1
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Dobersberger M, Sumesgutner D, Zajc CU, Salzer B, Laurent E, Emminger D, Sylvander E, Lehner E, Teufl M, Seigner J, Bobbili MR, Kunert R, Lehner M, Traxlmayr MW. An engineering strategy to target activated EGFR with CAR T cells. CELL REPORTS METHODS 2024; 4:100728. [PMID: 38492569 PMCID: PMC11045874 DOI: 10.1016/j.crmeth.2024.100728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 01/18/2024] [Accepted: 02/16/2024] [Indexed: 03/18/2024]
Abstract
Chimeric antigen receptor (CAR) T cells have shown remarkable response rates in hematological malignancies. In contrast, CAR T cell treatment of solid tumors is associated with several challenges, in particular the expression of most tumor-associated antigens at lower levels in vital organs, resulting in on-target/off-tumor toxicities. Thus, innovative approaches to improve the tumor specificity of CAR T cells are urgently needed. Based on the observation that many human solid tumors activate epidermal growth factor receptor (EGFR) on their surface through secretion of EGFR ligands, we developed an engineering strategy for CAR-binding domains specifically directed against the ligand-activated conformation of EGFR. We show, in several experimental systems, that the generated binding domains indeed enable CAR T cells to distinguish between active and inactive EGFR. We anticipate that this engineering concept will be an important step forward to improve the tumor specificity of CAR T cells directed against EGFR-positive solid cancers.
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Affiliation(s)
- Markus Dobersberger
- Department of Chemistry, Institute of Biochemistry, BOKU University, 1190 Vienna, Austria
| | - Delia Sumesgutner
- Department of Chemistry, Institute of Biochemistry, BOKU University, 1190 Vienna, Austria; CD Laboratory for Next Generation CAR T Cells, 1090 Vienna, Austria
| | - Charlotte U Zajc
- Department of Chemistry, Institute of Biochemistry, BOKU University, 1190 Vienna, Austria; CD Laboratory for Next Generation CAR T Cells, 1090 Vienna, Austria
| | - Benjamin Salzer
- CD Laboratory for Next Generation CAR T Cells, 1090 Vienna, Austria; St. Anna Children's Cancer Research Institute, CCRI, 1090 Vienna, Austria
| | - Elisabeth Laurent
- BOKU Core Facility Biomolecular & Cellular Analysis, BOKU University, 1190 Vienna, Austria
| | - Dominik Emminger
- CD Laboratory for Next Generation CAR T Cells, 1090 Vienna, Austria; St. Anna Children's Cancer Research Institute, CCRI, 1090 Vienna, Austria
| | - Elise Sylvander
- CD Laboratory for Next Generation CAR T Cells, 1090 Vienna, Austria; St. Anna Children's Cancer Research Institute, CCRI, 1090 Vienna, Austria
| | - Elisabeth Lehner
- Department of Chemistry, Institute of Biochemistry, BOKU University, 1190 Vienna, Austria; CD Laboratory for Next Generation CAR T Cells, 1090 Vienna, Austria
| | - Magdalena Teufl
- Department of Chemistry, Institute of Biochemistry, BOKU University, 1190 Vienna, Austria; CD Laboratory for Next Generation CAR T Cells, 1090 Vienna, Austria
| | - Jacqueline Seigner
- Department of Chemistry, Institute of Biochemistry, BOKU University, 1190 Vienna, Austria; Department of Biotechnology, Institute of Animal Cell Technology and Systems Biology, BOKU University, 1190 Vienna, Austria
| | - Madhusudhan Reddy Bobbili
- Department of Biotechnology, Institute of Molecular Biotechnology, BOKU University, 1190 Vienna, Austria; Ludwig Boltzmann Institute for Traumatology, Research Center in Cooperation with AUVA, 1200 Vienna, Austria
| | - Renate Kunert
- Department of Biotechnology, Institute of Animal Cell Technology and Systems Biology, BOKU University, 1190 Vienna, Austria
| | - Manfred Lehner
- CD Laboratory for Next Generation CAR T Cells, 1090 Vienna, Austria; St. Anna Children's Cancer Research Institute, CCRI, 1090 Vienna, Austria; St. Anna Children's Hospital, Department of Pediatrics, Medical University of Vienna, 1090 Vienna, Austria
| | - Michael W Traxlmayr
- Department of Chemistry, Institute of Biochemistry, BOKU University, 1190 Vienna, Austria; CD Laboratory for Next Generation CAR T Cells, 1090 Vienna, Austria.
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2
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Moeller T, Shah SB, Lai K, Lopez-Barbosa N, Desai P, Wang W, Zhong Z, Redmond D, Singh A, DeLisa MP. Profiling Germinal Center-like B Cell Responses to Conjugate Vaccines Using Synthetic Immune Organoids. ACS CENTRAL SCIENCE 2023; 9:787-804. [PMID: 37122450 PMCID: PMC10141597 DOI: 10.1021/acscentsci.2c01473] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Indexed: 05/03/2023]
Abstract
Glycoengineered bacteria have emerged as a cost-effective platform for rapid and controllable biosynthesis of designer conjugate vaccines. However, little is known about the engagement of such conjugates with naïve B cells to induce the formation of germinal centers (GC), a subanatomical microenvironment that converts naïve B cells into antibody-secreting plasma cells. Using a three-dimensional biomaterials-based B-cell follicular organoid system, we demonstrate that conjugates triggered robust expression of hallmark GC markers, B cell receptor clustering, intracellular signaling, and somatic hypermutation. These responses depended on the relative immunogenicity of the conjugate and correlated with the humoral response in vivo. The occurrence of these mechanisms was exploited for the discovery of high-affinity antibodies against components of the conjugate on a time scale that was significantly shorter than for typical animal immunization-based workflows. Collectively, these findings highlight the potential of synthetic organoids for rapidly predicting conjugate vaccine efficacy as well as expediting antigen-specific antibody discovery.
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Affiliation(s)
- Tyler
D. Moeller
- Robert
F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Shivem B. Shah
- Nancy
E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Kristine Lai
- George
W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Natalia Lopez-Barbosa
- Robert
F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Primit Desai
- Biochemistry,
Molecular and Cell Biology, Cornell University, Ithaca, New York 14853, United States
| | - Weiyao Wang
- Robert
F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Zhe Zhong
- George
W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - David Redmond
- Institute
for Computational Biomedicine, Weill Cornell Medicine, Cornell University, New York, New York 10021, United States
- Department
of Physiology and Biophysics, Weill Cornell Medicine, Cornell University, New York, New York 10021, United States
| | - Ankur Singh
- George
W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- Wallace
H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Matthew P. DeLisa
- Robert
F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
- Nancy
E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York 14853, United States
- Biochemistry,
Molecular and Cell Biology, Cornell University, Ithaca, New York 14853, United States
- Cornell
Institute of Biotechnology, Cornell University, Ithaca, New York 14853, United States
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3
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Rezhdo A, Lessard CT, Islam M, Van Deventer JA. Strategies for enriching and characterizing proteins with inhibitory properties on the yeast surface. Protein Eng Des Sel 2023; 36:gzac017. [PMID: 36648434 PMCID: PMC10365883 DOI: 10.1093/protein/gzac017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 10/20/2022] [Accepted: 11/07/2022] [Indexed: 01/18/2023] Open
Abstract
Display technologies are powerful tools for discovering binding proteins against a broad range of biological targets. However, it remains challenging to adapt display technologies for the discovery of proteins that inhibit the enzymatic activities of targets. Here, we investigate approaches for discovering and characterizing inhibitory antibodies in yeast display format using a well-defined series of constructs and the target matrix metalloproteinase-9. Three previously reported antibodies were used to create model libraries consisting of inhibitory, non-inhibitory, and non-binding constructs. Conditions that preferentially enrich for inhibitory clones were identified for both magnetic bead-based enrichments and fluorescence-activated cell sorting. Half maximal inhibitory concentration (IC50) was obtained through yeast titration assays. The IC50 of the inhibitory antibody obtained in yeast display format falls within the confidence interval of the IC50 value determined in soluble form. Overall, this study identifies strategies for the discovery and characterization of inhibitory clones directly in yeast display format.
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Affiliation(s)
- Arlinda Rezhdo
- Chemical and Biological Engineering Department, Tufts University, Medford, MA 02155, USA
| | - Catherine T Lessard
- Chemical and Biological Engineering Department, Tufts University, Medford, MA 02155, USA
| | - Mariha Islam
- Chemical and Biological Engineering Department, Tufts University, Medford, MA 02155, USA
| | - James A Van Deventer
- Chemical and Biological Engineering Department, Tufts University, Medford, MA 02155, USA
- Biomedical Engineering Department, Tufts University, Medford, MA 02155, USA
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4
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Engineering Proteins Containing Noncanonical Amino Acids on the Yeast Surface. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2491:491-559. [PMID: 35482204 DOI: 10.1007/978-1-0716-2285-8_23] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Yeast display has been used to advance many critical research areas, including the discovery of unique protein binders and biological therapeutics. In parallel, noncanonical amino acids (ncAAs) have been used to tailor antibody-drug conjugates and enable discovery of therapeutic leads. Together, these two technologies have allowed for generation of synthetic antibody libraries, where the introduction of ncAAs in yeast-displayed proteins allows for library screening for therapeutically relevant targets. The combination of yeast display with genetically encoded ncAAs increases the available chemistry in proteins and advances applications that require high-throughput strategies. In this chapter, we discuss methods for displaying proteins containing ncAAs on the yeast surface, generating and screening libraries of proteins containing ncAAs, preparing bioconjugates on the yeast surface in large scale, generating and screening libraries of aminoacyl-tRNA synthetases (aaRSs) for encoding ncAAs by using reporter constructs, and characterizing ncAA-containing proteins secreted from yeast. The experimental designs laid out in this chapter are generalizable for discovery of protein binders to a variety of targets and aaRS evolution to continue expanding the genetic code beyond what is currently available in yeast.
