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Xu RG, Tiede C, Calabrese AN, Cheah LT, Adams TL, Gauer JS, Hindle MS, Webb BA, Yates DM, Slater A, Duval C, Naseem KM, Herr AB, Tomlinson DC, Watson SP, Ariëns RAS. Affimer reagents as tool molecules to modulate platelet GPVI-ligand interactions and specifically bind GPVI dimer. Blood Adv 2024; 8:3917-3928. [PMID: 38838227 DOI: 10.1182/bloodadvances.2024012689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 05/24/2024] [Accepted: 05/27/2024] [Indexed: 06/07/2024] Open
Abstract
ABSTRACT Glycoprotein VI (GPVI) plays a key role in collagen-induced platelet aggregation. Affimers are engineered binding protein alternatives to antibodies. We screened and characterized GPVI-binding Affimers as novel tools to probe GPVI function. Among the positive clones, M17, D22, and D18 bound GPVI with the highest affinities (dissociation constant (KD) in the nanomolar range). These Affimers inhibited GPVI-collagen-related peptide (CRP)-XL/collagen interactions, CRP-XL/collagen-induced platelet aggregation, and D22 also inhibited in vitro thrombus formation on a collagen surface under flow. D18 bound GPVI dimer but not monomer. GPVI binding was increased for D18 but not M17/D22 upon platelet activation by CRP-XL and adenosine 5'-diphosphate. D22 but not M17/D18 displaced nanobody 2 (Nb2) binding to GPVI, indicating similar epitopes for D22 with Nb2 but not for M17/D18. Mapping of binding sites revealed that D22 binds a site that overlaps with Nb2 on the D1 domain, whereas M17 targets a site on the D2 domain, overlapping in part with the glenzocimab binding site, a humanized GPVI antibody fragment antigen-binding fragment. D18 targets a new region on the D2 domain. We found that D18 is a stable noncovalent dimer and forms a stable complex with dimeric GPVI with 1:1 stoichiometry. Taken together, our data demonstrate that Affimers modulate GPVI-ligand interactions and bind different sites on GPVI D1/D2 domains. D18 is dimer-specific and could be used as a tool to detect GPVI dimerization or clustering in platelets. A dimeric epitope regulating ligand binding was identified on the GPVI D2 domain, which could be used for the development of novel bivalent antithrombotic agents selectively targeting GPVI dimer on platelets.
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Affiliation(s)
- Rui-Gang Xu
- Discovery and Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, United Kingdom
| | - Christian Tiede
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Antonio N Calabrese
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Lih T Cheah
- Discovery and Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, United Kingdom
| | - Thomas L Adams
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Julia S Gauer
- Discovery and Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, United Kingdom
| | - Matthew S Hindle
- Discovery and Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, United Kingdom
- Centre for Biomedical Science Research, School of Health, Leeds Beckett University, Leeds, United Kingdom
| | - Beth A Webb
- Discovery and Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, United Kingdom
| | - Daisie M Yates
- Discovery and Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, United Kingdom
| | - Alexandre Slater
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Cédric Duval
- Discovery and Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, United Kingdom
| | - Khalid M Naseem
- Discovery and Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, United Kingdom
| | - Andrew B Herr
- Division of Immunobiology and Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Darren C Tomlinson
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Steve P Watson
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Robert A S Ariëns
- Discovery and Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, United Kingdom
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2
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Giang KA, Boxaspen T, Diao Y, Nilvebrant J, Kosugi-Kanaya M, Kanaya M, Krokeide SZ, Lehmann F, Svensson Gelius S, Malmberg KJ, Nygren PÅ. Affibody-based hBCMA x CD16 dual engagers for NK cell-mediated killing of multiple myeloma cells. N Biotechnol 2023; 77:139-148. [PMID: 37673373 DOI: 10.1016/j.nbt.2023.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/16/2023] [Accepted: 09/03/2023] [Indexed: 09/08/2023]
Abstract
We describe the development and characterization of the (to date) smallest Natural Killer (NK) cell re-directing human B Cell Maturation Antigen (hBCMA) x CD16 dual engagers for potential treatment of multiple myeloma, based on combinations of small 58 amino acid, non-immunoglobulin, affibody affinity proteins. Affibody molecules to human CD16a were selected from a combinatorial library by phage display resulting in the identification of three unique binders with affinities (KD) for CD16a in the range of 100 nM-3 µM. The affibody exhibiting the highest affinity demonstrated insensitivity towards the CD16a allotype (158F/V) and did not interfere with IgG (Fc) binding to CD16a. For the construction of hBCMA x CD16 dual engagers, different CD16a binding arms, including bi-paratopic affibody combinations, were genetically fused to a high-affinity hBCMA-specific affibody. Such 15-23 kDa dual engager constructs showed simultaneous hBCMA and CD16a binding ability and could efficiently activate resting primary NK cells and trigger specific lysis of a panel of hBCMA-positive multiple myeloma cell lines. Hence, we report a novel class of uniquely small NK cell engagers with specific binding properties and potent functional profiles.
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Affiliation(s)
- Kim Anh Giang
- Department of Protein Science, Div. Protein Engineering, AlbaNova University Center, KTH Royal Institute of Technology, S-114 21 Stockholm, Sweden
| | - Thorstein Boxaspen
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, N-0424 Oslo, Norway; Precision Immunotherapy Alliance, Institute of Clinical Medicine, University of Oslo, N-0313 Oslo, Norway
| | - Yumei Diao
- Oncopeptides AB, S-171 48 Stockholm, Sweden
| | - Johan Nilvebrant
- Department of Protein Science, Div. Protein Engineering, AlbaNova University Center, KTH Royal Institute of Technology, S-114 21 Stockholm, Sweden
| | - Mizuha Kosugi-Kanaya
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, N-0424 Oslo, Norway; Precision Immunotherapy Alliance, Institute of Clinical Medicine, University of Oslo, N-0313 Oslo, Norway
| | - Minoru Kanaya
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, N-0424 Oslo, Norway; Precision Immunotherapy Alliance, Institute of Clinical Medicine, University of Oslo, N-0313 Oslo, Norway
| | - Silje Zandstra Krokeide
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, N-0424 Oslo, Norway; Precision Immunotherapy Alliance, Institute of Clinical Medicine, University of Oslo, N-0313 Oslo, Norway
| | | | | | - Karl-Johan Malmberg
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, N-0424 Oslo, Norway; Precision Immunotherapy Alliance, Institute of Clinical Medicine, University of Oslo, N-0313 Oslo, Norway.
| | - Per-Åke Nygren
- Department of Protein Science, Div. Protein Engineering, AlbaNova University Center, KTH Royal Institute of Technology, S-114 21 Stockholm, Sweden; Science For Life Laboratory, S-171 65 Solna, Sweden.
