1
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Weng D, Yang L, Xie Y. Engineering and characterization of GFP-targeting nanobody: Expression, purification, and post-translational modification analysis. Protein Expr Purif 2024; 221:106501. [PMID: 38782081 DOI: 10.1016/j.pep.2024.106501] [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: 02/21/2024] [Revised: 05/07/2024] [Accepted: 05/09/2024] [Indexed: 05/25/2024]
Abstract
Nanobodies are single-variable domain antibodies with excellent properties, which are evolving as versatile tools to guide cognate antigens in vitro and in vivo for biological research, diagnosis, and treatment. Given their simple structure, nanobodies are readily produced in multiple systems. However, selecting an appropriate expression system is crucial because different conditions might cause proteins to produce different folds or post-translational modifications (PTMs), and these differences often result in different functions. At present, the strategies of PTMs are rarely reported. The GFP nanobody can specifically target the GFP protein. Here, we engineered a GFP nanobody fused with 6 × His tag and Fc tag, respectively, and expressed in bacteria and mammalian cells. The 6 × His-GFP-nanobody was produced from Escherichia coli at high yields and the pull-down assay indicated that it can precipitate the GFP protein. Meanwhile, the Fc-GFP-nanobody can be expressed in HEK293T cells, and the co-immunoprecipitation experiment can trace and target the GFP-tagged protein in vivo. Furthermore, some different PTMs in antigen-binding regions have been identified after using mass spectrometry (MS) to analyze the GFP nanobodies, which are expressed in prokaryotes and eukaryotes. In this study, a GFP nanobody was designed, and its binding ability was verified by using the eukaryotic and prokaryotic protein expression systems. In addition, this GFP nanobody was transformed into a useful instrument for more in-depth functional investigations of GFP fusion proteins. MS was further used to explore the reason for the difference in binding ability, providing a novel perspective for the study of GFP nanobodies and protein expression purification.
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Affiliation(s)
- Dunchu Weng
- The Ministry of Education Key Laboratory of Laboratory Medical Diagnostics, The College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Lin Yang
- The Ministry of Education Key Laboratory of Laboratory Medical Diagnostics, The College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Yajun Xie
- The Ministry of Education Key Laboratory of Laboratory Medical Diagnostics, The College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China.
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2
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Das PK, Sahoo A, Veeranki VD. Recombinant monoclonal antibody production in yeasts: Challenges and considerations. Int J Biol Macromol 2024; 266:131379. [PMID: 38580014 DOI: 10.1016/j.ijbiomac.2024.131379] [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: 10/29/2023] [Revised: 04/01/2024] [Accepted: 04/02/2024] [Indexed: 04/07/2024]
Abstract
Monoclonal antibodies (mAbs) are laboratory-based engineered protein molecules with a monovalent affinity or multivalent avidity towards a specific target or antigen, which can mimic natural antibodies that are produced in the human immune systems to fight against detrimental pathogens. The recombinant mAb is one of the most effective classes of biopharmaceuticals produced in vitro by cloning and expressing synthetic antibody genes in a suitable host. Yeast is one of the potential hosts among others for the successful production of recombinant mAbs. However, there are very few yeast-derived mAbs that got the approval of the regulatory agencies for direct use for treatment purposes. Certain challenges encountered by yeasts for recombinant antibody productions need to be overcome and a few considerations related to antibody structure, host engineering, and culturing strategies should be followed for the improved production of mAbs in yeasts. In this review, the drawbacks related to the metabolic burden of the host, culturing conditions including induction mechanism and secretion efficiency, solubility and stability, downstream processing, and the pharmacokinetic behavior of the antibody are discussed, which will help in developing the yeast hosts for the efficient production of recombinant mAbs.
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Affiliation(s)
- Prabir Kumar Das
- Biochemical Engineering Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Ansuman Sahoo
- Biochemical Engineering Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Venkata Dasu Veeranki
- Biochemical Engineering Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
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3
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Wang X, Chang W, Khosraviani M, Phung W, Peng L, Cohen S, Andrews BT, Sun Y, Davies CW, Koerber JT, Yang J, Song A. Application of N-Terminal Site-Specific Biotin and Digoxigenin Conjugates to Clinical Anti-drug Antibody Assay Development. Bioconjug Chem 2024; 35:174-186. [PMID: 38050929 DOI: 10.1021/acs.bioconjchem.3c00421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Biotin- and digoxigenin (DIG)-conjugated therapeutic drugs are critical reagents used for the development of anti-drug antibody (ADA) assays for the assessment of immunogenicity. The current practice of generating biotin and DIG conjugates is to label a therapeutic antibody with biotin or DIG via primary amine groups on lysine or N-terminal residues. This approach modifies lysine residues nonselectively, which can impact the ability of an ADA assay to detect those ADAs that recognize epitopes located at or near the modified lysine residue(s). The impact of the lysine modification is considered greater for therapeutic antibodies that have a limited number of lysine residues, such as the variable heavy domain of heavy chain (VHH) antibodies. In this paper, for the first time, we report the application of site-specifically conjugated biotin- and DIG-VHH reagents to clinical ADA assay development using a model molecule, VHHA. The site-specific conjugation of biotin or DIG to VHHA was achieved by using an optimized reductive alkylation approach, which enabled the majority of VHHA molecules labeled with biotin or DIG at the desirable N-terminus, thereby minimizing modification of the protein after labeling and reducing the possibility of missing detection of ADAs. Head-to-head comparison of biophysical characterization data revealed that the site-specific biotin and DIG conjugates demonstrated overall superior quality to biotin- and DIG-VHHA prepared using the conventional amine coupling method, and the performance of the ADA assay developed using site-specific biotin and DIG conjugates met all acceptance criteria. The approach described here can be applied to the production of other therapeutic-protein- or antibody-based critical reagents that are used to support ligand binding assays.