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5
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Wang EY, Dai Y, Rosen CE, Schmitt MM, Dong MX, Ferré EM, Liu F, Yang Y, González-Hernández JA, Meffre E, Hinchcliff M, Koumpouras F, Lionakis MS, Ring AM. High-throughput identification of autoantibodies that target the human exoproteome. CELL REPORTS METHODS 2022; 2:100172. [PMID: 35360706 PMCID: PMC8967185 DOI: 10.1016/j.crmeth.2022.100172] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 11/30/2021] [Accepted: 01/27/2022] [Indexed: 12/11/2022]
Abstract
Autoantibodies that recognize extracellular proteins (the exoproteome) exert potent biological effects but are challenging to detect. Here, we developed rapid extracellular antigen profiling (REAP), a high-throughput technique for the comprehensive discovery of exoproteome-targeting autoantibodies. Patient samples are applied to a genetically barcoded yeast surface display library containing 2,688 human extracellular proteins. Antibody-coated yeast are isolated, and sequencing of barcodes is used to identify displayed antigens. To benchmark REAP's performance, we screened 77 patients with autoimmune polyglandular syndrome type 1 (APS-1). REAP sensitively and specifically detected both known and previously unidentified autoantibodies in APS-1. We further screened 106 patients with systemic lupus erythematosus (SLE) and identified numerous autoantibodies, several of which were associated with disease severity or specific clinical manifestations and exerted functional effects on cell signaling ex vivo. These findings demonstrate the utility of REAP to atlas the expansive landscape of exoproteome-targeting autoantibodies and their impacts on patient health outcomes.
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Affiliation(s)
- Eric Y. Wang
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Yile Dai
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Connor E. Rosen
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Monica M. Schmitt
- Fungal Pathogenesis Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy & Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mei X. Dong
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06510, USA
| | - Elise M.N. Ferré
- Fungal Pathogenesis Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy & Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Feimei Liu
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Yi Yang
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
| | | | - Eric Meffre
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Monique Hinchcliff
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06510, USA
| | - Fotios Koumpouras
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06510, USA
| | - Michail S. Lionakis
- Fungal Pathogenesis Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy & Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Aaron M. Ring
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 06510, USA
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6
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Laurent E, Sieber A, Salzer B, Wachernig A, Seigner J, Lehner M, Geyeregger R, Kratzer B, Jäger U, Kunert R, Pickl WF, Traxlmayr MW. Directed Evolution of Stabilized Monomeric CD19 for Monovalent CAR Interaction Studies and Monitoring of CAR-T Cell Patients. ACS Synth Biol 2021; 10:1184-1198. [PMID: 33843201 PMCID: PMC8155657 DOI: 10.1021/acssynbio.1c00010] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
CD19 is among the most relevant targets in cancer immunotherapy. However, its extracellular domain (ECD) is prone to aggregation and misfolding, representing a major obstacle for the development and analysis of CD19-targeted therapeutics. Here, we engineered stabilized CD19-ECD (termed SuperFolder) variants, which also showed improved expression rates and, in contrast to the wild type protein, they could be efficiently purified in their monomeric forms. Despite being considerably more stable, these engineered mutants largely preserved the wild type sequence (>98.8%). We demonstrate that the variant SF05 enabled the determination of the monovalent affinity between CD19 and a clinically approved FMC63-based CAR, as well as monitoring and phenotypic characterization of CD19-directed CAR-T cells in the blood of lymphoma patients. We anticipate that the SuperFolder mutants generated in this study will be highly valuable tools for a range of applications in basic immunology and CD19-targeted cancer immunotherapy.
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Affiliation(s)
- Elisabeth Laurent
- Department of Biotechnology and BOKU Core Facility Biomolecular and Cellular Analysis, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Anna Sieber
- Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Benjamin Salzer
- St. Anna Children’s Cancer Research Institute, Zimmermannplatz 10, 1090 Vienna, Austria
| | - Anna Wachernig
- Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Jacqueline Seigner
- Department of Chemistry, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Manfred Lehner
- St. Anna Children’s Cancer Research Institute, Zimmermannplatz 10, 1090 Vienna, Austria
| | - René Geyeregger
- St. Anna Children’s Cancer Research Institute, Zimmermannplatz 10, 1090 Vienna, Austria
| | - Bernhard Kratzer
- Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Lazarettgasse 19, 1090 Vienna, Austria
| | - Ulrich Jäger
- Department of Internal Medicine, Division of Hematology and Hemostaseology, Medical University of Vienna, Währinger Gürtel 18-20, 1090 Vienna, Austria
| | - Renate Kunert
- Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Winfried F. Pickl
- Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Lazarettgasse 19, 1090 Vienna, Austria
| | - Michael W. Traxlmayr
- Department of Chemistry, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
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7
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Mutational and biophysical robustness in a prestabilized monobody. J Biol Chem 2021; 296:100447. [PMID: 33617878 PMCID: PMC8010708 DOI: 10.1016/j.jbc.2021.100447] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/15/2021] [Accepted: 02/18/2021] [Indexed: 12/14/2022] Open
Abstract
The fibronectin type III (FN3) monobody domain is a promising non-antibody scaffold, which features a less complex architecture than an antibody while maintaining analogous binding loops. We previously developed FN3Con, a hyperstable monobody derivative with diagnostic and therapeutic potential. Prestabilization of the scaffold mitigates the stability–function trade-off commonly associated with evolving a protein domain toward biological activity. Here, we aimed to examine if the FN3Con monobody could take on antibody-like binding to therapeutic targets, while retaining its extreme stability. We targeted the first of the Adnectin derivative of monobodies to reach clinical trials, which was engineered by directed evolution for binding to the therapeutic target VEGFR2; however, this function was gained at the expense of large losses in thermostability and increased oligomerization. In order to mitigate these losses, we grafted the binding loops from Adnectin-anti-VEGFR2 (CT-322) onto the prestabilized FN3Con scaffold to produce a domain that successfully bound with high affinity to the therapeutic target VEGFR2. This FN3Con-anti-VEGFR2 construct also maintains high thermostability, including remarkable long-term stability, retaining binding activity after 2 years of storage at 36 °C. Further investigations into buffer excipients doubled the presence of monomeric monobody in accelerated stability trials. These data suggest that loop grafting onto a prestabilized scaffold is a viable strategy for the development of monobody domains with desirable biophysical characteristics and that FN3Con is therefore well-suited to applications such as the evolution of multiple paratopes or shelf-stable diagnostics and therapeutics.
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8
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Lown PS, Cai JJ, Ritter SC, Otolski JJ, Wong R, Hackel BJ. Extended yeast surface display linkers enhance the enrichment of ligands in direct mammalian cell selections. Protein Eng Des Sel 2021; 34:gzab004. [PMID: 33880560 PMCID: PMC8058008 DOI: 10.1093/protein/gzab004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 02/12/2021] [Accepted: 02/12/2021] [Indexed: 12/21/2022] Open
Abstract
Selections of yeast-displayed ligands on mammalian cell monolayers benefit from high target expression and nanomolar affinity, which are not always available. Prior work extending the yeast-protein linker from 40 to 80 amino acids improved yield and enrichment but is hypothesized to be below the optimal length, prompting evaluation of an extended amino acid linker. A 641-residue linker provided enhanced enrichment with a 2-nM affinity fibronectin ligand and 105 epidermal growth factor receptors (EGFR) per cell (14 ± 2 vs. 8 ± 1, P = 0.008) and a >600-nM affinity ligand, 106 EGFR per cell system (23 ± 7 vs. 0.8 ± 0.2, P = 0.004). Enhanced enrichment was also observed with a 310-nM affinity affibody ligand and 104 CD276 per cell, suggesting a generalizable benefit to other scaffolds and targets. Spatial modeling of the linker suggests that improved extracellular accessibility of ligand enables the observed enrichment under conditions not previously possible.
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Affiliation(s)
- Patrick S Lown
- Department of Chemical Engineering and Materials Science, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA
| | - Jessy J Cai
- Department of Chemical Engineering and Materials Science, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA
| | - Seth C Ritter
- Department of Chemical Engineering and Materials Science, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA
| | - Jacob J Otolski
- Department of Chemical Engineering and Materials Science, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA
| | - Ryan Wong
- Department of Chemical Engineering and Materials Science, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA
| | - Benjamin J Hackel
- Department of Chemical Engineering and Materials Science, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA
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9
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Casey GR, Zhou X, Lesiak L, Xu B, Fang Y, Becker DF, Stains CI. An Evolutionary Strategy for Identification of Higher Order, Green Fluorescent Host-Guest Pairs Compatible with Living Systems. Chemistry 2020; 26:16721-16726. [PMID: 32725914 DOI: 10.1002/chem.202002423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 07/26/2020] [Indexed: 11/09/2022]
Abstract
Engineered miniprotein host-small-molecule guest pairs could be utilized to design new processes within cells as well as investigate fundamental aspects of cell signaling mechanisms. However, the development of host-guest pairs capable of functioning in living systems has proven challenging. Moreover, few examples of host-guest pairs with stoichiometries other than 2:1 exist, significantly hindering the ability to study the influence of oligomerization state on signaling fidelity. Herein, we present an approach to identify host-guest systems for relatively small green fluorescent guests by incorporation into cyclic peptides. The optimal host-guest pair produced a 10-fold increase in green fluorescence signal upon binding. Biophysical characterization clearly demonstrated higher order supramolecular assembly, which could be visualized on the surface of living yeast cells using a turn-on fluorescence readout. This work further defines evolutionary design principles to afford host-guest pairs with stoichiometries other than 2:1 and enables the identification of spectrally orthogonal host-guest pairs.
