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Maynard JA, Segatori L. Editorial overview: Tissue, cell, and pathway engineering: Recent innovations in biomedical technologies. Curr Opin Biotechnol 2023; 83:102981. [PMID: 37591033 DOI: 10.1016/j.copbio.2023.102981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Affiliation(s)
- Jennifer A Maynard
- Department of Chemical Engineering, University of Texas, Austin, TX 78712, USA.
| | - Laura Segatori
- Systems, Synthetic, and Physical Biology, Rice University, Houston, United States; Department of Bioengineering, Rice University, Houston, United States; Department of Chemical and Biomolecular Engineering, Rice University, Houston, United States; Department of Biosciences, Rice University, Houston, United States.
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2
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Osickova A, Knoblochova S, Bumba L, Man P, Kalaninova Z, Lepesheva A, Jurnecka D, Cizkova M, Biedermannova L, Goldsmith JA, Maynard JA, McLellan JS, Osicka R, Sebo P, Masin J. A conserved tryptophan in the acylated segment of RTX toxins controls their β 2 integrin-independent cell penetration. J Biol Chem 2023; 299:104978. [PMID: 37390987 PMCID: PMC10392135 DOI: 10.1016/j.jbc.2023.104978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/20/2023] [Accepted: 06/22/2023] [Indexed: 07/02/2023] Open
Abstract
The acylated Repeats in ToXins (RTX) leukotoxins, the adenylate cyclase toxin (CyaA) or α-hemolysin (HlyA), bind β2 integrins of leukocytes but also penetrate cells lacking these receptors. We show that the indoles of conserved tryptophans in the acylated segments, W876 of CyaA and W579 of HlyA, are crucial for β2 integrin-independent membrane penetration. Substitutions of W876 by aliphatic or aromatic residues did not affect acylation, folding, or the activities of CyaA W876L/F/Y variants on cells expressing high amounts of the β2 integrin CR3. However, toxin activity of CyaA W876L/F/Y on cells lacking CR3 was strongly impaired. Similarly, a W579L substitution selectively reduced HlyA W579L cytotoxicity towards cells lacking β2 integrins. Intriguingly, the W876L/F/Y substitutions increased the thermal stability (Tm) of CyaA by 4 to 8 °C but locally enhanced the accessibility to deuteration of the hydrophobic segment and of the interface of the two acylated loops. W876Q substitution (showing no increase in Tm), or combination of W876F with a cavity-filling V822M substitution (this combination decreasing the Tm closer to that of CyaA), yielded a milder defect of toxin activity on erythrocytes lacking CR3. Furthermore, the activity of CyaA on erythrocytes was also selectively impaired when the interaction of the pyrrolidine of P848 with the indole of W876 was ablated. Hence, the bulky indoles of residues W876 of CyaA, or W579 of HlyA, rule the local positioning of the acylated loops and enable a membrane-penetrating conformation in the absence of RTX toxin docking onto the cell membrane by β2 integrins.
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Affiliation(s)
- Adriana Osickova
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Sarka Knoblochova
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Ladislav Bumba
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Petr Man
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Zuzana Kalaninova
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic; Faculty of Sciences, Charles University, Prague, Czech Republic
| | - Anna Lepesheva
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic; Faculty of Sciences, Charles University, Prague, Czech Republic
| | - David Jurnecka
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Monika Cizkova
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Lada Biedermannova
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec, Czech Republic
| | - Jory A Goldsmith
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, USA
| | - Jennifer A Maynard
- Department of Chemical Engineering, The University of Texas at Austin, Austin, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, USA
| | - Radim Osicka
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Peter Sebo
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic.
| | - Jiri Masin
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic.
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Qerqez AN, Silva RP, Maynard JA. Outsmarting Pathogens with Antibody Engineering. Annu Rev Chem Biomol Eng 2023; 14:217-241. [PMID: 36917814 PMCID: PMC10330301 DOI: 10.1146/annurev-chembioeng-101121-084508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
There is growing interest in identifying antibodies that protect against infectious diseases, especially for high-risk individuals and pathogens for which no vaccine is yet available. However, pathogens that manifest as opportunistic or latent infections express complex arrays of virulence-associated proteins and are adept at avoiding immune responses. Some pathogens have developed strategies to selectively destroy antibodies, whereas others create decoy epitopes that trick the host immune system into generating antibodies that are at best nonprotective and at worst enhance pathogenesis. Antibody engineering strategies can thwart these efforts by accessing conserved neutralizing epitopes, generating Fc domains that resist capture or degradation and even accessing pathogens hidden inside cells. Design of pathogen-resistant antibodies can enhance protection and guide development of vaccine immunogens against these complex pathogens. Here, we discuss general strategies for design of antibodies resistant to specific pathogen defense mechanisms.
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Affiliation(s)
- Ahlam N Qerqez
- Department of Chemical Engineering, The University of Texas, Austin, Texas, USA;
| | - Rui P Silva
- Department of Molecular Biosciences, The University of Texas, Austin, Texas, USA
| | - Jennifer A Maynard
- Department of Chemical Engineering, The University of Texas, Austin, Texas, USA;
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4
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Yount KS, Hall JM, Caution K, Shamseldin MM, Guo M, Marion K, Fullen AR, Huang Y, Maynard JA, Quataert SA, Deora R, Dubey P. Systemic priming and intranasal booster with a BcfA-adjuvanted acellular pertussis vaccine generates CD4+ IL-17+ nasal tissue resident T cells and reduces B. pertussis nasal colonization. Front Immunol 2023; 14:1181876. [PMID: 37275891 PMCID: PMC10232778 DOI: 10.3389/fimmu.2023.1181876] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/04/2023] [Indexed: 06/07/2023] Open
Abstract
Introduction Resurgence of pertussis, caused by Bordetella pertussis, necessitates novel vaccines and vaccination strategies to combat this disease. Alum-adjuvanted acellular pertussis vaccines (aPV) delivered intramuscularly reduce bacterial numbers in the lungs of immunized animals and humans, but do not reduce nasal colonization. Thus, aPV-immunized individuals are sources of community transmission. We showed previously that modification of a commercial aPV (Boostrix) by addition of the Th1/17 polarizing adjuvant Bordetella Colonization Factor A (BcfA) attenuated Th2 responses elicited by alum and accelerated clearance of B. pertussis from mouse lungs. Here we tested whether a heterologous immunization strategy with systemic priming and mucosal booster (prime-pull) would reduce nasal colonization. Methods Adult male and female mice were immunized intramuscularly (i.m.) with aPV or aPV/BcfA and boosted either i.m. or intranasally (i.n.) with the same formulation. Tissue-resident memory (TRM) responses in the respiratory tract were quantified by flow cytometry, and mucosal and systemic antibodies were quantified by ELISA. Immunized and naïve mice were challenged i.n. with Bordetella pertussis and bacterial load in the nose and lungs enumerated at days 1-14 post-challenge. Results We show that prime-pull immunization with Boostrix plus BcfA (aPV/BcfA) generated IFNγ+ and IL-17+ CD4+ lung resident memory T cells (TRM), and CD4+IL-17+ TRM in the nose. In contrast, aPV alone delivered by the same route generated IL-5+ CD4+ resident memory T cells in the lungs and nose. Importantly, nasal colonization was only reduced in mice immunized with aPV/BcfA by the prime-pull regimen. Conclusions These results suggest that TH17 polarized TRM generated by aPV/BcfA may reduce nasal colonization thereby preventing pertussis transmission and subsequent resurgence.
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Affiliation(s)
- Kacy S. Yount
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, United States
| | - Jesse M. Hall
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, United States
| | - Kyle Caution
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, United States
| | - Mohamed M. Shamseldin
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, United States
| | - Myra Guo
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, United States
| | - Keirsten Marion
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, United States
| | - Audra R. Fullen
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, United States
| | - Yimin Huang
- Department of Chemical Engineering, University of Texas-Austin, Austin, TX, United States
| | - Jennifer A. Maynard
- Department of Chemical Engineering, University of Texas-Austin, Austin, TX, United States
| | - Sally A. Quataert
- Respiratory Pathogens Research Center, University of Rochester Medical Center, Rochester, NY, United States
| | - Rajendar Deora
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, United States
- Department of Microbiology, The Ohio State University, Columbus, OH, United States
| | - Purnima Dubey
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, United States
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5
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Silva RP, Huang Y, Nguyen AW, Hsieh CL, Olaluwoye OS, Kaoud TS, Wilen RE, Qerqez AN, Park JG, Khalil AM, Azouz LR, Le KC, Bohanon AL, DiVenere AM, Liu Y, Lee AG, Amengor DA, Shoemaker SR, Costello SM, Padlan EA, Marqusee S, Martinez-Sobrido L, Dalby KN, D'Arcy S, McLellan JS, Maynard JA. Identification of a conserved S2 epitope present on spike proteins from all highly pathogenic coronaviruses. eLife 2023; 12:e83710. [PMID: 36942851 PMCID: PMC10030117 DOI: 10.7554/elife.83710] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 03/04/2023] [Indexed: 03/23/2023] Open
Abstract
To address the ongoing SARS-CoV-2 pandemic and prepare for future coronavirus outbreaks, understanding the protective potential of epitopes conserved across SARS-CoV-2 variants and coronavirus lineages is essential. We describe a highly conserved, conformational S2 domain epitope present only in the prefusion core of β-coronaviruses: SARS-CoV-2 S2 apex residues 980-1006 in the flexible hinge. Antibody RAY53 binds the native hinge in MERS-CoV and SARS-CoV-2 spikes on the surface of mammalian cells and mediates antibody-dependent cellular phagocytosis and cytotoxicity against SARS-CoV-2 spike in vitro. Hinge epitope mutations that ablate antibody binding compromise pseudovirus infectivity, but changes elsewhere that affect spike opening dynamics, including those found in Omicron BA.1, occlude the epitope and may evade pre-existing serum antibodies targeting the S2 core. This work defines a third class of S2 antibody while providing insights into the potency and limitations of S2 core epitope targeting.
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Affiliation(s)
- Rui P Silva
- Department of Molecular Biosciences, The University of Texas at AustinAustinUnited States
| | - Yimin Huang
- Department of Molecular Biosciences, The University of Texas at AustinAustinUnited States
| | - Annalee W Nguyen
- Department of Chemical Engineering, The University of Texas at AustinAustinUnited States
| | - Ching-Lin Hsieh
- Department of Molecular Biosciences, The University of Texas at AustinAustinUnited States
| | - Oladimeji S Olaluwoye
- Department of Chemistry and Biochemistry, The University of Texas at DallasDallasUnited States
| | - Tamer S Kaoud
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at AustinAustinUnited States
| | - Rebecca E Wilen
- Department of Chemical Engineering, The University of Texas at AustinAustinUnited States
| | - Ahlam N Qerqez
- Department of Chemical Engineering, The University of Texas at AustinAustinUnited States
| | - Jun-Gyu Park
- Texas Biomedical Research InstituteSan AntonioUnited States
- Laboratory of Veterinary Zoonosis, College of Veterinary Medicine, Chonnam National UniversityGwangjuRepublic of Korea
| | - Ahmed M Khalil
- Texas Biomedical Research InstituteSan AntonioUnited States
| | - Laura R Azouz
- Department of Chemical Engineering, The University of Texas at AustinAustinUnited States
| | - Kevin C Le
- Department of Chemical Engineering, The University of Texas at AustinAustinUnited States
| | - Amanda L Bohanon
- Department of Molecular Biosciences, The University of Texas at AustinAustinUnited States
| | - Andrea M DiVenere
- Department of Chemical Engineering, The University of Texas at AustinAustinUnited States
| | - Yutong Liu
- Department of Chemical Engineering, The University of Texas at AustinAustinUnited States
| | - Alison G Lee
- Department of Molecular Biosciences, The University of Texas at AustinAustinUnited States
| | - Dzifa A Amengor
- Department of Molecular Biosciences, The University of Texas at AustinAustinUnited States
| | - Sophie R Shoemaker
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Shawn M Costello
- Biophysics Graduate Program, University of California, BerkeleyBerkeleyUnited States
| | | | - Susan Marqusee
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
- Department of Chemistry, University of California, BerkeleyBerkeleyUnited States
| | | | - Kevin N Dalby
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at AustinAustinUnited States
| | - Sheena D'Arcy
- Department of Chemistry and Biochemistry, The University of Texas at DallasDallasUnited States
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at AustinAustinUnited States
- LaMontagne Center for Infectious Diseases, The University of Texas at AustinAustinUnited States
| | - Jennifer A Maynard
- Department of Chemical Engineering, The University of Texas at AustinAustinUnited States
- LaMontagne Center for Infectious Diseases, The University of Texas at AustinAustinUnited States
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6
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Bowen JE, Park YJ, Stewart C, Brown JT, Sharkey WK, Walls AC, Joshi A, Sprouse KR, McCallum M, Tortorici MA, Franko NM, Logue JK, Mazzitelli IG, Nguyen AW, Silva RP, Huang Y, Low JS, Jerak J, Tiles SW, Ahmed K, Shariq A, Dan JM, Zhang Z, Weiskopf D, Sette A, Snell G, Posavad CM, Iqbal NT, Geffner J, Bandera A, Gori A, Sallusto F, Maynard JA, Crotty S, Van Voorhis WC, Simmerling C, Grifantini R, Chu HY, Corti D, Veesler D. SARS-CoV-2 spike conformation determines plasma neutralizing activity elicited by a wide panel of human vaccines. Sci Immunol 2022; 7:eadf1421. [PMID: 36356052 PMCID: PMC9765460 DOI: 10.1126/sciimmunol.adf1421] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 11/07/2022] [Indexed: 11/12/2022]
Abstract
Numerous safe and effective coronavirus disease 2019 vaccines have been developed worldwide that use various delivery technologies and engineering strategies. We show here that vaccines containing prefusion-stabilizing S mutations elicit antibody responses in humans with enhanced recognition of S and the S1 subunit relative to postfusion S as compared with vaccines lacking these mutations or natural infection. Prefusion S and S1 antibody binding titers positively and equivalently correlated with neutralizing activity, and depletion of S1-directed antibodies completely abrogated plasma neutralizing activity. We show that neutralizing activity is almost entirely directed to the S1 subunit and that variant cross-neutralization is mediated solely by receptor binding domain-specific antibodies. Our data provide a quantitative framework for guiding future S engineering efforts to develop vaccines with higher resilience to the emergence of variants than current technologies.
