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Krohl PJ, Fine J, Yang H, VanDyke D, Ang Z, Kim KB, Thomas-Tikhonenko A, Spangler JB. Discovery of antibodies targeting multipass transmembrane proteins using a suspension cell-based evolutionary approach. Cell Rep Methods 2023; 3:100429. [PMID: 37056366 PMCID: PMC10088246 DOI: 10.1016/j.crmeth.2023.100429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 01/06/2023] [Accepted: 02/21/2023] [Indexed: 04/15/2023]
Abstract
Due to their critical functions in cell sensing and signal processing, membrane proteins are highly preferred as pharmacological targets, and antibody drugs constitute the fastest growing category of therapeutic agents on the pharmaceutical market. However, major limitations exist in developing antibodies that recognize complex, multipass transmembrane proteins, such as G-protein-coupled receptors (GPCRs). These challenges, largely due to difficulties with recombinant expression of multipass transmembrane proteins, can be overcome using whole-cell screening techniques, which enable presentation of the functional antigen in its native conformation. Here, we developed suspension cell-based whole-cell panning methodologies to screen for specific binders against GPCRs within a naive yeast-displayed antibody library. We implemented our strategy to discover high-affinity antibodies against four distinct GPCR target proteins, demonstrating the potential for our cell-based screening workflow to advance the discovery of antibody therapeutics targeting membrane proteins.
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Affiliation(s)
- Patrick J. Krohl
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21208, USA
| | - Justyn Fine
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD 21208, USA
| | - Huilin Yang
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21208, USA
| | - Derek VanDyke
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21208, USA
| | - Zhiwei Ang
- Division of Cancer Pathobiology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Kook Bum Kim
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21208, USA
| | - Andrei Thomas-Tikhonenko
- Division of Cancer Pathobiology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology & Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jamie B. Spangler
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21208, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD 21208, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21208, USA
- Translational Tissue Engineering Center, Johns Hopkins University, Baltimore, MD 21231, USA
- Department of Oncology, Johns Hopkins University, Baltimore, MD 21231, USA
- Bloomberg∼Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University, Baltimore, MD 21287, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University Baltimore, MD 21231, USA
- Department of Ophthalmology, Johns Hopkins University, Baltimore, MD 21287, USA
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Panton RA, Stern LA. Ligand Selection by Combination of Recombinant and Cell Panning Selection Techniques. Methods Mol Biol 2022; 2491:217-233. [PMID: 35482193 DOI: 10.1007/978-1-0716-2285-8_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
High-throughput protein selection methods are a cornerstone for protein engineering and pharmaceutical development. Traditional high-throughput selection strategies rely largely on recombinant antigen to generate target specificity. Though effective, this selection strategy can be limited by soluble target quality, particularly in the case of recombinant extracellular domains of transmembrane proteins. Recent advances in cell-based selection techniques provide new opportunities for improving the outcomes of ligand selection campaigns but can introduce technical challenges in maintaining antigen specificity due to the heterogeneity of biomacromolecule expression on the mammalian cell surface. Here, we describe a combination technique using recombinant antigen to "train" library target specificity followed by cell panning selections to ensure that isolated ligands bind cell-expressed target, as well as a facile microscopy technique for assessing target specificity on a clonal basis without the need to produce soluble ligand.
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Affiliation(s)
- Rojhae A Panton
- Department of Chemical, Biological, and Materials Engineering, University of South Florida, Tampa, FL, USA
| | - Lawrence A Stern
- Department of Chemical, Biological, and Materials Engineering, University of South Florida, Tampa, FL, USA.
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Bacon K, Blain A, Bowen J, Burroughs M, McArthur N, Menegatti S, Rao BM. Quantitative Yeast-Yeast Two Hybrid for the Discovery and Binding Affinity Estimation of Protein-Protein Interactions. ACS Synth Biol 2021; 10:505-514. [PMID: 33587591 DOI: 10.1021/acssynbio.0c00472] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Quantifying the binding affinity of protein-protein interactions is important for elucidating connections within biochemical signaling pathways, as well as characterization of binding proteins isolated from combinatorial libraries. We describe a quantitative yeast-yeast two-hybrid (qYY2H) system that not only enables the discovery of specific protein-protein interactions but also efficient, quantitative estimation of their binding affinities (KD). In qYY2H, the bait and prey proteins are expressed as yeast cell surface fusions using yeast surface display. We developed a semiempirical framework for estimating the KD of monovalent bait-prey interactions, using measurements of bait-prey yeast-yeast binding, which is mediated by multivalent interactions between yeast-displayed bait and prey. Using qYY2H, we identified interaction partners of SMAD3 and the tandem WW domains of YAP from a cDNA library and characterized their binding affinities. Finally, we showed that qYY2H could also quantitatively evaluate binding interactions mediated by post-translational modifications on the bait protein.
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Affiliation(s)
- Kaitlyn Bacon
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Abigail Blain
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - John Bowen
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Matthew Burroughs
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Nikki McArthur
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Stefano Menegatti
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
- Golden LEAF Biomanufacturing Training and Education Center, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Balaji M. Rao
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
- Golden LEAF Biomanufacturing Training and Education Center, North Carolina State University, Raleigh, North Carolina 27695, United States
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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Krohl PJ, Kim KB, Lew L, VanDyke D, Ludwig SD, Spangler JB. A suspension cell‐based interaction platform for interrogation of membrane proteins. AIChE J 2020. [DOI: 10.1002/aic.16995] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Patrick J. Krohl
- Department of Chemical & Biomolecular Engineering Johns Hopkins University Baltimore Maryland USA
| | - Kook Bum Kim
- Department of Chemical & Biomolecular Engineering Johns Hopkins University Baltimore Maryland USA
| | - Lance Lew
- Department of Biophysics Johns Hopkins University Baltimore Maryland USA
| | - Derek VanDyke
- Department of Chemical & Biomolecular Engineering Johns Hopkins University Baltimore Maryland USA
| | - Seth D. Ludwig
- Department of Chemical & Biomolecular Engineering Johns Hopkins University Baltimore Maryland USA
| | - Jamie B. Spangler
- Department of Chemical & Biomolecular Engineering Johns Hopkins University Baltimore Maryland USA
- Department of Biomedical Engineering Johns Hopkins University School of Medicine Baltimore Maryland USA
- Translational Tissue Engineering Center Johns Hopkins University School of Medicine Baltimore Maryland USA
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