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3
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Roper BWR, Tiede C, Abdul-Zani I, Cuthbert GA, Jade D, Al-Aufi A, Critchley WR, Saikia Q, Homer-Vanniasinkam S, Sawamura T, McPherson MJ, Harrison MA, Tomlinson DC, Ponnambalam S. "Affimer" synthetic protein scaffolds block oxidized LDL binding to the LOX-1 scavenger receptor and inhibit ERK1/2 activation. J Biol Chem 2023; 299:105325. [PMID: 37805141 PMCID: PMC10641530 DOI: 10.1016/j.jbc.2023.105325] [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: 01/20/2023] [Revised: 09/11/2023] [Accepted: 09/21/2023] [Indexed: 10/09/2023] Open
Abstract
In multicellular organisms, a variety of lipid-protein particles control the systemic flow of triacylglycerides, cholesterol, and fatty acids between cells in different tissues. The chemical modification by oxidation of these particles can trigger pathological responses, mediated by a group of membrane proteins termed scavenger receptors. The lectin-like oxidized low-density lipoprotein (LOX-1) scavenger receptor binds to oxidized low-density lipoprotein (oxLDL) and mediates both signaling and trafficking outcomes. Here, we identified five synthetic proteins termed Affimers from a phage display library, each capable of binding recombinant LOX-1 extracellular (oxLDL-binding) domain with high specificity. These Affimers, based on a phytocystatin scaffold with loop regions of variable sequence, were able to bind to the plasma membrane of HEK293T cells exclusively when human LOX-1 was expressed. Binding and uptake of fluorescently labeled oxLDL by the LOX-1-expressing cell model was inhibited with subnanomolar potency by all 5 Affimers. ERK1/2 activation, stimulated by oxLDL binding to LOX-1, was also significantly inhibited (p < 0.01) by preincubation with LOX-1-specific Affimers, but these Affimers had no direct agonistic effect. Molecular modeling indicated that the LOX-1-specific Affimers bound predominantly via their variable loop regions to the surface of the LOX-1 lectin-like domain that contains a distinctive arrangement of arginine residues previously implicated in oxLDL binding, involving interactions with both subunits of the native, stable scavenger receptor homodimer. These data provide a new class of synthetic tools to probe and potentially modulate the oxLDL/LOX-1 interaction that plays an important role in vascular disease.
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Affiliation(s)
- Barnaby W R Roper
- School of Molecular & Cellular Biology, University of Leeds, Leeds, UK
| | - Christian Tiede
- School of Molecular & Cellular Biology, University of Leeds, Leeds, UK
| | - Izma Abdul-Zani
- School of Molecular & Cellular Biology, University of Leeds, Leeds, UK
| | - Gary A Cuthbert
- School of Molecular & Cellular Biology, University of Leeds, Leeds, UK; Leeds Vascular Institute, Leeds General Infirmary, Leeds, UK
| | - Dhananjay Jade
- School of Biomedical Sciences, University of Leeds, Leeds, UK
| | - Ahmed Al-Aufi
- School of Molecular & Cellular Biology, University of Leeds, Leeds, UK; Leeds Vascular Institute, Leeds General Infirmary, Leeds, UK
| | | | - Queen Saikia
- School of Molecular & Cellular Biology, University of Leeds, Leeds, UK
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4
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Martin HL, Turner AL, Higgins J, Tang AA, Tiede C, Taylor T, Siripanthong S, Adams TL, Manfield IW, Bell SM, Morrison EE, Bond J, Trinh CH, Hurst CD, Knowles MA, Bayliss RW, Tomlinson DC. Affimer-mediated locking of p21-activated kinase 5 in an intermediate activation state results in kinase inhibition. Cell Rep 2023; 42:113184. [PMID: 37776520 DOI: 10.1016/j.celrep.2023.113184] [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: 01/26/2023] [Revised: 07/17/2023] [Accepted: 09/13/2023] [Indexed: 10/02/2023] Open
Abstract
Kinases are important therapeutic targets, and their inhibitors are classified according to their mechanism of action, which range from blocking ATP binding to covalent inhibition. Here, a mechanism of inhibition is highlighted by capturing p21-activated kinase 5 (PAK5) in an intermediate state of activation using an Affimer reagent that binds in the P+1 pocket. PAK5 was identified from a non-hypothesis-driven high-content imaging RNAi screen in urothelial cancer cells. Silencing of PAK5 resulted in reduced cell number, G1/S arrest, and enlargement of cells, suggesting it to be important in urothelial cancer cell line survival and proliferation. Affimer reagents were isolated to identify mechanisms of inhibition. The Affimer PAK5-Af17 recapitulated the phenotype seen with siRNA. Co-crystallization revealed that PAK5-Af17 bound in the P+1 pocket of PAK5, locking the kinase into a partial activation state. This mechanism of inhibition indicates that another class of kinase inhibitors is possible.
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Affiliation(s)
- Heather L Martin
- BioScreening Technology Group, Leeds Institutes of Molecular Medicine, University of Leeds, Leeds LS9 7TF, UK; Division of Molecular Medicine, Leeds Institute of Medical Research at St James's University Hospital, University of Leeds, Leeds LS9 7TF, UK; School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Amy L Turner
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK; Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Julie Higgins
- BioScreening Technology Group, Leeds Institutes of Molecular Medicine, University of Leeds, Leeds LS9 7TF, UK
| | - Anna A Tang
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK; Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Christian Tiede
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK; Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Thomas Taylor
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Sitthinon Siripanthong
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK; Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Thomas L Adams
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK; Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Iain W Manfield
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK; Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Sandra M Bell
- BioScreening Technology Group, Leeds Institutes of Molecular Medicine, University of Leeds, Leeds LS9 7TF, UK; Division of Molecular Medicine, Leeds Institute of Medical Research at St James's University Hospital, University of Leeds, Leeds LS9 7TF, UK
| | - Ewan E Morrison
- BioScreening Technology Group, Leeds Institutes of Molecular Medicine, University of Leeds, Leeds LS9 7TF, UK; Division of Molecular Medicine, Leeds Institute of Medical Research at St James's University Hospital, University of Leeds, Leeds LS9 7TF, UK
| | - Jacquelyn Bond
- BioScreening Technology Group, Leeds Institutes of Molecular Medicine, University of Leeds, Leeds LS9 7TF, UK; Division of Molecular Medicine, Leeds Institute of Medical Research at St James's University Hospital, University of Leeds, Leeds LS9 7TF, UK
| | - Chi H Trinh
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK; Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Carolyn D Hurst
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James's University Hospital, University of Leeds, Leeds LS9 7TF, UK
| | - Margaret A Knowles
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James's University Hospital, University of Leeds, Leeds LS9 7TF, UK
| | - Richard W Bayliss
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK; Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Darren C Tomlinson
- BioScreening Technology Group, Leeds Institutes of Molecular Medicine, University of Leeds, Leeds LS9 7TF, UK; School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK; Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.
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5
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Mijit A, Wang X, Li Y, Xu H, Chen Y, Xue W. Mapping synthetic binding proteins epitopes on diverse protein targets by protein structure prediction and protein-protein docking. Comput Biol Med 2023; 163:107183. [PMID: 37352638 DOI: 10.1016/j.compbiomed.2023.107183] [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: 04/16/2023] [Revised: 06/12/2023] [Accepted: 06/13/2023] [Indexed: 06/25/2023]
Abstract
Synthetic binding proteins (SBPs) are a class of artificial proteins engineered from privileged protein scaffolds, which can form highly specific molecular recognition interfaces with a variety of targets. Due to the characteristics of small size, high stability, and good tissue permeability, SBPs have important applications in biomedical research, disease diagnosis and treatment. However, knowledge of SBPs epitopes on the structures of target proteins is still limited, which hinder the development of novel SBPs. In this study, based on the currently available information of SBPs and their targets, 96 pairs of interacting proteins referring to 96 representative SBPs and 80 different targets, were systemically investigated using the state-of-the-art computational modeling techniques including AlphaFold2 protein structure prediction and Rosetta protein-protein docking. As a result, 71 out of the 96 pairs were successfully docked, of which 18, 33, and 20 pairs were defined as models with high, medium, and acceptable quality, respectively. In addition, the interface information was analyzed to decipher the interaction types driven SBPs and targets recognition. Overall, this work not only provides important structural information for understanding the mechanism of action of other SBPs with same protein scaffold, but also for aiding the rational protein engineering and to design of novel SBPs with biomedical applications.