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Affiliation(s)
- John E. Bowen
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Cameron Stewart
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Jack T. Brown
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - William K. Sharkey
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Alexandra C. Walls
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Anshu Joshi
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Kaitlin R. Sprouse
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Matthew McCallum
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | | | - Nicholas M. Franko
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
| | - Jennifer K. Logue
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
| | - Ignacio G. Mazzitelli
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), Facultad de Medicina, Buenos Aires C1121ABG, Argentina
| | - Annalee W. Nguyen
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX
| | - Rui P. Silva
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX
| | - Yimin Huang
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX
| | - Jun Siong Low
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland
| | - Josipa Jerak
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland
| | - Sasha W Tiles
- Center for Emerging and Re-emerging Infectious Diseases, Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Kumail Ahmed
- Department of Paediatrics and Child Health, and Biological & Biomedical Sciences, Aga Khan University, Karachi 74800, Pakistan
| | - Asefa Shariq
- Department of Paediatrics and Child Health, and Biological & Biomedical Sciences, Aga Khan University, Karachi 74800, Pakistan
| | - Jennifer M. Dan
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA UC92037, USA
| | - Zeli Zhang
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA UC92037, USA
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA UC92037, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA UC92037, USA
| | | | - Christine M. Posavad
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Najeeha Talat Iqbal
- Department of Paediatrics and Child Health, and Biological & Biomedical Sciences, Aga Khan University, Karachi 74800, Pakistan
| | - Jorge Geffner
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), Facultad de Medicina, Buenos Aires C1121ABG, Argentina
| | - Alessandra Bandera
- Infectious Diseases Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Andrea Gori
- Infectious Diseases Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Federica Sallusto
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland
| | - Jennifer A. Maynard
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX
| | - Shane Crotty
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA UC92037, USA
| | - Wesley C. Van Voorhis
- Center for Emerging and Re-emerging Infectious Diseases, Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Carlos Simmerling
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, United States
| | - Renata Grifantini
- INGM, Istituto Nazionale Genetica Molecolare “Romeo ed Enrica Invernizzi”, 20122 Milan, Italy
| | - Helen Y. Chu
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
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7
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Liu Y, Nguyen AW, Maynard JA. Engineering antibodies for conditional activity in the solid tumor microenvironment. Curr Opin Biotechnol 2022; 78:102809. [PMID: 36182870 DOI: 10.1016/j.copbio.2022.102809] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/25/2022] [Accepted: 08/30/2022] [Indexed: 12/14/2022]
Abstract
Antibody-based therapeutics enjoy considerable clinical and commercial successes as cancer treatments. However, they can also cause serious toxicities due to recognition of tumor-associated antigens in noncancerous tissues, which can prevent antibody use in certain patient populations and therapeutic modalities. Here, we discuss recent efforts to develop advanced antibody therapeutics with activities restricted to the solid tumor microenvironment. With the intent of decreasing toxicities and expanding therapeutic windows, protein engineering strategies can render ligand binding sensitive to multiple tumor-specific characteristics. These triggers can be intrinsic to solid tumor microenvironments, such as low pH, high extracellular ATP, and the presence of specific proteases. Emerging strategies rely instead on exogenous triggers such as light and ultrasound to provide spatial and temporal control over antibody activation. These multilayered approaches to targeting diseased tissues are expected to usher in a new generation of precision therapeutics.
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Affiliation(s)
- Yutong Liu
- Department of Chemical Engineering, University of Texas, Austin, TX 78712, USA
| | - Annalee W Nguyen
- Department of Chemical Engineering, University of Texas, Austin, TX 78712, USA.
| | - Jennifer A Maynard
- Department of Chemical Engineering, University of Texas, Austin, TX 78712, USA.
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8
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Goldsmith JA, DiVenere AM, Maynard JA, McLellan JS. Structural basis for non-canonical integrin engagement by Bordetella adenylate cyclase toxin. Cell Rep 2022; 40:111196. [PMID: 35977491 PMCID: PMC9416875 DOI: 10.1016/j.celrep.2022.111196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 06/08/2022] [Accepted: 07/20/2022] [Indexed: 11/29/2022] Open
Abstract
Integrins are ubiquitous cell-surface heterodimers that are exploited by pathogens and toxins, including leukotoxins that target β2 integrins on phagocytes. The Bordetella adenylate cyclase toxin (ACT) uses the αMβ2 integrin as a receptor, but the structural basis for integrin binding and neutralization by antibodies is poorly understood. Here, we use cryoelectron microscopy to determine a 2.7 Å resolution structure of an ACT fragment bound to αMβ2. This structure reveals that ACT interacts with the headpiece and calf-2 of the αM subunit in a non-canonical manner specific to bent, inactive αMβ2. Neutralizing antibody epitopes map to ACT residues involved in αM binding, providing the basis for antibody-mediated attachment inhibition. Furthermore, binding to αMβ2 positions the essential ACT acylation sites, which are conserved among toxins exported by type I secretion systems, at the cell membrane. These findings reveal a structural mechanism for integrin-mediated attachment and explain antibody-mediated neutralization of ACT intoxication.
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Affiliation(s)
- Jory A Goldsmith
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Andrea M DiVenere
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| | - Jennifer A Maynard
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712, USA.
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.
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9
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Costello SM, Shoemaker SR, Hobbs HT, Nguyen AW, Hsieh CL, Maynard JA, McLellan JS, Pak JE, Marqusee S. The SARS-CoV-2 spike reversibly samples an open-trimer conformation exposing novel epitopes. Nat Struct Mol Biol 2022; 29:229-238. [PMID: 35236990 PMCID: PMC9007726 DOI: 10.1038/s41594-022-00735-5] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 01/21/2022] [Indexed: 11/09/2022]
Abstract
Current COVID-19 vaccines and many clinical diagnostics are based on the structure and function of the SARS-CoV-2 spike ectodomain. Using hydrogen-deuterium exchange monitored by mass spectrometry, we have uncovered that, in addition to the prefusion structure determined by cryo-electron microscopy, this protein adopts an alternative conformation that interconverts slowly with the canonical prefusion structure. This new conformation-an open trimer-contains easily accessible receptor-binding domains. It exposes the conserved trimer interface buried in the prefusion conformation, thus exposing potential epitopes for pan-coronavirus antibody and ligand recognition. The population of this state and kinetics of interconversion are modulated by temperature, receptor binding, antibody binding, and sequence variants observed in the natural population. Knowledge of the structure and populations of this conformation will help improve existing diagnostics, therapeutics, and vaccines.
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Affiliation(s)
- Shawn M Costello
- Biophysics Graduate Program, University of California, Berkeley, CA, USA
| | - Sophie R Shoemaker
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Helen T Hobbs
- Department of Chemistry, University of California, Berkeley, CA, USA
| | - Annalee W Nguyen
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Ching-Lin Hsieh
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Jennifer A Maynard
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - John E Pak
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Susan Marqusee
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
- Department of Chemistry, University of California, Berkeley, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA.
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10
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Silva RP, DiVenere AM, Amengor D, Maynard JA. Antibodies binding diverse pertactin epitopes protect mice from B. pertussis infection. J Biol Chem 2022; 298:101715. [PMID: 35151691 PMCID: PMC8931430 DOI: 10.1016/j.jbc.2022.101715] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 02/03/2022] [Accepted: 02/08/2022] [Indexed: 11/27/2022] Open
Abstract
Infection by the bacterium Bordetella pertussis continues to cause considerable morbidity and mortality worldwide. Many current acellular pertussis vaccines include the antigen pertactin, which has presumptive adhesive and immunomodulatory activities, but is rapidly lost from clinical isolates after the introduction of these vaccines. To better understand the contributions of pertactin antibodies to protection and pertactin's role in pathogenesis, we isolated and characterized recombinant antibodies binding four distinct epitopes on pertactin. We demonstrate that four of these antibodies bind epitopes that are conserved across all three classical Bordetella strains, and competition assays further showed that antibodies binding these epitopes are also elicited by B. pertussis infection of baboons. Surprisingly, we found that representative antibodies binding each epitope protected mice against experimental B. pertussis infection. A cocktail of antibodies from each epitope group protected mice against a subsequent lethal dose of B. pertussis and greatly reduced lung colonization levels after sublethal challenge. Each antibody reduced B. pertussis lung colonization levels up to 100-fold when administered individually, which was significantly reduced when antibody effector functions were impaired, with no antibody mediating antibody-dependent complement-induced lysis. These data suggest that antibodies binding multiple pertactin epitopes protect primarily by the same bactericidal mechanism, which overshadows contributions from blockade of other pertactin functions. These antibodies expand the available tools to further dissect pertactin's role in infection and understand the impact of antipertactin antibodies on bacterial fitness.
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11
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Schaub JM, Chou CW, Kuo HC, Javanmardi K, Hsieh CL, Goldsmith J, DiVenere AM, Le KC, Wrapp D, Byrne PO, Hjorth CK, Johnson NV, Ludes-Meyers J, Nguyen AW, Wang N, Lavinder JJ, Ippolito GC, Maynard JA, McLellan JS, Finkelstein IJ. Expression and characterization of SARS-CoV-2 spike proteins. Nat Protoc 2021; 16:5339-5356. [PMID: 34611365 PMCID: PMC9665560 DOI: 10.1038/s41596-021-00623-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 09/06/2021] [Indexed: 02/08/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 spike protein is a critical component of coronavirus disease 2019 vaccines and diagnostics and is also a therapeutic target. However, the spike protein is difficult to produce recombinantly because it is a large trimeric class I fusion membrane protein that is metastable and heavily glycosylated. We recently developed a prefusion-stabilized spike variant, termed HexaPro for six stabilizing proline substitutions, that can be expressed with a yield of >30 mg/L in ExpiCHO cells. This protocol describes an optimized workflow for expressing and biophysically characterizing rationally engineered spike proteins in Freestyle 293 and ExpiCHO cell lines. Although we focus on HexaPro, this protocol has been used to purify over a hundred different spike variants in our laboratories. We also provide guidance on expression quality control, long-term storage, and uses in enzyme-linked immunosorbent assays. The entire protocol, from transfection to biophysical characterization, can be completed in 7 d by researchers with basic tissue cell culture and protein purification expertise.
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Affiliation(s)
- Jeffrey M Schaub
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Chia-Wei Chou
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Hung-Che Kuo
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Kamyab Javanmardi
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Ching-Lin Hsieh
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Jory Goldsmith
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Andrea M DiVenere
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Kevin C Le
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Daniel Wrapp
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Patrick O Byrne
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Christy K Hjorth
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Nicole V Johnson
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - John Ludes-Meyers
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Annalee W Nguyen
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Nianshuang Wang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Jason J Lavinder
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Gregory C Ippolito
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
| | - Jennifer A Maynard
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
- Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA.