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Affiliation(s)
- Garrett R Casey
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.,Department of Chemistry and Physics, Southeast Missouri State University, Cape Girardeau, MO, 63701, USA
| | - Xinqi Zhou
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Lauren Lesiak
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Bi Xu
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Yuan Fang
- Department of Chemistry, University of Virginia, Charlottesville, VA, 22904, USA
| | - Donald F Becker
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Cliff I Stains
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.,Department of Chemistry, University of Virginia, Charlottesville, VA, 22904, USA.,Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.,Cancer Genes and Molecular Regulation Program, Fred & Pamela Buffet Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA.,University of Virginia Cancer Center, University of Virginia, Charlottesville, VA, 22904, USA
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10
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A conformation-specific ON-switch for controlling CAR T cells with an orally available drug. Proc Natl Acad Sci U S A 2020; 117:14926-14935. [PMID: 32554495 PMCID: PMC7334647 DOI: 10.1073/pnas.1911154117] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Molecular ON-switches in which a chemical compound induces protein-protein interactions can allow cellular function to be controlled with small molecules. ON-switches based on clinically applicable compounds and human proteins would greatly facilitate their therapeutic use. Here, we developed an ON-switch system in which the human retinol binding protein 4 (hRBP4) of the lipocalin family interacts with engineered hRBP4 binders in a small molecule-dependent manner. Two different protein scaffolds were engineered to bind to hRBP4 when loaded with the orally available small molecule A1120. The crystal structure of an assembled ON-switch shows that the engineered binder specifically recognizes the conformational changes induced by A1120 in two loop regions of hRBP4. We demonstrate that this conformation-specific ON-switch is highly dependent on the presence of A1120, as demonstrated by an ∼500-fold increase in affinity upon addition of the small molecule drug. Furthermore, the ON-switch successfully regulated the activity of primary human CAR T cells in vitro. We anticipate that lipocalin-based ON-switches have the potential to be broadly applied for the safe pharmacological control of cellular therapeutics.
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11
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Mehta NK, Pradhan RV, Soleimany AP, Moynihan KD, Rothschilds AM, Momin N, Rakhra K, Mata-Fink J, Bhatia SN, Wittrup KD, Irvine DJ. Pharmacokinetic tuning of protein-antigen fusions enhances the immunogenicity of T-cell vaccines. Nat Biomed Eng 2020; 4:636-648. [PMID: 32483299 DOI: 10.1038/s41551-020-0563-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 04/27/2020] [Indexed: 12/21/2022]
Abstract
The formulations of peptide-based antitumour vaccines being tested in clinical studies are generally associated with weak potency. Here, we show that pharmacokinetically tuning the responses of peptide vaccines by fusing the peptide epitopes to carrier proteins optimizes vaccine immunogenicity in mice. In particular, we show in immunized mice that the carrier protein transthyretin simultaneously optimizes three factors: efficient antigen uptake in draining lymphatics from the site of injection, protection of antigen payloads from proteolytic degradation and reduction of antigen presentation in uninflamed distal lymphoid organs. Optimizing these factors increases vaccine immunogenicity by up to 90-fold and maximizes the responses to viral antigens, tumour-associated antigens, oncofetal antigens and shared neoantigens. Protein-peptide epitope fusions represent a facile and generalizable strategy for enhancing the T-cell responses elicited by subunit vaccines.
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Affiliation(s)
- Naveen K Mehta
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Roma V Pradhan
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ava P Soleimany
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.,Harvard Graduate Program in Biophysics, Harvard University, Boston, MA, USA
| | - Kelly D Moynihan
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Adrienne M Rothschilds
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Noor Momin
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kavya Rakhra
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jordi Mata-Fink
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.,Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sangeeta N Bhatia
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Harvard-MIT Health Sciences and Technology Program, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.,Howard Hughes Medical Institute, Cambridge, MA, USA
| | - K Dane Wittrup
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Darrell J Irvine
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA. .,The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA. .,Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Howard Hughes Medical Institute, Cambridge, MA, USA.
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12
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Lown PS, Hackel BJ. Magnetic Bead-Immobilized Mammalian Cells Are Effective Targets to Enrich Ligand-Displaying Yeast. ACS COMBINATORIAL SCIENCE 2020; 22:274-284. [PMID: 32283920 DOI: 10.1021/acscombsci.0c00036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Yeast surface display empowers selection of protein binding ligands, typically using recombinant soluble antigens. However, ectodomain fragments of transmembrane targets may fail to recapitulate their true, membrane-bound form. Direct selections against adhered mammalian cells empower enrichment of genuine binders yet benefit from high target expression, robustly adherent mammalian cells, and nanomolar affinity ligands. This study evaluates a modified format with mammalian cells immobilized to magnetic beads; yeast-displayed fibronectin domain and affibody ligands of known affinities and cells with expression ranges of epidermal growth factor receptor (EGFR) and CD276 elucidate important parameters to ligand enrichment and yield in cell suspension panning with comparison to adherent panning. Cell suspension panning is hindered by significant background of nondisplaying yeast but exhibits yield advantages in model EGFR systems for a high affinity (KD = 2 nM) binder on cells with both high (106 per cell) target expression (9.6 ± 0.6% vs 3.2 ± 0.4%, p < 0.0001) and mid (105) target expression (2.3 ± 0.5% vs 0.41 ± 0.09%, p = 0.0008), as well as for a low affinity (KD > 600 nM) binder on high target expression cells (2.0 ± 0.5% vs 0.017 ± 0.005%; p = 0.001). Significant enrichment was observed for all EGFR systems except the low-affinity, high expression system. The CD276 system failed to provide significant enrichment, indicating that this technique may not be suitable for all targets. Collectively, this study highlights new approaches that yield successful enrichment of yeast-displayed ligands via panning on immobilized mammalian cells.
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Affiliation(s)
- Patrick S. Lown
- Department of Chemical Engineering and Materials Science, University of Minnesota−Twin Cities, 421 Washington Avenue Southeast, 356 Amundson Hall, Minneapolis, Minnesota 55455, United States
| | - Benjamin J. Hackel
- Department of Chemical Engineering and Materials Science, University of Minnesota−Twin Cities, 421 Washington Avenue Southeast, 356 Amundson Hall, Minneapolis, Minnesota 55455, United States
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13
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Chandler PG, Buckle AM. Development and Differentiation in Monobodies Based on the Fibronectin Type 3 Domain. Cells 2020; 9:E610. [PMID: 32143310 PMCID: PMC7140400 DOI: 10.3390/cells9030610] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/24/2020] [Accepted: 03/01/2020] [Indexed: 12/13/2022] Open
Abstract
As a non-antibody scaffold, monobodies based on the fibronectin type III (FN3) domain overcome antibody size and complexity while maintaining analogous binding loops. However, antibodies and their derivatives remain the gold standard for the design of new therapeutics. In response, clinical-stage therapeutic proteins based on the FN3 domain are beginning to use native fibronectin function as a point of differentiation. The small and simple structure of monomeric monobodies confers increased tissue distribution and reduced half-life, whilst the absence of disulphide bonds improves stability in cytosolic environments. Where multi-specificity is challenging with an antibody format that is prone to mis-pairing between chains, multiple FN3 domains in the fibronectin assembly already interact with a large number of molecules. As such, multiple monobodies engineered for interaction with therapeutic targets are being combined in a similar beads-on-a-string assembly which improves both efficacy and pharmacokinetics. Furthermore, full length fibronectin is able to fold into multiple conformations as part of its natural function and a greater understanding of how mechanical forces allow for the transition between states will lead to advanced applications that truly differentiate the FN3 domain as a therapeutic scaffold.
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Affiliation(s)
- Peter G. Chandler
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, Australia;
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14
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Stern LA, Lown PS, Hackel BJ. Ligand Engineering via Yeast Surface Display and Adherent Cell Panning. Methods Mol Biol 2020; 2070:303-320. [PMID: 31625103 PMCID: PMC6996137 DOI: 10.1007/978-1-4939-9853-1_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
High-throughput ligand discovery and evolution-via genotype-phenotype linkage strategies-empower molecularly targeted therapy, diagnostics, and fundamental science. Maintaining high-quality target antigen in these selections, particularly for membrane targets, is often a technical challenge. Panning yeast-displayed ligand libraries on intact mammalian cells expressing the molecular target has emerged as an effective strategy. Herein we describe the techniques used to select target-binding ligands via this approach including the use of target-negative cells to deplete non-specific binders and avidity reduction to preferentially select high-affinity ligands.
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Affiliation(s)
- Lawrence A Stern
- Department of Hematology and Hematopoietic Cell Transplantation, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Patrick S Lown
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Benjamin J Hackel
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, Minneapolis, MN, USA.
