recently, its potentiality as a cancer biomarker has been demonstrated but no antibody suitable for in vivo tumor targeting and treatment has been characterized so far. In this paper we describe the first successful attempt to recover recombinant antibodies against the FSHR and that: i) are directly panned from a pre-immune library using whole cells expressing the target receptor at their surface; ii) show inhibitory activity towards the FSH-induced cAMP accumulation; iii) do not share the same epitope with the natural binder FSH; iv) can be produced inexpensively as mono- or bivalent functional molecules in the bacterial cytoplasm. We expect that the proposed biopanning strategy will be profitable to identify useful functional antibodies for further members of the GPCR class.
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Affiliation(s)
- Ronan Crepin
- Tumor Target and Therapeutic Antibody - Identification Platform (TAb-IP), PSL Research University, Institut Curie, 26, Rue D'Ulm, Paris, France; CIC IGR Curie 1428, France
| | - Gianluca Veggiani
- Tumor Target and Therapeutic Antibody - Identification Platform (TAb-IP), PSL Research University, Institut Curie, 26, Rue D'Ulm, Paris, France
| | - Selma Djender
- Tumor Target and Therapeutic Antibody - Identification Platform (TAb-IP), PSL Research University, Institut Curie, 26, Rue D'Ulm, Paris, France; CIC IGR Curie 1428, France
| | - Anne Beugnet
- Tumor Target and Therapeutic Antibody - Identification Platform (TAb-IP), PSL Research University, Institut Curie, 26, Rue D'Ulm, Paris, France; CIC IGR Curie 1428, France
| | - François Planeix
- Translational Research Department, PSL Research University, Institut Curie, 26 Rue D'Ulm, F75248 Paris Cedex 05, France
| | - Christophe Pichon
- Translational Research Department, PSL Research University, Institut Curie, 26 Rue D'Ulm, F75248 Paris Cedex 05, France
| | - Sandrine Moutel
- Tumor Target and Therapeutic Antibody - Identification Platform (TAb-IP), PSL Research University, Institut Curie, 26, Rue D'Ulm, Paris, France; Translational Research Department, PSL Research University, Institut Curie, 26 Rue D'Ulm, F75248 Paris Cedex 05, France
| | - Sebastian Amigorena
- INSERM U932, PSL Research University, Institut Curie, 26 Rue D'Ulm, F75248 Paris, France; SIRIC INCa-DGOS-4654, France; CIC IGR Curie 1428, France
| | - Franck Perez
- UMR144, PSL Research University, Institut Curie, 12 Lhomond, 75005, Paris, France
| | - Nicolae Ghinea
- Translational Research Department, PSL Research University, Institut Curie, 26 Rue D'Ulm, F75248 Paris Cedex 05, France
| | - Ario de Marco
- Tumor Target and Therapeutic Antibody - Identification Platform (TAb-IP), PSL Research University, Institut Curie, 26, Rue D'Ulm, Paris, France; SIRIC INCa-DGOS-4654, France; CIC IGR Curie 1428, France; Dept. of Biomedical Sciences and Engineering, University of Nova Gorica (UNG), Glavni Trg 9, SI-5261, Vipava, Slovenia.
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Ju MS, Min SW, Lee SM, Kwon HS, Park JC, Lee JC, Jung ST. A synthetic library for rapid isolation of humanized single-domain antibodies. BIOTECHNOL BIOPROC E 2017. [DOI: 10.1007/s12257-017-0082-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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46
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Ambrosetti E, Paoletti P, Bosco A, Parisse P, Scaini D, Tagliabue E, de Marco A, Casalis L. Quantification of Circulating Cancer Biomarkers via Sensitive Topographic Measurements on Single Binder Nanoarrays. ACS OMEGA 2017; 2:2618-2629. [PMID: 30023671 PMCID: PMC6044866 DOI: 10.1021/acsomega.7b00284] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 04/28/2017] [Indexed: 01/10/2023]
Abstract
Early detection of cancer plays a crucial role in disease prognosis. It requires the recognition and quantification of low amounts of specific molecular biomarkers, either free or transported inside nanovesicles, through the development of novel sensitive diagnostic technologies. In this context, we have developed a nanoarray platform for the noninvasive quantification of cancer biomarkers circulating in the bloodstream. The assay is based on molecular manipulation to create functional spots of surface-immobilized binders and differential topography measurements. It is label-free and requires just a single binder per antigen, and when it is implemented with fluorescence labeling/readout, it can be used for epitope mapping. As a benchmark, we focused on the plasma release of Her2 extracellular domain (ECD), a proposed biomarker for the progression of Her2-positive tumors and response to anticancer therapies. By employing robust, easily engineered camelid nanobodies as binders, we measured ECD-Her2 concentrations in the range of the actual clinical cutoff value for Her2-positive breast cancer. The specificity for Her2 detection was preserved when it was measured in parallel with other potential biomarkers, demonstrating a forthcoming implementation of this approach for multiplexing analysis. Prospectively, this nanorarray platform may be customized to allow for the detection of promising new classes of circulating biomarkers, such as exosomes and microvesicles.