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12
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Patterson-Orazem AC, Qerqez AN, Azouz LR, Ma MT, Hill SE, Ku Y, Schildmeyer LA, Maynard JA, Lieberman RL. Recombinant antibodies recognize conformation-dependent epitopes of the leucine zipper of misfolding-prone myocilin. J Biol Chem 2021; 297:101067. [PMID: 34384785 PMCID: PMC8408531 DOI: 10.1016/j.jbc.2021.101067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/02/2021] [Accepted: 08/06/2021] [Indexed: 11/11/2022] Open
Abstract
Recombinant antibodies with well-characterized epitopes and known conformational specificities are critical reagents to support robust interpretation and reproducibility of immunoassays across biomedical research. For myocilin, a protein prone to misfolding that is associated with glaucoma and an emerging player in other human diseases, currently available antibodies are unable to differentiate among the numerous disease-associated protein states. This fundamentally constrains efforts to understand the connection between myocilin structure, function, and disease. To address this concern, we used protein engineering methods to develop new recombinant antibodies that detect the N-terminal leucine zipper structural domain of myocilin and that are cross-reactive for human and mouse myocilin. After harvesting spleens from immunized mice and in vitro library panning, we identified two antibodies, 2A4 and 1G12. 2A4 specifically recognizes a folded epitope while 1G12 recognizes a range of conformations. We matured antibody 2A4 for improved biophysical properties, resulting in variant 2H2. In a human IgG1 format, 2A4, 1G12, and 2H2 immunoprecipitate full-length folded myocilin present in the spent media of human trabecular meshwork (TM) cells, and 2H2 can visualize myocilin in fixed human TM cells using fluorescence microscopy. These new antibodies should find broad application in glaucoma and other research across multiple species platforms.
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Affiliation(s)
| | - Ahlam N Qerqez
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, USA
| | - Laura R Azouz
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, USA
| | - Minh Thu Ma
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Shannon E Hill
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Yemo Ku
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Lisa A Schildmeyer
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Jennifer A Maynard
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, USA; Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA.
| | - Raquel L Lieberman
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA.
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13
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Yuan SF, Brooks SM, Nguyen AW, Lin WL, Johnston TG, Maynard JA, Nelson A, Alper HS. Bioproduced Proteins On Demand (Bio-POD) in hydrogels using Pichia pastoris. Bioact Mater 2021; 6:2390-2399. [PMID: 33553823 PMCID: PMC7846901 DOI: 10.1016/j.bioactmat.2021.01.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 10/23/2020] [Accepted: 01/14/2021] [Indexed: 12/20/2022] Open
Abstract
Traditional production of industrial and therapeutic proteins by eukaryotic cells typically requires large-scale fermentation capacity. As a result, these systems are not easily portable or reusable for on-demand protein production applications. In this study, we employ Bioproduced Proteins On Demand (Bio-POD), a F127-bisurethane methacrylate hydrogel-based technique that immobilizes engineered Pichia pastoris for preservable, on-demand production and secretion of medium- and high-molecular weight proteins (in this case, SEAP, α-amylase, and anti-HER2). The gel samples containing encapsulated-yeast demonstrated sustained protein production and exhibited productivity immediately after lyophilization and rehydration. The hydrogel platform described here is the first hydrogel immobilization using a P. pastoris system to produce recombinant proteins of this breadth. These results highlight the potential of this formulation to establish a cost-effective bioprocessing strategy for on-demand protein production.
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Affiliation(s)
- Shuo-Fu Yuan
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA
| | - Sierra M. Brooks
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Annalee W. Nguyen
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Wen-Ling Lin
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA
| | - Trevor G. Johnston
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA, USA
| | - Jennifer A. Maynard
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Alshakim Nelson
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA, USA
| | - Hal S. Alper
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
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14
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Thust SC, Maynard JA, Benenati M, Wastling SJ, Mancini L, Jaunmuktane Z, Brandner S, Jäger HR. Regional and Volumetric Parameters for Diffusion-Weighted WHO Grade II and III Glioma Genotyping: A Method Comparison. AJNR Am J Neuroradiol 2021; 42:441-447. [PMID: 33414227 DOI: 10.3174/ajnr.a6965] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 10/19/2020] [Indexed: 12/21/2022]
Abstract
BACKGROUND AND PURPOSE Studies consistently report lower ADC values in isocitrate dehydrogenase (IDH) wild-type gliomas than in IDH mutant tumors, but their methods and thresholds vary. This research aimed to compare volumetric and regional ADC measurement techniques for glioma genotyping, with a focus on IDH status prediction. MATERIALS AND METHODS Treatment-naïve World Health Organization grade II and III gliomas were analyzed by 3 neuroradiologist readers blinded to tissue results. ADC minimum and mean ROIs were defined in tumor and in normal-appearing white matter to calculate normalized values. T2-weighted tumor VOIs were registered to ADC maps with histogram parameters (mean, 2nd and 5th percentiles) extracted. Nonparametric testing (eta2 and ANOVA) was performed to identify associations between ADC metrics and glioma genotypes. Logistic regression was used to probe the ability of VOI and ROI metrics to predict IDH status. RESULTS The study included 283 patients with 79 IDH wild-type and 204 IDH mutant gliomas. Across the study population, IDH status was most accurately predicted by ROI mean normalized ADC and VOI mean normalized ADC, with areas under the curve of 0.83 and 0.82, respectively. The results for ROI-based genotyping of nonenhancing and solid-patchy enhancing gliomas were comparable with volumetric parameters (area under the curve = 0.81-0.84). In rim-enhancing, centrally necrotic tumors (n = 23), only volumetric measurements were predictive (0.90). CONCLUSIONS Regional normalized mean ADC measurements are noninferior to volumetric segmentation for defining solid glioma IDH status. Partially necrotic, rim-enhancing tumors are unsuitable for ROI assessment and may benefit from volumetric ADC quantification.
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Affiliation(s)
- S C Thust
- From the Neuroradiological Academic Unit (S.C.T., J.A.M, S.J.W., L.M., H.R.J.), Department of Brain, Repair and Rehabilitation, UCL Institute of Neurology, London, UK
- Lysholm Department of Neuroradiology (S.C.T., J.A.M., M.B., S.J.W., L.M., H.R.J.), National Hospital for Neurology and Neurosurgery, London, UK
- Imaging Department (S.C.T., H.R.J.), University College London Foundation Hospital, London, UK
| | - J A Maynard
- From the Neuroradiological Academic Unit (S.C.T., J.A.M, S.J.W., L.M., H.R.J.), Department of Brain, Repair and Rehabilitation, UCL Institute of Neurology, London, UK
- Lysholm Department of Neuroradiology (S.C.T., J.A.M., M.B., S.J.W., L.M., H.R.J.), National Hospital for Neurology and Neurosurgery, London, UK
| | - M Benenati
- Lysholm Department of Neuroradiology (S.C.T., J.A.M., M.B., S.J.W., L.M., H.R.J.), National Hospital for Neurology and Neurosurgery, London, UK
- Dipartimento di Diagnostica per Immagini (M.B.), Radioterapia, Oncologia ed Ematologia, Fondazione Policlinico Universitario A. Gemelli Institute for Research, Hospitalization and Health Care, Rome, Italy
| | - S J Wastling
- From the Neuroradiological Academic Unit (S.C.T., J.A.M, S.J.W., L.M., H.R.J.), Department of Brain, Repair and Rehabilitation, UCL Institute of Neurology, London, UK
- Lysholm Department of Neuroradiology (S.C.T., J.A.M., M.B., S.J.W., L.M., H.R.J.), National Hospital for Neurology and Neurosurgery, London, UK
| | - L Mancini
- From the Neuroradiological Academic Unit (S.C.T., J.A.M, S.J.W., L.M., H.R.J.), Department of Brain, Repair and Rehabilitation, UCL Institute of Neurology, London, UK
- Lysholm Department of Neuroradiology (S.C.T., J.A.M., M.B., S.J.W., L.M., H.R.J.), National Hospital for Neurology and Neurosurgery, London, UK
| | - Z Jaunmuktane
- Department of Clinical and Movement Neurosciences (Z.J.)
| | - S Brandner
- Neurodegenerative Disease (S.B.), UCL Queen Square Institute of Neurology, and Division of Neuropathology, National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, London, UK
| | - H R Jäger
- From the Neuroradiological Academic Unit (S.C.T., J.A.M, S.J.W., L.M., H.R.J.), Department of Brain, Repair and Rehabilitation, UCL Institute of Neurology, London, UK
- Lysholm Department of Neuroradiology (S.C.T., J.A.M., M.B., S.J.W., L.M., H.R.J.), National Hospital for Neurology and Neurosurgery, London, UK
- Imaging Department (S.C.T., H.R.J.), University College London Foundation Hospital, London, UK
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15
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Hsieh CL, Goldsmith JA, Schaub JM, DiVenere AM, Kuo HC, Javanmardi K, Le KC, Wrapp D, Lee AG, Liu Y, Chou CW, Byrne PO, Hjorth CK, Johnson NV, Ludes-Meyers J, Nguyen AW, Park J, Wang N, Amengor D, Lavinder JJ, Ippolito GC, Maynard JA, Finkelstein IJ, McLellan JS. Structure-based design of prefusion-stabilized SARS-CoV-2 spikes. Science 2020. [PMID: 32703906 DOI: 10.1126/science:abd0826] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has led to accelerated efforts to develop therapeutics and vaccines. A key target of these efforts is the spike (S) protein, which is metastable and difficult to produce recombinantly. We characterized 100 structure-guided spike designs and identified 26 individual substitutions that increased protein yields and stability. Testing combinations of beneficial substitutions resulted in the identification of HexaPro, a variant with six beneficial proline substitutions exhibiting higher expression than its parental construct (by a factor of 10) as well as the ability to withstand heat stress, storage at room temperature, and three freeze-thaw cycles. A cryo-electron microscopy structure of HexaPro at a resolution of 3.2 angstroms confirmed that it retains the prefusion spike conformation. High-yield production of a stabilized prefusion spike protein will accelerate the development of vaccines and serological diagnostics for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
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Affiliation(s)
- Ching-Lin Hsieh
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Jory A Goldsmith
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Jeffrey M Schaub
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Andrea M DiVenere
- Department of Chemical Engineering, University of Texas, Austin, TX 78712, USA
| | - Hung-Che Kuo
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Kamyab Javanmardi
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Kevin C Le
- Department of Chemical Engineering, University of Texas, Austin, TX 78712, USA
| | - Daniel Wrapp
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Alison G Lee
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Yutong Liu
- Department of Chemical Engineering, University of Texas, Austin, TX 78712, USA
| | - Chia-Wei Chou
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Patrick O Byrne
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Christy K Hjorth
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Nicole V Johnson
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - John Ludes-Meyers
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Annalee W Nguyen
- Department of Chemical Engineering, University of Texas, Austin, TX 78712, USA
| | - Juyeon Park
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Nianshuang Wang
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Dzifa Amengor
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Jason J Lavinder
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
- Department of Chemical Engineering, University of Texas, Austin, TX 78712, USA
| | - Gregory C Ippolito
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
- Department of Oncology, Dell Medical School, University of Texas, Austin, TX 78712, USA
| | - Jennifer A Maynard
- Department of Chemical Engineering, University of Texas, Austin, TX 78712, USA.
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA.
- Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA.
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16
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Hsieh CL, Goldsmith JA, Schaub JM, DiVenere AM, Kuo HC, Javanmardi K, Le KC, Wrapp D, Lee AG, Liu Y, Chou CW, Byrne PO, Hjorth CK, Johnson NV, Ludes-Meyers J, Nguyen AW, Park J, Wang N, Amengor D, Lavinder JJ, Ippolito GC, Maynard JA, Finkelstein IJ, McLellan JS. Structure-based design of prefusion-stabilized SARS-CoV-2 spikes. Science 2020; 369:1501-1505. [PMID: 32703906 PMCID: PMC7402631 DOI: 10.1126/science.abd0826] [Citation(s) in RCA: 792] [Impact Index Per Article: 198.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 07/13/2020] [Indexed: 12/16/2022]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has led to accelerated efforts to develop therapeutics and vaccines. A key target of these efforts is the spike (S) protein, which is metastable and difficult to produce recombinantly. We characterized 100 structure-guided spike designs and identified 26 individual substitutions that increased protein yields and stability. Testing combinations of beneficial substitutions resulted in the identification of HexaPro, a variant with six beneficial proline substitutions exhibiting higher expression than its parental construct (by a factor of 10) as well as the ability to withstand heat stress, storage at room temperature, and three freeze-thaw cycles. A cryo-electron microscopy structure of HexaPro at a resolution of 3.2 angstroms confirmed that it retains the prefusion spike conformation. High-yield production of a stabilized prefusion spike protein will accelerate the development of vaccines and serological diagnostics for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
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Affiliation(s)
- Ching-Lin Hsieh
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Jory A Goldsmith
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Jeffrey M Schaub
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Andrea M DiVenere
- Department of Chemical Engineering, University of Texas, Austin, TX 78712, USA
| | - Hung-Che Kuo
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Kamyab Javanmardi
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Kevin C Le
- Department of Chemical Engineering, University of Texas, Austin, TX 78712, USA
| | - Daniel Wrapp
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Alison G Lee
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Yutong Liu
- Department of Chemical Engineering, University of Texas, Austin, TX 78712, USA
| | - Chia-Wei Chou
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Patrick O Byrne
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Christy K Hjorth
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Nicole V Johnson
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - John Ludes-Meyers
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Annalee W Nguyen
- Department of Chemical Engineering, University of Texas, Austin, TX 78712, USA
| | - Juyeon Park
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Nianshuang Wang
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Dzifa Amengor
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Jason J Lavinder
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
- Department of Chemical Engineering, University of Texas, Austin, TX 78712, USA
| | - Gregory C Ippolito
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
- Department of Oncology, Dell Medical School, University of Texas, Austin, TX 78712, USA
| | - Jennifer A Maynard
- Department of Chemical Engineering, University of Texas, Austin, TX 78712, USA.