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Affiliation(s)
- Arzu Mijit
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, China
| | - Xiaona Wang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, China
| | - Yanlin Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, China
| | - Hangwei Xu
- School of Medicine, Hangzhou City University, Hangzhou, 310000, China
| | - Yingjun Chen
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, China.
| | - Weiwei Xue
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, China.
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6
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Liang Y, Li X, Peng F, Ye X, Wang W, Cen T, Li F, Lu Y, Liu Z, Liu H, Ding K, Ye K, Yu Y, Ma T, Zhang S, Huang Y, Wang Y, Yang X, Fu R, Zhang H. Self-assembly of X-shaped antibody to combine the activity of IgG and IgA for enhanced tumor killing. Am J Cancer Res 2022; 12:7729-7744. [PMID: 36451853 PMCID: PMC9706586 DOI: 10.7150/thno.74903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 10/13/2022] [Indexed: 12/02/2022] Open
Abstract
Rationale: IgA can induce activation of neutrophils which are the most abundant cell type in blood, but the development of IgA as therapeutic has been confounded by its short half-life and a weak ability to recruit NK cells as effector cells. Therefore, we generated an X-shaped antibody (X-body) based on the principle of molecular self-assembly that combines the activities of both IgG and IgA, which can effectively recruit and activate NK cells, macrophages, and neutrophils to kill tumor cells. Methods: X-body was generated by using a self-assembly strategy. The affinity of the X-body with the antigen and Fc receptors was tested by surface plasmon resonance. The shape of X-body was examined using negative staining transmission electron microscopy. The tumor cell killing activity of X-body was assessed in vitro and in multiple syngeneic mouse models. To explore the mechanism of X-body, tumor-infiltrating immune cells were analyzed by single-cell RNA-seq and flow cytometry. The dependence of neutrophil, macrophage, and NK cells for the X-body efficacy was confirmed by in vivo depletion of immune cell subsets. Results: The X-body versions of rituximab and trastuzumab combined the full spectrum activity of IgG and IgA and recruited NK cells, macrophages, and neutrophils as effector cells for eradication of tumor cells. Treatment with anti-hCD20 and anti-hHER2 X-bodies leads to a greater reduction in tumor burden in tumor-bearing mice compared with the IgA or IgG counterpart, and no obvious adverse effect is observed upon X-body treatment. Moreover, the X-body has a serum half-life and drug stability comparable to IgG. Conclusions: The X-body, as a myeloid-cell-centered therapeutic strategy, holds promise for the development of more effective cancer-targeting therapies than the current state of the art.
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Affiliation(s)
- Yuexia Liang
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin 300350, PR China.,Frontiers Science Center for Cell Responses, Nankai University, Tianjin 300350, PR China
| | - Xin Li
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin 300350, PR China.,Frontiers Science Center for Cell Responses, Nankai University, Tianjin 300350, PR China
| | - Fengping Peng
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin 300052, PR China
| | - Xiaohan Ye
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin 300350, PR China.,Frontiers Science Center for Cell Responses, Nankai University, Tianjin 300350, PR China
| | - Wei Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, PR China
| | - Tianyi Cen
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin 300350, PR China.,Frontiers Science Center for Cell Responses, Nankai University, Tianjin 300350, PR China
| | - Fan Li
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin 300350, PR China.,Frontiers Science Center for Cell Responses, Nankai University, Tianjin 300350, PR China
| | - Yue Lu
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin 300350, PR China
| | - Zhaoyun Liu
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin 300052, PR China
| | - Hui Liu
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin 300052, PR China
| | - Kai Ding
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin 300052, PR China
| | - Kai Ye
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin 300350, PR China.,Frontiers Science Center for Cell Responses, Nankai University, Tianjin 300350, PR China
| | - Yang Yu
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin 300350, PR China.,Frontiers Science Center for Cell Responses, Nankai University, Tianjin 300350, PR China
| | - Tianyu Ma
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin 300350, PR China.,Frontiers Science Center for Cell Responses, Nankai University, Tianjin 300350, PR China
| | - Sihe Zhang
- Department of Cell Biology, School of Medicine, Nankai University, Tianjin 300350, PR China
| | - Yi Huang
- Shanghai Tanshi Biotechnology Company, Shanghai, 201206, PR China
| | - Yuan Wang
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin 300350, PR China.,Frontiers Science Center for Cell Responses, Nankai University, Tianjin 300350, PR China
| | - Xue Yang
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin 300350, PR China
| | - Rong Fu
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin 300052, PR China.,✉ Corresponding authors: Hongkai Zhang, E-mail: ; Rong Fu, E-mail:
| | - Hongkai Zhang
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin 300350, PR China.,Frontiers Science Center for Cell Responses, Nankai University, Tianjin 300350, PR China.,Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, PR China.,✉ Corresponding authors: Hongkai Zhang, E-mail: ; Rong Fu, E-mail:
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7
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Lüscher B, Verheirstraeten M, Krieg S, Korn P. Intracellular mono-ADP-ribosyltransferases at the host-virus interphase. Cell Mol Life Sci 2022; 79:288. [PMID: 35536484 PMCID: PMC9087173 DOI: 10.1007/s00018-022-04290-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/15/2022] [Accepted: 04/05/2022] [Indexed: 01/22/2023]
Abstract
The innate immune system, the primary defense mechanism of higher organisms against pathogens including viruses, senses pathogen-associated molecular patterns (PAMPs). In response to PAMPs, interferons (IFNs) are produced, allowing the host to react swiftly to viral infection. In turn the expression of IFN-stimulated genes (ISGs) is induced. Their products disseminate the antiviral response. Among the ISGs conserved in many species are those encoding mono-ADP-ribosyltransferases (mono-ARTs). This prompts the question whether, and if so how, mono-ADP-ribosylation affects viral propagation. Emerging evidence demonstrates that some mono-ADP-ribosyltransferases function as PAMP receptors and modify both host and viral proteins relevant for viral replication. Support for mono-ADP-ribosylation in virus–host interaction stems from the findings that some viruses encode mono-ADP-ribosylhydrolases, which antagonize cellular mono-ARTs. We summarize and discuss the evidence linking mono-ADP-ribosylation and the enzymes relevant to catalyze this reversible modification with the innate immune response as part of the arms race between host and viruses.
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Affiliation(s)
- Bernhard Lüscher
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany.
| | - Maud Verheirstraeten
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany
| | - Sarah Krieg
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany
| | - Patricia Korn
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany.
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8
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An antibody Fc engineered for conditional antibody-dependent cellular cytotoxicity at the low tumor microenvironment pH. J Biol Chem 2022; 298:101798. [PMID: 35248534 PMCID: PMC9006656 DOI: 10.1016/j.jbc.2022.101798] [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: 01/08/2022] [Revised: 02/28/2022] [Accepted: 03/01/2022] [Indexed: 11/20/2022] Open
Abstract
Despite the exquisite specificity and high affinity of antibody-based cancer therapies, treatment side effects can occur since the tumor-associated antigens targeted are also present on healthy cells. However, the low pH of the tumor microenvironment provides an opportunity to develop conditionally active antibodies with enhanced tumor specificity. Here, we engineered the human IgG1 Fc domain to enhance pH-selective binding to the receptor FcγRIIIa and subsequent antibody-dependent cellular cytotoxicity (ADCC). We displayed the Fc domain on the surface of mammalian cells and generated a site-directed library by altering Fc residues at the Fc-FcγRIIIa interface to support interactions with positively charged histidine residues. We then used a competitive staining and flow cytometric selection strategy to isolate Fc variants exhibiting reduced FcγRIIIa affinities at neutral pH, but physiological affinities at the tumor-typical pH 6.5. We demonstrate that antibodies composed of Fab arms binding the breast cell epithelial marker Her2 and the lead Fc variant, termed acid-Fc, exhibited an ∼2-fold pH-selectivity for FcγRIIIa binding based on the ratio of equilibrium dissociation constants Kd,7.4/Kd,6.5, due to a faster dissociation rate at pH 7.4. Finally, in vitro ADCC assays with human FcγRIIIa-positive natural killer and Her2-positive target cells demonstrated similar activities for anti-Her2 antibodies bearing the wild-type or acid-Fc at pH 6.5, but nearly 20-fold reduced ADCC for acid-Fc at pH 7.4, based on EC50 ratios. This work shows the promise of mammalian cell display for Fc engineering and the feasibility of pH-selective Fc activation to provide a second dimension of selective tumor cell targeting.
