1
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Deacy AM, Gan SKE. The influence of variable-heavy chain families on IgG 2, 3, 4, FcγRs and B-cell superantigens protein G and L binding using biolayer interferometry. Antib Ther 2023; 6:182-193. [PMID: 37680351 PMCID: PMC10481891 DOI: 10.1093/abt/tbad016] [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: 03/26/2023] [Revised: 06/16/2023] [Accepted: 06/28/2023] [Indexed: 09/09/2023] Open
Abstract
As the most abundant immunoglobulin in blood and the most common human isotype used for therapeutic monoclonal antibodies, the engagement and activation of its Fc receptors by IgGs are crucial for antibody function. Assumed to be relatively constant within subtypes, recent studies reveal that antibody variable regions exert distal effects of modulating antibody-receptor interactions on antibody isotypes. These variable (V)-region distal effects are also expected for the IgG subtypes. With an in-depth understanding of the V-region effects, researchers can make a more informed antibody engineering approach and antibody purification strategy accounting for the functions of microbial immune evasion . In this study, we created a panel of IgG2/IgG3/IgG4 antibodies by changing the VH family (VH1-7) frameworks while retaining the complementary determining regions of pertumuzab and measured their interactions with FcγRIa, FcγRIIaH167, FcγRIIaR167, FcγRIIb/c, FcγRIIIaF176, FcγRIIIaV176, FcγRIIIbNA1 and FcγRIIIbNA2 receptors alongside B-cell superantigens Protein L and G using biolayer interferometry. The panel of 21 IgGs demonstrated that the VH frameworks influenced receptor binding sites on the constant region in a non-canonical manner. However, there was minimal influence on the binding of bacterial B-cell superantigens Proteins L and Protein G on the IgGs, showing their robustness against V-region effects. These results demonstrate the role of V-regions during the humanization of therapeutic antibodies that can influence FcR-dependent immune responses while retaining binding by bacterial B-cell superantigens for antibody purification. These in vitro measurements provide a clue to detailed antibody engineering and understanding of antibody superantigen functions that would be relevant with in vivo validation.
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Affiliation(s)
- Anthony M Deacy
- Antibody& Product Development Lab, Agency for Science, Technology and Research (ASTAR), Singapore, and Wenzhou-Kean University, Wenzhou, Zhejiang, China
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Samuel Ken-En Gan
- Antibody& Product Development Lab, Agency for Science, Technology and Research (ASTAR), Singapore, and Wenzhou-Kean University, Wenzhou, Zhejiang, China
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Zhejiang Bioinformatics International Science and Technology Cooperation Centre, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China
- Wenzhou Municipal Key Lab of Applied Biomedical and Biopharmaceutical Informatics, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China
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2
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Kallolimath S, Palt R, Föderl-Höbenreich E, Sun L, Chen Q, Pruckner F, Eidenberger L, Strasser R, Zatloukal K, Steinkellner H. Glyco engineered pentameric SARS-CoV-2 IgMs show superior activities compared to IgG1 orthologues. Front Immunol 2023; 14:1147960. [PMID: 37359564 PMCID: PMC10285447 DOI: 10.3389/fimmu.2023.1147960] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 05/22/2023] [Indexed: 06/28/2023] Open
Abstract
Immunoglobulin M (IgM) is the largest antibody isotype with unique features like extensive glycosylation and oligomerization. Major hurdles in characterizing its properties are difficulties in the production of well-defined multimers. Here we report the expression of two SARS-CoV-2 neutralizing monoclonal antibodies in glycoengineered plants. Isotype switch from IgG1 to IgM resulted in the production of IgMs, composed of 21 human protein subunits correctly assembled into pentamers. All four recombinant monoclonal antibodies carried a highly reproducible human-type N-glycosylation profile, with a single dominant N-glycan species at each glycosite. Both pentameric IgMs exhibited increased antigen binding and virus neutralization potency, up to 390-fold, compared to the parental IgG1. Collectively, the results may impact on the future design of vaccines, diagnostics and antibody-based therapies and emphasize the versatile use of plants for the expression of highly complex human proteins with targeted posttranslational modifications.
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Affiliation(s)
- Somanath Kallolimath
- Institute of Plant Biotechnology and Cell Biology, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Roman Palt
- Institute of Plant Biotechnology and Cell Biology, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | | | - Lin Sun
- Institute of Plant Biotechnology and Cell Biology, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Qiang Chen
- The Biodesign Institute and School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Florian Pruckner
- Institute of Plant Biotechnology and Cell Biology, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Lukas Eidenberger
- Institute of Plant Biotechnology and Cell Biology, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Richard Strasser
- Institute of Plant Biotechnology and Cell Biology, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Kurt Zatloukal
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Herta Steinkellner
- Institute of Plant Biotechnology and Cell Biology, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
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3
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Ling WL, Su CTT, Lua WH, Yeo JY, Poh JJ, Ng YL, Wipat A, Gan SKE. Variable-heavy (VH) families influencing IgA1&2 engagement to the antigen, FcαRI and superantigen proteins G, A, and L. Sci Rep 2022; 12:6510. [PMID: 35444201 PMCID: PMC9020155 DOI: 10.1038/s41598-022-10388-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 04/07/2022] [Indexed: 12/18/2022] Open
Abstract
Interest in IgA as an alternative antibody format has increased over the years with much remaining to be investigated in relation to interactions with immune cells. Considering the recent whole antibody investigations showing significant distal effects between the variable (V) and constant (C)- regions that can be mitigated by the hinge regions of both human IgA subtypes A1 and A2, we performed an in-depth mechanistic investigation using a panel of 28 IgA1s and A2s of both Trastuzumab and Pertuzumab models. FcαRI binding were found to be mitigated by the differing glycosylation patterns in IgA1 and 2 with contributions from the CDRs. On their interactions with antigen-Her2 and superantigens PpL, SpG and SpA, PpL was found to sterically hinder Her2 antigen binding with unexpected findings of IgAs binding SpG at the CH2-3 region alongside SpA interacting with IgAs at the CH1. Although the VH3 framework (FWR) is commonly used in CDR grafting, we found the VH1 framework (FWR) to be a possible alternative when grafting IgA1 and 2 owing to its stronger binding to antigen Her2 and weaker interactions to superantigen Protein L and A. These findings lay the foundation to understanding the interactions between IgAs and microbial superantigens, and also guide the engineering of IgAs for future antibody applications and targeting of superantigen-producing microbes.