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15
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Heinzelman P, Low A, Simeon R, Wright GA, Chen Z. De Novo Isolation & Affinity Maturation of yeast-displayed Virion-binding human fibronectin domains by flow cytometric screening against Virions. J Biol Eng 2019; 13:76. [PMID: 31636701 PMCID: PMC6796422 DOI: 10.1186/s13036-019-0203-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 09/04/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The promise of biopharmaceuticals comprising one or more binding domains motivates the development of novel methods for de novo isolation and affinity maturation of virion-binding domains. Identifying avenues for overcoming the challenges associated with using virions as screening reagents is paramount given the difficulties associated with obtaining high-purity virus-associated proteins that retain the conformation exhibited on the virion surface. RESULTS Fluorescence activated cell sorting (FACS) of 1.5 × 107 clones taken from a naïve yeast surface-displayed human fibronectin domain (Fn3) against whole virions yielded two unique binders to Zika virions. Construction and FACS of site-directed binding loop mutant libraries based on one of these binders yielded multiple progeny clones with enhanced Zika-binding affinities. These affinity-matured clones bound Zika virions with low double- or single-digit nanomolar affinity in ELISA assays, and expressed well as soluble proteins in E. coli shake flask culture, with post-purification yields exceeding 10 mg/L. CONCLUSIONS FACS of a yeast-displayed binding domain library is an efficient method for de novo isolation of virion-binding domains. Affinities of isolated virion-binding clones are readily enhanced via FACS screening of mutant progeny libraries. Given that most binding domains are compatible with yeast display, the approach taken in this work may be broadly utilized for generating virion-binding domains against many different viruses for use in passive immunotherapy and the prevention of viral infection.
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Affiliation(s)
- Pete Heinzelman
- Department of Microbial Pathogenesis & Immunology, Texas A&M University, College Station, Texas 77843 USA
| | - Alyssa Low
- Department of Microbial Pathogenesis & Immunology, Texas A&M University, College Station, Texas 77843 USA
| | - Rudo Simeon
- Department of Microbial Pathogenesis & Immunology, Texas A&M University, College Station, Texas 77843 USA
| | - Gus A. Wright
- Department of Veterinary Pathobiology, Texas A&M University, College Station, Texas 77843 USA
| | - Zhilei Chen
- Department of Microbial Pathogenesis & Immunology, Texas A&M University, College Station, Texas 77843 USA
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16
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Stern LA, Lown PS, Kobe AC, Abou-Elkacem L, Willmann JK, Hackel BJ. Cellular-Based Selections Aid Yeast-Display Discovery of Genuine Cell-Binding Ligands: Targeting Oncology Vascular Biomarker CD276. ACS COMBINATORIAL SCIENCE 2019; 21:207-222. [PMID: 30620189 PMCID: PMC6411437 DOI: 10.1021/acscombsci.8b00156] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Yeast surface display is a proven tool for the selection and evolution of ligands with novel binding activity. Selections from yeast surface display libraries against transmembrane targets are generally carried out using recombinant soluble extracellular domains. Unfortunately, these molecules may not be good models of their true, membrane-bound form for a variety of reasons. Such selection campaigns often yield ligands that bind a recombinant target but not target-expressing cells or tissues. Advances in cell-based selections with yeast surface display may aid the frequency of evolving ligands that do bind true, membrane-bound antigens. This study aims to evaluate ligand selection strategies using both soluble target-driven and cellular selection techniques to determine which methods yield translatable ligands most efficiently and generate novel binders against CD276 (B7-H3) and Thy1, two promising tumor vasculature targets. Out of four ligand selection campaigns carried out using only soluble extracellular domains, only an affibody library sorted against CD276 yielded translatable binders. In contrast, fibronectin domains against CD276 and affibodies against CD276 were discovered in campaigns that either combined soluble target and cellular selection methods or used cellular selection methods alone. A high frequency of non target-specific ligands discovered from the use of cellular selection methods alone motivated the development of a depletion scheme using disadhered, antigen-negative mammalian cells as a blocking agent. Affinity maturation of CD276-binding affibodies by error-prone PCR and helix walking resulted in strong, specific cellular CD276 affinity ( Kd = 0.9 ± 0.6 nM). Collectively, these results motivate the use of cellular selections in tandem with recombinant selections and introduce promising affibody molecules specific to CD276 for further applications.
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Affiliation(s)
- Lawrence A. Stern
- Department of Chemical Engineering and Materials Science, University of Minnesota–Twin Cities, Minneapolis, MN
| | - Patrick S. Lown
- Department of Chemical Engineering and Materials Science, University of Minnesota–Twin Cities, Minneapolis, MN
| | - Alexandra C. Kobe
- Department of Chemical Engineering and Materials Science, University of Minnesota–Twin Cities, Minneapolis, MN
| | | | | | - Benjamin J. Hackel
- Department of Chemical Engineering and Materials Science, University of Minnesota–Twin Cities, Minneapolis, MN
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17
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Abstract
Access to well-defined ubiquitin conjugates has been key to elucidating the biochemical functions of proteins in the ubiquitin signaling network. Yet, we have a poor understanding of how deubiquitinases and ubiquitin-binding proteins respond to ubiquitin modifications when anchored to a protein other than ubiquitin or a ubiquitin-like protein. This is due to the difficulty of synthesizing ubiquitinated proteins comprised of native isopeptide bonds. Here we report on the evolution of a deubiquitinase capable of site-specifically modifying itself with defined ubiquitin chains. Following mutagenesis and yeast display screening, we identify a variant of the yeast ubiquitin C-terminal hydrolase Yuh1 that has a 28-fold improvement in the transamidation to hydrolysis ratio relative to the wild type enzyme. The switch in activity enables robust autoubiquitination of a lysine in the crossover loop to form an isopeptide bond. We demonstrate the utility of autoubiquitinating the evolved Yuh1 variant by investigating the consequences of ubiquitin chain anchoring on the activities of other deubiquitinases. Much to our surprise, we find that certain deubiquitinases are exquisitely sensitive to chain anchoring. These results highlight the importance of investigating the biochemical activities of deubiquitinases with both substrate-anchored and unanchored ubiquitin chains.
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18
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Shingarova LN, Petrovskaya LE, Zlobinov AV, Gapizov SS, Kryukova EA, Birikh KR, Boldyreva EF, Yakimov SA, Dolgikh DA, Kirpichnikov MP. Construction of Artificial TNF-Binding Proteins Based on the 10th Human Fibronectin Type III Domain Using Bacterial Display. BIOCHEMISTRY (MOSCOW) 2018; 83:708-716. [PMID: 30195327 DOI: 10.1134/s0006297918060081] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Construction of antibody mimetics on the base of alternative scaffold proteins is a promising strategy for obtaining new products for medicine and biotechnology. The aim of our work was to optimize the cell display system for the 10th human fibronectin type III domain (10Fn3) scaffold protein based on the AT877 autotransporter from Psychrobacter cryohalolentis K5T and to construct new artificial TNF-binding proteins. We obtained a 10Fn3 gene combinatorial library and screened it using the bacterial display method. After expression of the selected 10Fn3 variants in Escherichia coli cells and analysis of their TNF-binding activity, we identified proteins that display high affinity for TNF and characterized their properties.
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Affiliation(s)
- L N Shingarova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
| | - L E Petrovskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - A V Zlobinov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.,Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234, Russia
| | - S Sh Gapizov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.,Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234, Russia
| | - E A Kryukova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - K R Birikh
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - E F Boldyreva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - S A Yakimov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - D A Dolgikh
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.,Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234, Russia
| | - M P Kirpichnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.,Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234, Russia
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19
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Case BA, Kruziki MA, Johnson SM, Hackel BJ. Engineered Charge Redistribution of Gp2 Proteins through Guided Diversity for Improved PET Imaging of Epidermal Growth Factor Receptor. Bioconjug Chem 2018; 29:1646-1658. [PMID: 29579383 PMCID: PMC6051758 DOI: 10.1021/acs.bioconjchem.8b00144] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The Gp2 domain is a protein scaffold for synthetic ligand engineering. However, the native protein function results in a heterogeneous distribution of charge on the conserved surface, which may hinder further development and utility. We aim to modulate charge, without diminishing function, which is challenging in small proteins where each mutation is a significant fraction of protein structure. We constructed rationally guided combinatorial libraries with charge-neutralizing or charge-flipping mutations and sorted them, via yeast display and flow cytometry, for stability and target binding. Deep sequencing of functional variants revealed effective mutations both in clone-dependent contexts and broadly across binders to epidermal growth factor receptor (EGFR), insulin receptor, and immunoglobulin G. Functional mutants averaged 4.3 charge neutralizing mutations per domain while maintaining net negative charge. We evolved an EGFR-targeted Gp2 mutant that reduced charge density by 33%, maintained net charge, and improved charge distribution homogeneity while elevating thermal stability ( Tm = 87 ± 1 °C), improving binding specificity, and maintaining affinity ( Kd = 8.8 ± 0.6 nM). This molecule was conjugated with 1,4,7-triazacyclononane,1-glutaric acid-4,7-acetic acid for 64Cu chelation and evaluated for physiological distribution in mice with xenografted A431 (EGFRhigh) and MDA-MB-435 (EGFRlow) tumors. Excised tissue gamma counting and positron emission tomography/computed tomography imaging revealed good EGFRhigh tumor signal (4.7 ± 0.5%ID/g) at 2 h post-injection and molecular specificity evidenced by low uptake in EGFRlow tumors (0.6 ± 0.1%ID/g, significantly lower than for non-charge-modified Gp2, p = 0.01). These results provide charge mutations for an improved Gp2 framework, validate an effective approach to charge engineering, and advance performance of physiological EGFR targeting for molecular imaging.