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA.
- Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA.
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17
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Hsieh CL, Goldsmith JA, Schaub JM, DiVenere AM, Kuo HC, Javanmardi K, Le KC, Wrapp D, Lee AGW, Liu Y, Chou CW, Byrne PO, Hjorth CK, Johnson NV, Ludes-Meyers J, Nguyen AW, Park J, Wang N, Amengor D, Maynard JA, Finkelstein IJ, McLellan JS. Structure-based Design of Prefusion-stabilized SARS-CoV-2 Spikes. bioRxiv 2020:2020.05.30.125484. [PMID: 32577660 PMCID: PMC7302215 DOI: 10.1101/2020.05.30.125484] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
The COVID-19 pandemic caused by the novel coronavirus SARS-CoV-2 has led to accelerated efforts to develop therapeutics, diagnostics, and vaccines to mitigate this public health emergency. A key target of these efforts is the spike (S) protein, a large trimeric class I fusion protein that is metastable and difficult to produce recombinantly in large quantities. Here, we designed and expressed over 100 structure-guided spike variants based upon a previously determined cryo-EM structure of the prefusion SARS-CoV-2 spike. Biochemical, biophysical and structural characterization of these variants identified numerous individual substitutions that increased protein yields and stability. The best variant, HexaPro, has six beneficial proline substitutions leading to ~10-fold higher expression than its parental construct and is able to withstand heat stress, storage at room temperature, and multiple freeze-thaws. A 3.2 Å-resolution cryo-EM structure of HexaPro confirmed that it retains the prefusion spike conformation. High-yield production of a stabilized prefusion spike protein will accelerate the development of vaccines and serological diagnostics for SARS-CoV-2.
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Affiliation(s)
- Ching-Lin Hsieh
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Jory A. Goldsmith
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Jeffrey M. Schaub
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Andrea M. DiVenere
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712
| | - Hung-Che Kuo
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Kamyab Javanmardi
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Kevin C. Le
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712
| | - Daniel Wrapp
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Alison Gene-Wei Lee
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Yutong Liu
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712
| | - Chia-Wei Chou
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Patrick O. Byrne
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Christy K. Hjorth
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Nicole V. Johnson
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - John Ludes-Meyers
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Annalee W. Nguyen
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712
| | - Juyeon Park
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Nianshuang Wang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Dzifa Amengor
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Jennifer A. Maynard
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712
| | - Ilya J. Finkelstein
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas 78712
| | - Jason S. McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
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18
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Tanno H, McDaniel JR, Stevens CA, Voss WN, Li J, Durrett R, Lee J, Gollihar J, Tanno Y, Delidakis G, Pothukuchy A, Ellefson JW, Goronzy JJ, Maynard JA, Ellington AD, Ippolito GC, Georgiou G. A facile technology for the high-throughput sequencing of the paired VH:VL and TCRβ:TCRα repertoires. Sci Adv 2020; 6:eaay9093. [PMID: 32426460 PMCID: PMC7176429 DOI: 10.1126/sciadv.aay9093] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 01/27/2020] [Indexed: 05/27/2023]
Abstract
Natively paired sequencing (NPS) of B cell receptors [variable heavy (VH) and light (VL)] and T cell receptors (TCRb and TCRa) is essential for the understanding of adaptive immunity in health and disease. Despite many recent technical advances, determining the VH:VL or TCRb:a repertoire with high accuracy and throughput remains challenging. We discovered that the recently engineered xenopolymerase, RTX, is exceptionally resistant to cell lysate inhibition in single-cell emulsion droplets. We capitalized on the characteristics of this enzyme to develop a simple, rapid, and inexpensive in-droplet overlap extension reverse transcription polymerase chain reaction method for NPS not requiring microfluidics or other specialized equipment. Using this technique, we obtained high yields (5000 to >20,000 per sample) of paired VH:VL or TCRb:a clonotypes at low cost. As a demonstration, we performed NPS on peripheral blood plasmablasts and T follicular helper cells following seasonal influenza vaccination and discovered high-affinity influenza-specific antibodies and TCRb:a.
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Affiliation(s)
- Hidetaka Tanno
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
| | - Jonathan R. McDaniel
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
| | | | - William N. Voss
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
| | - Jie Li
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
| | - Russell Durrett
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Jiwon Lee
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA
| | - Jimmy Gollihar
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
- U.S. Army Research Laboratory South, Austin, TX, USA
| | - Yuri Tanno
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
| | - George Delidakis
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Arti Pothukuchy
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Jared W. Ellefson
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Jörg J. Goronzy
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA, USA
- Department of Medicine, VA Palo Alto Health Care System, Palo Alto, CA, USA
| | - Jennifer A. Maynard
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Andrew D. Ellington
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Gregory C. Ippolito
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - George Georgiou
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
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19
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Nguyen AW, DiVenere AM, Papin JF, Connelly S, Kaleko M, Maynard JA. Neutralization of pertussis toxin by a single antibody prevents clinical pertussis in neonatal baboons. Sci Adv 2020; 6:eaay9258. [PMID: 32076653 PMCID: PMC7002138 DOI: 10.1126/sciadv.aay9258] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 11/20/2019] [Indexed: 05/13/2023]
Abstract
Pertussis continues to cause considerable infant mortality world-wide, which could be addressed in part by passive immunization strategies. Antibody hu1B7 is a candidate therapeutic that potently neutralizes pertussis toxin in vitro, prevents leukocytosis in mice and treats established disease in weanling baboons as part of an antibody cocktail. Here, we evaluated the potential for hu1B7 and an extended half-life hu1B7 variant to prevent death, leukocytosis and other clinical symptoms in a newborn baboon model that mimics many aspects of human disease. We administered a single antibody dose to newborn baboons five weeks prior to experimental infection. While all animals were heavily colonized with Bordetella pertussis, prophylaxed animals showed significantly greater survival (P < 0.005), delayed and suppressed leukocytosis (P < 0.01) and enhanced clinical outcomes, including coughing (P < 0.01), as compared to controls. Together, this work demonstrates that a single neutralizing anti-PTx antibody is sufficient to prevent clinical pertussis symptoms.
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Affiliation(s)
- Annalee W. Nguyen
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Andrea M. DiVenere
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - James F. Papin
- Division of Comparative Medicine, Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Sheila Connelly
- Synthetic Biologics, 9605 Medical Center Dr., Suite 270, Rockville, MD 20850, USA
| | - Michael Kaleko
- Synthetic Biologics, 9605 Medical Center Dr., Suite 270, Rockville, MD 20850, USA
| | - Jennifer A. Maynard
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712, USA
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20
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Abstract
While antibody libraries are traditionally screened in phage, bacterial, or yeast display formats, they are produced in large scale for pharmaceutical and commercial use in mammalian cell lines. The simpler organisms used for screening have significantly different folding and glycosylation machinery than mammalian cells; consequently, clones resulting from these libraries may require further optimization for mammalian cell expression. To streamline the antibody discovery process, we developed a Chinese hamster ovary (CHO) cell-based selection system that allows for long-term display of antibody Fab fragments. This system is facilitated by a semi-stable Epi-CHO episomal platform to maintain antibody expression for up to 2 months and is compatible with standard PCR-based mutagenesis strategies. This protocol describes the simple and accessible use of CHO display coupled with flow cytometry to enrich for antibody variants with increased ligand-binding affinity from large libraries of ~106 variants, using HER2-binding antibodies as an example.
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Affiliation(s)
- Annalee W Nguyen
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA.
| | - Kevin Le
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Jennifer A Maynard
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
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21
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Wagner EK, Qerqez AN, Stevens CA, Nguyen AW, Delidakis G, Maynard JA. Human cytomegalovirus-specific T-cell receptor engineered for high affinity and soluble expression using mammalian cell display. J Biol Chem 2019; 294:5790-5804. [PMID: 30796163 PMCID: PMC6463697 DOI: 10.1074/jbc.ra118.007187] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 02/07/2019] [Indexed: 01/01/2023] Open
Abstract
T-cell receptors (TCR) have considerable potential as therapeutics and antibody-like reagents to monitor disease progression and vaccine efficacy. Whereas antibodies recognize only secreted and surface-bound proteins, TCRs recognize otherwise inaccessible disease-associated intracellular proteins when they are presented as processed peptides bound to major histocompatibility complexes (pMHC). TCRs have been primarily explored for cancer therapy applications but could also target infectious diseases such as cytomegalovirus (CMV). However, TCRs are more difficult to express and engineer than antibodies, and advanced methods are needed to enable their widespread use. Here, we engineered the human CMV-specific TCR RA14 for high-affinity and robust soluble expression. To achieve this, we adapted our previously reported mammalian display system to present TCR extracellular domains and used this to screen CDR3 libraries for clones with increased pMHC affinity. After three rounds of selection, characterized clones retained peptide specificity and activation when expressed on the surface of human Jurkat T cells. We obtained high yields of soluble, monomeric protein by fusing the TCR extracellular domains to antibody hinge and Fc constant regions, adding a stabilizing disulfide bond between the constant domains and disrupting predicted glycosylation sites. One variant exhibited 50 nm affinity for its cognate pMHC, as measured by surface plasmon resonance, and specifically stained cells presenting this pMHC. Our work has identified a human TCR with high affinity for the immunodominant CMV peptide and offers a new strategy to rapidly engineer soluble TCRs for biomedical applications.
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Affiliation(s)
- Ellen K Wagner
- From the McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712
| | - Ahlam N Qerqez
- From the McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712
| | - Christopher A Stevens
- From the McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712
| | - Annalee W Nguyen
- From the McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712
| | - George Delidakis
- From the McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712
| | - Jennifer A Maynard
- From the McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712.
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22
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Nguyen AW, Le KC, Maynard JA. Identification of high affinity HER2 binding antibodies using CHO Fab surface display. Protein Eng Des Sel 2019; 31:91-101. [PMID: 29566240 DOI: 10.1093/protein/gzy004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 02/02/2018] [Indexed: 12/27/2022] Open
Abstract
Discovery of monoclonal antibodies is most commonly performed using phage or yeast display but mammalian cells are used for production because of the complex antibody structure, including the multiple disulfide bonds and glycosylation, required for function. As this transition between host organisms is often accompanied by impaired binding, folding or expression, development pipelines include laborious plate-based screening or engineering strategies to adapt an antibody to mammalian expression. To circumvent these problems, we developed a plasmid-based Fab screening platform on Chinese hamster ovary (CHO) cells which allows for antibody selection in the production host and in the presence of the same post-translational modifications as the manufactured product. A hu4D5 variant with low affinity for the human epidermal growth factor receptor (HER2) growth factor receptor was mutagenized and this library of ~10(6) unique clones was screened to identify variants with up to 400-fold enhanced HER2 binding. After two rounds of fluorescence activated cell sorting (FACS), four unique clones exhibited improved antigen binding when expressed on the CHO surface or as purified human IgG. Three of the four clones contained free cysteines in third complementarity determining region of the antibody heavy chain, which did not impair expression or cause aggregation. The improved clones had similar yields and stabilities as hu4D5 and similar sub-nanomolar affinities as measured by equilibrium binding to target cells. The limited size of mammalian libraries restricts the utility of this approach for naïve antibody library screening, but it is a powerful approach for antibody affinity maturation or specificity enhancement and is readily generalizable to engineering other surface receptors, including T-cell receptors and chimeric antigen receptors.