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Affiliation(s)
- Xiangdan Wang
- BioAnalytical Sciences, Genentech, South San Francisco, California 94080, United States
| | - Wenping Chang
- Department of Peptide Therapeutics, Genentech, South San Francisco, California 94080, United States
| | - Mehraban Khosraviani
- BioAnalytical Sciences, Genentech, South San Francisco, California 94080, United States
| | - Wilson Phung
- Department of Microchemistry, Proteomics, and Lipidomics, Genentech, South San Francisco, California 94080, United States
| | - Lingling Peng
- Department of Peptide Therapeutics, Genentech, South San Francisco, California 94080, United States
| | - Sivan Cohen
- BioAnalytical Sciences, Genentech, South San Francisco, California 94080, United States
| | - Benjamin T Andrews
- BioAnalytical Sciences, Genentech, South San Francisco, California 94080, United States
| | - Yonglian Sun
- Antibody Engineering, Genentech, South San Francisco, California 94080, United States
| | - Christopher W Davies
- Antibody Engineering, Genentech, South San Francisco, California 94080, United States
| | - James T Koerber
- Antibody Engineering, Genentech, South San Francisco, California 94080, United States
| | - Jihong Yang
- BioAnalytical Sciences, Genentech, South San Francisco, California 94080, United States
| | - Aimin Song
- Department of Peptide Therapeutics, Genentech, South San Francisco, California 94080, United States
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4
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Harmsen MM, Ackerschott B, de Smit H. Serum immunoglobulin or albumin binding single-domain antibodies that enable tailored half-life extension of biologics in multiple animal species. Front Immunol 2024; 15:1346328. [PMID: 38352869 PMCID: PMC10862077 DOI: 10.3389/fimmu.2024.1346328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 01/12/2024] [Indexed: 02/16/2024] Open
Abstract
Single-domain antibody fragments (sdAbs) can be isolated from heavy-chain-only antibodies that occur in camelids or the heavy chain of conventional antibodies, that also occur in camelids. Therapeutic application of sdAbs is often complicated by their low serum half-life. Fusion to sdAb that bind to long-lived serum proteins albumin or IgG can prolong serum half-life of fusion partners. Such studies mostly focused on human application. For half-life prolongation in multiple animal species novel species cross-reacting sdAb are needed. We here describe the isolation from immunized llamas of sdAbs G6 and G13 that bound IgG of 9-10 species analysed, including horse, dog, cat, and swine, as well as sdAb A12 that bound horse, dog, swine and cat albumin. A12 bound albumin with 13 to 271 nM affinity dependent on the species. G13 affinity was difficult to determine by biolayer interferometry due to low and heterogeneous signals. G13 and G6 compete for the same binding domain on Fab fragments. Furthermore, they both lack the hallmark residues typical of camelid sdAbs derived from heavy-chain antibodies and had sequence characteristics typical of human sdAbs with high solubility and stability. This suggests they are derived from conventional llama antibodies. They most likely bind IgG through pairing with VL domains at the VH-VL interface rather than a paratope involving complementarity determining regions. None of the isolated sdAb interfered with FcRn binding to albumin or IgG, and thus do not prevent endosomal albumin/IgG-sdAb complex recycling. Fusions of albumin-binding sdAb A12 to several tetanus neurotoxin (TeNT) binding sdAbs prolonged the terminal serum half-life in piglets to about 4 days, comparable to authentic swine albumin. However, G13 conferred a much lower half-life of 0.84 days. Similarly, in horse, G13 prolonged half-life to only 1.2 days whereas A12 fused to two TeNT binding domains (T6T16A12) had a half-life of 21 days. The high half-life of T6T16A12, which earlier proved to be a highly potent TeNT antitoxin, further supports its therapeutic value. Furthermore, we have identified several additional sdAbs that enable tailored half-life extension of biologicals in multiple animal species.
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Affiliation(s)
- Michiel M. Harmsen
- Wageningen Bioveterinary Research, Wageningen University & Research, Lelystad, Netherlands
| | | | - Hans de Smit
- Research and Development, Smivet B.V., Wijchen, Netherlands
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5
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Struijf EM, De la O Becerra KI, Ruyken M, de Haas CJC, van Oosterom F, Siere DY, van Keulen JE, Heesterbeek DAC, Dolk E, Heukers R, Bardoel BW, Gros P, Rooijakkers SHM. Inhibition of cleavage of human complement component C5 and the R885H C5 variant by two distinct high affinity anti-C5 nanobodies. J Biol Chem 2023; 299:104956. [PMID: 37356719 PMCID: PMC10374974 DOI: 10.1016/j.jbc.2023.104956] [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: 03/06/2023] [Revised: 06/09/2023] [Accepted: 06/12/2023] [Indexed: 06/27/2023] Open
Abstract
The human complement system plays a crucial role in immune defense. However, its erroneous activation contributes to many serious inflammatory diseases. Since most unwanted complement effector functions result from C5 cleavage into C5a and C5b, development of C5 inhibitors, such as clinically approved monoclonal antibody eculizumab, are of great interest. Here, we developed and characterized two anti-C5 nanobodies, UNbC5-1 and UNbC5-2. Using surface plasmon resonance, we determined a binding affinity of 119.9 pM for UNbC5-1 and 7.7 pM for UNbC5-2. Competition experiments determined that the two nanobodies recognize distinct epitopes on C5. Both nanobodies efficiently interfered with C5 cleavage in a human serum environment, as they prevented red blood cell lysis via membrane attack complexes (C5b-9) and the formation of chemoattractant C5a. The cryo-EM structure of UNbC5-1 and UNbC5-2 in complex with C5 (3.6 Å resolution) revealed that the binding interfaces of UNbC5-1 and UNbC5-2 overlap with known complement inhibitors eculizumab and RaCI3, respectively. UNbC5-1 binds to the MG7 domain of C5, facilitated by a hydrophobic core and polar interactions, and UNbC5-2 interacts with the C5d domain mostly by salt bridges and hydrogen bonds. Interestingly, UNbC5-1 potently binds and inhibits C5 R885H, a genetic variant of C5 that is not recognized by eculizumab. Altogether, we identified and characterized two different, high affinity nanobodies against human C5. Both nanobodies could serve as diagnostic and/or research tools to detect C5 or inhibit C5 cleavage. Furthermore, the residues targeted by UNbC5-1 hold important information for therapeutic inhibition of different polymorphic variants of C5.
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Affiliation(s)
- Eva M Struijf
- Department Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Karla I De la O Becerra
- Structural Biochemistry Group, Faculty of Science, Department of Chemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Maartje Ruyken
- Department Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Carla J C de Haas
- Department Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Fleur van Oosterom
- Department Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Danique Y Siere
- Department Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Joanne E van Keulen
- Department Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Dani A C Heesterbeek
- Department Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | | | | | - Bart W Bardoel
- Department Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Piet Gros
- Structural Biochemistry Group, Faculty of Science, Department of Chemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Suzan H M Rooijakkers
- Department Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.
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6
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Bocancia-Mateescu LA, Stan D, Mirica AC, Ghita MG, Stan D, Ruta LL. Nanobodies as Diagnostic and Therapeutic Tools for Cardiovascular Diseases (CVDs). Pharmaceuticals (Basel) 2023; 16:863. [PMID: 37375810 PMCID: PMC10301117 DOI: 10.3390/ph16060863] [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: 05/10/2023] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
The aim of this review is to summarize some of the most recent work in the field of cardiovascular disease (CVD) diagnosis and therapy, focusing mainly on the role of nanobodies in the development of non-invasive imaging methods, diagnostic devices, and advanced biotechnological therapy tools. In the context of the increased number of people suffering from CVDs due to a variety of factors such as sedentariness, poor nutrition, stress, and smoking, there is an urgent need for new and improved diagnostic and therapeutic methods. Nanobodies can be easily produced in prokaryotes, lower eukaryotes, and plant and mammalian cells, and offer great advantages. In the diagnosis domain, they are mainly used as labeled probes that bind to certain surface receptors or other target molecules and give important information on the severity and extent of atherosclerotic lesions, using imaging methods such as contrast-enhanced ultrasound molecular imaging (CEUMI), positron emission tomography (PET), single-photon emission computed tomography coupled with computed tomography (SPECT/CT), and PET/CT. As therapy tools, nanobodies have been used either for transporting drug-loaded vesicles to specific targets or as inhibitors for certain enzymes and receptors, demonstrated to be involved in various CVDs.
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Affiliation(s)
| | - Dana Stan
- DDS Diagnostic, 7 Vulcan Judetu, 031427 Bucharest, Romania; (L.-A.B.-M.); (D.S.); (A.-C.M.); (M.G.G.); (D.S.)