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Affiliation(s)
- Wei-Li Ling
- Antibody & Product Development Lab, Experimental Drug Development Centre, Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,Newcastle University Singapore, Singapore, Singapore
| | - Chinh Tran-To Su
- Antibody & Product Development Lab, Experimental Drug Development Centre, Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Wai-Heng Lua
- Antibody & Product Development Lab, Experimental Drug Development Centre, Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Joshua Yi Yeo
- Antibody & Product Development Lab, Experimental Drug Development Centre, Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Jun-Jie Poh
- Antibody & Product Development Lab, Experimental Drug Development Centre, Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Yuen-Ling Ng
- Newcastle University Singapore, Singapore, Singapore
| | - Anil Wipat
- School of Computing, Newcastle University, Newcastle upon Tyne, UK
| | - Samuel Ken-En Gan
- Antibody & Product Development Lab, Experimental Drug Development Centre, Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore. .,James Cook University, Singapore, Singapore. .,Zhejiang Bioinformatics International Science and Technology Cooperation Center, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China. .,Wenzhou Municipal Key Lab of Applied Biomedical and Biopharmaceutical Informatics, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China.
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4
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Gan SKE, Derrick JP, Fraternali F. Editorial: Understanding and Engineering Antibody-Superantigen Interactions. Front Immunol 2022; 13:857339. [PMID: 35222446 PMCID: PMC8865624 DOI: 10.3389/fimmu.2022.857339] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 01/24/2022] [Indexed: 12/04/2022] Open
Affiliation(s)
- Samuel Ken-En Gan
- Antibody & Product Development (APD) Lab, Agency for Science, Technology, and Research (ASTAR), Singapore, Singapore.,APD SKEG Pte Ltd, Singapore, Singapore.,James Cook University, Singapore, Singapore
| | - Jeremy P Derrick
- School of Biological Sciences, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester, United Kingdom
| | - Franca Fraternali
- Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom.,The Francis Crick Institute, London, United Kingdom.,The Thomas Young Centre for Theory and Simulation of Materials, London, United Kingdom
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5
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Gan SKE, Phua SX, Yeo JY. Sagacious epitope selection for vaccines, and both antibody-based therapeutics and diagnostics: tips from virology and oncology. Antib Ther 2022; 5:63-72. [PMID: 35372784 PMCID: PMC8972324 DOI: 10.1093/abt/tbac005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/24/2022] [Accepted: 02/12/2022] [Indexed: 11/12/2022] Open
Abstract
Abstract
The target of an antibody plays a significant role in the success of antibody-based therapeutics and diagnostics, and vaccine development. This importance is focused on the target binding site—epitope, where epitope selection as a part of design thinking beyond traditional antigen selection using whole cell or whole protein immunization can positively impact success. With purified recombinant protein production and peptide synthesis to display limited/selected epitopes, intrinsic factors that can affect the functioning of resulting antibodies can be more easily selected for. Many of these factors stem from the location of the epitope that can impact accessibility of the antibody to the epitope at a cellular or molecular level, direct inhibition of target antigen activity, conservation of function despite escape mutations, and even non-competitive inhibition sites. By incorporating novel computational methods for predicting antigen changes to model-informed drug discovery and development, superior vaccines and antibody-based therapeutics or diagnostics can be easily designed to mitigate failures. With detailed examples, this review highlights the new opportunities, factors and methods of predicting antigenic changes for consideration in sagacious epitope selection.