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Affiliation(s)
- Brett A. Case
- University of Minnesota – Twin Cities, Department of Chemical Engineering and Materials Science, 421 Washington Avenue SE, Minneapolis, MN 55455
| | - Max A. Kruziki
- University of Minnesota – Twin Cities, Department of Chemical Engineering and Materials Science, 421 Washington Avenue SE, Minneapolis, MN 55455
| | - Sadie M. Johnson
- University of Minnesota – Twin Cities, Department of Chemical Engineering and Materials Science, 421 Washington Avenue SE, Minneapolis, MN 55455
| | - Benjamin J. Hackel
- University of Minnesota – Twin Cities, Department of Chemical Engineering and Materials Science, 421 Washington Avenue SE, Minneapolis, MN 55455
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20
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Sirois AR, Deny DA, Baierl SR, George KS, Moore SJ. Fn3 proteins engineered to recognize tumor biomarker mesothelin internalize upon binding. PLoS One 2018; 13:e0197029. [PMID: 29738555 PMCID: PMC5940182 DOI: 10.1371/journal.pone.0197029] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 03/20/2018] [Indexed: 11/19/2022] Open
Abstract
Mesothelin is a cell surface protein that is overexpressed in numerous cancers, including breast, ovarian, lung, liver, and pancreatic tumors. Aberrant expression of mesothelin has been shown to promote tumor progression and metastasis through interaction with established tumor biomarker CA125. Therefore, molecules that specifically bind to mesothelin have potential therapeutic and diagnostic applications. However, no mesothelin-targeting molecules are currently approved for routine clinical use. While antibodies that target mesothelin are in development, some clinical applications may require a targeting molecule with an alternative protein fold. For example, non-antibody proteins are more suitable for molecular imaging and may facilitate diverse chemical conjugation strategies to create drug delivery complexes. In this work, we engineered variants of the fibronectin type III domain (Fn3) non-antibody protein scaffold to bind to mesothelin with high affinity, using directed evolution and yeast surface display. Lead engineered Fn3 variants were solubly produced and purified from bacterial culture at high yield. Upon specific binding to mesothelin on human cancer cell lines, the engineered Fn3 proteins internalized and co-localized to early endosomes. To our knowledge, this is the first report of non-antibody proteins engineered to bind mesothelin. The results validate that non-antibody proteins can be engineered to bind to tumor biomarker mesothelin, and encourage the continued development of engineered variants for applications such as targeted diagnostics and therapeutics.
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Affiliation(s)
- Allison R. Sirois
- Molecular and Cellular Biology Program, University of Massachusetts, Amherst, Amherst, Massachusetts, United States of America
- Picker Engineering Program, Smith College, Northampton, Massachusetts, United States of America
| | - Daniela A. Deny
- Department of Biochemistry, Smith College, Northampton, Massachusetts, United States of America
| | - Samantha R. Baierl
- Picker Engineering Program, Smith College, Northampton, Massachusetts, United States of America
| | - Katia S. George
- Department of Biochemistry, Smith College, Northampton, Massachusetts, United States of America
| | - Sarah J. Moore
- Molecular and Cellular Biology Program, University of Massachusetts, Amherst, Amherst, Massachusetts, United States of America
- Picker Engineering Program, Smith College, Northampton, Massachusetts, United States of America
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, United States of America
- * E-mail:
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21
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Chen TF, Li KK, Zhu EF, Opel CF, Kauke MJ, Kim H, Atolia E, Wittrup KD. Artificial Anti-Tumor Opsonizing Proteins with Fibronectin Scaffolds Engineered for Specificity to Each of the Murine FcγR Types. J Mol Biol 2018; 430:1786-1798. [PMID: 29704491 DOI: 10.1016/j.jmb.2018.04.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 04/14/2018] [Accepted: 04/16/2018] [Indexed: 10/17/2022]
Abstract
We have engineered a panel of novel Fn3 scaffold-based proteins that bind with high specificity and affinity to each of the individual mouse Fcγ receptors (mFcγR). These binders were expressed as fusions to anti-tumor antigen single-chain antibodies and mouse serum albumin, creating opsonizing agents that invoke only a single mFcγR response rather than the broader activity of natural Fc isotypes, as well as all previously reported Fc mutants. This panel isolated the capability of each of the four mFcγRs to contribute to macrophage phagocytosis of opsonized tumor cells and in vivo tumor growth control with these monospecific opsonizing fusion proteins. All activating receptors (mFcγRI, mFcγRIII, and mFcγRIV) were capable of driving specific tumor cell phagocytosis to an equivalent extent, while mFcγRII, the inhibitory receptor, did not drive phagocytosis. Monospecific opsonizing fusion proteins that bound mFcγRI alone controlled tumor growth to an extent similar to the most active IgG2a murine isotype. As expected, binding to the inhibitory mFcγRII did not delay tumor growth, but unexpectedly, mFcγRIII also failed to control tumor growth. mFcγRIV exhibited detectable but lesser tumor-growth control leading to less overall survival compared to mFcγRI. Interestingly, in vivo macrophage depletion demonstrates their importance in tumor control with mFcγRIV engagement, but not with mFcγRI. This panel of monospecific mFcγR-binding proteins provides a toolkit for isolating the functional effects of each mFcγR in the context of an intact immune system.
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Affiliation(s)
- Tiffany F Chen
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, United States; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, United States
| | - Kevin K Li
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, United States; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, United States
| | - Eric F Zhu
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, United States; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, United States
| | - Cary F Opel
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, United States; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, United States
| | - Monique J Kauke
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, United States; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, United States
| | - Heeyoon Kim
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, United States
| | - Eta Atolia
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, United States
| | - K Dane Wittrup
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, United States; Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, United States; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, United States.
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22
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Könning D, Kolmar H. Beyond antibody engineering: directed evolution of alternative binding scaffolds and enzymes using yeast surface display. Microb Cell Fact 2018; 17:32. [PMID: 29482656 PMCID: PMC6389260 DOI: 10.1186/s12934-018-0881-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 02/22/2018] [Indexed: 01/08/2023] Open
Abstract
Pioneered exactly 20 years ago, yeast surface display (YSD) continues to take a major role in protein engineering among the high-throughput display methodologies that have been developed to date. The classical yeast display technology relies on tethering an engineered protein to the cell wall by genetic fusion to one subunit of a dimeric yeast-mating agglutination receptor complex. This method enables an efficient genotype-phenotype linkage while exploiting the benefits of a eukaryotic expression machinery. Over the past two decades, a plethora of protein engineering efforts encompassing conventional antibody Fab and scFv fragments have been reported. In this review, we will focus on the versatility of YSD beyond conventional antibody engineering and, instead, place the focus on alternative scaffold proteins and enzymes which have successfully been tailored for purpose with regard to improving binding, activity or specificity.
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Affiliation(s)
- Doreen Könning
- Antibody-Drug Conjugates and Targeted NBE Therapeutics, Merck KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, 64287 Darmstadt, Germany
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, 64287 Darmstadt, Germany
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23
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Fusion with the cold-active esterase facilitates autotransporter-based surface display of the 10th human fibronectin domain in Escherichia coli. Extremophiles 2017; 22:141-150. [PMID: 29256084 DOI: 10.1007/s00792-017-0990-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 12/08/2017] [Indexed: 10/24/2022]
Abstract
Cell surface display is a popular approach for the construction of whole-cell biocatalysts, live vaccines, and screening of combinatorial libraries. To develop a novel surface display system for the popular scaffold protein 10th human fibronectin type III domain (10Fn3) in Escherichia coli cells, we have used an α-helical linker and a C-terminal translocator domain from previously characterized autotransporter from Psychrobacter cryohalolentis K5T. The level of 10Fn3 passenger exposure at the cell surface provided by the hybrid autotransporter Fn877 and its C-terminal variants was low. To improve it, the fusion proteins containing 10Fn3 and the native autotransporter passenger Est877 or the cold-active esterase EstPc in different orientations were constructed and expressed as passenger domains. Using the whole-cell ELISA and activity assays, we have demonstrated that N-terminal position of EstPc in the passenger significantly improves the efficiency of the surface display of 10Fn3 in E. coli cells.
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24
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Huang Y, Chen DH, Liu BY, Shen WH, Ruan Y. Conservation and diversification of polycomb repressive complex 2 (PRC2) proteins in the green lineage. Brief Funct Genomics 2017; 16:106-119. [PMID: 27032420 DOI: 10.1093/bfgp/elw007] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The polycomb group (PcG) proteins are key epigenetic regulators of gene expression in animals and plants. They act in multiprotein complexes, of which the best characterized is the polycomb repressive complex 2 (PRC2), which catalyses the trimethylation of histone H3 at lysine 27 (H3K27me3) at chromatin targets. In Arabidopsis thaliana, PRC2 proteins are involved in the regulation of diverse developmental processes, including cell fate determination, vegetative growth and development, flowering time control and embryogenesis. Here, we systematically analysed the evolutionary conservation and diversification of PRC2 components in lower and higher plants. We searched for and identified PRC2 homologues from the sequenced genomes of several green lineage species, from the unicellular green alga Ostreococcus lucimarinus to more complicated angiosperms. We found that some PRC2 core components, e.g. E(z), ESC/FIE and MSI/p55, are ancient and have multiplied coincidently with multicellular evolution. For one component, some members are newly formed, especially in the Cruciferae. During evolution, higher plants underwent copy number multiplication of various PRC2 components, which occurred independently for each component, without any obvious co-amplification of PRC2 members. Among the amplified members, usually one was well-conserved and the others were more diversified. Gene amplification occurred at different times for different PcG members during green lineage evolution. Certain PRC2 core components or members of them were highly conserved. Our study provides an insight into the evolutionary conservation and diversification of PcG proteins and may guide future functional characterization of these important epigenetic regulators in plants other than Arabidopsis.