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Olaleye O, Spanov B, Ford R, Govorukhina N, van de Merbel NC, Bischoff R. Enrichment and Liquid Chromatography-Mass Spectrometry Analysis of Trastuzumab and Pertuzumab Using Affimer Reagents. Anal Chem 2021; 93:13597-13605. [PMID: 34582688 PMCID: PMC8515351 DOI: 10.1021/acs.analchem.1c02807] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Trastuzumab and pertuzumab are monoclonal antibodies used in the treatment of human epidermal growth factor receptor-2 (HER2)-positive breast cancer. Therapeutic proteins may undergo chemical modifications that may affect the results of bioanalytical assays, as well as their therapeutic efficacy. Modifications may arise during production and storage, as well as after administration to patients. Studying in vivo biotransformation of monoclonal, therapeutic antibodies requires their enrichment from plasma to discriminate them from endogenous antibodies, as well as from other plasma proteins. To this end, we screened Affimer reagents for selectivity toward trastuzumab or pertuzumab. Affimer reagents are alternative binding proteins possessing two variable binding loops that are based on the human protease inhibitor stefin A or phytocystatin protein scaffolds. Affimer reagents were selected from an extensive library by phage display. The four best-performing binders for each therapeutic antibody were prioritized using a microtiter plate-based approach combined with liquid chromatography-mass spectrometry (LC-MS) in the selected reaction monitoring (SRM) mode. These Affimer reagents were immobilized via engineered 6-His or Cys tags to Ni2+- or maleimide beads, respectively. Recovery values of 70% and higher were obtained for both trastuzumab and pertuzumab when spiked at 100, 150, and 200 μg/mL concentrations in human plasma followed by trypsin digestion in the presence of 0.5% sodium deoxycholate and 10 mM dithiothreitol (DTT). Notably, the maleimide beads showed undetectable unspecific binding to endogenous immunoglobulin G (IgGs) or other plasma proteins when analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The enrichment method was applied to samples from stress tests of the antibodies at 37 °C to mimic in vivo conditions.
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Affiliation(s)
- Oladapo Olaleye
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Baubek Spanov
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Robert Ford
- Avacta Life Sciences Limited, Unit 20, Ash Way, Thorp Arch Estate, Wetherby LS23 7FA, United Kingdom
| | - Natalia Govorukhina
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Nico C van de Merbel
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands.,Bioanalytical Laboratory, PRA Health Sciences, Early Development Services, Amerikaweg 18, Assen 9407 TK, The Netherlands
| | - Rainer Bischoff
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
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10
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POLArIS, a versatile probe for molecular orientation, revealed actin filaments associated with microtubule asters in early embryos. Proc Natl Acad Sci U S A 2021; 118:2019071118. [PMID: 33674463 DOI: 10.1073/pnas.2019071118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Biomolecular assemblies govern the physiology of cells. Their function often depends on the changes in molecular arrangements of constituents, both in the positions and orientations. While recent advancements of fluorescence microscopy including super-resolution microscopy have enabled us to determine the positions of fluorophores with unprecedented accuracy, monitoring the orientation of fluorescently labeled molecules within living cells in real time is challenging. Fluorescence polarization microscopy (FPM) reports the orientation of emission dipoles and is therefore a promising solution. For imaging with FPM, target proteins need labeling with fluorescent probes in a sterically constrained manner, but because of difficulties in the rational three-dimensional design of protein connection, a universal method for constrained tagging with fluorophore was not available. Here, we report POLArIS, a genetically encoded and versatile probe for molecular orientation imaging. Instead of using a direct tagging approach, we used a recombinant binder connected to a fluorescent protein in a sterically constrained manner that can target specific biomolecules of interest by combining with phage display screening. As an initial test case, we developed POLArISact, which specifically binds to F-actin in living cells. We confirmed that the orientation of F-actin can be monitored by observing cells expressing POLArISact with FPM. In living starfish early embryos expressing POLArISact, we found actin filaments radially extending from centrosomes in association with microtubule asters during mitosis. By taking advantage of the genetically encoded nature, POLArIS can be used in a variety of living specimens, including whole bodies of developing embryos and animals, and also be expressed in a cell type/tissue specific manner.
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11
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Yasui N, Nakamura K, Yamashita A. A sweet protein monellin as a non-antibody scaffold for synthetic binding proteins. J Biochem 2021; 169:585-599. [PMID: 33386843 DOI: 10.1093/jb/mvaa147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/07/2020] [Indexed: 11/13/2022] Open
Abstract
Synthetic binding proteins that have the ability to bind with molecules can be generated using various protein domains as non-antibody scaffolds. These designer proteins have been used widely in research studies, as their properties overcome the disadvantages of using antibodies. Here, we describe the first application of a phage display to generate synthetic binding proteins using a sweet protein, monellin, as a non-antibody scaffold. Single-chain monellin (scMonellin), in which two polypeptide chains of natural monellin are connected by a short linker, has two loops on one side of the molecule. We constructed phage display libraries of scMonellin, in which the amino acid sequence of the two loops is diversified. To validate the performance of these libraries, we sorted them against the folding mutant of the green fluorescent protein variant (GFPuv) and yeast small ubiquitin-related modifier. We successfully obtained scMonellin variants exhibiting moderate but significant affinities for these target proteins. Crystal structures of one of the GFPuv-binding variants in complex with GFPuv revealed that the two diversified loops were involved in target recognition. scMonellin, therefore, represents a promising non-antibody scaffold in the design and generation of synthetic binding proteins. We termed the scMonellin-derived synthetic binding proteins 'SWEEPins'.
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Affiliation(s)
- Norihisa Yasui
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1, Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Kazuaki Nakamura
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1, Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Atsuko Yamashita
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1, Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
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12
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RAS-inhibiting biologics identify and probe druggable pockets including an SII-α3 allosteric site. Nat Commun 2021; 12:4045. [PMID: 34193876 PMCID: PMC8245420 DOI: 10.1038/s41467-021-24316-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 06/04/2021] [Indexed: 11/09/2022] Open
Abstract
RAS mutations are the most common oncogenic drivers across human cancers, but there remains a paucity of clinically-validated pharmacological inhibitors of RAS, as druggable pockets have proven difficult to identify. Here, we identify two RAS-binding Affimer proteins, K3 and K6, that inhibit nucleotide exchange and downstream signaling pathways with distinct isoform and mutant profiles. Affimer K6 binds in the SI/SII pocket, whilst Affimer K3 is a non-covalent inhibitor of the SII region that reveals a conformer of wild-type RAS with a large, druggable SII/α3 pocket. Competitive NanoBRET between the RAS-binding Affimers and known RAS binding small-molecules demonstrates the potential to use Affimers as tools to identify pharmacophores. This work highlights the potential of using biologics with small interface surfaces to select unseen, druggable conformations in conjunction with pharmacophore identification for hard-to-drug proteins. Oncogenic RAS mutants remain difficult to target with small molecules. Here, the authors show that RAS-binding Affimer proteins inhibit RAS signaling while binding diverse regions on the RAS surface, suggesting the potential to use Affimers as tools to identify new binding pockets and pharmacophores.