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Affiliation(s)
- Annalee W Nguyen
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| | - Kevin C Le
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| | - Jennifer A Maynard
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
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23
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Boehm DT, Hall JM, Wong TY, DiVenere AM, Sen-Kilic E, Bevere JR, Bradford SD, Blackwood CB, Elkins CM, DeRoos KA, Gray MC, Cooper CG, Varney ME, Maynard JA, Hewlett EL, Barbier M, Damron FH. Evaluation of Adenylate Cyclase Toxoid Antigen in Acellular Pertussis Vaccines by Using a Bordetella pertussis Challenge Model in Mice. Infect Immun 2018; 86:e00857-17. [PMID: 30012638 PMCID: PMC6204743 DOI: 10.1128/iai.00857-17] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 07/10/2018] [Indexed: 12/21/2022] Open
Abstract
Bordetella pertussis is the primary causative agent of pertussis (whooping cough), which is a respiratory infection that leads to a violent cough and can be fatal in infants. There is a need to develop more effective vaccines because of the resurgence of cases of pertussis in the United States since the switch from the whole-cell pertussis vaccines (wP) to the acellular pertussis vaccines (aP; diphtheria-tetanus-acellular-pertussis vaccine/tetanus-diphtheria-pertussis vaccine). Adenylate cyclase toxin (ACT) is a major virulence factor of B. pertussis that is (i) required for establishment of infection, (ii) an effective immunogen, and (iii) a protective antigen. The C-terminal repeats-in-toxin domain (RTX) of ACT is sufficient to induce production of toxin-neutralizing antibodies. In this study, we characterized the effectiveness of vaccines containing the RTX antigen against experimental murine infection with B. pertussis RTX was not protective as a single-antigen vaccine against B. pertussis challenge, and adding RTX to 1/5 human dose of aP did not enhance protection. Since the doses of aP used in murine studies are not proportionate to mouse/human body masses, we titrated the aP from 1/20 to 1/160 of the human dose. Mice receiving 1/80 human aP dose had bacterial burden comparable to those of naive controls. Adding RTX antigen to the 1/80 aP base resulted in enhanced bacterial clearance. Inclusion of RTX induced production of antibodies recognizing RTX, enhanced production of anti-pertussis toxin, decreased secretion of proinflammatory cytokines, such as interleukin-6, and decreased recruitment of total macrophages in the lung. This study shows that adding RTX antigen to an appropriate dose of aP can enhance protection against B. pertussis challenge in mice.
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Affiliation(s)
- Dylan T Boehm
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, West Virginia, USA
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, West Virginia, USA
| | - Jesse M Hall
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, West Virginia, USA
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, West Virginia, USA
| | - Ting Y Wong
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, West Virginia, USA
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, West Virginia, USA
| | - Andrea M DiVenere
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, USA
| | - Emel Sen-Kilic
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, West Virginia, USA
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, West Virginia, USA
| | - Justin R Bevere
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, West Virginia, USA
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, West Virginia, USA
| | - Shelby D Bradford
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, West Virginia, USA
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, West Virginia, USA
| | - Catherine B Blackwood
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, West Virginia, USA
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, West Virginia, USA
| | - Cody M Elkins
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, West Virginia, USA
| | - Katherine A DeRoos
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, West Virginia, USA
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, West Virginia, USA
| | - Mary C Gray
- Department of Medicine, Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - C Garret Cooper
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, West Virginia, USA
- Department of Medicine, Section of Infectious Diseases, West Virginia University, Morgantown, West Virginia, USA
| | - Melinda E Varney
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, West Virginia, USA
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, West Virginia, USA
| | - Jennifer A Maynard
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, USA
| | - Erik L Hewlett
- Department of Medicine, Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - Mariette Barbier
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, West Virginia, USA
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, West Virginia, USA
| | - F Heath Damron
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, West Virginia, USA
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, West Virginia, USA
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24
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Acquaye-Seedah E, Huang Y, Sutherland JN, DiVenere AM, Maynard JA. Humanised monoclonal antibodies neutralise pertussis toxin by receptor blockade and reduced retrograde trafficking. Cell Microbiol 2018; 20:e12948. [PMID: 30152075 PMCID: PMC6519169 DOI: 10.1111/cmi.12948] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Revised: 08/02/2018] [Accepted: 08/20/2018] [Indexed: 12/12/2022]
Abstract
Pertussis toxin (PTx) is a major protective antigen produced by Bordetella pertussis that is included in all current acellular vaccines. Of several well‐characterized monoclonal antibodies binding this toxin, the humanised hu1B7 and hu11E6 antibodies are highly protective in multiple in vitro and in vivo assays. In this study, we determine the molecular mechanisms of protection mediated by these antibodies. Neither antibody directly binds the B. pertussis bacterium nor supports antibody‐dependent complement cytotoxicity. Both antibodies, either individually or as a cocktail, form multivalent complexes with soluble PTx that bind the FcγRIIb receptor more tightly than antibody alone, suggesting that the antibodies may accelerate PTx clearance via immune complex formation. However, a receptor binding assay and cellular imaging indicate that the main mechanism used by hu11E6 is competitive inhibition of PTx binding to its cellular receptor. In contrast, the main hu1B7 neutralising mechanism appears to be inhibition of PTx internalisation and retrograde trafficking. We assessed the effects of hu1B7 on PTx retrograde trafficking in CHO‐K1 cells using quantitative immunofluorescence microscopy. In the absence of hu1B7 or after incubation with an isotype control antibody, PTx colocalizes to organelles in a manner consistent with retrograde transport. However, after preincubation with hu1B7, PTx appears restricted to the membrane surface with colocalization to organelles associated with retrograde transport significantly reduced. Together, these data support a model whereby hu11E6 and hu1B7 interfere with PTx receptor binding and PTx retrograde trafficking, respectively.
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Affiliation(s)
- Edith Acquaye-Seedah
- Department of Biochemistry, The University of Texas at Austin, Austin, Texas.,Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas
| | - Yimin Huang
- Department of Cell and Molecular Biology, The University of Texas at Austin, Austin, Texas.,Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas
| | - Jamie N Sutherland
- Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas
| | - Andrea M DiVenere
- Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas
| | - Jennifer A Maynard
- Department of Biochemistry, The University of Texas at Austin, Austin, Texas.,Department of Cell and Molecular Biology, The University of Texas at Austin, Austin, Texas.,Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas
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25
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Abstract
Serum therapy fell out of favor 80 years ago, but antibodies against infectious diseases are now experiencing a renaissance. With the evolution of antibiotic-resistant bacteria, the emergence of new pathogens, and a growing population of immunocompromised individuals coupled with improvements in antibody manufacturing and biological efficacy, antibodies are an increasingly attractive therapeutic option. In this review, we highlight successful clinical strategies and discuss recent applications of advanced antibody engineering approaches to combat infectious diseases. Case studies include antibody mixtures to neutralize Staphylococcus aureus; bispecific antibodies promoting Pseudomonas aeruginosa clearance; antibody-antibiotic conjugates to eradicate S. aureus from protected intracellular niches; and novel anti-RSV antibodies with extended serum half-life. These new designs are powerful strategies for targeting infectious diseases due to their abilities to target multiple antigens and induce novel clearance mechanisms.
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Affiliation(s)
- Ellen K Wagner
- Department of Chemical Engineering, The University of Texas at Austin, Austin TX USA, 78712
| | - Jennifer A Maynard
- Department of Chemical Engineering, The University of Texas at Austin, Austin TX USA, 78712
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26
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Ha Y, Ko S, Kim I, Huang Y, Mohanty K, Huh C, Maynard JA. Recent Advances Incorporating Superparamagnetic Nanoparticles into Immunoassays. ACS Appl Nano Mater 2018; 1:512-521. [PMID: 29911680 PMCID: PMC5999228 DOI: 10.1021/acsanm.7b00025] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 01/31/2018] [Indexed: 05/09/2023]
Abstract
Superparamagnetic nanoparticles (SPMNPs) have attracted interest for various biomedical applications due to their unique magnetic behavior, excellent biocompatibility, easy surface modification, and low cost. Their unique magnetic properties, superparamagnetism, and magnetophoretic mobility have led to their inclusion in immunoassays to enhance biosensor sensitivity and allow for rapid detection of various analytes. In this review, we describe SPMNP characteristics valuable for incorporation into biosensors, including the use of SPMNPs to increase detection capabilities of surface plasmon resonance and giant magneto-resistive biosensors. The current status of SPMNP-based immunoassays to improve the sensitivity of rapid diagnostic tests is reviewed, and suggested strategies for the successful adoption of SPMNPs for immunoassays are presented.
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Affiliation(s)
- Yeonjeong Ha
- Department
of Chemical Engineering and Petroleum and Geosystems Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
- E-mail: . (J.A.M.)
| | - Saebom Ko
- Department
of Chemical Engineering and Petroleum and Geosystems Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Ijung Kim
- Department
of Civil and Environmental Engineering, Western New England University, Springfield, Massachusetts 01119, United States
| | - Yimin Huang
- Department
of Chemical Engineering and Petroleum and Geosystems Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Kishore Mohanty
- Department
of Chemical Engineering and Petroleum and Geosystems Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Chun Huh
- Department
of Chemical Engineering and Petroleum and Geosystems Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jennifer A. Maynard
- Department
of Chemical Engineering and Petroleum and Geosystems Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
- E-mail: . (Y.-J.H.)
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27
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Laber JR, Dear BJ, Martins ML, Jackson DE, DiVenere A, Gollihar JD, Ellington AD, Truskett TM, Johnston KP, Maynard JA. Charge Shielding Prevents Aggregation of Supercharged GFP Variants at High Protein Concentration. Mol Pharm 2017; 14:3269-3280. [PMID: 28870080 DOI: 10.1021/acs.molpharmaceut.7b00322] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Understanding protein stability is central to combatting protein aggregation diseases and developing new protein therapeutics. At the high concentrations often present in biological systems, purified proteins can exhibit undesirable high solution viscosities and poor solubilities mediated by short-range electrostatic and hydrophobic protein-protein interactions. The interplay between protein amino acid sequence, protein structure, and solvent conditions to minimize protein-protein interactions is key to designing well-behaved pharmaceutical proteins. However, theoretical approaches have yet to yield a general framework to address these problems. Here, we analyzed the high concentration behavior of superfolder GFP (sfGFP) and two supercharged sfGFP variants engineered to have formal charges of -18 or +15. Under low cosolute conditions, sfGFP and the -18 variant formed a gel or phase separated at ∼10 mg/mL. Under conditions that screen surface charges, including formulations with high histidine or high NaCl concentrations, all three variants attained concentrations up to 250 mg/mL with moderate viscosities. Moreover, all three variants exhibited very similar viscosity-concentration profiles over this range. This effect was not mimicked by high sugar concentrations that exert excluded-volume effects without shielding charge. Collectively, these data demonstrate that charge shielding neutralizes not only long-range electrostatic interactions but also, surprisingly, short-range electrostatic effects due to surface charge anisotropy. This work shows that supercharged sfGFP behavior under high ionic strength is largely determined by particle geometry, a conclusion that is supported by colloid models and may be applicable to pharmaceutically relevant proteins.
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Affiliation(s)
- Joshua R Laber
- Departments of †Chemical Engineering and ‡Molecular Biosciences, University of Texas at Austin , Austin, Texas 78712, United States
| | - Barton J Dear
- Departments of †Chemical Engineering and ‡Molecular Biosciences, University of Texas at Austin , Austin, Texas 78712, United States
| | - Matheus L Martins
- Departments of †Chemical Engineering and ‡Molecular Biosciences, University of Texas at Austin , Austin, Texas 78712, United States
| | - Devin E Jackson
- Departments of †Chemical Engineering and ‡Molecular Biosciences, University of Texas at Austin , Austin, Texas 78712, United States
| | - Andrea DiVenere
- Departments of †Chemical Engineering and ‡Molecular Biosciences, University of Texas at Austin , Austin, Texas 78712, United States
| | - Jimmy D Gollihar
- Departments of †Chemical Engineering and ‡Molecular Biosciences, University of Texas at Austin , Austin, Texas 78712, United States
| | - Andrew D Ellington
- Departments of †Chemical Engineering and ‡Molecular Biosciences, University of Texas at Austin , Austin, Texas 78712, United States
| | - Thomas M Truskett
- Departments of †Chemical Engineering and ‡Molecular Biosciences, University of Texas at Austin , Austin, Texas 78712, United States
| | - Keith P Johnston
- Departments of †Chemical Engineering and ‡Molecular Biosciences, University of Texas at Austin , Austin, Texas 78712, United States
| | - Jennifer A Maynard
- Departments of †Chemical Engineering and ‡Molecular Biosciences, University of Texas at Austin , Austin, Texas 78712, United States
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28
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Entzminger KC, Hyun JM, Pantazes RJ, Patterson-Orazem AC, Qerqez AN, Frye ZP, Hughes RA, Ellington AD, Lieberman RL, Maranas CD, Maynard JA. De novo design of antibody complementarity determining regions binding a FLAG tetra-peptide. Sci Rep 2017; 7:10295. [PMID: 28860479 PMCID: PMC5579192 DOI: 10.1038/s41598-017-10737-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 08/14/2017] [Indexed: 12/30/2022] Open
Abstract
Computational antibody engineering efforts to date have focused on improving binding affinities or biophysical characteristics. De novo design of antibodies binding specific epitopes could greatly accelerate discovery of therapeutics as compared to conventional immunization or synthetic library selection strategies. Here, we employed de novo complementarity determining region (CDR) design to engineer targeted antibody-antigen interactions using previously described in silico methods. CDRs predicted to bind the minimal FLAG peptide (Asp-Tyr-Lys-Asp) were grafted onto a single-chain variable fragment (scFv) acceptor framework. Fifty scFvs comprised of designed heavy and light or just heavy chain CDRs were synthesized and screened for peptide binding by phage ELISA. Roughly half of the designs resulted in detectable scFv expression. Four antibodies, designed entirely in silico, bound the minimal FLAG sequence with high specificity and sensitivity. When reformatted as soluble antigen-binding fragments (Fab), these clones expressed well, were predominantly monomeric and retained peptide specificity. In both formats, the antibodies bind the peptide only when present at the amino-terminus of a carrier protein and even conservative peptide amino acid substitutions resulted in a complete loss of binding. These results support in silico CDR design of antibody specificity as an emerging antibody engineering strategy.