- Medicine Doctoral School, Titu Maiorescu University, 031593 Bucharest, Romania
| | - Andreea-Cristina Mirica
- DDS Diagnostic, 7 Vulcan Judetu, 031427 Bucharest, Romania; (L.-A.B.-M.); (D.S.); (A.-C.M.); (M.G.G.); (D.S.)
- Advanced Polymer Materials Group, University Politehnica of Bucharest, 1–7 Gh. Polizu Street, 011061 Bucharest, Romania
| | - Miruna Gabriela Ghita
- DDS Diagnostic, 7 Vulcan Judetu, 031427 Bucharest, Romania; (L.-A.B.-M.); (D.S.); (A.-C.M.); (M.G.G.); (D.S.)
| | - Diana Stan
- DDS Diagnostic, 7 Vulcan Judetu, 031427 Bucharest, Romania; (L.-A.B.-M.); (D.S.); (A.-C.M.); (M.G.G.); (D.S.)
| | - Lavinia Liliana Ruta
- Faculty of Chemistry, University of Bucharest, 90-92 Panduri Street, 050663 Bucharest, Romania
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7
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Karaman E, Eyüpoğlu AE, Mahmoudi Azar L, Uysal S. Large-Scale Production of Anti-RNase A VHH Expressed in pyrG Auxotrophic Aspergillus oryzae. Curr Issues Mol Biol 2023; 45:4778-4795. [PMID: 37367053 DOI: 10.3390/cimb45060304] [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: 04/29/2023] [Revised: 05/15/2023] [Accepted: 05/18/2023] [Indexed: 06/28/2023] Open
Abstract
Nanobodies, also referred to as VHH antibodies, are the smallest fragments of naturally produced camelid antibodies and are ideal affinity reagents due to their remarkable properties. They are considered an alternative to monoclonal antibodies (mAbs) with potential utility in imaging, diagnostic, and other biotechnological applications given the difficulties associated with mAb expression. Aspergillus oryzae (A. oryzae) is a potential system for the large-scale expression and production of functional VHH antibodies that can be used to meet the demand for affinity reagents. In this study, anti-RNase A VHH was expressed under the control of the glucoamylase promoter in pyrG auxotrophic A. oryzae grown in a fermenter. The feature of pyrG auxotrophy, selected for the construction of a stable and efficient platform, was established using homologous recombination. Pull-down assay, size exclusion chromatography, and surface plasmon resonance were used to confirm the binding specificity of anti-RNase A VHH to RNase A. The affinity of anti-RNase A VHH was nearly 18.3-fold higher (1.9 nM) when expressed in pyrG auxotrophic A. oryzae rather than in Escherichia coli. This demonstrates that pyrG auxotrophic A. oryzae is a practical, industrially scalable, and promising biotechnological platform for the large-scale production of functional VHH antibodies with high binding activity.
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Affiliation(s)
- Elif Karaman
- Beykoz Institute of Life Sciences and Biotechnology, Bezmialem Vakif University, 34820 Istanbul, Turkey
- Department of Biotechnology, Institute of Health Sciences, Bezmialem Vakif University, 34093 Istanbul, Turkey
| | - Alp Ertunga Eyüpoğlu
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Bogazici University, 34450 Istanbul, Turkey
| | - Lena Mahmoudi Azar
- Beykoz Institute of Life Sciences and Biotechnology, Bezmialem Vakif University, 34820 Istanbul, Turkey
| | - Serdar Uysal
- Beykoz Institute of Life Sciences and Biotechnology, Bezmialem Vakif University, 34820 Istanbul, Turkey
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8
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van den Bor J, Bergkamp ND, Anbuhl SM, Dekker F, Comez D, Perez Almeria CV, Bosma R, White CW, Kilpatrick LE, Hill SJ, Siderius M, Smit MJ, Heukers R. NanoB 2 to monitor interactions of ligands with membrane proteins by combining nanobodies and NanoBRET. CELL REPORTS METHODS 2023; 3:100422. [PMID: 37056381 PMCID: PMC10088090 DOI: 10.1016/j.crmeth.2023.100422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 01/31/2023] [Accepted: 02/17/2023] [Indexed: 03/14/2023]
Abstract
The therapeutic potential of ligands targeting disease-associated membrane proteins is predicted by ligand-receptor binding constants, which can be determined using NanoLuciferase (NanoLuc)-based bioluminescence resonance energy transfer (NanoBRET) methods. However, the broad applicability of these methods is hampered by the restricted availability of fluorescent probes. We describe the use of antibody fragments, like nanobodies, as universal building blocks for fluorescent probes for use in NanoBRET. Our nanobody-NanoBRET (NanoB2) workflow starts with the generation of NanoLuc-tagged receptors and fluorescent nanobodies, enabling homogeneous, real-time monitoring of nanobody-receptor binding. Moreover, NanoB2 facilitates the assessment of receptor binding of unlabeled ligands in competition binding experiments. The broad significance is illustrated by the successful application of NanoB2 to different drug targets (e.g., multiple G protein-coupled receptors [GPCRs] and a receptor tyrosine kinase [RTK]) at distinct therapeutically relevant binding sites (i.e., extracellular and intracellular).
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Affiliation(s)
- Jelle van den Bor
- Receptor Biochemistry and Signaling group, Division of Medicinal Chemistry, Amsterdam Institute for Molecular and Life Science (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Nick D. Bergkamp
- Receptor Biochemistry and Signaling group, Division of Medicinal Chemistry, Amsterdam Institute for Molecular and Life Science (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Stephanie M. Anbuhl
- Receptor Biochemistry and Signaling group, Division of Medicinal Chemistry, Amsterdam Institute for Molecular and Life Science (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- QVQ Holding B.V., Utrecht, the Netherlands
| | - Françoise Dekker
- Receptor Biochemistry and Signaling group, Division of Medicinal Chemistry, Amsterdam Institute for Molecular and Life Science (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Dehan Comez
- Cell Signalling Research Group, Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, UK
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, the Midlands, UK
| | - Claudia V. Perez Almeria
- Receptor Biochemistry and Signaling group, Division of Medicinal Chemistry, Amsterdam Institute for Molecular and Life Science (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Reggie Bosma
- Receptor Biochemistry and Signaling group, Division of Medicinal Chemistry, Amsterdam Institute for Molecular and Life Science (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Carl W. White
- Cell Signalling Research Group, Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, UK
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, the Midlands, UK
| | - Laura E. Kilpatrick
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, the Midlands, UK
- Division of Bimolecular Science and Medicinal Chemistry, School of Pharmacy, Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | - Stephen J. Hill
- Cell Signalling Research Group, Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, UK
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, the Midlands, UK
| | - Marco Siderius
- Receptor Biochemistry and Signaling group, Division of Medicinal Chemistry, Amsterdam Institute for Molecular and Life Science (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Martine J. Smit
- Receptor Biochemistry and Signaling group, Division of Medicinal Chemistry, Amsterdam Institute for Molecular and Life Science (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Raimond Heukers
- Receptor Biochemistry and Signaling group, Division of Medicinal Chemistry, Amsterdam Institute for Molecular and Life Science (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- QVQ Holding B.V., Utrecht, the Netherlands
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9
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Zahrl RJ, Prielhofer R, Burgard J, Mattanovich D, Gasser B. Synthetic activation of yeast stress response improves secretion of recombinant proteins. N Biotechnol 2023; 73:19-28. [PMID: 36603701 DOI: 10.1016/j.nbt.2023.01.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 12/22/2022] [Accepted: 01/01/2023] [Indexed: 01/03/2023]
Abstract
Yeasts, such as Pichia pastoris (syn Komagataella spp.), are particularly suitable expression systems for emerging classes of recombinant proteins. Among them, recombinant antibody fragments, such as single-chain variable fragments (scFv) and single-domain antibodies (VHH), are credible alternatives to monoclonal antibodies. The availability of powerful genetic engineering and synthetic biology tools has facilitated improvement of this cell factory to overcome certain limitations. However, cell engineering to improve secretion often remains a trial-and-error approach and improvements are often specific to the protein produced. Where multiple genetic interventions are needed to remove bottlenecks in the process of recombinant protein secretion, this leads to a high number of combinatorial possibilities for creation of new production strains. Therefore, our aim was to exploit whole transcriptional programs (stress response pathways) in order to simplify the strain engineering of new production strains. Indeed, the artificial activation of the general stress response transcription factor Msn4, as well as synthetic versions thereof, could replace the secretion enhancing effect of several cytosolic chaperones. Greater than 4-fold improvements in recombinant protein secretion were achieved by overexpression of MSN4 or synMSN4, either alone or in combination with Hac1 or ER chaperones. With this concept we were able to successfully engineer strains reaching titers of more than 2.5 g/L scFv and 8 g/L VHH in bioreactor cultivations. This increased secretion capacity of different industrially relevant model proteins indicates that MSN4 overexpression most likely represents a general concept to improve recombinant protein production in yeast.