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13
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Tang AAS, Tiede C, McPherson MJ, Tomlinson DC. Isolation of Artificial Binding Proteins (Affimer Reagents) for Use in Molecular and Cellular Biology. Methods Mol Biol 2021; 2247:105-121. [PMID: 33301114 DOI: 10.1007/978-1-0716-1126-5_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Artificial binding proteins have been validated as alternatives to antibodies in their use as research reagents in molecular and cellular biology. For example, they have been used as inhibitors of protein-protein interactions to modulate activity, to facilitate crystallization, and as probes for cellular imaging.Phage display is a widely used approach for isolating target-specific binding reagents, and it has even been used to isolate isoform-specific binding proteins and binders that can distinguish between highly homologous protein domains.Here, we describe methods that have been employed in isolating highly specific artificial binding proteins against a wide range of target proteins.
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Affiliation(s)
- Anna A S Tang
- Astbury Centre for Structural and Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | - Christian Tiede
- Astbury Centre for Structural and Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | - Michael J McPherson
- Astbury Centre for Structural and Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | - Darren C Tomlinson
- Astbury Centre for Structural and Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, UK.
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14
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Selection and characterisation of Affimers specific for CEA recognition. Sci Rep 2021; 11:744. [PMID: 33436840 PMCID: PMC7804248 DOI: 10.1038/s41598-020-80354-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 12/18/2020] [Indexed: 02/06/2023] Open
Abstract
Carcinoembryonic antigen (CEA) is the only blood based protein biomarker at present, used for preoperative screening of advanced colorectal cancer (CRC) patients to determine the appropriate curative treatments and post-surveillance screening for tumour recurrence. Current diagnostics for CRC detection have several limitations and development of a highly sensitive, specific and rapid diagnostic device is required. The majority of such devices developed to date are antibody-based and suffer from shortcomings including multimeric binding, cost and difficulties in mass production. To circumvent antibody-derived limitations, the present study focused on the development of Affimer proteins as a novel alternative binding reagent for CEA detection. Here, we describe the selection, from a phage display library, of Affimers specific to CEA protein. Characterization of three anti-CEA Affimers reveal that these bind specifically and selectively to protein epitopes of CEA from cell culture lysate and on fixed cells. Kinetic binding analysis by SPR show that the Affimers bind to CEA with high affinity and within the nM range. Therefore, they have substantial potential for used as novel affinity reagents in diagnostic imaging, targeted CRC therapy, affinity purification and biosensor applications.
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15
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Miles JA, Hobor F, Trinh CH, Taylor J, Tiede C, Rowell PR, Jackson BR, Nadat FA, Ramsahye P, Kyle HF, Wicky BIM, Clarke J, Tomlinson DC, Wilson AJ, Edwards TA. Selective Affimers Recognise the BCL-2 Family Proteins BCL-x L and MCL-1 through Noncanonical Structural Motifs*. Chembiochem 2021; 22:232-240. [PMID: 32961017 PMCID: PMC7821230 DOI: 10.1002/cbic.202000585] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/17/2020] [Indexed: 12/26/2022]
Abstract
The BCL-2 family is a challenging group of proteins to target selectively due to sequence and structural homologies across the family. Selective ligands for the BCL-2 family regulators of apoptosis are useful as probes to understand cell biology and apoptotic signalling pathways, and as starting points for inhibitor design. We have used phage display to isolate Affimer reagents (non-antibody-binding proteins based on a conserved scaffold) to identify ligands for MCL-1, BCL-xL , BCL-2, BAK and BAX, then used multiple biophysical characterisation methods to probe the interactions. We established that purified Affimers elicit selective recognition of their target BCL-2 protein. For anti-apoptotic targets BCL-xL and MCL-1, competitive inhibition of their canonical protein-protein interactions is demonstrated. Co-crystal structures reveal an unprecedented mode of molecular recognition; where a BH3 helix is normally bound, flexible loops from the Affimer dock into the BH3 binding cleft. Moreover, the Affimers induce a change in the target proteins towards a desirable drug-bound-like conformation. These proof-of-concept studies indicate that Affimers could be used as alternative templates to inspire the design of selective BCL-2 family modulators and more generally other protein-protein interaction inhibitors.
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Affiliation(s)
- Jennifer A. Miles
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- School of ChemistryUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Fruzsina Hobor
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Chi H. Trinh
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - James Taylor
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Christian Tiede
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Philip R. Rowell
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Brian R. Jackson
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Protein Production FacilityUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Fatima A. Nadat
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Protein Production FacilityUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Pallavi Ramsahye
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Hannah F. Kyle
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Basile I. M. Wicky
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Jane Clarke
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Darren C. Tomlinson
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Andrew J. Wilson
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- School of ChemistryUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Thomas A. Edwards
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
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16
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Persistent Activation of Innate Immunity in Patients with Primary Antibody Deficiencies. J Immunol Res 2020; 2020:8317671. [PMID: 33274244 PMCID: PMC7695510 DOI: 10.1155/2020/8317671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 09/13/2020] [Accepted: 10/19/2020] [Indexed: 12/03/2022] Open
Abstract
Primary antibody deficiencies (PAD) represent a heterogeneous group of disorders, with common variable immunodeficiency being the most common with clinical significance. The main phenotypic defect resides in the inability of B cells to produce antibodies, and the cornerstone of therapy is immunoglobulin replacement treatment in order to fight infections. However, the management of the other inflammatory manifestations is inadequate, reinforcing the hypothesis that a complex genetic background affecting additional cell populations, such as polymorphonuclear cells (PMN) and monocytes, influences the expression of the clinical phenotype of the disease. In this study, we investigated by flow cytometry in different conditions (resting state, and after isolation and incubation, with and without stimuli) the expression pattern of several markers on PMN and monocytes, indicative of their maturation, capacity for chemotaxis, adhesion, opsonization, migration, and phagocytosis in 25 PAD patients, 12 healthy blood donors, and 4 septic patients. In this context, we also analyzed patients before and after the initiation of replacement treatment, as well as an untreated patient in different clinical conditions. Interestingly, we observed that PAD patients exhibit a chronic activation status of the innate immunity compartment, along with several differences in the expression of activation, maturation, and adhesion markers, with respect to different clinical conditions. Moreover, immunoglobulin replacement treatment had a favorable effect on PMN, as it was expressed by a more mature and less activated phenotype on basal state cells, and an enhanced activation capacity after LPS exposure. Thus, we conclude that PAD patients display a persistent innate immune cell activation, which is probably associated with the chronic inflammatory stress, usually observed in these disorders.
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17
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Carrington G, Tomlinson D, Peckham M. Exploiting nanobodies and Affimers for superresolution imaging in light microscopy. Mol Biol Cell 2020; 30:2737-2740. [PMID: 31609674 PMCID: PMC6789155 DOI: 10.1091/mbc.e18-11-0694] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Antibodies have long been the main approach used for localizing proteins of interest by light microscopy. In the past 5 yr or so, and with the advent of superresolution microscopy, the diversity of tools for imaging has rapidly expanded. One main area of expansion has been in the area of nanobodies, small single-chain antibodies from camelids or sharks. The other has been the use of artificial scaffold proteins, including Affimers. The small size of nanobodies and Affimers compared with the traditional antibody provides several advantages for superresolution imaging.