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Affiliation(s)
- Samuel Ken-En Gan
- Antibody & Product Development Lab, EDDC-BII, Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore
- APD SKEG Pte Ltd, Singapore 439444, Singapore
| | - Ser-Xian Phua
- Antibody & Product Development Lab, EDDC-BII, Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore
| | - Joshua Yi Yeo
- Antibody & Product Development Lab, EDDC-BII, Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore
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6
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Ling WL, Yeo JY, Ng YL, Wipat A, Gan SKE. More Than Meets the Kappa for Antibody Superantigen Protein L (PpL). Antibodies (Basel) 2022; 11:antib11010014. [PMID: 35225872 PMCID: PMC8883962 DOI: 10.3390/antib11010014] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/04/2022] [Accepted: 02/07/2022] [Indexed: 02/04/2023] Open
Abstract
Immunoglobulin superantigens play an important role in affinity purification of antibodies and the microbiota-immune axis at mucosal areas. Based on current understanding, Staphylococcal Protein A (SpA), Streptococcal Protein G (SpG) and Finegoldia Protein L (PpL) are thought to only bind specific regions of human antibodies, allowing for selective purification of antibody isotypes and chains. Clinically, these superantigens are often classified as toxins and increase the virulence of the producing pathogen through unspecific interactions with immune proteins. To perform an in-depth interaction study of these three superantigens with antibodies, bio-layer interferometry (BLI) measurements of their interactions with a permutation panel of 63 IgG1 variants of Pertuzumab and Trastuzumab CDRs grafted to the six human Vκ and seven human VH region families were tested. Through this holistic and systemic analysis of IgG1 variants with various antibody regions modified, comparisons revealed novel PpL–antibody interactions influenced by other non-canonical antibody known light-chain framework regions, whereas SpA and SpG showed relatively consistent interactions. These findings have implications on PpL-based affinity antibody purification and design that can guide the engineering and understanding of PpL-based microbiota-immune effects.
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Affiliation(s)
- Wei-Li Ling
- Antibody & Product Development Laboratory, Experimental Drug Development Centre—Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore; (W.-L.L.); (J.Y.Y.)
- Newcastle Research and Innovation Institute (NewRIIS), Singapore 609607, Singapore;
| | - Joshua Yi Yeo
- Antibody & Product Development Laboratory, Experimental Drug Development Centre—Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore; (W.-L.L.); (J.Y.Y.)
| | - Yuen-Ling Ng
- Newcastle Research and Innovation Institute (NewRIIS), Singapore 609607, Singapore;
| | - Anil Wipat
- School of Computing, Newcastle University, Newcastle upon Tyne NE1 7RU, UK;
| | - Samuel Ken-En Gan
- Antibody & Product Development Laboratory, Experimental Drug Development Centre—Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore; (W.-L.L.); (J.Y.Y.)
- James Cook University, Singapore 387380, Singapore
- Correspondence:
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7
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Yeo JY, Gan SKE. Peering into Avian Influenza A(H5N8) for a Framework towards Pandemic Preparedness. Viruses 2021; 13:2276. [PMID: 34835082 PMCID: PMC8622263 DOI: 10.3390/v13112276] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/20/2021] [Accepted: 11/12/2021] [Indexed: 12/13/2022] Open
Abstract
2014 marked the first emergence of avian influenza A(H5N8) in Jeonbuk Province, South Korea, which then quickly spread worldwide. In the midst of the 2020-2021 H5N8 outbreak, it spread to domestic poultry and wild waterfowl shorebirds, leading to the first human infection in Astrakhan Oblast, Russia. Despite being clinically asymptomatic and without direct human-to-human transmission, the World Health Organization stressed the need for continued risk assessment given the nature of Influenza to reassort and generate novel strains. Given its promiscuity and easy cross to humans, the urgency to understand the mechanisms of possible species jumping to avert disastrous pandemics is increasing. Addressing the epidemiology of H5N8, its mechanisms of species jumping and its implications, mutational and reassortment libraries can potentially be built, allowing them to be tested on various models complemented with deep-sequencing and automation. With knowledge on mutational patterns, cellular pathways, drug resistance mechanisms and effects of host proteins, we can be better prepared against H5N8 and other influenza A viruses.
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Affiliation(s)
- Joshua Yi Yeo
- Antibody & Product Development Lab, EDDC-BII, Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore;
| | - Samuel Ken-En Gan
- Antibody & Product Development Lab, EDDC-BII, Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore;
- APD SKEG Pte Ltd., Singapore 439444, Singapore
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8
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Deacy AM, Gan SKE, Derrick JP. Superantigen Recognition and Interactions: Functions, Mechanisms and Applications. Front Immunol 2021; 12:731845. [PMID: 34616400 PMCID: PMC8488440 DOI: 10.3389/fimmu.2021.731845] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/30/2021] [Indexed: 12/27/2022] Open
Abstract
Superantigens are unconventional antigens which recognise immune receptors outside their usual recognition sites e.g. complementary determining regions (CDRs), to elicit a response within the target cell. T-cell superantigens crosslink T-cell receptors and MHC Class II molecules on antigen-presenting cells, leading to lymphocyte recruitment, induction of cytokine storms and T-cell anergy or apoptosis among many other effects. B-cell superantigens, on the other hand, bind immunoglobulins on B-cells, affecting opsonisation, IgG-mediated phagocytosis, and driving apoptosis. Here, through a review of the structural basis for recognition of immune receptors by superantigens, we show that their binding interfaces share specific physicochemical characteristics when compared with other protein-protein interaction complexes. Given that antibody-binding superantigens have been exploited extensively in industrial antibody purification, these observations could facilitate further protein engineering to optimize the use of superantigens in this and other areas of biotechnology.