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Affiliation(s)
- Kevin C Entzminger
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
| | - Jeong-Min Hyun
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
| | - Robert J Pantazes
- Department of Chemical Engineering, Auburn University, Auburn, AL, 36849, USA
| | | | - Ahlam N Qerqez
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Zach P Frye
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Randall A Hughes
- Applied Research Laboratories, University of Texas at Austin, Austin, TX, 78712, USA
| | - Andrew D Ellington
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
| | - Raquel L Lieberman
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Costas D Maranas
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania, PA, 16802, USA
| | - Jennifer A Maynard
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA. .,Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712, USA.
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29
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Wang X, Stapleton JA, Klesmith JR, Hewlett EL, Whitehead TA, Maynard JA. Fine Epitope Mapping of Two Antibodies Neutralizing the Bordetella Adenylate Cyclase Toxin. Biochemistry 2017; 56:1324-1336. [PMID: 28177609 DOI: 10.1021/acs.biochem.6b01163] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Adenylate cyclase toxin (ACT) is an important Bordetella pertussis virulence factor that is not included in current acellular pertussis vaccines. We previously demonstrated that immunization with the repeat-in-toxin (RTX) domain of ACT elicits neutralizing antibodies in mice and discovered the first two antibodies to neutralize ACT activities by occluding the receptor-binding site. Here, we fully characterize these antibodies and their epitopes. Both antibodies bind ACT with low nanomolar affinity and cross-react with ACT homologues produced by B. parapertussis and B. bronchiseptica. Antibody M1H5 binds B. pertussis RTX751 ∼100-fold tighter than RTX751 from the other two species, while antibody M2B10 has similar affinity for all three variants. To initially map the antibody epitopes, we generated a series of ACT chimeras and truncation variants, which implicated the repeat blocks II-III. To identify individual epitope residues, we displayed randomly mutated RTX751 libraries on yeast and isolated clones with decreased antibody binding by flow cytometry. Next-generation sequencing identified candidate epitope residues on the basis of enrichment of clones with mutations at specific positions. These epitopes form two adjacent surface patches on a predicted structural model of the RTX751 domain, one for each antibody. Notably, the cellular receptor also binds within blocks II-III and shares at least one residue with the M1H5 epitope. The RTX751 model supports the notion that the antibody and receptor epitopes overlap. These data provide insight into mechanisms of ACT neutralization and guidance for engineering more stable RTX variants that may be more appropriate vaccine antigens.
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Affiliation(s)
- Xianzhe Wang
- Department of Chemical Engineering, University of Texas at Austin , Austin, Texas 78712, United States
| | - James A Stapleton
- Department of Chemical Engineering and Materials Science, Michigan State University , East Lansing, Michigan 48824, United States
| | - Justin R Klesmith
- Department of Biochemistry and Molecular Biology, Michigan State University , East Lansing, Michigan 48824, United States
| | - Erik L Hewlett
- Department of Medicine, University of Virginia , Charlottesville, Virginia 22906, United States
| | - Timothy A Whitehead
- Department of Chemical Engineering and Materials Science, Michigan State University , East Lansing, Michigan 48824, United States.,Department of Biosystems and Agricultural Engineering, Michigan State University , East Lansing, Michigan 48824, United States
| | - Jennifer A Maynard
- Department of Chemical Engineering, University of Texas at Austin , Austin, Texas 78712, United States
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30
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Borwankar AU, Dear BJ, Twu A, Hung JJ, Dinin AK, Wilson BK, Yue J, Maynard JA, Truskett TM, Johnston KP. Viscosity Reduction of a Concentrated Monoclonal Antibody with Arginine·HCl and Arginine·Glutamate. Ind Eng Chem Res 2016. [DOI: 10.1021/acs.iecr.6b02042] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Ameya U. Borwankar
- McKetta Department of Chemical
Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Barton J. Dear
- McKetta Department of Chemical
Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - April Twu
- McKetta Department of Chemical
Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jessica J. Hung
- McKetta Department of Chemical
Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Aileen K. Dinin
- McKetta Department of Chemical
Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Brian K. Wilson
- McKetta Department of Chemical
Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jingyan Yue
- McKetta Department of Chemical
Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jennifer A. Maynard
- McKetta Department of Chemical
Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Thomas M. Truskett
- McKetta Department of Chemical
Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Keith P. Johnston
- McKetta Department of Chemical
Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
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31
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Nguyen AW, Wagner EK, Posada L, Liu X, Connelly S, Papin JF, Wolf RF, Kaleko M, Maynard JA. Prior exposure to Bordetella species as an exclusion criterion in the baboon model of pertussis. J Vet Med Sci 2016; 79:60-64. [PMID: 27666464 PMCID: PMC5289237 DOI: 10.1292/jvms.16-0427] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The baboon model of Bordetella pertussis infection is the newest and most clinically accurate model of the human disease to date. However, among the 15 experimentally infected baboons in this study, a subset of baboons did not exhibit the expected high bacterial colonization levels or increase in white blood cell count. Moreover, cultures of nasopharyngeal wash samples from several baboons suggested B. bronchiseptica coinfection. Analysis of serum antibodies recognizing filamentous hemagglutinin, pertussis toxin and B. pertussis lipo-oligosaccharide indicated that several baboons had likely been previously exposed to Bordetella species and that prior exposure correlated with partial protection from B. pertussis infection. Notably, all animals with a baseline Fha titer of 5 IU/ml or below exhibited symptoms typical of the model, suggesting this value can be used as inclusion criteria for animals prior to study enrollment. While B. pertussis infection is endemic to human populations and B. bronchiseptica is common in wild small mammals, this study illustrates that baboons can readily harbor both organisms. Awareness of Bordetella species that share antigens capable of generating protective immune responses and tracking of prior exposure to those species is required for successful use of the baboon model of pertussis.
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Affiliation(s)
- Annalee W Nguyen
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712, U.S.A
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32
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Nguyen AW, Wagner EK, Laber JR, Goodfield LL, Smallridge WE, Harvill ET, Papin JF, Wolf RF, Padlan EA, Bristol A, Kaleko M, Maynard JA. A cocktail of humanized anti-pertussis toxin antibodies limits disease in murine and baboon models of whooping cough. Sci Transl Med 2016; 7:316ra195. [PMID: 26631634 DOI: 10.1126/scitranslmed.aad0966] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Despite widespread vaccination, pertussis rates are rising in industrialized countries and remain high worldwide. With no specific therapeutics to treat disease, pertussis continues to cause considerable infant morbidity and mortality. The pertussis toxin is a major contributor to disease, responsible for local and systemic effects including leukocytosis and immunosuppression. We humanized two murine monoclonal antibodies that neutralize pertussis toxin and expressed them as human immunoglobulin G1 molecules with no loss of affinity or in vitro neutralization activity. When administered prophylactically to mice as a binary cocktail, antibody treatment completely mitigated the Bordetella pertussis-induced rise in white blood cell counts and decreased bacterial colonization. When administered therapeutically to baboons, antibody-treated, but not untreated control animals, experienced a blunted rise in white blood cell counts and accelerated bacterial clearance rates. These preliminary findings support further investigation into the use of these antibodies to treat human neonatal pertussis in conjunction with antibiotics and supportive care.
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Affiliation(s)
- Annalee W Nguyen
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Ellen K Wagner
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Joshua R Laber
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Laura L Goodfield
- Department of Veterinary and Biomedical Science, Pennsylvania State University, University Park, PA 16802, USA
| | - William E Smallridge
- Department of Veterinary and Biomedical Science, Pennsylvania State University, University Park, PA 16802, USA
| | - Eric T Harvill
- Department of Veterinary and Biomedical Science, Pennsylvania State University, University Park, PA 16802, USA
| | - James F Papin
- Department of Comparative Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Roman F Wolf
- Department of Comparative Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Eduardo A Padlan
- The Marine Science Institute, College of Science, University of the Philippines Diliman, Quezon City 1101, Philippines
| | - Andy Bristol
- Synthetic Biologics, 155 Gibbs Street, Suite 412, Rockville, MD 20850, USA
| | - Michael Kaleko
- Synthetic Biologics, 155 Gibbs Street, Suite 412, Rockville, MD 20850, USA
| | - Jennifer A Maynard
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712, USA
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33
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Ha Y, Wang X, Liljestrand HM, Maynard JA, Katz LE. Bioavailability of Fullerene under Environmentally Relevant Conditions: Effects of Humic Acid and Fetal Bovine Serum on Accumulation in Lipid Bilayers and Cellular Uptake. Environ Sci Technol 2016; 50:6717-6727. [PMID: 26943027 DOI: 10.1021/acs.est.5b04964] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Carbon fullerene (C60) has emerged at the forefront of nanoscale research and application due to its unique properties. As the production of this nanoparticle rapidly increases, it can be released into natural aquatic environments and can accumulate in biological systems. This research examined the effects of humic acid and fetal bovine serum (FBS), which are ubiquitous in aquatic environments and representative of blood plasma in living organisms, respectively, on bioavailability of fullerene. Bioavailability was investigated using in vitro methods for lipid membrane accumulation and cellular uptake studies. Humic acid and FBS significantly changed the characteristics of fullerene including its particle size and surface charge. The effects of humic acid on lipid accumulation of fullerene depended on the lipid head charge. FBS also significantly decreased the lipid accumulation when positively charged and zwitterionic head groups were present on the lipids, possibly due to the higher steric repulsion of the protein coated nanoparticles. In addition, both humic acid and FBS protein effectively lowered the amounts of fullerene taken up by Caco-2 cells, which are derived from a human colorectal adenocarcinoma and have similar functions to the small intestinal epithelium. Results of this study suggest that surface modification of fullerene by environmentally relevant matrices can significantly affect the biological transport, as well as the possible toxicity of this nanomaterial.
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Affiliation(s)
- Yeonjeong Ha
- Department of Civil, Architectural and Environmental Engineering, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Xianzhe Wang
- Department of Biochemistry, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Howard M Liljestrand
- Department of Civil, Architectural and Environmental Engineering, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Jennifer A Maynard
- Department of Chemical Engineering, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Lynn E Katz
- Department of Civil, Architectural and Environmental Engineering, The University of Texas at Austin , Austin, Texas 78712, United States
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34
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Affiliation(s)
- Tarik A. Khan
- Departments of Chemical Engineering and ‡Biochemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Xianzhe Wang
- Departments of Chemical Engineering and ‡Biochemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Jennifer A. Maynard
- Departments of Chemical Engineering and ‡Biochemistry, University of Texas at Austin, Austin, Texas 78712, United States
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35
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Wang X, Gray MC, Hewlett EL, Maynard JA. The Bordetella adenylate cyclase repeat-in-toxin (RTX) domain is immunodominant and elicits neutralizing antibodies. J Biol Chem 2015; 290:23025. [PMID: 26386047 DOI: 10.1074/jbc.a114.585281] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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36
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Kowalsky CA, Faber MS, Nath A, Dann HE, Kelly VW, Liu L, Shanker P, Wagner EK, Maynard JA, Chan C, Whitehead TA. Rapid fine conformational epitope mapping using comprehensive mutagenesis and deep sequencing. J Biol Chem 2015; 290:26457-70. [PMID: 26296891 DOI: 10.1074/jbc.m115.676635] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Indexed: 12/29/2022] Open
Abstract
Knowledge of the fine location of neutralizing and non-neutralizing epitopes on human pathogens affords a better understanding of the structural basis of antibody efficacy, which will expedite rational design of vaccines, prophylactics, and therapeutics. However, full utilization of the wealth of information from single cell techniques and antibody repertoire sequencing awaits the development of a high throughput, inexpensive method to map the conformational epitopes for antibody-antigen interactions. Here we show such an approach that combines comprehensive mutagenesis, cell surface display, and DNA deep sequencing. We develop analytical equations to identify epitope positions and show the method effectiveness by mapping the fine epitope for different antibodies targeting TNF, pertussis toxin, and the cancer target TROP2. In all three cases, the experimentally determined conformational epitope was consistent with previous experimental datasets, confirming the reliability of the experimental pipeline. Once the comprehensive library is generated, fine conformational epitope maps can be prepared at a rate of four per day.