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Affiliation(s)
- Richard J Zahrl
- ACIB GmbH, Muthgasse 11, 1190 Vienna, Austria; Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Roland Prielhofer
- ACIB GmbH, Muthgasse 11, 1190 Vienna, Austria; Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Jonas Burgard
- ACIB GmbH, Muthgasse 11, 1190 Vienna, Austria; Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Diethard Mattanovich
- ACIB GmbH, Muthgasse 11, 1190 Vienna, Austria; Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Brigitte Gasser
- ACIB GmbH, Muthgasse 11, 1190 Vienna, Austria; Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190 Vienna, Austria.
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10
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Zahrl RJ, Prielhofer R, Ata Ö, Baumann K, Mattanovich D, Gasser B. Pushing and pulling proteins into the yeast secretory pathway enhances recombinant protein secretion. Metab Eng 2022; 74:36-48. [PMID: 36057427 DOI: 10.1016/j.ymben.2022.08.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 11/26/2022]
Abstract
Yeasts and especially Pichia pastoris (syn Komagataella spp.) are popular microbial expression systems for the production of recombinant proteins. One of the key advantages of yeast host systems is their ability to secrete the recombinant protein into the culture media. However, secretion of some recombinant proteins is less efficient. These proteins include antibody fragments such as Fabs or scFvs. We have recently identified translocation of nascent Fab fragments from the cytosol into the endoplasmic reticulum (ER) as one major bottleneck. Conceptually, this bottleneck requires engineering to increase the flux of recombinant proteins at the translocation step by pushing on the cytosolic side and pulling on the ER side. This engineering strategy is well-known in the field of metabolic engineering. To apply the push-and-pull strategy to recombinant protein secretion, we chose to modulate the cytosolic and ER Hsp70 cycles, which have a key impact on the translocation process. After identifying the relevant candidate factors of the Hsp70 cycles, we combined the push-and-pull factors in a single strain and achieved synergistic effects for antibody fragment secretion. With this concept we were able to successfully engineer strains and improve protein secretion up to 5-fold for different model protein classes. Overall, titers of more than 1.3 g/L Fab and scFv were reached in bioreactor cultivations.
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Affiliation(s)
- Richard J Zahrl
- ACIB GmbH, Muthgasse 11, 1190, Vienna, Austria; Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria
| | - Roland Prielhofer
- ACIB GmbH, Muthgasse 11, 1190, Vienna, Austria; Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria
| | - Özge Ata
- ACIB GmbH, Muthgasse 11, 1190, Vienna, Austria; Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria
| | - Kristin Baumann
- ACIB GmbH, Muthgasse 11, 1190, Vienna, Austria; Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria
| | - Diethard Mattanovich
- ACIB GmbH, Muthgasse 11, 1190, Vienna, Austria; Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria
| | - Brigitte Gasser
- ACIB GmbH, Muthgasse 11, 1190, Vienna, Austria; Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria.
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11
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Schriek AI, van Haaren MM, Poniman M, Dekkers G, Bentlage AEH, Grobben M, Vidarsson G, Sanders RW, Verrips T, Geijtenbeek TBH, Heukers R, Kootstra NA, de Taeye SW, van Gils MJ. Anti-HIV-1 Nanobody-IgG1 Constructs With Improved Neutralization Potency and the Ability to Mediate Fc Effector Functions. Front Immunol 2022; 13:893648. [PMID: 35651621 PMCID: PMC9150821 DOI: 10.3389/fimmu.2022.893648] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 04/13/2022] [Indexed: 11/13/2022] Open
Abstract
The most effective treatment for HIV-1, antiretroviral therapy, suppresses viral replication and averts the disease from progression. Nonetheless, there is a need for alternative treatments as it requires daily administration with the possibility of side effects and occurrence of drug resistance. Broadly neutralizing antibodies or nanobodies targeting the HIV-1 envelope glycoprotein are explored as alternative treatment, since they mediate viral suppression and contribute to the elimination of virus-infected cells. Besides neutralization potency and breadth, Fc-mediated effector functions of bNAbs also contribute to the in vivo efficacy. In this study multivalent J3, 2E7 and 1F10 anti-HIV-1 broadly neutralizing nanobodies were generated to improve neutralization potency and IgG1 Fc fusion was utilized to gain Fc-mediated effector functions. Bivalent and trivalent nanobodies, coupled using long glycine-serine linkers, showed increased binding to the HIV-1 Env and enhanced neutralization potency compared to the monovalent variant. Fusion of an IgG1 Fc domain to J3 improved neutralization potency compared to the J3-bihead and restored Fc-mediated effector functions such as antibody-dependent cellular phagocytosis and trogocytosis, and natural killer cell activation. Due to their neutralization breadth and potency and their ability to induce effector functions these nanobody-IgG1 constructs may prove to be valuable towards alternative HIV-1 therapies.