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Affiliation(s)
- Anthony M. Deacy
- School of Biological Sciences, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester, United Kingdom
| | - Samuel Ken-En Gan
- Antibody & Product Development Lab, Experimental Drug Development Centre – Bioinformatics Institute (EDDC-BII), Agency for Science Technology and Research (ASTAR), Singapore, Singapore
- James Cook University, Singapore, Singapore
| | - Jeremy P. Derrick
- School of Biological Sciences, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester, United Kingdom
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9
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Su CTT, Lua WH, Poh JJ, Ling WL, Yeo JY, Gan SKE. Molecular Insights of Nickel Binding to Therapeutic Antibodies as a Possible New Antibody Superantigen. Front Immunol 2021; 12:676048. [PMID: 34305906 PMCID: PMC8296638 DOI: 10.3389/fimmu.2021.676048] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 05/24/2021] [Indexed: 11/21/2022] Open
Abstract
The binding of nickel by immune proteins can manifest as Type IV contact dermatitis (Ni-specific T cells mediated) and less frequently as Type I hypersensitivity with both mechanisms remaining unknown to date. Since there are reports of patients co-manifesting the two hypersensitivities, a common mechanism may underlie both the TCR and IgE nickel binding. Focusing on Trastuzumab and Pertuzumab IgE variants as serendipitous investigation models, we found Ni-NTA interactions independent of Her2 binding to be due to glutamine stretches. These stretches are both Ni-inducible and in fixed pockets at the antibody complementarity-determining regions (CDRs) and framework regions (FWRs) of both the antibody heavy and light chains with influence from the heavy chain constant region. Comparisons with TCRs structures revealed similar interactions, demonstrating the possible underlying mechanism in selecting for Ni-binding IgEs and TCRs respectively. With the elucidation of the interaction, future therapeutic antibodies could also be sagaciously engineered to utilize such nickel binding for biotechnological purposes.
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Affiliation(s)
- Chinh Tran-To Su
- Antibody & Product Development Lab, Experimental Drug Development Centre, Bioinformatics Institute, Agency for Science, Technology, and Research (ASTAR), Singapore, Singapore
| | - Wai-Heng Lua
- Antibody & Product Development Lab, Experimental Drug Development Centre, Bioinformatics Institute, Agency for Science, Technology, and Research (ASTAR), Singapore, Singapore
| | - Jun-Jie Poh
- Antibody & Product Development Lab, Experimental Drug Development Centre, Bioinformatics Institute, Agency for Science, Technology, and Research (ASTAR), Singapore, Singapore
| | - Wei-Li Ling
- Antibody & Product Development Lab, Experimental Drug Development Centre, Bioinformatics Institute, Agency for Science, Technology, and Research (ASTAR), Singapore, Singapore
| | - Joshua Yi Yeo
- Antibody & Product Development Lab, Experimental Drug Development Centre, Bioinformatics Institute, Agency for Science, Technology, and Research (ASTAR), Singapore, Singapore
| | - Samuel Ken-En Gan
- Antibody & Product Development Lab, Experimental Drug Development Centre, Bioinformatics Institute, Agency for Science, Technology, and Research (ASTAR), Singapore, Singapore.,James Cook University, Singapore, Singapore.,APD SKEG Pte Ltd, Singapore, Singapore
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10
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Yeo JY, Koh DWS, Yap P, Goh GR, Gan SKE. Spontaneous Mutations in HIV-1 Gag, Protease, RT p66 in the First Replication Cycle and How They Appear: Insights from an In Vitro Assay on Mutation Rates and Types. Int J Mol Sci 2020; 22:E370. [PMID: 33396460 PMCID: PMC7796399 DOI: 10.3390/ijms22010370] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 12/25/2020] [Accepted: 12/29/2020] [Indexed: 02/07/2023] Open
Abstract
While drug resistant mutations in HIV-1 are largely credited to its error prone HIV-1 RT, the time point in the infection cycle that these mutations can arise and if they appear spontaneously without selection pressures both remained enigmatic. Many HIV-1 RT mutational in vitro studies utilized reporter genes (LacZ) as a template to investigate these questions, thereby not accounting for the possible contribution of viral codon usage. To address this gap, we investigated HIV-1 RT mutation rates and biases on its own Gag, protease, and RT p66 genes in an in vitro selection pressure free system. We found rare clinical mutations with a general avoidance of crucial functional sites in the background mutations rates for Gag, protease, and RT p66 at 4.71 × 10-5, 6.03 × 10-5, and 7.09 × 10-5 mutations/bp, respectively. Gag and p66 genes showed a large number of 'A to G' mutations. Comparisons with silently mutated p66 sequences showed an increase in mutation rates (1.88 × 10-4 mutations/bp) and that 'A to G' mutations occurred in regions reminiscent of ADAR neighbor sequence preferences. Mutational free energies of the 'A to G' mutations revealed an avoidance of destabilizing effects, with the natural p66 gene codon usage providing barriers to disruptive amino acid changes. Our study demonstrates the importance of studying mutation emergence in HIV genes in a RT-PCR in vitro selection pressure free system to understand how fast drug resistance can emerge, providing transferable applications to how new viral diseases and drug resistances can emerge.
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Affiliation(s)
- Joshua Yi Yeo
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore; (J.Y.Y.); (D.W.-S.K.); (P.Y.); (G.-R.G.)
- Experimental Drug Development Centre, A*STAR, 10 Biopolis Road Chromos #05-01, Singapore 138670, Singapore
| | - Darius Wen-Shuo Koh
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore; (J.Y.Y.); (D.W.-S.K.); (P.Y.); (G.-R.G.)
- Experimental Drug Development Centre, A*STAR, 10 Biopolis Road Chromos #05-01, Singapore 138670, Singapore
| | - Ping Yap
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore; (J.Y.Y.); (D.W.-S.K.); (P.Y.); (G.-R.G.)
| | - Ghin-Ray Goh
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore; (J.Y.Y.); (D.W.-S.K.); (P.Y.); (G.-R.G.)
| | - Samuel Ken-En Gan
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore; (J.Y.Y.); (D.W.-S.K.); (P.Y.); (G.-R.G.)