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Affiliation(s)
- Glenn Carrington
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Darren Tomlinson
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Michelle Peckham
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
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18
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Baxter EW, Graham AE, Re NA, Carr IM, Robinson JI, Mackie SL, Morgan AW. Standardized protocols for differentiation of THP-1 cells to macrophages with distinct M(IFNγ+LPS), M(IL-4) and M(IL-10) phenotypes. J Immunol Methods 2020; 478:112721. [PMID: 32033786 DOI: 10.1016/j.jim.2019.112721] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 12/01/2019] [Accepted: 12/04/2019] [Indexed: 12/28/2022]
Abstract
In vitro models of differing macrophage functions are useful since human monocyte-derived macrophages are short-lived, finite and vary from donor to donor. Published protocols using the promonocytic cell line THP-1 have tended to result in cells that closely resemble classically-activated macrophages, differentiated in IFNγ and LPS. However, no protocol, to date, has fully recapitulated polarization of THP-1 to the M(IL-4) or M(IL-10) macrophage phenotypes seen when human monocyte-derived macrophages are exposed to each cytokine. Here we present protocols that can be used to prepare M(IL-4) polarized THP-1 that transcribe CCL17, CCL26, CD200R and MRC1 and M(IL-10) cells which transcribe CD163, C1QA and SEPP1. We show that the inhibitory Fcγ Receptor IIb is preferentially expressed on the surface of M(IL-4) cells, altering the balance of activating to inhibitory Fcγ Receptors. Adoption of standardized experimental conditions for macrophage polarization will make it easier to compare downstream effector functions of different macrophage polarization states, where the impact of PMA exposure is minimized and rest periods and cytokine exposure have been optimized.
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Affiliation(s)
- E W Baxter
- Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds, UK; NIHR Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - A E Graham
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, School of Medicine, University of Leeds, Leeds, UK
| | - N A Re
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, School of Medicine, University of Leeds, Leeds, UK
| | - I M Carr
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, Leeds, UK
| | - J I Robinson
- Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds, UK; NIHR Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - S L Mackie
- NIHR Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK; Leeds Institute of Rheumatic and Musculoskeletal Medicine, School of Medicine, University of Leeds, Leeds, UK
| | - A W Morgan
- Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds, UK; NIHR Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK.
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19
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Adamson H, Nicholl A, Tiede C, Tang AA, Davidson A, Curd H, Wignall A, Ford R, Nuttall J, McPherson MJ, Johnson M, Tomlinson DC. Affimers as anti-idiotypic affinity reagents for pharmacokinetic analysis of biotherapeutics. Biotechniques 2019; 67:261-269. [DOI: 10.2144/btn-2019-0089] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Therapeutic antibodies are the fastest growing class of drugs in the treatment of cancer, and autoimmune and inflammatory diseases that require the concomitant development of assays to monitor therapeutic antibody levels. Here, we demonstrate that the use of Affimer nonantibody binding proteins provides an advantage over current antibody-based detection systems. For four therapeutic antibodies, we used phage display to isolate highly specific anti-idiotypic Affimer reagents, which selectively bind to the therapeutic antibody idiotype. For each antibody target the calibration curves met US Food and Drug Administration criteria and the dynamic range compared favorably with commercially available reagents. Affimer proteins therefore represent promising anti-idiotypic reagents that are simple to select and manufacture, and that offer the sensitivity, specificity and consistency required for pharmacokinetic assays.
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Affiliation(s)
- Hope Adamson
- School of Molecular & Cellular Biology, Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Amanda Nicholl
- Avacta Life Sciences, Ash Way, Thorp Arch Estate, Wetherby, LS23 7FA, UK
| | - Christian Tiede
- School of Molecular & Cellular Biology, Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Anna A Tang
- School of Molecular & Cellular Biology, Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Alex Davidson
- Avacta Life Sciences, Ash Way, Thorp Arch Estate, Wetherby, LS23 7FA, UK
| | - Helen Curd
- Avacta Life Sciences, Ash Way, Thorp Arch Estate, Wetherby, LS23 7FA, UK
| | - Alex Wignall
- Avacta Life Sciences, Ash Way, Thorp Arch Estate, Wetherby, LS23 7FA, UK
| | - Robert Ford
- Avacta Life Sciences, Ash Way, Thorp Arch Estate, Wetherby, LS23 7FA, UK
| | - James Nuttall
- Avacta Life Sciences, Ash Way, Thorp Arch Estate, Wetherby, LS23 7FA, UK
| | - Michael J McPherson
- School of Molecular & Cellular Biology, Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Matt Johnson
- Avacta Life Sciences, Ash Way, Thorp Arch Estate, Wetherby, LS23 7FA, UK
| | - Darren C Tomlinson
- School of Molecular & Cellular Biology, Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
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20
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Gebauer M, Skerra A. Engineering of binding functions into proteins. Curr Opin Biotechnol 2019; 60:230-241. [DOI: 10.1016/j.copbio.2019.05.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 05/07/2019] [Indexed: 12/13/2022]
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21
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Affimer reagents as tools in diagnosing plant virus diseases. Sci Rep 2019; 9:7524. [PMID: 31101847 PMCID: PMC6525157 DOI: 10.1038/s41598-019-43945-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 04/24/2019] [Indexed: 12/19/2022] Open
Abstract
Plant viruses can cause devastating losses to agriculture and are therefore a major threat to food security. The rapid identification of virally-infected crops allowing containment is essential to limit such threats, but plant viral diseases can be extremely challenging to diagnose. An ideal method for plant virus diagnosis would be a device which can be implemented easily in the field. Such devices require a binding reagent that is specific for the virus of interest. We chose to investigate the use of Affimer reagents, artificial binding proteins and a model plant virus Cowpea Mosaic virus (CPMV) empty virus like particles (eVLPs). CPMV-eVLP mimic the morphology of wild-type (WT) CPMV but lack any infectious genomic material and so do not have biocontainment issues. We have produced and purified an Affimer reagent selected for its ability to bind to CPMV-eVLP and have shown that the selected Affimer also specifically binds to WT CPMV. We have produced a 3.4 Å structure of WT CPMV bound to the Affimer using cryo-electron microscopy. Finally, we have shown that this Affimer is capable of reliably detecting the virus in crude extracts of CPMV-infected leaves and can therefore form the basis for the future development of diagnostic tests.
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22
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Toxin Neutralization Using Alternative Binding Proteins. Toxins (Basel) 2019; 11:toxins11010053. [PMID: 30658491 PMCID: PMC6356946 DOI: 10.3390/toxins11010053] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 01/07/2019] [Accepted: 01/12/2019] [Indexed: 12/20/2022] Open
Abstract
Animal toxins present a major threat to human health worldwide, predominantly through snakebite envenomings, which are responsible for over 100,000 deaths each year. To date, the only available treatment against snakebite envenoming is plasma-derived antivenom. However, despite being key to limiting morbidity and mortality among snakebite victims, current antivenoms suffer from several drawbacks, such as immunogenicity and high cost of production. Consequently, avenues for improving envenoming therapy, such as the discovery of toxin-sequestering monoclonal antibodies against medically important target toxins through phage display selection, are being explored. However, alternative binding protein scaffolds that exhibit certain advantages compared to the well-known immunoglobulin G scaffold, including high stability under harsh conditions and low cost of production, may pose as possible low-cost alternatives to antibody-based therapeutics. There is now a plethora of alternative binding protein scaffolds, ranging from antibody derivatives (e.g., nanobodies), through rationally designed derivatives of other human proteins (e.g., DARPins), to derivatives of non-human proteins (e.g., affibodies), all exhibiting different biochemical and pharmacokinetic profiles. Undeniably, the high level of engineerability and potentially low cost of production, associated with many alternative protein scaffolds, present an exciting possibility for the future of snakebite therapeutics and merit thorough investigation. In this review, a comprehensive overview of the different types of binding protein scaffolds is provided together with a discussion on their relevance as potential modalities for use as next-generation antivenoms.