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Affiliation(s)
- Yong Huang
- College of Bioscience and Biotechnology, International Associated Laboratory of CNRS-FU-HAU On Plant Epigenome Research, Hunan Agricultural University, Changsha, China.,Key Laboratory of Education, Department of Hunan Province On Plant Genetics and Molecular Biology, Hunan Agricultural University, Changsha, China
| | - Dong-Hong Chen
- College of Bioscience and Biotechnology, International Associated Laboratory of CNRS-FU-HAU On Plant Epigenome Research, Hunan Agricultural University, Changsha, China.,Key Laboratory of Education, Department of Hunan Province On Plant Genetics and Molecular Biology, Hunan Agricultural University, Changsha, China
| | - Bo-Yu Liu
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha, China
| | - Wen-Hui Shen
- College of Bioscience and Biotechnology, International Associated Laboratory of CNRS-FU-HAU On Plant Epigenome Research, Hunan Agricultural University, Changsha, China.,Institut de Biologie Moléculaire Des Plantes Du CNRS, Université de Strasbourg, 12 Rue Du Général Zimmer, Strasbourg Cedex, France
| | - Ying Ruan
- College of Bioscience and Biotechnology, International Associated Laboratory of CNRS-FU-HAU On Plant Epigenome Research, Hunan Agricultural University, Changsha, China.,Key Laboratory of Education, Department of Hunan Province On Plant Genetics and Molecular Biology, Hunan Agricultural University, Changsha, China.,Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha, China
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25
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Newby GA, Kiriakov S, Hallacli E, Kayatekin C, Tsvetkov P, Mancuso CP, Bonner JM, Hesse WR, Chakrabortee S, Manogaran AL, Liebman SW, Lindquist S, Khalil AS. A Genetic Tool to Track Protein Aggregates and Control Prion Inheritance. Cell 2017; 171:966-979.e18. [PMID: 29056345 DOI: 10.1016/j.cell.2017.09.041] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 07/20/2017] [Accepted: 09/25/2017] [Indexed: 01/05/2023]
Abstract
Protein aggregation is a hallmark of many diseases but also underlies a wide range of positive cellular functions. This phenomenon has been difficult to study because of a lack of quantitative and high-throughput cellular tools. Here, we develop a synthetic genetic tool to sense and control protein aggregation. We apply the technology to yeast prions, developing sensors to track their aggregation states and employing prion fusions to encode synthetic memories in yeast cells. Utilizing high-throughput screens, we identify prion-curing mutants and engineer "anti-prion drives" that reverse the non-Mendelian inheritance pattern of prions and eliminate them from yeast populations. We extend our technology to yeast RNA-binding proteins (RBPs) by tracking their propensity to aggregate, searching for co-occurring aggregates, and uncovering a group of coalescing RBPs through screens enabled by our platform. Our work establishes a quantitative, high-throughput, and generalizable technology to study and control diverse protein aggregation processes in cells.
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Affiliation(s)
- Gregory A Newby
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Szilvia Kiriakov
- Program in Molecular Biology, Cell Biology, and Biochemistry, Boston University, Boston, MA 02215, USA; Biological Design Center, Boston University, Boston, MA 02215, USA
| | - Erinc Hallacli
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Ann Romney Center for Neurologic Disease, Department of Neurology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Can Kayatekin
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Peter Tsvetkov
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Christopher P Mancuso
- Biological Design Center, Boston University, Boston, MA 02215, USA; Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - J Maeve Bonner
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - William R Hesse
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Anita L Manogaran
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201, USA
| | - Susan W Liebman
- Department of Pharmacology, University of Nevada, Reno, NV 89557, USA
| | - Susan Lindquist
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Cambridge, MA 02139, USA
| | - Ahmad S Khalil
- Biological Design Center, Boston University, Boston, MA 02215, USA; Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA.
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26
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Stern LA, Csizmar CM, Woldring DR, Wagner CR, Hackel BJ. Titratable Avidity Reduction Enhances Affinity Discrimination in Mammalian Cellular Selections of Yeast-Displayed Ligands. ACS COMBINATORIAL SCIENCE 2017; 19:315-323. [PMID: 28322543 DOI: 10.1021/acscombsci.6b00191] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Yeast surface display selections against mammalian cell monolayers have proven effective in isolating proteins with novel binding activity. Recent advances in this technique allow for the recovery of clones with even micromolar binding affinities. However, no efficient method has been shown for affinity-based selection in this context. This study demonstrates the effectiveness of titratable avidity reduction using dithiothreitol to achieve this goal. A series of epidermal growth factor receptor binding fibronectin domains with a range of affinities are used to quantitatively identify the number of ligands per yeast cell that yield the strongest selectivity between strong, moderate, and weak affinities. Notably, reduction of ligand display to 3,000-6,000 ligands per yeast cell of a 2 nM binder yields 16-fold better selectivity than that to a 17 nM binder. These lessons are applied to affinity maturation of an EpCAM-binding fibronectin population, yielding an enriched pool of ligands with significantly stronger affinity than that of an analogous pool sorted by standard cellular selection methods. Collectively, this study offers a facile approach for affinity selection of yeast-displayed ligands against full-length cellular targets and demonstrates the effectiveness of this method by generating EpCAM-binding ligands that are promising for further applications.
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Affiliation(s)
- Lawrence A. Stern
- Department
of Chemical Engineering and Materials Science and ‡Department of Medicinal Chemistry, University of Minnesota−Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Clifford M. Csizmar
- Department
of Chemical Engineering and Materials Science and ‡Department of Medicinal Chemistry, University of Minnesota−Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Daniel R. Woldring
- Department
of Chemical Engineering and Materials Science and ‡Department of Medicinal Chemistry, University of Minnesota−Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Carston R. Wagner
- Department
of Chemical Engineering and Materials Science and ‡Department of Medicinal Chemistry, University of Minnesota−Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Benjamin J. Hackel
- Department
of Chemical Engineering and Materials Science and ‡Department of Medicinal Chemistry, University of Minnesota−Twin Cities, Minneapolis, Minnesota 55455, United States
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27
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de Picciotto S, Dickson PM, Traxlmayr MW, Marques BS, Socher E, Zhao S, Cheung S, Kiefer JD, Wand AJ, Griffith LG, Imperiali B, Wittrup KD. Design Principles for SuCESsFul Biosensors: Specific Fluorophore/Analyte Binding and Minimization of Fluorophore/Scaffold Interactions. J Mol Biol 2016; 428:4228-4241. [PMID: 27448945 PMCID: PMC5048519 DOI: 10.1016/j.jmb.2016.07.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 06/30/2016] [Accepted: 07/04/2016] [Indexed: 11/18/2022]
Abstract
Quantifying protein location and concentration is critical for understanding function in situ. Scaffold conjugated to environment-sensitive fluorophore (SuCESsFul) biosensors, in which a reporting fluorophore is conjugated to a binding scaffold, can, in principle, detect analytes of interest with high temporal and spatial resolution. However, their adoption has been limited due to the extensive empirical screening required for their development. We sought to establish design principles for this class of biosensor by characterizing over 400 biosensors based on various protein analytes, binding proteins, and fluorophores. We found that the brightest readouts are attained when a specific binding pocket for the fluorophore is present on the analyte. Also, interaction of the fluorophore with the binding protein it is conjugated to can raise background fluorescence, considerably limiting sensor dynamic range. Exploiting these two concepts, we designed biosensors that attain a 100-fold increase in fluorescence upon binding to analyte, an order of magnitude improvement over the previously best-reported SuCESsFul biosensor. These design principles should facilitate the development of improved SuCESsFul biosensors.
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Affiliation(s)
- Seymour de Picciotto
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Paige M Dickson
- Department of Chemistry, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA
| | - Michael W Traxlmayr
- Koch Institute for Integrative Cancer Research, 500 Main Street, Cambridge, MA 02139, USA
| | - Bryan S Marques
- Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Elke Socher
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 01239, USA
| | - Sixing Zhao
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Stephanie Cheung
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 01239, USA
| | - Jonathan D Kiefer
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology, Zurich, 8093, Switzerland
| | - A Joshua Wand
- Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Linda G Griffith
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Barbara Imperiali
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 01239, USA; Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - K Dane Wittrup
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, 500 Main Street, Cambridge, MA 02139, USA; Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
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28
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Traxlmayr MW, Kiefer JD, Srinivas RR, Lobner E, Tisdale AW, Mehta NK, Yang NJ, Tidor B, Wittrup KD. Strong Enrichment of Aromatic Residues in Binding Sites from a Charge-neutralized Hyperthermostable Sso7d Scaffold Library. J Biol Chem 2016; 291:22496-22508. [PMID: 27582495 PMCID: PMC5077188 DOI: 10.1074/jbc.m116.741314] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 08/23/2016] [Indexed: 11/06/2022] Open
Abstract
The Sso7d protein from the hyperthermophilic archaeon Sulfolobus solfataricus is an attractive binding scaffold because of its small size (7 kDa), high thermal stability (Tm of 98 °C), and absence of cysteines and glycosylation sites. However, as a DNA-binding protein, Sso7d is highly positively charged, introducing a strong specificity constraint for binding epitopes and leading to nonspecific interaction with mammalian cell membranes. In the present study, we report charge-neutralized variants of Sso7d that maintain high thermal stability. Yeast-displayed libraries that were based on this reduced charge Sso7d (rcSso7d) scaffold yielded binders with low nanomolar affinities against mouse serum albumin and several epitopes on human epidermal growth factor receptor. Importantly, starting from a charge-neutralized scaffold facilitated evolutionary adaptation of binders to differentially charged epitopes on mouse serum albumin and human epidermal growth factor receptor, respectively. Interestingly, the distribution of amino acids in the small and rigid binding surface of enriched rcSso7d-based binders is very different from that generally found in more flexible antibody complementarity-determining region loops but resembles the composition of antibody-binding energetic hot spots. Particularly striking was a strong enrichment of the aromatic residues Trp, Tyr, and Phe in rcSso7d-based binders. This suggests that the rigidity and small size of this scaffold determines the unusual amino acid composition of its binding sites, mimicking the energetic core of antibody paratopes. Despite the high frequency of aromatic residues, these rcSso7d-based binders are highly expressed, thermostable, and monomeric, suggesting that the hyperstability of the starting scaffold and the rigidness of the binding surface confer a high tolerance to mutation.