- Experimental Drug Development Centre, A*STAR, 10 Biopolis Road Chromos #05-01, Singapore 138670, Singapore
- p53 Laboratory, A*STAR, 8A Biomedical Grove, #06-04/05 Neuros/Immunos, Singapore 138648, Singapore
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11
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Chan KF, Su CTT, Krah A, Phua SX, Yeo JY, Ling WL, Bond PJ, Gan SKE. An Alternative HIV-1 Non-Nucleoside Reverse Transcriptase Inhibition Mechanism: Targeting the p51 Subunit. Molecules 2020; 25:E5902. [PMID: 33322154 PMCID: PMC7763519 DOI: 10.3390/molecules25245902] [Citation(s) in RCA: 5] [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: 11/29/2020] [Revised: 12/09/2020] [Accepted: 12/11/2020] [Indexed: 01/08/2023] Open
Abstract
The ongoing development of drug resistance in HIV continues to push for the need of alternative drug targets in inhibiting HIV. One such target is the Reverse transcriptase (RT) enzyme which is unique and critical in the viral life cycle-a rational target that is likely to have less off-target effects in humans. Serendipitously, we found two chemical scaffolds from the National Cancer Institute (NCI) Diversity Set V that inhibited HIV-1 RT catalytic activity. Computational structural analyses and subsequent experimental testing demonstrated that one of the two chemical scaffolds binds to a novel location in the HIV-1 RT p51 subunit, interacting with residue Y183, which has no known association with previously reported drug resistance. This finding supports the possibility of a novel druggable site on p51 for a new class of non-nucleoside RT inhibitors that may inhibit HIV-1 RT allosterically. Although inhibitory activity was shown experimentally to only be in the micromolar range, the scaffolds serve as a proof-of-concept of targeting the HIV RT p51 subunit, with the possibility of medical chemistry methods being applied to improve inhibitory activity towards more effective drugs.
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Affiliation(s)
- Kwok-Fong Chan
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore; (K.-F.C.); (C.T.-T.S.); (A.K.); (S.-X.P.); (J.Y.Y.); (W.-L.L.); (P.J.B.)
| | - Chinh Tran-To Su
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore; (K.-F.C.); (C.T.-T.S.); (A.K.); (S.-X.P.); (J.Y.Y.); (W.-L.L.); (P.J.B.)
- Experimental Drug Development Centre, A*STAR, 10 Biopolis Road Chromos #05-01, Singapore 138670, Singapore
| | - Alexander Krah
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore; (K.-F.C.); (C.T.-T.S.); (A.K.); (S.-X.P.); (J.Y.Y.); (W.-L.L.); (P.J.B.)
| | - Ser-Xian Phua
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore; (K.-F.C.); (C.T.-T.S.); (A.K.); (S.-X.P.); (J.Y.Y.); (W.-L.L.); (P.J.B.)
| | - Joshua Yi Yeo
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore; (K.-F.C.); (C.T.-T.S.); (A.K.); (S.-X.P.); (J.Y.Y.); (W.-L.L.); (P.J.B.)
- Experimental Drug Development Centre, A*STAR, 10 Biopolis Road Chromos #05-01, Singapore 138670, Singapore
| | - Wei-Li Ling
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore; (K.-F.C.); (C.T.-T.S.); (A.K.); (S.-X.P.); (J.Y.Y.); (W.-L.L.); (P.J.B.)
- Experimental Drug Development Centre, A*STAR, 10 Biopolis Road Chromos #05-01, Singapore 138670, Singapore
| | - Peter J. Bond
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore; (K.-F.C.); (C.T.-T.S.); (A.K.); (S.-X.P.); (J.Y.Y.); (W.-L.L.); (P.J.B.)
| | - Samuel Ken-En Gan
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore; (K.-F.C.); (C.T.-T.S.); (A.K.); (S.-X.P.); (J.Y.Y.); (W.-L.L.); (P.J.B.)
- Experimental Drug Development Centre, A*STAR, 10 Biopolis Road Chromos #05-01, Singapore 138670, Singapore
- p53 Laboratory, A*STAR, 8A Biomedical Grove, #06-04/05 Neuros/Immunos, Singapore 138648, Singapore
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12
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Ling WL, Su CTT, Lua WH, Poh JJ, Ng YL, Wipat A, Gan SKE. Essentially Leading Antibody Production: An Investigation of Amino Acids, Myeloma, and Natural V-Region Signal Peptides in Producing Pertuzumab and Trastuzumab Variants. Front Immunol 2020; 11:604318. [PMID: 33365032 PMCID: PMC7750424 DOI: 10.3389/fimmu.2020.604318] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 11/05/2020] [Indexed: 11/29/2022] Open
Abstract
Boosting the production of recombinant therapeutic antibodies is crucial in both academic and industry settings. In this work, we investigated the usage of varying signal peptides by antibody V-genes and their roles in recombinant transient production, systematically comparing myeloma and the native signal peptides of both heavy and light chains in 168 antibody permutation variants. We found that amino acids count and types (essential or non-essential) were important factors in a logistic regression equation model for predicting transient co-transfection protein production rates. Deeper analysis revealed that the culture media were often incomplete and that the supplementation of essential amino acids can improve the recombinant protein yield. While these findings are derived from transient HEK293 expression, they also provide insights to the usage of the large repertoire of antibody signal peptides, where by varying the number of specific amino acids in the signal peptides attached to the variable regions, bottlenecks in amino acid availability can be mitigated.