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23
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Affimer proteins as a tool to modulate fibrinolysis, stabilize the blood clot, and reduce bleeding complications. Blood 2018; 133:1233-1244. [PMID: 30545831 DOI: 10.1182/blood-2018-06-856195] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 12/02/2018] [Indexed: 12/17/2022] Open
Abstract
Bleeding complications secondary to surgery, trauma, or coagulation disorders are important causes of morbidity and mortality. Although fibrin sealants are considered to minimize blood loss, this is not widely adopted because of its high cost and/or risk for infection. We present a novel methodology employing nonantibody fibrinogen-binding proteins, termed Affimers, to stabilize fibrin networks with the potential to control excessive bleeding. Two fibrinogen-specific Affimer proteins, F5 and G2, were identified and characterized for their effects on clot structure/fibrinolysis, using turbidimetric and permeation analyses and confocal and electron microscopy. Binding studies and molecular modeling identified interaction sites, whereas plasmin generation assays determined effects on plasminogen activation. In human plasma, F5 and G2 prolonged clot lysis time from 9.8 ± 1.1 minutes in the absence of Affimers to 172.6 ± 7.4 and more than 180 minutes (P < .0001), respectively, and from 7.6 ± 0.2 to 28.7 ± 5.8 (P < .05) and 149.3 ± 9.7 (P < .0001) minutes in clots made from purified fibrinogen. Prolongation in fibrinolysis was consistent across plasma samples from healthy control patients and individuals at high bleeding risk. F5 and G2 had a differential effect on clot structure and G2 profoundly altered fibrin fiber arrangement, whereas F5 maintained physiological clot structure. Affimer F5 reduced fibrin-dependent plasmin generation and was predicted to bind fibrinogen D fragment close to tissue plasminogen activator (tPA; residues γ312-324) and plasminogen (α148-160) binding sites, thus interfering with tPA-plasminogen interaction and representing 1 potential mechanism for modulation of fibrinolysis. Our Affimer proteins provide a novel methodology for stabilizing fibrin networks with potential future clinical implications to reduce bleeding risk.
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24
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Roberts JT, Barb AW. A single amino acid distorts the Fc γ receptor IIIb/CD16b structure upon binding immunoglobulin G1 and reduces affinity relative to CD16a. J Biol Chem 2018; 293:19899-19908. [PMID: 30361439 DOI: 10.1074/jbc.ra118.005273] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 10/15/2018] [Indexed: 12/31/2022] Open
Abstract
Therapeutic mAbs engage Fc γ receptor III (CD16) to elicit a protective cell-mediated response and destroy the target tissue. Newer drugs designed to bind CD16a with increased affinity surprisingly also elicit protective CD16b-mediated responses. However, it is unclear why IgG binds CD16a with more than 10-fold higher affinity than CD16b even though these receptors share more than 97% identity. Here we identified one residue, Gly-129, that contributes to the greater IgG binding affinity of CD16a. The CD16b variant D129G bound IgG1 Fc with 2-fold higher affinity than CD16a and with 90-fold higher affinity than the WT. Conversely, the binding affinity of CD16a-G129D was decreased 128-fold relative to WT CD16a and comparably to that of WT CD16b. The interaction of IgG1 Fc with CD16a, but not with CD16b, is known to be sensitive to the composition of the asparagine-linked carbohydrates (N-glycans) attached to the receptor. CD16a and CD16b-D129G displaying minimally processed oligomannose N-glycans bound to IgG1 Fc with about 5.2-fold increased affinity compared with variants with highly processed complex-type N-glycans. CD16b and the CD16a-G129D variant exhibited a smaller 1.9-fold affinity increase with oligomannose N-glycans. A model of glycosylated CD16b bound to IgG1 Fc determined to 2.2 Å resolution combined with a 250-ns all-atom molecular dynamics simulation showed that the larger Asp-129 residue deformed the Fc-binding surface. These results reveal how Asp-129 in CD16b affects its binding affinity for IgG1 Fc and suggest that antibodies engineered to engage CD16b with high affinity must accommodate the Asp-129 side chain.
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Affiliation(s)
- Jacob T Roberts
- From the Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011
| | - Adam W Barb
- From the Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011
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25
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Klont F, Hadderingh M, Horvatovich P, Ten Hacken NHT, Bischoff R. Affimers as an Alternative to Antibodies in an Affinity LC-MS Assay for Quantification of the Soluble Receptor of Advanced Glycation End-Products (sRAGE) in Human Serum. J Proteome Res 2018; 17:2892-2899. [PMID: 30005571 PMCID: PMC6079930 DOI: 10.1021/acs.jproteome.8b00414] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
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Antibodies are indispensable tools
in biomedical research, but
their size, complexity, and sometimes lack of reproducibility created
a need for the development of alternative binders to overcome these
limitations. Affimers are a novel class of affinity binders based
on a structurally robust protease inhibitor scaffold (i.e., Cystatin
A), which are selected by phage display and produced in a rapid and
simple E. coli protein expression system. These binders
have a defined amino acid sequence with defined binding regions and
are versatile, thereby allowing for easy engineering. Here we present
an affimer-based liquid chromatography–mass spectrometry (LC–MS)
method for quantification of the soluble Receptor of Advanced Glycation
End-products (sRAGE), a promising biomarker for chronic obstructive
pulmonary disease. The method was validated according to European
Medicines Agency and U.S. Food and Drug Administration guidelines
and enabled quantitation of serum sRAGE between 0.2 and 10 ng/mL.
Comparison between the affimer-based method and a previously developed,
validated antibody-based method showed good correlation (R2 = 0.88) and indicated that 25% lower sRAGE levels are
reported by the affimer-based assay. In conclusion, we show the first-time
application of affimers in a quantitative LC–MS method, which
supports the potential of affimers as robust alternatives to antibodies.