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Affiliation(s)
- Angela I Schriek
- Department of Medical Microbiology, Amsterdam UMC, Amsterdam Institute for Infection and Immunity, University of Amsterdam, Amsterdam, Netherlands
| | - Marlies M van Haaren
- Department of Medical Microbiology, Amsterdam UMC, Amsterdam Institute for Infection and Immunity, University of Amsterdam, Amsterdam, Netherlands
| | - Meliawati Poniman
- Department of Medical Microbiology, Amsterdam UMC, Amsterdam Institute for Infection and Immunity, University of Amsterdam, Amsterdam, Netherlands
| | | | - Arthur E H Bentlage
- Department of Experimental Immunohematology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Marloes Grobben
- Department of Medical Microbiology, Amsterdam UMC, Amsterdam Institute for Infection and Immunity, University of Amsterdam, Amsterdam, Netherlands
| | - Gestur Vidarsson
- Department of Experimental Immunohematology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Rogier W Sanders
- Department of Medical Microbiology, Amsterdam UMC, Amsterdam Institute for Infection and Immunity, University of Amsterdam, Amsterdam, Netherlands.,Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, United States
| | - Theo Verrips
- Department of Biology, Faculty of Sciences, Utrecht University, Utrecht, Netherlands.,VerLin BV, Utrecht, Netherlands
| | - Teunis B H Geijtenbeek
- Department of Experimental Immunology, Amsterdam UMC, Amsterdam Institute for Infection and Immunity, University of Amsterdam, Amsterdam, Netherlands
| | | | - Neeltje A Kootstra
- Department of Experimental Immunology, Amsterdam UMC, Amsterdam Institute for Infection and Immunity, University of Amsterdam, Amsterdam, Netherlands
| | - Steven W de Taeye
- Department of Medical Microbiology, Amsterdam UMC, Amsterdam Institute for Infection and Immunity, University of Amsterdam, Amsterdam, Netherlands
| | - Marit J van Gils
- Department of Medical Microbiology, Amsterdam UMC, Amsterdam Institute for Infection and Immunity, University of Amsterdam, Amsterdam, Netherlands
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12
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Harmsen MM, van Hagen-van Setten M, Willemsen PTJ. Small-Scale Secretory VHH Expression in Saccharomyces cerevisiae. Methods Mol Biol 2022; 2446:159-179. [PMID: 35157273 DOI: 10.1007/978-1-0716-2075-5_8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
After isolation of a single-domain antibody (VHH) binding to an antigen of interest, the soluble VHH is often produced in Escherichia coli. However, targeting VHH expression to the secretory pathway of Saccharomyces cerevisiae (baker's yeast) enables the secretion of correctly folded, soluble, disulfide-bonded, and N-glycosylated VHHs into the culture medium. Here, we describe the small-scale production of VHHs in baker's yeast in shaker flasks using both an episomal vector and a vector requiring genomic integration for higher VHH expression levels. This expression system results in the production of VHHs linked to the natural llama long hinge region including a single cysteine residue for partial dimerization. This format is especially suitable for the development of double antibody sandwich ELISAs by passive adsorption of unlabeled VHHs to polystyrene ELISA plates, antigen capture, and detection of the antigen of interest using a second biotinylated VHH. The procedures described here for detection of foot-and-mouth disease virus can also be applied to other antigens for which suitable VHHs are available.
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13
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Mashayekhi V, Schooten E, van Bergen En Henegouwen PMP, Kijanka MM, Oliveira S. Nanobody-Targeted Photodynamic Therapy: Nanobody Production and Purification. Methods Mol Biol 2022; 2451:481-493. [PMID: 35505026 DOI: 10.1007/978-1-0716-2099-1_21] [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 have recently been introduced to the field of photodynamic therapy (PDT) as a very promising strategy to target photosensitizers selectively to cancer cells. Nanobodies are known for their characteristic small size (15 kDa), high specificity, and high binding affinities. These features allow rapid accumulation of nanobody-photosensitizer conjugates at the tumor site and rapid clearance of unbound fractions, and thus illumination for activation is possible 1 or 2 h postinjection. Preclinical studies have shown extensive tumor damage after nanobody-targeted PDT . This chapter addresses the first steps toward preparing nanobody-photosensitizer conjugates, which are the nanobody production and purification. The protocol for nanobody production addresses either medium- or large-scale bacterial expression, while the nanobody purification is described for two main strategies: affinity chromatography and ion-exchange chromatography. For the first strategy, protocols are described for different affinity tags and purification from either medium-scale or large-scale productions. For the second strategy, the protocol given is for purification from a large-scale production.
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Affiliation(s)
- Vida Mashayekhi
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | | | | | | | - Sabrina Oliveira
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands.
- Pharmaceutics, Department of Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, The Netherlands.
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14
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de Smit H, Ackerschott B, Tierney R, Stickings P, Harmsen MM. A novel single-domain antibody multimer that potently neutralizes tetanus neurotoxin. Vaccine X 2021; 8:100099. [PMID: 34169269 PMCID: PMC8207222 DOI: 10.1016/j.jvacx.2021.100099] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 04/17/2021] [Accepted: 05/27/2021] [Indexed: 11/30/2022] Open
Abstract
Tetanus antitoxin, produced in animals, has been used for the prevention and treatment of tetanus for more than 100 years. The availability of antitoxins, ethical issues around production, and risks involved in the use of animal derived serum products are a concern. We therefore developed a llama derived single-domain antibody (VHH) multimer to potentially replace the conventional veterinary product. In total, 28 different tetanus neurotoxin (TeNT) binding VHHs were isolated, 14 of which were expressed in yeast for further characterization. Four VHH monomers (T2, T6, T15 and T16) binding TeNT with high affinity (KD < 1 nM), covering different antigenic domains as revealed by epitope binning, and including 3 monomers (T6, T15 and T16) that inhibited TeNT binding to neuron gangliosides, were chosen as building blocks to generate 11 VHH multimers. These multimers contained either 1 or 2 different TeNT binding VHHs fused to 1 VHH binding to either albumin (A12) or immunoglobulin (G13) to extend serum half-life in animals. Multimers consisting of 2 TeNT binding VHHs showed more than a 10-fold increase in affinity (KD of 4-23 pM) when compared to multimers containing only one TeNT binding VHH. The T6 and T16 VHHs showed synergistic in vivo TeNT neutralization and, when incorporated into a single VHH trimer (T6T16A12), they showed a very high TeNT neutralizing capacity (1,510 IU/mg).