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Affiliation(s)
- Wei-Li Ling
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Newcastle Research and Innovation Institute (NewRIIS), Singapore, Singapore
- Experimental Drug Development Centre, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Chinh Tran-To Su
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Experimental Drug Development Centre, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Wai-Heng Lua
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Jun-Jie Poh
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Yuen-Ling Ng
- Newcastle Research and Innovation Institute (NewRIIS), Singapore, Singapore
| | - Anil Wipat
- School of Computing, Newcastle University, Singapore, Singapore
| | - Samuel Ken-En Gan
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Experimental Drug Development Centre, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
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13
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Chan KF, Poh JJ, Wu WL, Gan SKE. Augmented reality in scientific visualization and communications: a new dawn of looking at antibody interactions. Antib Ther 2020; 3:221-226. [PMID: 33928229 PMCID: PMC7990256 DOI: 10.1093/abt/tbaa021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/12/2020] [Accepted: 09/02/2020] [Indexed: 01/01/2023] Open
Abstract
The use of augmented reality (AR) in providing three-dimensional (3D) visual support and image depth have been applied in education, tourism, historical studies, and medical training. In research and development, there has been a slow but growing use of AR tools in chemical and drug discovery, but little has been implemented for whole 3D antibody structures (IgE, IgM, IgA, IgG, and IgD) and in communicating their interactions with the antigens or receptors in publications. Given that antibody interactions can vary significantly between different monoclonal antibodies, a convenient and easy to use 3D visualization can convey structural mechanisms clearer to readers, especially in how residues may interact with one another. While this was previously constrained to the use of stereo images on printed material or molecular visualization software on the computer, the revolution of smartphone and phablets now allows visualization of whole molecular structures on-the-go, allowing rotations, zooming in and out, and even animations without complex devices or the training of visual prowess. While not yet as versatile as molecular visualization software on the computer, such technology is an improvement from stereo-images and bridges the gap with molecular visualization tools. In this report, we discuss the use of AR and how they can be employed in the holistic view of antibodies and the future of the technology for better scientific communication.
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Affiliation(s)
- Kwok-Fong Chan
- Antibody & Product Development Lab, Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Jun-Jie Poh
- Antibody & Product Development Lab, Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Wei-Ling Wu
- Antibody & Product Development Lab, Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Samuel Ken-En Gan
- Antibody & Product Development Lab, Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
- Experimental Drug Development Centre, ASTAR, 10 Biopolis Road, #05-01, Chromos, Singapore 138670
- p53 Laboratory, ASTAR, 8A Biomedical Grove, #06-04/05 Neuros/Immunos, Singapore 138648
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14
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Allosteric drugs and mutations: chances, challenges, and necessity. Curr Opin Struct Biol 2020; 62:149-157. [DOI: 10.1016/j.sbi.2020.01.010] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 01/16/2020] [Indexed: 12/22/2022]
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15
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Bachert C, Humbert M, Hanania NA, Zhang N, Holgate S, Buhl R, Bröker BM. Staphylococcus aureus and its IgE-inducing enterotoxins in asthma: current knowledge. Eur Respir J 2020; 55:13993003.01592-2019. [PMID: 31980492 DOI: 10.1183/13993003.01592-2019] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 12/31/2019] [Indexed: 02/06/2023]
Abstract
While immunoglobulin (Ig) E is a prominent biomarker for early-onset, its levels are often elevated in non-allergic late-onset asthma. However, the pattern of IgE expression in the latter is mostly polyclonal, with specific IgEs low or below detection level albeit with an increased total IgE. In late-onset severe asthma patients, specific IgE to Staphylococcal enterotoxins (se-IgE) can frequently be detected in serum, and has been associated with asthma, with severe asthma defined by hospitalisations, oral steroid use and decrease in lung function. Recently, se-IgE was demonstrated to even predict the development into severe asthma with exacerbations over the next decade. Staphylococcus aureus manipulates the airway mucosal immunology at various levels via its proteins, including superantigens, serine-protease-like proteins (Spls), or protein A (SpA) and possibly others. Release of IL-33 from respiratory epithelium and activation of innate lymphoid cells (ILCs) via its receptor ST2, type 2 cytokine release from those ILCs and T helper (Th) 2 cells, mast cell degranulation, massive local B-cell activation and IgE formation, and finally eosinophil attraction with consequent release of extracellular traps, adding to the epithelial damage and contributing to disease persistence via formation of Charcot-Leyden crystals are the most prominent hallmarks of the manipulation of the mucosal immunity by S. aureus In summary, S. aureus claims a prominent role in the orchestration of severe airway inflammation and in current and future disease severity. In this review, we discuss current knowledge in this field and outline the needs for future research to fully understand the impact of S. aureus and its proteins on asthma.