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Affiliation(s)
- Frank Klont
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy , University of Groningen , Antonius Deusinglaan 1 , 9713 AV Groningen , The Netherlands
| | - Marrit Hadderingh
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy , University of Groningen , Antonius Deusinglaan 1 , 9713 AV Groningen , The Netherlands
| | - Péter Horvatovich
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy , University of Groningen , Antonius Deusinglaan 1 , 9713 AV Groningen , The Netherlands
| | - Nick H T Ten Hacken
- Department of Pulmonary Diseases, University Medical Center Groningen , University of Groningen , Hanzeplein 1 , 9713 GZ Groningen , The Netherlands
| | - Rainer Bischoff
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy , University of Groningen , Antonius Deusinglaan 1 , 9713 AV Groningen , The Netherlands
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26
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Schlichthaerle T, Eklund AS, Schueder F, Strauss MT, Tiede C, Curd A, Ries J, Peckham M, Tomlinson DC, Jungmann R. Ortsspezifische Funktionalisierung von Affimeren für die DNA-PAINT-Mikroskopie. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201804020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Thomas Schlichthaerle
- Fakultät für Physik und Center for Nanoscience; LMU München; München Deutschland
- Max-Planck-Institut für Biochemie; Martinsried Deutschland
| | - Alexandra S. Eklund
- Fakultät für Physik und Center for Nanoscience; LMU München; München Deutschland
- Max-Planck-Institut für Biochemie; Martinsried Deutschland
| | - Florian Schueder
- Fakultät für Physik und Center for Nanoscience; LMU München; München Deutschland
- Max-Planck-Institut für Biochemie; Martinsried Deutschland
| | - Maximilian T. Strauss
- Fakultät für Physik und Center for Nanoscience; LMU München; München Deutschland
- Max-Planck-Institut für Biochemie; Martinsried Deutschland
| | - Christian Tiede
- Astbury Centre for Structural and Molecular Biology; University of Leeds; Leeds Großbritannien
- School of Molecular and Cellular Biology; University of Leeds; Leeds Großbritannien
| | - Alistair Curd
- Astbury Centre for Structural and Molecular Biology; University of Leeds; Leeds Großbritannien
- School of Molecular and Cellular Biology; University of Leeds; Leeds Großbritannien
| | - Jonas Ries
- European Molecular Biology Laboratory; Cell Biology and Biophysics Unit; Heidelberg Deutschland
| | - Michelle Peckham
- Astbury Centre for Structural and Molecular Biology; University of Leeds; Leeds Großbritannien
- School of Molecular and Cellular Biology; University of Leeds; Leeds Großbritannien
| | - Darren C. Tomlinson
- Astbury Centre for Structural and Molecular Biology; University of Leeds; Leeds Großbritannien
- School of Molecular and Cellular Biology; University of Leeds; Leeds Großbritannien
| | - Ralf Jungmann
- Fakultät für Physik und Center for Nanoscience; LMU München; München Deutschland
- Max-Planck-Institut für Biochemie; Martinsried Deutschland
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27
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Schlichthaerle T, Eklund AS, Schueder F, Strauss MT, Tiede C, Curd A, Ries J, Peckham M, Tomlinson DC, Jungmann R. Site-Specific Labeling of Affimers for DNA-PAINT Microscopy. Angew Chem Int Ed Engl 2018; 57:11060-11063. [PMID: 29873161 DOI: 10.1002/anie.201804020] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 05/11/2018] [Indexed: 12/17/2022]
Abstract
Optical super-resolution techniques allow fluorescence imaging below the classical diffraction limit of light. From a technology standpoint, recent methods are approaching molecular-scale spatial resolution. However, this remarkable achievement is not easily translated to imaging of cellular components, since current labeling approaches are limited by either large label sizes (antibodies) or the sparse availability of small and efficient binders (nanobodies, aptamers, genetically-encoded tags). In this work, we combined recently developed Affimer reagents with site-specific DNA modification for high-efficiency labeling and imaging using DNA-PAINT. We assayed our approach using an actin Affimer. The small DNA-conjugated affinity binders could provide a solution for efficient multitarget super-resolution imaging in the future.
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Affiliation(s)
- Thomas Schlichthaerle
- Faculty of Physics and Center for Nanoscience, LMU Munich, Munich, Germany.,Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Alexandra S Eklund
- Faculty of Physics and Center for Nanoscience, LMU Munich, Munich, Germany.,Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Florian Schueder
- Faculty of Physics and Center for Nanoscience, LMU Munich, Munich, Germany.,Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Maximilian T Strauss
- Faculty of Physics and Center for Nanoscience, LMU Munich, Munich, Germany.,Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Christian Tiede
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, UK.,School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | - Alistair Curd
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, UK.,School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | - Jonas Ries
- European Molecular Biology Laboratory, Cell Biology and Biophysics Unit, Heidelberg, Germany
| | - Michelle Peckham
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, UK.,School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | - Darren C Tomlinson
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, UK.,School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | - Ralf Jungmann
- Faculty of Physics and Center for Nanoscience, LMU Munich, Munich, Germany.,Max Planck Institute of Biochemistry, Martinsried, Germany
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28
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Identifying Recrudescent Plasmodium falciparum in Treated Malaria Patients by Real-time PCR and High Resolution Melt Analysis of Genetic Diversity. Sci Rep 2018; 8:10097. [PMID: 29973679 PMCID: PMC6031682 DOI: 10.1038/s41598-018-28179-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 06/18/2018] [Indexed: 12/24/2022] Open
Abstract
Recurrent parasitaemia during follow up of clinical trials of antimalarial drug efficacy results from either recrudescence of parasites surviving treatment or from parasites newly emerging from the hepatic stage of infection. Nested PCR is used to distinguish these two possibilities and the technique is difficult to standardise. There is risk of both false positive and false negative results, leading to misclassification errors. The high-resolution melt (HRM) assay was developed with pairs of conserved primers targeting blocks of merozoite surface protein 1 and 2 (msp1 and msp2) genes, and polymorphisms were compared using sequence-confirmed Plasmodium falciparum DNA samples from laboratory isolates. In this study, the HRM dissociation profiles of msp1 and msp2 amplicons were determined and validated against parasite isolates from malaria patients. The msp1 and msp2 profiles of both laboratory and clinical isolates were reproducibly differentiated by HRM. These rapid assays are performed in a closed-tube system, and so avoid cross-contamination while increasing throughput, which are two major advantages. The HRM assays offer significant gains in simplicity, speed and interpretation of results, and reduced analysis cost, for studies that require discrimination of parasite clones. Assay performance in large-scale studies utilizing DNA samples derived from filter-paper bloodspots should now be evaluated.
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29
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Lopata A, Hughes R, Tiede C, Heissler SM, Sellers JR, Knight PJ, Tomlinson D, Peckham M. Affimer proteins for F-actin: novel affinity reagents that label F-actin in live and fixed cells. Sci Rep 2018; 8:6572. [PMID: 29700342 PMCID: PMC5920084 DOI: 10.1038/s41598-018-24953-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 04/10/2018] [Indexed: 01/21/2023] Open
Abstract
Imaging the actin cytoskeleton in cells uses a wide range of approaches. Typically, a fluorescent derivative of the small cyclic peptide phalloidin is used to image F-actin in fixed cells. Lifeact and F-tractin are popular for imaging the cytoskeleton in live cells. Here we characterised novel affinity reagents called Affimers that specifically bind to F-actin in vitro to determine if they are suitable alternatives as eGFP-fusion proteins, to label actin in live cells, or for labeling F-actin in fixed cells. In vitro experiments showed that 3 out of the 4 Affimers (Affimers 6, 14 and 24) tested bind tightly to purified F-actin, and appear to have overlapping binding sites. As eGFP-fusion proteins, the same 3 Affimers label F-actin in live cells. FRAP experiments suggest that eGFP-Affimer 6 behaves most similarly to F-tractin and Lifeact. However, it does not colocalise with mCherry-actin in dynamic ruffles, and may preferentially bind stable actin filaments. All 4 Affimers label F-actin in methanol fixed cells, while only Affimer 14 labels F-actin after paraformaldehyde fixation. eGFP-Affimer 6 has potential for use in selectively imaging the stable actin cytoskeleton in live cells, while all 4 Affimers are strong alternatives to phalloidin for labelling F-actin in fixed cells.
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Affiliation(s)
- Anna Lopata
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK.,Laboratory of Molecular Physiology, National Heart, Lung, and Blood Institute, Bethesda, MD, 20892, USA
| | - Ruth Hughes
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Christian Tiede
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Sarah M Heissler
- Laboratory of Molecular Physiology, National Heart, Lung, and Blood Institute, Bethesda, MD, 20892, USA
| | - James R Sellers
- Laboratory of Molecular Physiology, National Heart, Lung, and Blood Institute, Bethesda, MD, 20892, USA
| | - Peter J Knight
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Darren Tomlinson
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Michelle Peckham
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK. .,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK.
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