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Affiliation(s)
- Hans de Smit
- R&D, Smivet B.V., Diemewei 4110, 6605XC Wijchen, the Netherlands
| | - Bart Ackerschott
- R&D, Smivet B.V., Diemewei 4110, 6605XC Wijchen, the Netherlands
| | - Robert Tierney
- Division of Bacteriology, National Institute for Biological Standards and Control (NIBSC), MHRA, Potters Bar, Hertfordshire EN6 3QG, UK
| | - Paul Stickings
- Division of Bacteriology, National Institute for Biological Standards and Control (NIBSC), MHRA, Potters Bar, Hertfordshire EN6 3QG, UK
| | - Michiel M. Harmsen
- Wageningen Bioveterinary Research, P.O. Box 65, 8200 AB Lelystad, the Netherlands
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15
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A Novel Nanobody Scaffold Optimized for Bacterial Expression and Suitable for the Construction of Ribosome Display Libraries. Mol Biotechnol 2019; 62:43-55. [DOI: 10.1007/s12033-019-00224-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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16
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Miura N, Miyamoto K, Ohtani Y, Yaginuma K, Aburaya S, Kitagawa Y, Aoki W, Ueda M. Domain swapping of complementarity-determining region in nanobodies produced by Pichia pastoris. AMB Express 2019; 9:107. [PMID: 31309388 PMCID: PMC6629726 DOI: 10.1186/s13568-019-0833-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 07/05/2019] [Indexed: 11/10/2022] Open
Abstract
Easy preparation of chimeric nanobodies with various scaffolds is important for customizing abilities of nanobodies toward practical utilization. To accomplish high-throughput production of various nanobodies, utilization of microbes is an attractive option. In the present study, various chimeric nanobodies were prepared using the methylotrophic yeast Pichia pastoris. We designed chimeric nanobodies with complementarity-determining regions (CDRs) against green fluorescent protein (GFP) or cluster of differentiation 4 (CD4) based on the scaffold of GFP-nanobody. FLAG-tagged chimeric nanobodies were prepared by one-step cloning and produced using P. pastoris. Secreted chimeric nanobodies were purified from the culture media of P. pastoris transformants. Relative binding abilities of purified chimeric nanobodies to GFP and CD4 was tested using a BIACORE T-200. P. pastoris successfully produced a high yield of FLAG-tagged chimeric nanobodies. FLAG-tagged GFP- and CD4-nanobodies were shown to specifically bind to GFP and CD4, respectively. Chimeric nanobodies, in which the CDR2 or 3 of GFP-nanobody was replaced with CDRs of CD4-nanobody, acquired the ability to bind to CD4 without binding to GFP. These results demonstrate successful production of functional chimeric nanobodies using P. pastoris. These results also suggest that swapping of CDRs, especially CDRs 2 or 3, potentially enables a novel method of creating nanobodies.
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17
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Heukers R, Mashayekhi V, Ramirez-Escudero M, de Haard H, Verrips TC, van Bergen En Henegouwen PMP, Oliveira S. VHH-Photosensitizer Conjugates for Targeted Photodynamic Therapy of Met-Overexpressing Tumor Cells. Antibodies (Basel) 2019; 8:antib8020026. [PMID: 31544832 PMCID: PMC6640711 DOI: 10.3390/antib8020026] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 03/09/2019] [Accepted: 03/28/2019] [Indexed: 01/10/2023] Open
Abstract
Photodynamic therapy (PDT) is an approach that kills (cancer) cells by the local production of toxic reactive oxygen species upon the local illumination of a photosensitizer (PS). The specificity of PDT has been further enhanced by the development of a new water-soluble PS and by the specific delivery of PS via conjugation to tumor-targeting antibodies. To improve tissue penetration and shorten photosensitivity, we have recently introduced nanobodies, also known as VHH (variable domains from the heavy chain of llama heavy chain antibodies), for targeted PDT of cancer cells overexpressing the epidermal growth factor receptor (EGFR). Overexpression and activation of another cancer-related receptor, the hepatocyte growth factor receptor (HGFR, c-Met or Met) is also involved in the progression and metastasis of a large variety of malignancies. In this study we evaluate whether anti-Met VHHs conjugated to PS can also serve as a biopharmaceutical for targeted PDT. VHHs targeting the SEMA (semaphorin-like) subdomain of Met were provided with a C-terminal tag that allowed both straightforward purification from yeast supernatant and directional conjugation to the PS IRDye700DX using maleimide chemistry. The generated anti-Met VHH-PS showed nanomolar binding affinity and, upon illumination, specifically killed MKN45 cells with nanomolar potency. This study shows that Met can also serve as a membrane target for targeted PDT.
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Affiliation(s)
- Raimond Heukers
- QVQ Holding BV, Yalelaan 1, 3584 CL Utrecht, The Netherlands.
| | - Vida Mashayekhi
- Cell Biology Division, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
| | - Mercedes Ramirez-Escudero
- Crystal & Structural Chemistry, Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
| | - Hans de Haard
- Argenx BVBA, Industriepark-Zwijnaarde 7, 9052 Gent, Belgium.
| | - Theo C Verrips
- QVQ Holding BV, Yalelaan 1, 3584 CL Utrecht, The Netherlands.
| | - Paul M P van Bergen En Henegouwen
- Cell Biology Division, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
| | - Sabrina Oliveira
- Cell Biology Division, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
- Pharmaceutics Division, Department of Pharmaceutical Sciences, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands.
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18
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Suzuki T, Mochizuki Y, Kimura S, Akazawa-Ogawa Y, Hagihara Y, Nemoto N. Anti-survivin single-domain antibodies derived from an artificial library including three synthetic random regions by in vitro selection using cDNA display. Biochem Biophys Res Commun 2018; 503:2054-2060. [DOI: 10.1016/j.bbrc.2018.07.158] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 07/31/2018] [Indexed: 12/21/2022]
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19
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Kumar R, Kumari R, Khan L, Sankhyan A, Parray HA, Tiwari A, Wig N, Sinha S, Luthra K. Isolation and Characterization of Cross-Neutralizing Human Anti-V3 Single-Chain Variable Fragments (scFvs) Against HIV-1 from an Antigen Preselected Phage Library. Appl Biochem Biotechnol 2018; 187:1011-1027. [DOI: 10.1007/s12010-018-2862-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 08/13/2018] [Indexed: 02/07/2023]
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20
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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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21
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Koskela EV, de Ruijter JC, Frey AD. Following nature's roadmap: folding factors from plasma cells led to improvements in antibody secretion in S. cerevisiae. Biotechnol J 2017; 12. [PMID: 28429845 DOI: 10.1002/biot.201600631] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Revised: 04/12/2017] [Accepted: 04/20/2017] [Indexed: 12/21/2022]
Abstract
Therapeutic protein production in yeast is a reality in industry with an untapped potential to expand to more complex proteins, such as full-length antibodies. Despite numerous engineering approaches, cellular limitations are preventing the use of Saccharomyces cerevisiae as the titers of recombinant antibodies are currently not competitive. Instead of a host specific approach, the possibility of adopting the features from native producers of antibodies, plasma cells, to improve antibody production in yeast. A subset of mammalian folding factors upregulated in plasma cells for expression in yeast and screened for beneficial effects on antibody secretion using a high-throughput ELISA platform was selected. Co-expression of the mammalian chaperone BiP, the co-chaperone GRP170, or the peptidyl-prolyl isomerase FKBP2, with the antibody improved specific product yields up to two-fold. By comparing strains expressing FKBP2 or the yeast PPIase Cpr5p, the authors demonstrate that speeding up peptidyl-prolyl isomerization by upregulation of catalyzing enzymes is a key factor to improve antibody titers in yeast. The findings show that following the route of plasma cells can improve product titers and contribute to developing an alternative yeast-based antibody factory.