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Affiliation(s)
- Michael W Traxlmayr
- From the Koch Institute for Integrative Cancer Research and .,Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 and
| | | | | | - Elisabeth Lobner
- Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Alison W Tisdale
- From the Koch Institute for Integrative Cancer Research and.,Departments of Biological Engineering and
| | - Naveen K Mehta
- From the Koch Institute for Integrative Cancer Research and.,Departments of Biological Engineering and
| | - Nicole J Yang
- From the Koch Institute for Integrative Cancer Research and.,Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 and
| | | | - K Dane Wittrup
- From the Koch Institute for Integrative Cancer Research and .,Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 and.,Departments of Biological Engineering and
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29
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Hunter SA, Cochran JR. Cell-Binding Assays for Determining the Affinity of Protein-Protein Interactions: Technologies and Considerations. Methods Enzymol 2016; 580:21-44. [PMID: 27586327 PMCID: PMC6067677 DOI: 10.1016/bs.mie.2016.05.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Determining the equilibrium-binding affinity (Kd) of two interacting proteins is essential not only for the biochemical study of protein signaling and function but also for the engineering of improved protein and enzyme variants. One common technique for measuring protein-binding affinities uses flow cytometry to analyze ligand binding to proteins presented on the surface of a cell. However, cell-binding assays require specific considerations to accurately quantify the binding affinity of a protein-protein interaction. Here we will cover the basic assumptions in designing a cell-based binding assay, including the relevant equations and theory behind determining binding affinities. Further, two major considerations in measuring binding affinities-time to equilibrium and ligand depletion-will be discussed. As these conditions have the potential to greatly alter the Kd, methods through which to avoid or minimize them will be provided. We then outline detailed protocols for performing direct- and competitive-binding assays against proteins displayed on the surface of yeast or mammalian cells that can be used to derive accurate Kd values. Finally, a comparison of cell-based binding assays to other types of binding assays will be presented.
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Affiliation(s)
- S A Hunter
- Stanford University, Stanford, CA, United States
| | - J R Cochran
- Stanford University, Stanford, CA, United States.
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30
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Wronska MA, O'Connor IB, Tilbury MA, Srivastava A, Wall JG. Adding Functions to Biomaterial Surfaces through Protein Incorporation. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2016; 28:5485-5508. [PMID: 27164952 DOI: 10.1002/adma.201504310] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 03/16/2016] [Indexed: 06/05/2023]
Abstract
The concept of biomaterials has evolved from one of inert mechanical supports with a long-term, biologically inactive role in the body into complex matrices that exhibit selective cell binding, promote proliferation and matrix production, and may ultimately become replaced by newly generated tissues in vivo. Functionalization of material surfaces with biomolecules is critical to their ability to evade immunorecognition, interact productively with surrounding tissues and extracellular matrix, and avoid bacterial colonization. Antibody molecules and their derived fragments are commonly immobilized on materials to mediate coating with specific cell types in fields such as stent endothelialization and drug delivery. The incorporation of growth factors into biomaterials has found application in promoting and accelerating bone formation in osteogenerative and related applications. Peptides and extracellular matrix proteins can impart biomolecule- and cell-specificities to materials while antimicrobial peptides have found roles in preventing biofilm formation on devices and implants. In this progress report, we detail developments in the use of diverse proteins and peptides to modify the surfaces of hard biomaterials in vivo and in vitro. Chemical approaches to immobilizing active biomolecules are presented, as well as platform technologies for isolation or generation of natural or synthetic molecules suitable for biomaterial functionalization.
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Affiliation(s)
- Małgorzata A Wronska
- Microbiology and Center for Research in Medical Devices (CÚRAM), National University of Ireland, Galway, Ireland
| | - Iain B O'Connor
- Microbiology and Center for Research in Medical Devices (CÚRAM), National University of Ireland, Galway, Ireland
| | - Maura A Tilbury
- Microbiology and Center for Research in Medical Devices (CÚRAM), National University of Ireland, Galway, Ireland
| | - Akshay Srivastava
- Microbiology and Center for Research in Medical Devices (CÚRAM), National University of Ireland, Galway, Ireland
| | - J Gerard Wall
- Microbiology and Center for Research in Medical Devices (CÚRAM), National University of Ireland, Galway, Ireland
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31
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Stern LA, Schrack IA, Johnson SM, Deshpande A, Bennett NR, Harasymiw LA, Gardner MK, Hackel BJ. Geometry and expression enhance enrichment of functional yeast-displayed ligands via cell panning. Biotechnol Bioeng 2016; 113:2328-41. [PMID: 27144954 DOI: 10.1002/bit.26001] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Revised: 03/23/2016] [Accepted: 04/25/2016] [Indexed: 01/10/2023]
Abstract
Yeast surface display has proven to be an effective tool in the discovery and evolution of ligands with new or improved binding activity. Selections for binding activity are generally carried out using immobilized or fluorescently labeled soluble domains of target molecules such as recombinant ectodomain fragments. While this method typically provides ligands with high affinity and specificity for the soluble molecular target, translation to binding true membrane-bound cellular target is commonly problematic. Direct selections against mammalian cell surfaces can be carried out either exclusively or in combination with soluble target-based selections to further direct towards ligands for genuine cellular target. Using a series of fibronectin domain, affibody, and Gp2 ligands and human cell lines expressing a range of their targets, epidermal growth factor receptor and carcinoembryonic antigen, this study quantitatively identifies the elements that dictate ligand enrichment and yield. Most notably, extended flexible linkers between ligand and yeast enhance enrichment ratios from 1.4 ± 0.8 to 62 ± 57 for a low-affinity (>600 nM) binder on cells with high target expression and from 14 ± 13 to 74 ± 25 for a high-affinity binder (2 nM) on cells with medium valency. Inversion of the yeast display fusion from C-terminal display to N-terminal display still enables enrichment albeit with 40-97% reduced efficacy. Collectively, this study further enlightens the conditions-while highlighting new approaches-that yield successful enrichment of yeast-displayed binding ligands via panning on mammalian cells. Biotechnol. Bioeng. 2016;113: 2328-2341. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Lawrence A Stern
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, Minneapolis, Minnesota, 55455
| | - Ian A Schrack
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, Minneapolis, Minnesota, 55455
| | - Sadie M Johnson
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, Minneapolis, Minnesota, 55455
| | - Aakash Deshpande
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, Minneapolis, Minnesota, 55455
| | - Nathaniel R Bennett
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, Minneapolis, Minnesota, 55455
| | - Lauren A Harasymiw
- Department of Genetics, Cell Biology, and Development, University of Minnesota-Twin Cities, Minneapolis, Minnesota
| | - Melissa K Gardner
- Department of Genetics, Cell Biology, and Development, University of Minnesota-Twin Cities, Minneapolis, Minnesota
| | - Benjamin J Hackel
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, Minneapolis, Minnesota, 55455.
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32
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Xu B, Zhou X, Stains CI. An improved miniprotein host for fluorogenic supramolecular assembly on the surface of living cells. RSC Adv 2016. [DOI: 10.1039/c6ra01215a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
A new host–guest pair produces a significant increase in the brightness of supramolecular complexes on the surface of living cells.
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Affiliation(s)
- Bi Xu
- Department of Chemistry
- University of Nebraska – Lincoln
- Lincoln
- USA
| | - Xinqi Zhou
- Department of Chemistry
- University of Nebraska – Lincoln
- Lincoln
- USA
| | - Cliff I. Stains
- Department of Chemistry
- University of Nebraska – Lincoln
- Lincoln
- USA
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33
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Xu B, Zhou X, Stains CI. Supramolecular Assembly of an Evolved Miniprotein Host and Fluorogenic Guest Pair. J Am Chem Soc 2015; 137:14252-5. [DOI: 10.1021/jacs.5b09494] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Bi Xu
- Department of Chemistry, University of Nebraska—Lincoln, Lincoln, Nebraska 68588, United States
| | - Xinqi Zhou
- Department of Chemistry, University of Nebraska—Lincoln, Lincoln, Nebraska 68588, United States
| | - Cliff I. Stains
- Department of Chemistry, University of Nebraska—Lincoln, Lincoln, Nebraska 68588, United States
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34
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Yang NJ, Liu DV, Sklaviadis D, Gui DY, Vander Heiden MG, Wittrup KD. Antibody-mediated neutralization of perfringolysin o for intracellular protein delivery. Mol Pharm 2015; 12:1992-2000. [PMID: 25881713 PMCID: PMC4876977 DOI: 10.1021/mp500797n] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Perfringolysin O (PFO) is a member of the cholesterol-dependent cytolysin (CDC) family of bacterial pore-forming proteins, which are highly efficient in delivering exogenous proteins to the cytoplasm. However, the indiscriminate and potent cytotoxicity of PFO limits its practical use as an intracellular delivery system. In this study, we describe the design and engineering of a bispecific, neutralizing antibody against PFO, which targets reversibly attenuated PFO to endocytic compartments via receptor-mediated internalization. This PFO-based system efficiently mediated the endosomal release of a co-targeted gelonin construct with high specificity and minimal toxicity in vitro. Consequently, the therapeutic window of PFO was improved by more than 5 orders of magnitude. Our results demonstrating that the activity of pore-forming proteins can be controlled by antibody-mediated neutralization present a novel strategy for utilizing these potent membrane-lytic agents as a safe and effective intracellular delivery vehicle.