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Affiliation(s)
- Claus Bachert
- Upper Airways Research Laboratory, Ghent University, Ghent, Belgium .,Division of ENT diseases, CLINTEC, Karolinska Institute, University of Stockholm, Stockholm, Sweden
| | - Marc Humbert
- Service de Pneumologie, Hôpital Bicêtre, Le Kremlin Bicêtre, France
| | - Nicola A Hanania
- Section of Pulmonary and Critical Care Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Nan Zhang
- Upper Airways Research Laboratory, Ghent University, Ghent, Belgium
| | - Stephen Holgate
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, The Sir Henry Wellcome Research Laboratories, Southampton General Hospital, Southampton, UK
| | - Roland Buhl
- Pulmonary Dept, Mainz University Hospital, Mainz, Germany
| | - Barbara M Bröker
- Dept of Immunology, University Medicine Greifswald, Greifswald, Germany
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16
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Ling WL, Lua WH, Gan SKE. Sagacity in antibody humanization for therapeutics, diagnostics and research purposes: considerations of antibody elements and their roles. Antib Ther 2020; 3:71-79. [PMID: 33928226 PMCID: PMC7990220 DOI: 10.1093/abt/tbaa005] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/27/2020] [Accepted: 04/07/2020] [Indexed: 12/15/2022] Open
Abstract
The humanization of antibodies for therapeutics is a critical process that can determine the success of antibody drug development. However, the science underpinning this process remains elusive with different laboratories having very different methods. Well-funded laboratories can afford automated high-throughput screening methods to derive their best binder utilizing a very expensive initial set of equipment affordable only to a few. Often within these high-throughput processes, only standard key parameters, such as production, binding and aggregation are analyzed. Given the lack of suitable animal models, it is only at clinical trials that immunogenicity and allergy adverse effects are detected through anti-human antibodies as per FDA guidelines. While some occurrences that slip through can be mitigated by additional desensitization protocols, such adverse reactions to grafted humanized antibodies can be prevented at the humanization step. Considerations such as better antibody localization, avoidance of unspecific interactions to superantigens and the tailoring of antibody dependent triggering of immune responses, the antibody persistence on cells, can all be preemptively considered through a holistic sagacious approach, allowing for better outcomes in therapy and for research and diagnostic purposes.
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Affiliation(s)
- Wei-Li Ling
- Antibody & Product Development Lab, Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Wai-Heng Lua
- Antibody & Product Development Lab, Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Samuel Ken-En Gan
- Antibody & Product Development Lab, Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
- p53 Laboratory, ASTAR, 8A Biomedical Grove, #06-04/05 Neuros/Immunos, Singapore 138648
- Experimental Drug Development Center, ASTAR, 10 Biopolis Road, #05-01, Chromos, Singapore 138670
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17
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Samsudin F, Yeo JY, Gan SKE, Bond PJ. Not all therapeutic antibody isotypes are equal: the case of IgM versus IgG in Pertuzumab and Trastuzumab. Chem Sci 2020; 11:2843-2854. [PMID: 32206268 PMCID: PMC7069520 DOI: 10.1039/c9sc04722k] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 02/12/2020] [Indexed: 01/06/2023] Open
Abstract
The therapeutic potential of immunoglobulin M (IgM) is of considerable interest in immunotherapy due to its complement-activating and cell-agglutinating abilities. Pertuzumab and Trastuzumab are monoclonal antibodies used to treat human epidermal growth factor receptor 2 (HER2)-positive breast cancer but exhibit significantly different binding affinities as IgM when compared to its IgG isotype. Using integrative multiscale modelling and simulations of complete antibody assemblies, we show that Pertuzumab IgM is able to utilize all of its V-regions to bind multiple HER2 receptors simultaneously, while similar binding in Trastuzumab IgM is prohibited by steric clashes caused by the large globular domain of HER2. This is subsequently validated by confirming that Pertuzumab IgM inhibits proliferation in HER2 over-expressing live cells more effectively than its IgG counterpart and Trastuzumab IgM. Our study highlights the importance of understanding the molecular details of antibody-antigen interactions for the design and isotype selection of therapeutic antibodies.
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Affiliation(s)
- Firdaus Samsudin
- Bioinformatics Institute (ASTAR) , 30 Biopolis Street, #07-01 Matrix , Singapore 138671 , Singapore . ;
| | - Joshua Yi Yeo
- Bioinformatics Institute (ASTAR) , 30 Biopolis Street, #07-01 Matrix , Singapore 138671 , Singapore . ;
| | - Samuel Ken-En Gan
- Bioinformatics Institute (ASTAR) , 30 Biopolis Street, #07-01 Matrix , Singapore 138671 , Singapore . ;
- p53 Laboratory (ASTAR) , 8A Biomedical Grove, #06-04/05 Neuros/Immunos , Singapore 138648
- Experimental Drug Development Center (ASTAR) , 10 Biopolis Road Chromos #05-01 , Singapore 138670
| | - Peter J Bond
- Bioinformatics Institute (ASTAR) , 30 Biopolis Street, #07-01 Matrix , Singapore 138671 , Singapore . ;
- Department of Biological Sciences , National University of Singapore , 14 Science Drive 4 , Singapore 117543 , Singapore
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18
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Liu J, Cao Z. Protective Effect of Circular RNA (CircRNA) Ddx17 in Ovalbumin (OVA)-Induced Allergic Rhinitis (AR) Mice. Med Sci Monit 2020; 26:e919083. [PMID: 31999672 PMCID: PMC7003661 DOI: 10.12659/msm.919083] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Background CircRNAs are involved in multiple biological processes, especially when they act as sponges of miRNA. Thus, the present study investigated the effect of circDdx17 on allergic rhinitis (AR) in an animal model, and determined the miRNA that was involved in this effect. Material/Methods The AR model was created by repetitive stimulation of ovalbumin (OVA). The levels of mRNAs in plasma were determined by qPCR. CircDdx17 stability was assessed using RNase R. The interaction between circDdx17 and miR-17-5p was predicted by bioinformatics and confirmed by dual luciferase assay. Moreover, the frequencies of rubbing and sneezing and pathological changes were recorded, and OVA-specific IgE, tumor necrosis factor (TNF)-α, interleukin (IL)-4, and IL-5 levels were detected by ELISA. Results Levels of circDdx17 were decreased in OVA-induced AR mice, and miR-17-5p interacted with circDdx17 in spleen cells derived from mice. Moreover, circDdx17 overexpression reduced the expression of miR-17-5p, OVA-specific IgE, TNF-α, IL-4, and IL-5, as well as the frequencies of rubbing and sneezing, and alleviated pathological changes in OVA-induced AR mice. Conclusions CircDdx17 appears to have a protective effect on mice in the progression of AR. Specifically, overexpression of circDdx17 inhibited the expression of miR-17-5p and alleviated the condition of AR. Therefore, circDdx17 appears to be a good candidate for use in prevention of AR. However, the detailed mechanism underlying the circDdx17/miR-17-5p regulatory pathway requires further study.