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Affiliation(s)
- Elena Ambrosetti
- NanoInnovation
Lab, Elettra-Sincrotone S.C.p.A., ss 14 km 163.5 in Area Science Park, 34149 Basovizza-Trieste, Italy
- PhD
School in Nanotechnology, University of Trieste, Piazzale Europa
1, 34127 Trieste, Italy
- INSTM−ST Unit, ss 14 km 163.5
in Area Science Park, 34149 Basovizza-Trieste, Italy
| | - Pamela Paoletti
- NanoInnovation
Lab, Elettra-Sincrotone S.C.p.A., ss 14 km 163.5 in Area Science Park, 34149 Basovizza-Trieste, Italy
- International School for Advanced Studies (SISSA), Via Bonomea 265, 34136 Trieste, Italy
| | - Alessandro Bosco
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles väg, 17177 Stockholm, Sweden
| | - Pietro Parisse
- NanoInnovation
Lab, Elettra-Sincrotone S.C.p.A., ss 14 km 163.5 in Area Science Park, 34149 Basovizza-Trieste, Italy
| | - Denis Scaini
- NanoInnovation
Lab, Elettra-Sincrotone S.C.p.A., ss 14 km 163.5 in Area Science Park, 34149 Basovizza-Trieste, Italy
- PhD
School in Nanotechnology, University of Trieste, Piazzale Europa
1, 34127 Trieste, Italy
| | - Elda Tagliabue
- Department
of Experimental Oncology and Molecular Medicine, Fondazione IRCCS−Istituto Nazionale dei Tumori, Via Amadeo 42, 20133 Milano, Italy
| | - Ario de Marco
- Center
for Biomedical Sciences and Engineering, University of Nova Gorica, Dvorec Lanthieri, Glavni Trg 8, 5271 Vipava, Slovenia
| | - Loredana Casalis
- NanoInnovation
Lab, Elettra-Sincrotone S.C.p.A., ss 14 km 163.5 in Area Science Park, 34149 Basovizza-Trieste, Italy
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47
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Cytoplasmic versus periplasmic expression of site-specifically and bioorthogonally functionalized nanobodies using expressed protein ligation. Protein Expr Purif 2017; 133:25-34. [DOI: 10.1016/j.pep.2017.02.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 02/07/2017] [Accepted: 02/21/2017] [Indexed: 01/27/2023]
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48
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Crépin R, Gentien D, Duché A, Rapinat A, Reyes C, Némati F, Massonnet G, Decaudin D, Djender S, Moutel S, Desrumeaux K, Cassoux N, Piperno-Neumann S, Amigorena S, Perez F, Roman-Roman S, de Marco A. Nanobodies against surface biomarkers enable the analysis of tumor genetic heterogeneity in uveal melanoma patient-derived xenografts. Pigment Cell Melanoma Res 2017; 30:317-327. [DOI: 10.1111/pcmr.12577] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 01/23/2017] [Indexed: 12/13/2022]
Affiliation(s)
- Ronan Crépin
- Tumor Target and Therapeutic Antibody - Identification Platform (TAb-IP); Paris Cedex 05 France
| | - David Gentien
- Translational Research Department; Institut Curie; PSL Research University; Paris France
| | - Angeline Duché
- Translational Research Department; Institut Curie; PSL Research University; Paris France
| | - Audrey Rapinat
- Translational Research Department; Institut Curie; PSL Research University; Paris France
| | - Cecile Reyes
- Translational Research Department; Institut Curie; PSL Research University; Paris France
| | - Fariba Némati
- Translational Research Department; Institut Curie; PSL Research University; Paris France
| | - Gérald Massonnet
- Translational Research Department; Institut Curie; PSL Research University; Paris France
| | - Didier Decaudin
- Translational Research Department; Institut Curie; PSL Research University; Paris France
- Medical Oncology Department; Institut Curie; Paris Cedex 05 France
| | - Selma Djender
- Tumor Target and Therapeutic Antibody - Identification Platform (TAb-IP); Paris Cedex 05 France
- Institut Curie; PSL Research University; Paris Cedex 05 France
| | - Sandrine Moutel
- Translational Research Department; Institut Curie; PSL Research University; Paris France
- Institut Curie; PSL Research University; Paris Cedex 05 France