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Affiliation(s)
- Nicole J. Yang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - David V. Liu
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Demetra Sklaviadis
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Dan Y. Gui
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Matthew G. Vander Heiden
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - K. Dane Wittrup
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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35
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Heinzelman P, Krais J, Ruben E, Pantazes R. Engineering pH responsive fibronectin domains for biomedical applications. J Biol Eng 2015; 9:6. [PMID: 26106447 PMCID: PMC4477602 DOI: 10.1186/s13036-015-0004-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 05/01/2015] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Engineered antibodies with pH responsive cell surface target antigen-binding affinities that decrease at the acidic pH (5.5-5.8) within the endosomes have been found to have reduced susceptibility to degradation within the lysosomes and increased serum half-life. Such pH responsive recombinant antibodies have been developed for the treatment of cancer and cardiovascular disease. Engineered tenth type III human fibronectin (Fn3) domains are emerging as a class of target antigen-binding biopharmaceuticals that could complement or be superior to recombinant antibodies in a number of biomedical contexts. As such, there is strong motivation for demonstrating the feasibility of engineering Fn3s with pH responsive antigen binding behavior that could lead to improved Fn3 pharmacokinetics. RESULTS A yeast surface-displayed Fn3 histidine (His) mutant library screening approach yielded epidermal growth factor receptor (EGFR)-binding Fn3 domains with EGFR binding affinities that markedly decrease at endosomal pH; the first reported case of engineering Fn3s with pH responsive antigen binding. Yeast surface-displayed His mutant Fn3s, which contain either one or two His mutations, have equilibrium binding dissociation constants (KDs) that increase up to four-fold relative to wild type when pH is decreased from 7.4 to 5.5. Assays in which Fn3-displaying yeast were incubated with soluble EGFR after ligand-free incubation in respective neutral and acidic buffers showed that His mutant Fn3 pH responsiveness is due to reversible changes in Fn3 conformation and/or EGFR binding interface properties rather than irreversible unfolding. CONCLUSIONS We have established a generalizable method for efficiently constructing and screening Fn3 His mutant libraries that could enable both our laboratory and others to develop pH responsive Fn3s for use in a wide range of biomedical applications.
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Affiliation(s)
- Pete Heinzelman
- Department of Chemical, Biological & Materials Engineering, University of Oklahoma, Sarkeys Energy Center, 100 East Boyd Street, Room T-301, 73019 Norman, OK USA
| | - John Krais
- Department of Chemical, Biological & Materials Engineering, University of Oklahoma, Sarkeys Energy Center, 100 East Boyd Street, Room T-301, 73019 Norman, OK USA
| | - Eliza Ruben
- Department of Chemistry & Biochemistry, University of Oklahoma, 73019 Norman, OK USA
| | - Robert Pantazes
- Department of Chemical Engineering, University of California-Santa Barbara, 93106 Santa Barbara, CA USA
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36
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AlDeghaither D, Smaglo BG, Weiner LM. Beyond peptides and mAbs--current status and future perspectives for biotherapeutics with novel constructs. J Clin Pharmacol 2015; 55 Suppl 3:S4-20. [PMID: 25707963 PMCID: PMC4340091 DOI: 10.1002/jcph.407] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 09/29/2014] [Indexed: 12/26/2022]
Abstract
Biotherapeutics are attractive anti-cancer agents due to their high specificity and limited toxicity compared to conventional small molecules. Antibodies are widely used in cancer therapy, either directly or conjugated to a cytotoxic payload. Peptide therapies, though not as prevalent, have been utilized in hormonal therapy and imaging. The limitations associated with unmodified forms of both types of biotherapeutics have led to the design and development of novel structures, which incorporate key features and structures that have improved the molecules' abilities to bind to tumor targets, avoid degradation, and exhibit favorable pharmacokinetics. In this review, we highlight the current status of monoclonal antibodies and peptides, and provide a perspective on the future of biotherapeutics using novel constructs.
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Affiliation(s)
- Dalal AlDeghaither
- Georgetown Lombardi Comprehensive Cancer Center, Department of Oncology, Georgetown University Medical Center, 3970 Reservoir Road NW, Washington DC 20057
| | - Brandon G Smaglo
- Medstar Georgetown University Hospital, Department of Medicine, Division of Hematology/Oncology, 3800 Reservoir Road NW, Washington DC 20007
| | - Louis M. Weiner
- Georgetown Lombardi Comprehensive Cancer Center, Department of Oncology, Georgetown University Medical Center, 3970 Reservoir Road NW, Washington DC 20057
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Deyev SM, Lebedenko EN, Petrovskaya LE, Dolgikh DA, Gabibov AG, Kirpichnikov MP. Man-made antibodies and immunoconjugates with desired properties: function optimization using structural engineering. RUSSIAN CHEMICAL REVIEWS 2015. [DOI: 10.1070/rcr4459] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Zhang C, Tang B, Wang Q, Lai L. Discovery of binding proteins for a protein target using protein-protein docking-based virtual screening. Proteins 2014; 82:2472-82. [PMID: 24854898 DOI: 10.1002/prot.24611] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 05/06/2014] [Accepted: 05/09/2014] [Indexed: 12/18/2022]
Abstract
Target structure-based virtual screening, which employs protein-small molecule docking to identify potential ligands, has been widely used in small-molecule drug discovery. In the present study, we used a protein-protein docking program to identify proteins that bind to a specific target protein. In the testing phase, an all-to-all protein-protein docking run on a large dataset was performed. The three-dimensional rigid docking program SDOCK was used to examine protein-protein docking on all protein pairs in the dataset. Both the binding affinity and features of the binding energy landscape were considered in the scoring function in order to distinguish positive binding pairs from negative binding pairs. Thus, the lowest docking score, the average Z-score, and convergency of the low-score solutions were incorporated in the analysis. The hybrid scoring function was optimized in the all-to-all docking test. The docking method and the hybrid scoring function were then used to screen for proteins that bind to tumor necrosis factor-α (TNFα), which is a well-known therapeutic target for rheumatoid arthritis and other autoimmune diseases. A protein library containing 677 proteins was used for the screen. Proteins with scores among the top 20% were further examined. Sixteen proteins from the top-ranking 67 proteins were selected for experimental study. Two of these proteins showed significant binding to TNFα in an in vitro binding study. The results of the present study demonstrate the power and potential application of protein-protein docking for the discovery of novel binding proteins for specific protein targets.
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Affiliation(s)
- Changsheng Zhang
- BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Peking-Tsinghua Center for Life Sciences at College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
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Berkut AA, Usmanova DR, Peigneur S, Oparin PB, Mineev KS, Odintsova TI, Tytgat J, Arseniev AS, Grishin EV, Vassilevski AA. Structural similarity between defense peptide from wheat and scorpion neurotoxin permits rational functional design. J Biol Chem 2014; 289:14331-40. [PMID: 24671422 DOI: 10.1074/jbc.m113.530477] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
In this study, we present the spatial structure of the wheat antimicrobial peptide (AMP) Tk-AMP-X2 studied using NMR spectroscopy. This peptide was found to adopt a disulfide-stabilized α-helical hairpin fold and therefore belongs to the α-hairpinin family of plant defense peptides. Based on Tk-AMP-X2 structural similarity to cone snail and scorpion potassium channel blockers, a mutant molecule, Tk-hefu, was engineered by incorporating the functionally important residues from κ-hefutoxin 1 onto the Tk-AMP-X2 scaffold. The designed peptide contained the so-called essential dyad of amino acid residues significant for channel-blocking activity. Electrophysiological studies showed that although the parent peptide Tk-AMP-X2 did not present any activity against potassium channels, Tk-hefu blocked Kv1.3 channels with similar potency (IC50 ∼ 35 μm) to κ-hefutoxin 1 (IC50 ∼ 40 μm). We conclude that α-hairpinins are attractive in their simplicity as structural templates, which may be used for functional engineering and drug design.
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Affiliation(s)
- Antonina A Berkut
- From the M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia, Moscow Institute of Physics and Technology (State University), Moscow 117303, Russia
| | - Dinara R Usmanova
- From the M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia, Moscow Institute of Physics and Technology (State University), Moscow 117303, Russia
| | - Steve Peigneur
- Laboratory of Toxicology and Pharmacology, University of Leuven, Leuven 3000, Belgium, and
| | - Peter B Oparin
- From the M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Konstantin S Mineev
- From the M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Tatyana I Odintsova
- N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia
| | - Jan Tytgat
- Laboratory of Toxicology and Pharmacology, University of Leuven, Leuven 3000, Belgium, and
| | - Alexander S Arseniev
- From the M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Eugene V Grishin
- From the M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Alexander A Vassilevski
- From the M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia,
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40
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Stern LA, Case BA, Hackel BJ. Alternative Non-Antibody Protein Scaffolds for Molecular Imaging of Cancer. Curr Opin Chem Eng 2013; 2. [PMID: 24358455 DOI: 10.1016/j.coche.2013.08.009] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The development of improved methods for early detection and characterization of cancer presents a major clinical challenge. One approach that has shown excellent potential in preclinical and clinical evaluation is molecular imaging with small-scaffold, non-antibody based, engineered proteins. These novel diagnostic agents produce high contrast images due to their fast clearance from the bloodstream and healthy tissues, can be evolved to bind a multitude of cancer biomarkers, and are easily functionalized by site-specific bioconjugation methods. Several small protein scaffolds have been verified for in vivo molecular imaging including affibodies and their two-helix variants, knottins, fibronectins, DARPins, and several natural ligands. Further, the biodistribution of these engineered ligands can be optimized through rational mutation of the conserved regions, careful selection and placement of chelator, and modification of molecular size.
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Affiliation(s)
- Lawrence A Stern
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, Minneapolis, MN 55455
| | - Brett A Case
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, Minneapolis, MN 55455
| | - Benjamin J Hackel
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, Minneapolis, MN 55455
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