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Affiliation(s)
- Essi V Koskela
- Department of Bioproducts and Biosystems, Aalto University, Espoo, Finland
| | - Jorg C de Ruijter
- Department of Bioproducts and Biosystems, Aalto University, Espoo, Finland.,Current address: Department of Biocatalysis and Isotope Chemistry, Almac Sciences, Craigavon, Northern Ireland, United Kingdom
| | - Alexander D Frey
- Department of Bioproducts and Biosystems, Aalto University, Espoo, Finland
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22
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Li W, Prabakaran P, Chen W, Zhu Z, Feng Y, Dimitrov DS. Antibody Aggregation: Insights from Sequence and Structure. Antibodies (Basel) 2016; 5:antib5030019. [PMID: 31558000 PMCID: PMC6698864 DOI: 10.3390/antib5030019] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 08/03/2016] [Accepted: 08/04/2016] [Indexed: 12/12/2022] Open
Abstract
Monoclonal antibodies (mAbs) are the fastest-growing biological therapeutics with important applications ranging from cancers, autoimmunity diseases and metabolic disorders to emerging infectious diseases. Aggregation of mAbs continues to be a major problem in their developability. Antibody aggregation could be triggered by partial unfolding of its domains, leading to monomer-monomer association followed by nucleation and growth. Although the aggregation propensities of antibodies and antibody-based proteins can be affected by the external experimental conditions, they are strongly dependent on the intrinsic antibody properties as determined by their sequences and structures. In this review, we describe how the unfolding and aggregation susceptibilities of IgG could be related to their cognate sequences and structures. The impact of antibody domain structures on thermostability and aggregation propensities, and effective strategies to reduce aggregation are discussed. Finally, the aggregation of antibody-drug conjugates (ADCs) as related to their sequence/structure, linker payload, conjugation chemistry and drug-antibody ratio (DAR) is reviewed.
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Affiliation(s)
- Wei Li
- Protein Interactions Section, Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA.
| | | | - Weizao Chen
- Protein Interactions Section, Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA.
| | - Zhongyu Zhu
- Protein Interactions Section, Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA.
| | - Yang Feng
- Protein Interactions Section, Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA.
| | - Dimiter S Dimitrov
- Protein Interactions Section, Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA.
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23
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Bever CS, Dong JX, Vasylieva N, Barnych B, Cui Y, Xu ZL, Hammock BD, Gee SJ. VHH antibodies: emerging reagents for the analysis of environmental chemicals. Anal Bioanal Chem 2016; 408:5985-6002. [PMID: 27209591 DOI: 10.1007/s00216-016-9585-x] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Revised: 03/24/2016] [Accepted: 04/19/2016] [Indexed: 01/28/2023]
Abstract
A VHH antibody (or nanobody) is the antigen binding fragment of heavy chain only antibodies. Discovered nearly 25 years ago, they have been investigated for their use in clinical therapeutics and immunodiagnostics, and more recently for environmental monitoring applications. A new and valuable immunoreagent for the analysis of small molecular weight environmental chemicals, VHH will overcome many pitfalls encountered with conventional reagents. In the work so far, VHH antibodies often perform comparably to conventional antibodies for small molecule analysis, are amenable to numerous genetic engineering techniques, and show ease of adaption to other immunodiagnostic platforms for use in environmental monitoring. Recent reviews cover the structure and production of VHH antibodies as well as their use in clinical settings. However, no report focuses on the use of these VHH antibodies to detect small environmental chemicals (MW < 1500 Da). This review article summarizes the efforts made to produce VHHs to various environmental targets, compares the VHH-based assays with conventional antibody assays, and discusses the advantages and limitations in developing these new antibody reagents particularly to small molecule targets. Graphical Abstract Overview of the production of VHHs to small environmental chemicals and highlights of the utility of these new emerging reagents.
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Affiliation(s)
- Candace S Bever
- Department of Entomology and Nematology and UCD Comprehensive Cancer Center, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Jie-Xian Dong
- Department of Entomology and Nematology and UCD Comprehensive Cancer Center, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Natalia Vasylieva
- Department of Entomology and Nematology and UCD Comprehensive Cancer Center, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Bogdan Barnych
- Department of Entomology and Nematology and UCD Comprehensive Cancer Center, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Yongliang Cui
- Department of Entomology and Nematology and UCD Comprehensive Cancer Center, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA.,Department of Oral Biology, School of Dental Medicine, University of Buffalo, State University of New York, Buffalo, NY, 14214, USA
| | - Zhen-Lin Xu
- Department of Entomology and Nematology and UCD Comprehensive Cancer Center, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Bruce D Hammock
- Department of Entomology and Nematology and UCD Comprehensive Cancer Center, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Shirley J Gee
- Department of Entomology and Nematology and UCD Comprehensive Cancer Center, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA.
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24
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Neutralization of Clostridium difficile Toxin B Mediated by Engineered Lactobacilli That Produce Single-Domain Antibodies. Infect Immun 2015; 84:395-406. [PMID: 26573738 DOI: 10.1128/iai.00870-15] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Accepted: 11/08/2015] [Indexed: 02/06/2023] Open
Abstract
Clostridium difficile is the primary cause of nosocomial antibiotic-associated diarrhea in the Western world. The major virulence factors of C. difficile are two exotoxins, toxin A (TcdA) and toxin B (TcdB), which cause extensive colonic inflammation and epithelial damage manifested by episodes of diarrhea. In this study, we explored the basis for an oral antitoxin strategy based on engineered Lactobacillus strains expressing TcdB-neutralizing antibody fragments in the gastrointestinal tract. Variable domain of heavy chain-only (VHH) antibodies were raised in llamas by immunization with the complete TcdB toxin. Four unique VHH fragments neutralizing TcdB in vitro were isolated. When these VHH fragments were expressed in either secreted or cell wall-anchored form in Lactobacillus paracasei BL23, they were able to neutralize the cytotoxic effect of the toxin in an in vitro cell-based assay. Prophylactic treatment with a combination of two strains of engineered L. paracasei BL23 expressing two neutralizing anti-TcdB VHH fragments (VHH-B2 and VHH-G3) delayed killing in a hamster protection model where the animals were challenged with spores of a TcdA(-) TcdB(+) strain of C. difficile (P < 0.05). Half of the hamsters in the treated group survived until the termination of the experiment at day 5 and showed either no damage or limited inflammation of the colonic mucosa despite having been colonized with C. difficile for up to 4 days. The protective effect in the hamster model suggests that the strategy could be explored as a supplement to existing therapies for patients.
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de Marco A. Recombinant antibody production evolves into multiple options aimed at yielding reagents suitable for application-specific needs. Microb Cell Fact 2015; 14:125. [PMID: 26330219 PMCID: PMC4557595 DOI: 10.1186/s12934-015-0320-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Accepted: 08/20/2015] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Antibodies have been a pillar of basic research, while their relevance in clinical diagnostics and therapy is constantly growing. Consequently, the production of both conventional and fragment antibodies constantly faces more demanding challenges for the improvement of their quantity and quality. The answer to such an increasing need has been the development of a wide array of formats and alternative production platforms. This review offers a critical comparison and evaluation of the different options to help the researchers interested in expressing recombinant antibodies in their choice. RESULTS Rather than the compilation of an exhaustive list of the recent publications in the field, this review intendeds to analyze the development of the most innovative or fast-growing strategies. These have been illustrated with some significant examples and, when possible, compared with the existing alternatives. Space has also been given to those solutions that might represent interesting opportunities or that investigate critical aspects of the production optimization but for which the available data as yet do not allow for a definitive judgment. CONCLUSIONS The take-home message is that there is a clear process of progressive diversification concerning the antibody expression platforms and an effort to yield directly application-adapted immune-reagents rather than generic naked antibodies that need further in vitro modification steps before becoming usable.