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Affiliation(s)
| | | | | | - Hailey E Dann
- From the Department of Chemical Engineering and Materials Science
| | - Vince W Kelly
- From the Department of Chemical Engineering and Materials Science
| | - Li Liu
- Department of Microbiology and Molecular Genetics, and
| | - Purva Shanker
- From the Department of Chemical Engineering and Materials Science
| | - Ellen K Wagner
- the Department of Chemical Engineering, University of Texas, Austin, Texas 78712
| | - Jennifer A Maynard
- the Department of Chemical Engineering, University of Texas, Austin, Texas 78712
| | - Christina Chan
- From the Department of Chemical Engineering and Materials Science, Department of Biochemistry and Molecular Biology, Genetics Graduate Program
| | - Timothy A Whitehead
- From the Department of Chemical Engineering and Materials Science, Department of Biosystems and Agricultural Engineering, Michigan State University, East Lansing, Michigan 48824 and
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37
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Entzminger KC, Johnson JL, Hyun J, Lieberman RL, Maynard JA. Increased Fab thermoresistance via VH-targeted directed evolution. Protein Eng Des Sel 2015; 28:365-77. [PMID: 26283664 DOI: 10.1093/protein/gzv037] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 07/15/2015] [Indexed: 01/17/2023] Open
Abstract
Antibody aggregation is frequently mediated by the complementarity determining regions within the variable domains and can significantly decrease purification yields, shorten shelf-life and increase the risk of anti-drug immune responses. Aggregation-resistant antibodies could offset these risks; accordingly, we have developed a directed evolution strategy to improve Fab stability. A Fab-phage display vector was constructed and the VH domain targeted for mutagenesis by error-prone PCR. To enrich for thermoresistant clones, the resulting phage library was transiently heated, followed by selection for binding to an anti-light chain constant domain antibody. Five unique variants were identified, each possessing one to three amino acid substitutions. Each engineered Fab possessed higher, Escherichia coli expression yield, a 2-3°C increase in apparent melting temperature and improved aggregation resistance upon heating at high concentration. Select mutations were combined and shown to confer additive improvements to these biophysical characteristics. Finally, the wild-type and most stable triple variant Fab variant were converted into a human IgG1 and expressed in mammalian cells. Both expression level and aggregation resistance were similarly improved in the engineered IgG1. Analysis of the wild-type Fab crystal structure provided a structural rationale for the selected residues changes. This approach can help guide future Fab stabilization efforts.
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Affiliation(s)
| | - Jennifer L Johnson
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, GA 30332, USA
| | | | - Raquel L Lieberman
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, GA 30332, USA
| | - Jennifer A Maynard
- Chemical Engineering, University of Texas at Austin, 1 University Station, Austin, TX 78712, USA
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Johnson JL, Entzminger KC, Hyun J, Kalyoncu S, Heaner DP, Morales IA, Sheppard A, Gumbart JC, Maynard JA, Lieberman RL. Structural and biophysical characterization of an epitope-specific engineered Fab fragment and complexation with membrane proteins: implications for co-crystallization. Acta Crystallogr D Biol Crystallogr 2015; 71:896-906. [PMID: 25849400 PMCID: PMC4388267 DOI: 10.1107/s1399004715001856] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Accepted: 01/28/2015] [Indexed: 12/22/2022]
Abstract
Crystallization chaperones are attracting increasing interest as a route to crystal growth and structure elucidation of difficult targets such as membrane proteins. While strategies to date have typically employed protein-specific chaperones, a peptide-specific chaperone to crystallize multiple cognate peptide epitope-containing client proteins is envisioned. This would eliminate the target-specific chaperone-production step and streamline the co-crystallization process. Previously, protein engineering and directed evolution were used to generate a single-chain variable (scFv) antibody fragment with affinity for the peptide sequence EYMPME (scFv/EE). This report details the conversion of scFv/EE to an anti-EE Fab format (Fab/EE) followed by its biophysical characterization. The addition of constant chains increased the overall stability and had a negligible impact on the antigen affinity. The 2.0 Å resolution crystal structure of Fab/EE reveals contacts with larger surface areas than those of scFv/EE. Surface plasmon resonance, an enzyme-linked immunosorbent assay, and size-exclusion chromatography were used to assess Fab/EE binding to EE-tagged soluble and membrane test proteins: namely, the β-barrel outer membrane protein intimin and α-helical A2a G protein-coupled receptor (A2aR). Molecular-dynamics simulation of the intimin constructs with and without Fab/EE provides insight into the energetic complexities of the co-crystallization approach.
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Affiliation(s)
- Jennifer L. Johnson
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, GA 30332, USA
| | - Kevin C. Entzminger
- McKetta Department of Chemical Engineering, University of Texas at Austin, MC0400, 1 University Station, Austin, TX 78712, USA
| | - Jeongmin Hyun
- McKetta Department of Chemical Engineering, University of Texas at Austin, MC0400, 1 University Station, Austin, TX 78712, USA
| | - Sibel Kalyoncu
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, GA 30332, USA
| | - David P. Heaner
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, GA 30332, USA
| | - Ivan A. Morales
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, GA 30332, USA
| | - Aly Sheppard
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, GA 30332, USA
| | - James C. Gumbart
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, GA 30332, USA
- School of Physics, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, GA 30332, USA
| | - Jennifer A. Maynard
- McKetta Department of Chemical Engineering, University of Texas at Austin, MC0400, 1 University Station, Austin, TX 78712, USA
| | - Raquel L. Lieberman
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, GA 30332, USA
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39
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Wang X, Gray MC, Hewlett EL, Maynard JA. The Bordetella adenylate cyclase repeat-in-toxin (RTX) domain is immunodominant and elicits neutralizing antibodies. J Biol Chem 2014; 290:3576-91. [PMID: 25505186 DOI: 10.1074/jbc.m114.585281] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The adenylate cyclase toxin (ACT) is a multifunctional virulence factor secreted by Bordetella species. Upon interaction of its C-terminal hemolysin moiety with the cell surface receptor αMβ2 integrin, the N-terminal cyclase domain translocates into the host cell cytosol where it rapidly generates supraphysiological cAMP concentrations, which inhibit host cell anti-bacterial activities. Although ACT has been shown to induce protective immunity in mice, it is not included in any current acellular pertussis vaccines due to protein stability issues and a poor understanding of its role as a protective antigen. Here, we aimed to determine whether any single domain could recapitulate the antibody responses induced by the holo-toxin and to characterize the dominant neutralizing antibody response. We first immunized mice with ACT and screened antibody phage display libraries for binding to purified ACT. The vast majority of unique antibodies identified bound the C-terminal repeat-in-toxin (RTX) domain. Representative antibodies binding two nonoverlapping, neutralizing epitopes in the RTX domain prevented ACT association with J774A.1 macrophages and soluble αMβ2 integrin, suggesting that these antibodies inhibit the ACT-receptor interaction. Sera from mice immunized with the RTX domain showed similar neutralizing activity as ACT-immunized mice, indicating that this domain induced an antibody response similar to that induced by ACT. These data demonstrate that RTX can elicit neutralizing antibodies and suggest it may present an alternative to ACT.
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Affiliation(s)
| | - Mary C Gray
- Chemical Engineering, University of Texas at Austin, Austin, Texas 78712
| | - Erik L Hewlett
- Division of Infectious Diseases and International Health, Deparment of Medicine, University of Virginia, Charlottesville, Virginia, 22908
| | - Jennifer A Maynard
- Division of Infectious Diseases and International Health, Deparment of Medicine, University of Virginia, Charlottesville, Virginia, 22908
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40
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Beeden RJ, Turner MA, Dryden J, Merida F, Goudkamp K, Malone C, Marshall PA, Birtles A, Maynard JA. Rapid survey protocol that provides dynamic information on reef condition to managers of the Great Barrier Reef. Environ Monit Assess 2014; 186:8527-8540. [PMID: 25179944 DOI: 10.1007/s10661-014-4022-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 08/21/2014] [Indexed: 06/03/2023]
Abstract
Managing to support coral reef resilience as the climate changes requires strategic and responsive actions that reduce anthropogenic stress. Managers can only target and tailor these actions if they regularly receive information on system condition and impact severity. In large coral reef areas like the Great Barrier Reef Marine Park (GBRMP), acquiring condition and impact data with good spatial and temporal coverage requires using a large network of observers. Here, we describe the result of ~10 years of evolving and refining participatory monitoring programs used in the GBR that have rangers, tourism operators and members of the public as observers. Participants complete Reef Health and Impact Surveys (RHIS) using a protocol that meets coral reef managers' needs for up-to-date information on the following: benthic community composition, reef condition and impacts including coral diseases, damage, predation and the presence of rubbish. Training programs ensure that the information gathered is sufficiently precise to inform management decisions. Participants regularly report because the demands of the survey methodology have been matched to their time availability. Undertaking the RHIS protocol we describe involves three ~20 min surveys at each site. Participants enter data into an online data management system that can create reports for managers and participants within minutes of data being submitted. Since 2009, 211 participants have completed a total of more than 10,415 surveys at more than 625 different reefs. The two-way exchange of information between managers and participants increases the capacity to manage reefs adaptively, meets education and outreach objectives and can increase stewardship. The general approach used and the survey methodology are both sufficiently adaptable to be used in all reef regions.
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Affiliation(s)
- R J Beeden
- Great Barrier Reef Marine Park Authority, 2-68 Flinders Street, Townsville, QLD, 4810, Australia,
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Kalyoncu S, Hyun J, Pai JC, Johnson JL, Entzminger K, Jain A, Heaner DP, Morales IA, Truskett TM, Maynard JA, Lieberman RL. Effects of protein engineering and rational mutagenesis on crystal lattice of single chain antibody fragments. Proteins 2014; 82:1884-95. [PMID: 24615866 PMCID: PMC4142072 DOI: 10.1002/prot.24542] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 02/12/2014] [Accepted: 02/20/2014] [Indexed: 11/06/2022]
Abstract
Protein crystallization is dependent upon, and sensitive to, the intermolecular contacts that assist in ordering proteins into a three-dimensional lattice. Here we used protein engineering and mutagenesis to affect the crystallization of single chain antibody fragments (scFvs) that recognize the EE epitope (EYMPME) with high affinity. These hypercrystallizable scFvs are under development to assist difficult proteins, such as membrane proteins, in forming crystals, by acting as crystallization chaperones. Guided by analyses of intermolecular crystal lattice contacts, two second-generation anti-EE scFvs were produced, which bind to proteins with installed EE tags. Surprisingly, although noncomplementarity determining region (CDR) lattice residues from the parent scFv framework remained unchanged through the processes of protein engineering and rational design, crystal lattices of the derivative scFvs differ. Comparison of energy calculations and the experimentally-determined lattice interactions for this basis set provides insight into the complexity of the forces driving crystal lattice choice and demonstrates the availability of multiple well-ordered surface features in our scFvs capable of forming versatile crystal contacts.
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Affiliation(s)
- Sibel Kalyoncu
- School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, GA 30332-0400
| | - Jeongmin Hyun
- McKetta Department of Chemical Engineering, University of Texas at Austin, MC0400, 1 University Station, Austin, TX 78712
| | - Jennifer C. Pai
- McKetta Department of Chemical Engineering, University of Texas at Austin, MC0400, 1 University Station, Austin, TX 78712
| | - Jennifer L. Johnson
- School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, GA 30332-0400
| | - Kevin Entzminger
- McKetta Department of Chemical Engineering, University of Texas at Austin, MC0400, 1 University Station, Austin, TX 78712
| | - Avni Jain
- McKetta Department of Chemical Engineering, University of Texas at Austin, MC0400, 1 University Station, Austin, TX 78712
| | - David P. Heaner
- School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, GA 30332-0400
| | - Ivan A. Morales
- School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, GA 30332-0400
| | - Thomas M. Truskett
- McKetta Department of Chemical Engineering, University of Texas at Austin, MC0400, 1 University Station, Austin, TX 78712
| | - Jennifer A. Maynard
- McKetta Department of Chemical Engineering, University of Texas at Austin, MC0400, 1 University Station, Austin, TX 78712
| | - Raquel L. Lieberman
- School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, GA 30332-0400
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Kalyoncu S, Johnson JL, Heaner DP, Morales IA, Hyun J, Pai JC, Etzminger K, Maynard JA, Lieberman RL. The Use of Engineered Antibody Fragments to Promote Crystallization of Membrane Proteins. Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Abstract
Antibody therapeutics are one of the fastest growing classes of pharmaceuticals, with an annual US market over $20 billion, developed to treat a variety of diseases including cancer, auto-immune and infectious diseases. Most are currently administered as a single molecule to treat a single disease, however there is mounting evidence that cocktails of multiple antibodies, each with a unique binding specificity and protective mechanism, may improve clinical efficacy. Here, we review progress in the development of oligoclonal combinations of antibodies to treat disease, focusing on identification of synergistic antibodies. We then discuss the application of modern antibody engineering technologies to produce highly potent antibody preparations, including oligoclonal antibody cocktails and truly recombinant polyclonal antibodies. Specific examples illustrating the synergy conferred by multiple antibodies will be provided for diseases caused by botulinum toxin, cancer and immune thrombocytopenia. The bioprocessing and regulatory options for these preparations will be discussed.