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Affiliation(s)
- Jiao Liu
- Department of Otorhinolaryngology, Tongliao Hospital, Tongliao, Inner Mongolia, China (mainland)
| | - Zhiwei Cao
- Department of Otorhinolaryngology, Shengjing Hospital, China Medical University, Shenyang, Liaoning, China (mainland)
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19
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Ling WL, Ng YL, Wipat A, Lane DP, Gan SKE. The quantification of antibody elements and receptors subunit expression using qPCR: The design of VH, VL, CH, CL, FcR subunits primers for a more holistic view of the immune system. J Immunol Methods 2019; 476:112683. [PMID: 31682797 DOI: 10.1016/j.jim.2019.112683] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 08/20/2019] [Accepted: 10/09/2019] [Indexed: 12/18/2022]
Abstract
The expression levels of immunoglobulin elements and their receptors are important markers for health and disease. Within the immunoglobulin locus, the constant regions and the variable region families are associated with certain pathologies, yet a holistic view of the interaction between the expressions of the multiple genes remain to be fully characterized. There is thus an important need to quantify antibody elements, their receptors and the receptor subunits in blood (PBMC cDNA) for both screening and detailed studies of such associations. Leveraging on qPCR, we designed primers for all Vκ1-6, VH1-7, Vλ1-11, nine CH isotypes, Cκ, Cκ, Cλ1 &3, FcεRI α,β, and γ subunits, all three FcγR and their subunits, and FcαR. Validating this on a volunteer PBMC cDNA, we report a qPCR primer set repertoire that can quantify the relative expression of all the above genes to the GAPDH housekeeping gene, with implications and uses in both clinical monitoring and research.
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Affiliation(s)
- Wei-Li Ling
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore; Newcastle Research and Innovation Institute (NewRIIS), Singapore.
| | - Yuen-Ling Ng
- Newcastle Research and Innovation Institute (NewRIIS), Singapore.
| | - Anil Wipat
- School of Computing, Newcastle University, UK.
| | - David Philip Lane
- p53 Laboratory, Agency for Science, Technology and Research (A*STAR), Singapore.
| | - Samuel Ken-En Gan
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore; p53 Laboratory, Agency for Science, Technology and Research (A*STAR), Singapore.
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20
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Krokhotin A, Du H, Hirabayashi K, Popov K, Kurokawa T, Wan X, Ferrone S, Dotti G, Dokholyan NV. Computationally Guided Design of Single-Chain Variable Fragment Improves Specificity of Chimeric Antigen Receptors. MOLECULAR THERAPY-ONCOLYTICS 2019; 15:30-37. [PMID: 31650023 PMCID: PMC6804740 DOI: 10.1016/j.omto.2019.08.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 08/24/2019] [Indexed: 01/24/2023]
Abstract
Chimeric antigen receptor (CAR)-T cell-based immunotherapy of malignant disease relies on the specificity and association constant of single-chain variable fragments (scFvs). The latter are synthesized from parent antibodies by fusing their light (VL) and heavy (VH)-chain variable domains into a single chain using a flexible linker peptide. The fusion of VL and VH domains can distort their relative orientation, thereby compromising specificity and association constant of scFv, and reducing the lytic efficacy of CAR-T cells. Here, we circumvent the complications of domains' fusion by designing scFv mutants that stabilize interaction between scFv and its target, thereby rescuing scFv efficacy. We employ an iterative approach, based on structural modeling and mutagenesis driven by computational protein design. To demonstrate the power of this approach, we use the scFv derived from an antibody specific to a human leukocyte antigen A2 (HLA-A2)-HER2-derived peptide complex. Whereas the parental antibody is highly specific to its target, the scFv showed reduced specificity. Using our approach, we design mutations into scFvs that restore specificity of the original antibody.
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Affiliation(s)
- Andrey Krokhotin
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Hongwei Du
- Lineberger Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Koichi Hirabayashi
- Lineberger Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Konstantin Popov
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Tomohiro Kurokawa
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Xinhui Wan
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Soldano Ferrone
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Gianpietro Dotti
- Lineberger Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Nikolay V Dokholyan
- Departments of Pharmacology and Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA
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