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Affiliation(s)
- Ario de Marco
- Department of Biomedical Sciences and Engineering, University of Nova Gorica, Glavni Trg 9, 5261, Vipava, Slovenia.
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Mizukami M, Tokunaga H, Onishi H, Ueno Y, Hanagata H, Miyazaki N, Kiyose N, Ito Y, Ishibashi M, Hagihara Y, Arakawa T, Miyauchi A, Tokunaga M. Highly efficient production of VHH antibody fragments in Brevibacillus choshinensis expression system. Protein Expr Purif 2015; 105:23-32. [DOI: 10.1016/j.pep.2014.09.017] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 09/24/2014] [Accepted: 09/25/2014] [Indexed: 11/29/2022]
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Kim DY, To R, Kandalaft H, Ding W, van Faassen H, Luo Y, Schrag JD, St-Amant N, Hefford M, Hirama T, Kelly JF, MacKenzie R, Tanha J. Antibody light chain variable domains and their biophysically improved versions for human immunotherapy. MAbs 2014; 6:219-35. [PMID: 24423624 PMCID: PMC3929445 DOI: 10.4161/mabs.26844] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
We set out to gain deeper insight into the potential of antibody light chain variable domains (VLs) as immunotherapeutics. To this end, we generated a naïve human VL phage display library and, by using a method previously shown to select for non-aggregating antibody heavy chain variable domains (VHs), we isolated a diversity of VL domains by panning the library against B cell super-antigen protein L. Eight domains representing different germline origins were shown to be non-aggregating at concentrations as high as 450 µM, indicating VL repertoires are a rich source of non-aggregating domains. In addition, the VLs demonstrated high expression yields in E. coli, protein L binding and high reversibility of thermal unfolding. A side-by-side comparison with a set of non-aggregating human VHs revealed that the VLs had similar overall profiles with respect to melting temperature (Tm), reversibility of thermal unfolding and resistance to gastrointestinal proteases. Successful engineering of a non-canonical disulfide linkage in the core of VLs did not compromise the non-aggregation state or protein L binding properties. Furthermore, the introduced disulfide bond significantly increased their Tms, by 5.5–17.5 °C, and pepsin resistance, although it somewhat reduced expression yields and subtly changed the structure of VLs. Human VLs and engineered versions may make suitable therapeutics due to their desirable biophysical features. The disulfide linkage-engineered VLs may be the preferred therapeutic format because of their higher stability, especially for oral therapy applications that necessitate high resistance to the stomach’s acidic pH and pepsin.
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Affiliation(s)
- Dae Young Kim
- Human Health Therapeutics; National Research Council Canada; Ottawa, ON Canada
| | - Rebecca To
- Human Health Therapeutics; National Research Council Canada; Ottawa, ON Canada
| | - Hiba Kandalaft
- Human Health Therapeutics; National Research Council Canada; Ottawa, ON Canada
| | - Wen Ding
- Human Health Therapeutics; National Research Council Canada; Ottawa, ON Canada
| | - Henk van Faassen
- Human Health Therapeutics; National Research Council Canada; Ottawa, ON Canada
| | - Yan Luo
- Human Health Therapeutics; National Research Council Canada; Ottawa, ON Canada
| | - Joseph D Schrag
- Human Health Therapeutics; National Research Council Canada; Montréal, QC Canada
| | - Nadereh St-Amant
- Centre for Vaccine Evaluation; Biologics and Genetic Therapies Directorate;, Health Canada; Ottawa, ON Canada
| | - Mary Hefford
- Centre for Vaccine Evaluation; Biologics and Genetic Therapies Directorate;, Health Canada; Ottawa, ON Canada
| | - Tomoko Hirama
- Human Health Therapeutics; National Research Council Canada; Ottawa, ON Canada
| | - John F Kelly
- Human Health Therapeutics; National Research Council Canada; Ottawa, ON Canada
| | - Roger MacKenzie
- Human Health Therapeutics; National Research Council Canada; Ottawa, ON Canada; School of Environmental Sciences; Ontario Agricultural College; University of Guelph; Guelph, ON Canada
| | - Jamshid Tanha
- Human Health Therapeutics; National Research Council Canada; Ottawa, ON Canada; School of Environmental Sciences; Ontario Agricultural College; University of Guelph; Guelph, ON Canada; Department of Biochemistry, Microbiology, and Immunology; University of Ottawa; Ottawa, ON Canada
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De Meyer T, Muyldermans S, Depicker A. Nanobody-based products as research and diagnostic tools. Trends Biotechnol 2014; 32:263-70. [PMID: 24698358 DOI: 10.1016/j.tibtech.2014.03.001] [Citation(s) in RCA: 303] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 02/17/2014] [Accepted: 03/05/2014] [Indexed: 01/25/2023]
Abstract
Since the serendipitous discovery 20 years ago of bona fide camelid heavy-chain antibodies, their single-domain antigen-binding fragments, known as VHHs or nanobodies, have received a progressively growing interest. As a result of the beneficial properties of these stable recombinant entities, they are currently highly valued proteins for multiple applications, including fundamental research, diagnostics, and therapeutics. Today, with the original patents expiring, even more academic and industrial groups are expected to explore innovative VHH applications. Here, we provide a thorough overview of novel implementations of VHHs as research and diagnostic tools, and of the recently evaluated production platforms for several VHHs and VHH-derived antibody formats.
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Affiliation(s)
- Thomas De Meyer
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Serge Muyldermans
- Structural Biology Research Center, VIB, 1050 Brussel, Belgium; Research Unit of Cellular and Molecular Immunology, Vrije Universiteit Brussel, 1050 Brussel, Belgium
| | - Ann Depicker
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium.
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Frenzel A, Hust M, Schirrmann T. Expression of recombinant antibodies. Front Immunol 2013; 4:217. [PMID: 23908655 PMCID: PMC3725456 DOI: 10.3389/fimmu.2013.00217] [Citation(s) in RCA: 219] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 07/15/2013] [Indexed: 12/15/2022] Open
Abstract
Recombinant antibodies are highly specific detection probes in research, diagnostics, and have emerged over the last two decades as the fastest growing class of therapeutic proteins. Antibody generation has been dramatically accelerated by in vitro selection systems, particularly phage display. An increasing variety of recombinant production systems have been developed, ranging from Gram-negative and positive bacteria, yeasts and filamentous fungi, insect cell lines, mammalian cells to transgenic plants and animals. Currently, almost all therapeutic antibodies are still produced in mammalian cell lines in order to reduce the risk of immunogenicity due to altered, non-human glycosylation patterns. However, recent developments of glycosylation-engineered yeast, insect cell lines, and transgenic plants are promising to obtain antibodies with "human-like" post-translational modifications. Furthermore, smaller antibody fragments including bispecific antibodies without any glycosylation are successfully produced in bacteria and have advanced to clinical testing. The first therapeutic antibody products from a non-mammalian source can be expected in coming next years. In this review, we focus on current antibody production systems including their usability for different applications.
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Affiliation(s)
- André Frenzel
- Abteilung Biotechnologie, Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Braunschweig, Germany
| | - Michael Hust
- Abteilung Biotechnologie, Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Braunschweig, Germany
| | - Thomas Schirrmann
- Abteilung Biotechnologie, Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Braunschweig, Germany
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