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Affiliation(s)
- Xian-zhe Wang
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, United States
| | - Vincent W Coljee
- Department of Physics, Harvard University, Cambridge, MA 02138, United States
| | - Jennifer A Maynard
- Chemical Engineering, University of Texas at Austin, Austin, TX 78712, United States
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Panthani MG, Khan TA, Reid DK, Hellebusch DJ, Rasch MR, Maynard JA, Korgel BA. In vivo whole animal fluorescence imaging of a microparticle-based oral vaccine containing (CuInSe(x)S(2-x))/ZnS core/shell quantum dots. Nano Lett 2013; 13:4294-8. [PMID: 23915166 PMCID: PMC3796198 DOI: 10.1021/nl402054w] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Zinc sulfide-coated copper indium sulfur selenide (CuInSexS2-x/ZnS core/shell) nanocrystals were synthesized with size-tunable red to near-infrared (NIR) fluorescence with high quantum yield (40%) in water. These nanocrystals were tested as an imaging agent to track a microparticle-based oral vaccine administered to mice. Poly(lactic-co-glycolic acid) (PLGA) microparticle-encapsulated CuInSexSe2-x/ZnS quantum dots were orally administered to mice and were found to provide a distinct visible fluorescent marker in the gastrointestinal tract of living mice.
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Affiliation(s)
| | | | | | | | | | - Jennifer A. Maynard
- Corresponding authors: (T) +1-512-471-9188, (F): +1-512-471-7060, ; (T) +1-512-471-5633, (F) +1-512-471-7060k
| | - Brian A. Korgel
- Corresponding authors: (T) +1-512-471-9188, (F): +1-512-471-7060, ; (T) +1-512-471-5633, (F) +1-512-471-7060k
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45
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Miller MA, Rodrigues MA, Glass MA, Singh SK, Johnston KP, Maynard JA. Frozen-state storage stability of a monoclonal antibody: aggregation is impacted by freezing rate and solute distribution. J Pharm Sci 2013; 102:1194-208. [PMID: 23400717 DOI: 10.1002/jps.23473] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Revised: 01/08/2013] [Accepted: 01/22/2013] [Indexed: 01/13/2023]
Abstract
Freezing of protein solutions perturbs protein conformation, potentially leading to aggregate formation during long-term storage in the frozen state. Macroscopic protein concentration profiles in small cylindrical vessels were determined for a monoclonal antibody frozen in a trehalose-based formulation for various freezing protocols. Slow cooling rates led to concentration differences between outer edges of the tank and the center, up to twice the initial concentration. Fast cooling rates resulted in much smaller differences in protein distribution, likely due to the formation of dendritic ice, which traps solutes in micropockets, limiting their transport by convection and diffusion. Analysis of protein stability after more than 6 months storage at either -10°C or -20°C [above glass transition temperature (T'g )] or -80°C (below T'g ) revealed that aggregation correlated with the cooling rate. Slow-cooled vessels stored above T'g exhibited increased aggregation with time. In contrast, fast-cooled vessels and those stored below T'g showed small to no increase in aggregation at any position. Rapid entrapment of protein in a solute matrix by fast freezing results in improved stability even when stored above T'g . © 2013 Wiley Periodicals, Inc. and the American Pharmacists Association J Pharm Sci 102:1194-1208, 2013.
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Affiliation(s)
- Maria A Miller
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, USA
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46
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Abstract
T cell activation requires formation of a tri-molecular interaction between a major histocompatibility complex (MHC), peptide, and T cell receptor. In a common model system, the ovalbumin epitope 323–339 binds the murine class II MHC, I-Ad, in at least three distinct registers. The DO11.10 T cell recognizes the least stable of these, as determined by peptide-MHC dissociation rates. Using exogenous peptides and peptide insertions into a carrier protein in combination with IL-2 secretion assays, we show that the alternate registers do not competitively inhibit display of the active register four. In contrast, this weakly binding register is stabilized by the presence of n-terminal flanking residues active in MHC binding. The DO11.10 hybridoma is sensitive to the presence of specific wild-type residues extending to at least the P-3 peptide position. Transfer of the P-4 to P-2 flanking residues to a hen egg lysozyme epitope also presented by I-Ad increases the activity of that epitope substantially. These results illustrate the inherent complexity in delineating the interaction of multiple registers based on traditional thermodynamic measurements and demonstrate the potential of flanking residue modification for increasing the activity of weakly bound epitopes. The latter technique represents an alternative to substitution of anchor residues within a weakly bound register, which we show can significantly decrease the activity of the epitope to a responding T cell.
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Affiliation(s)
- Benjamin M. Roy
- Department of Chemical Engineering, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Chemical Engineering, University of Texas at Austin, Austin Texas, United States of America
| | - Dmitriy V. Zhukov
- Department of Chemical Engineering, University of Texas at Austin, Austin Texas, United States of America
| | - Jennifer A. Maynard
- Department of Chemical Engineering, University of Texas at Austin, Austin Texas, United States of America
- * E-mail:
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Miller MA, Khan TA, Kaczorowski KJ, Wilson BK, Dinin AK, Borwankar AU, Rodrigues MA, Truskett TM, Johnston KP, Maynard JA. Antibody nanoparticle dispersions formed with mixtures of crowding molecules retain activity and in vivo bioavailability. J Pharm Sci 2012; 101:3763-78. [PMID: 22777686 DOI: 10.1002/jps.23256] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Revised: 06/01/2012] [Accepted: 06/14/2012] [Indexed: 01/07/2023]
Abstract
Monoclonal antibodies continue to command a large market for treatment of a variety of diseases. In many cases, the doses required for therapeutic efficacy are large, limiting options for antibody delivery and administration. We report a novel formulation strategy based on dispersions of antibody nanoclusters that allows for subcutaneous injection of highly concentrated antibody (≈ 190 mg/mL). A solution of monoclonal antibody 1B7 was rapidly frozen and lyophilized using a novel spiral-wound in-situ freezing technology to generate amorphous particles. Upon gentle stirring, a translucent dispersion of approximately 430 nm protein clusters with low apparent viscosity (≈ 24 cp) formed rapidly in buffer containing the pharmaceutically acceptable crowding agents such as trehalose, polyethylene glycol, and n-methyl-2-pyrrolidone. Upon in vitro dilution of the dispersion, the nanoclusters rapidly reverted to monomeric protein with full activity, as monitored by dynamic light scattering and antigen binding. When administered to mice as an intravenous solution, subcutaneous solution, or subcutaneous dispersion at similar (4.6-7.3 mg/kg) or ultra-high dosages (51.6 mg/kg), the distribution and elimination kinetics were within error and the protein retained full activity. Overall, this method of generating high-concentration, low-viscosity dispersions of antibody nanoclusters could lead to improved administration and patient compliance, providing new opportunities for the biotechnology industry.
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Affiliation(s)
- Maria A Miller
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, USA
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Entzminger KC, Chang C, Myhre RO, McCallum KC, Maynard JA. The Skp chaperone helps fold soluble proteins in vitro by inhibiting aggregation. Biochemistry 2012; 51:4822-34. [PMID: 22650963 DOI: 10.1021/bi300412y] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The periplasmic seventeen kilodalton protein (Skp) chaperone has been characterized primarily for its role in outer membrane protein (OMP) biogenesis, during which the jellyfish-like trimeric protein encapsulates partially folded OMPs, protecting them from the aqueous environment until delivery to the BAM outer membrane protein insertion complex. However, Skp is increasingly recognized as a chaperone that also assists in folding soluble proteins in the bacterial periplasm. In this capacity, Skp coexpression increases the active yields of many recombinant proteins and bacterial virulence factors. Using a panel of single-chain antibodies and a single-chain T-cell receptor (collectively termed scFvs) possessing varying stabilities and biophysical characteristics, we performed in vivo expression and in vitro folding and aggregation assays in the presence or absence of Skp. For Skp-sensitive scFvs, the presence of Skp during in vitro refolding assays reduced aggregation but did not alter the observed folding rates, resulting in a higher overall yield of active protein. Of the proteins analyzed, Skp sensitivity in all assays correlated with the presence of folding intermediates, as observed with urea denaturation studies. These results are consistent with Skp acting as a holdase, sequestering partially folded intermediates and thereby preventing aggregation. Because not all soluble proteins are sensitive to Skp coexpression, we hypothesize that the presence of a long-lived protein folding intermediate renders a protein sensitive to Skp. Improved understanding of the bacterial periplasmic protein folding machinery may assist in high-level recombinant protein expression and may help identify novel approaches to block bacterial virulence.
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Affiliation(s)
- Kevin C Entzminger
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, USA
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49
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Johnston KP, Maynard JA, Truskett TM, Borwankar AU, Miller MA, Wilson BK, Dinin AK, Khan TA, Kaczorowski KJ. Concentrated dispersions of equilibrium protein nanoclusters that reversibly dissociate into active monomers. ACS Nano 2012; 6:1357-1369. [PMID: 22260218 DOI: 10.1021/nn204166z] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Stabilizing proteins at high concentration is of broad interest in drug delivery, for treatment of cancer and many other diseases. Herein, we create highly concentrated antibody dispersions (up to 260 mg/mL) comprising dense equilibrium nanoclusters of protein (monoclonal antibody 1B7, polyclonal sheep immunoglobulin G, and bovine serum albumin) molecules which, upon dilution in vitro or administration in vivo, remain conformationally stable and biologically active. The extremely concentrated environment within the nanoclusters (∼700 mg/mL) provides conformational stability to the protein through a novel self-crowding mechanism, as shown by computer simulation, while the primarily repulsive nanocluster interactions result in colloidally stable, transparent dispersions. The nanoclusters are formed by adding trehalose as a cosolute which strengthens the short-ranged attraction between protein molecules. The protein cluster diameter was reversibly tuned from 50 to 300 nm by balancing short-ranged attraction against long-ranged electrostatic repulsion of weakly charged protein at a pH near the isoelectric point. This behavior is described semiquantitatively with a free energy model which includes the fractal dimension of the clusters. Upon dilution of the dispersion in vitro, the clusters rapidly dissociated into fully active protein monomers as shown with biophysical analysis (SEC, DLS, CD, and SDS-PAGE) and sensitive biological assays. Since the concept of forming nanoclusters by tuning colloid interactions is shown to be general, it is likely applicable to a variety of biological therapeutics, mitigating the need to engineer protein stability through amino acid modification. In vivo subcutaneous injection into mice results in indistinguishable pharmacokinetics versus a standard antibody solution. Stable protein dispersions with low viscosities may potentially enable patient self-administration by subcutaneous injection of antibody therapeutics being discovered and developed.
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Affiliation(s)
- Keith P Johnston
- Department of Chemical Engineering, The University of Texas at Austin, 1 University Station C0400, Austin, Texas 78712-0231, United States.
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50
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Im H, Sutherland JN, Maynard JA, Oh SH. Nanohole-based surface plasmon resonance instruments with improved spectral resolution quantify a broad range of antibody-ligand binding kinetics. Anal Chem 2012; 84:1941-7. [PMID: 22235895 DOI: 10.1021/ac300070t] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We demonstrate an affordable low-noise surface plasmon resonance (SPR) instrument based on extraordinary optical transmission (EOT) in metallic nanohole arrays and quantify a broad range of antibody-ligand binding kinetics with equilibrium dissociation constants ranging from 200 pM to 40 nM. This nanohole-based SPR instrument is straightforward to construct, align, and operate, since it is built around a standard microscope and a portable fiber-optic spectrometer. The measured refractive index resolution of this platform is 3.1 × 10(-6) without on-chip cooling, which is among the lowest reported for SPR sensors based on EOT. This is accomplished via rapid full-spectrum acquisition in 10 ms followed by frame averaging of the EOT spectra, which is made possible by the production of template-stripped gold nanohole arrays with homogeneous optical properties over centimeter-sized areas. Sequential SPR measurements are performed using a 12-channel microfluidic flow cell after optimizing surface modification protocols and antibody injection conditions to minimize mass-transport artifacts. The immobilization of a model ligand, the protective antigen of anthrax on the gold surface, is monitored in real-time with a signal-to-noise ratio of ~860. Subsequently, real-time binding kinetic curves were measured quantitatively between the antigen and a panel of small, 25 kDa single-chain antibodies at concentrations down to 1 nM. These results indicate that nanohole-based SPR instruments have potential for quantitative antibody screening and as a general-purpose platform for integrating SPR sensors with other bioanalytical tools.
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Affiliation(s)
- Hyungsoon Im
- Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, Minnesota 55455, USA
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