- UMR144; Institut Curie; Paris France
| | - Klervi Desrumeaux
- Tumor Target and Therapeutic Antibody - Identification Platform (TAb-IP); Paris Cedex 05 France
| | | | | | - Sebastian Amigorena
- Institut Curie; PSL Research University; Paris Cedex 05 France
- INSERM Unit 932; Paris cedex 05 France
- SIRIC INCa-DGOS-4654; Paris France
- CIC IGR Curie 1428; Paris France
| | - Franck Perez
- Tumor Target and Therapeutic Antibody - Identification Platform (TAb-IP); Paris Cedex 05 France
- Institut Curie; PSL Research University; Paris Cedex 05 France
- UMR144; Institut Curie; Paris France
| | - Sergio Roman-Roman
- Translational Research Department; Institut Curie; PSL Research University; Paris France
| | - Ario de Marco
- Tumor Target and Therapeutic Antibody - Identification Platform (TAb-IP); Paris Cedex 05 France
- SIRIC INCa-DGOS-4654; Paris France
- CIC IGR Curie 1428; Paris France
- Department of Biomedical Sciences and Engineering; University of Nova Gorica (UNG); Vipava Slovenia
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49
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de Marco A. Acting on Folding Effectors to Improve Recombinant Protein Yields and Functional Quality. Methods Mol Biol 2017; 1586:197-210. [PMID: 28470606 DOI: 10.1007/978-1-4939-6887-9_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Molecular and chemical chaperones /foldases can strongly contribute to improve the amounts and the structural quality of recombinant proteins. Several methodologies have been proposed to optimize their beneficial effects. This chapter presents a condensed summary of the biotechnological opportunities offered by this approach followed by a protocol describing the method we use for expressing disulfide bond-dependent recombinant antibodies in the cytoplasm of bacteria engineered to overexpress sulfhydryl oxidase and DsbC isomerase. The system is based on the possibility to trigger the foldase expression independently and before the induction of the target protein. As a consequence, the recombinant antibody synthesis starts only after enough foldases have accumulated to promote correct folding of the antibody.
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Affiliation(s)
- Ario de Marco
- Department of Biomedical Sciences and Engineering, University of Nova Gorica, Glavni Trg 9, SI-5261, Vipava, Slovenia.
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50
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Molecular dynamics simulations and docking enable to explore the biophysical factors controlling the yields of engineered nanobodies. Sci Rep 2016; 6:34869. [PMID: 27721441 PMCID: PMC5056509 DOI: 10.1038/srep34869] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 09/20/2016] [Indexed: 02/08/2023] Open
Abstract
Nanobodies (VHHs) have proved to be valuable substitutes of conventional antibodies for molecular recognition. Their small size represents a precious advantage for rational mutagenesis based on modelling. Here we address the problem of predicting how Camelidae nanobody sequences can tolerate mutations by developing a simulation protocol based on all-atom molecular dynamics and whole-molecule docking. The method was tested on two sets of nanobodies characterized experimentally for their biophysical features. One set contained point mutations introduced to humanize a wild type sequence, in the second the CDRs were swapped between single-domain frameworks with Camelidae and human hallmarks. The method resulted in accurate scoring approaches to predict experimental yields and enabled to identify the structural modifications induced by mutations. This work is a promising tool for the in silico development of single-domain antibodies and opens the opportunity to customize single functional domains of larger macromolecules.
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