1
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Wang Y, Zhang K, Zhao Y, Li Y, Su W, Li S. Construction and Applications of Mammalian Cell-Based DNA-Encoded Peptide/Protein Libraries. ACS Synth Biol 2023; 12:1874-1888. [PMID: 37315219 DOI: 10.1021/acssynbio.3c00043] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
DNA-encoded peptide/protein libraries are the starting point for protein evolutionary modification and functional peptide/antibody selection. Different display technologies, protein directed evolution, and deep mutational scanning (DMS) experiments employ DNA-encoded libraries to provide sequence variations for downstream affinity- or function-based selections. Mammalian cells promise the inherent post-translational modification and near-to-natural conformation of exogenously expressed mammalian proteins and thus are the best platform for studying transmembrane proteins or human disease-related proteins. However, due to the current technical bottlenecks of constructing mammalian cell-based large size DNA-encoded libraries, the advantages of mammalian cells as screening platforms have not been fully exploited. In this review, we summarize the current efforts in constructing DNA-encoded libraries in mammalian cells and the existing applications of these libraries in different fields.
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Affiliation(s)
- Yi Wang
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin; Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Kaili Zhang
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin; Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Yanjie Zhao
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin; Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Yifan Li
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin; Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Weijun Su
- School of Medicine, Nankai University, Tianjin 300071, China
| | - Shuai Li
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin; Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
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2
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See K, Kadonosono T, Miyamoto K, Tsubaki T, Ota Y, Katsumi M, Ryo S, Aida K, Minegishi M, Isozaki T, Kuchimaru T, Kizaka-Kondoh S. Antibody-guided design and identification of CD25-binding small antibody mimetics using mammalian cell surface display. Sci Rep 2021; 11:22098. [PMID: 34764369 PMCID: PMC8585965 DOI: 10.1038/s41598-021-01603-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 11/01/2021] [Indexed: 11/09/2022] Open
Abstract
Small antibody mimetics that contain high-affinity target-binding peptides can be lower cost alternatives to monoclonal antibodies (mAbs). We have recently developed a method to create small antibody mimetics called FLuctuation-regulated Affinity Proteins (FLAPs), which consist of a small protein scaffold with a structurally immobilized target-binding peptide. In this study, to further develop this method, we established a novel screening system for FLAPs called monoclonal antibody-guided peptide identification and engineering (MAGPIE), in which a mAb guides selection in two manners. First, antibody-guided design allows construction of a peptide library that is relatively small in size, but sufficient to identify high-affinity binders in a single selection round. Second, in antibody-guided screening, the fluorescently labeled mAb is used to select mammalian cells that display FLAP candidates with high affinity for the target using fluorescence-activated cell sorting. We demonstrate the reliability and efficacy of MAGPIE using daclizumab, a mAb against human interleukin-2 receptor alpha chain (CD25). Three FLAPs identified by MAGPIE bound CD25 with dissociation constants of approximately 30 nM as measured by biolayer interferometry without undergoing affinity maturation. MAGPIE can be broadly adapted to any mAb to develop small antibody mimetics.
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Affiliation(s)
- Kyra See
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Tetsuya Kadonosono
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan.
| | - Kotaro Miyamoto
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Takuya Tsubaki
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Yumi Ota
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Marina Katsumi
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Sumoe Ryo
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Kazuki Aida
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Misa Minegishi
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Tatsuhiro Isozaki
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Takahiro Kuchimaru
- Center for Molecular Medicine, Jichi Medical University, Tochigi, 329-0498, Japan
| | - Shinae Kizaka-Kondoh
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
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3
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Rome KS, Stein SJ, Kurachi M, Petrovic J, Schwartz GW, Mack EA, Uljon S, Wu WW, DeHart AG, McClory SE, Xu L, Gimotty PA, Blacklow SC, Faryabi RB, Wherry EJ, Jordan MS, Pear WS. Trib1 regulates T cell differentiation during chronic infection by restraining the effector program. J Exp Med 2020; 217:133863. [PMID: 32150623 PMCID: PMC7201917 DOI: 10.1084/jem.20190888] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 11/02/2019] [Accepted: 02/04/2020] [Indexed: 12/24/2022] Open
Abstract
In chronic infections, the immune response fails to control virus, leading to persistent antigen stimulation and the progressive development of T cell exhaustion. T cell effector differentiation is poorly understood in the context of exhaustion, but targeting effector programs may provide new strategies for reinvigorating T cell function. We identified Tribbles pseudokinase 1 (Trib1) as a central regulator of antiviral T cell immunity, where loss of Trib1 led to a sustained enrichment of effector-like KLRG1+ T cells, enhanced function, and improved viral control. Single-cell profiling revealed that Trib1 restrains a population of KLRG1+ effector CD8 T cells that is transcriptionally distinct from exhausted cells. Mechanistically, we identified an interaction between Trib1 and the T cell receptor (TCR) signaling activator, MALT1, which disrupted MALT1 signaling complexes. These data identify Trib1 as a negative regulator of TCR signaling and downstream function, and reveal a link between Trib1 and effector versus exhausted T cell differentiation that can be targeted to improve antiviral immunity.
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Affiliation(s)
- Kelly S Rome
- Department of Pathology and Laboratory Medicine, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Sarah J Stein
- Department of Pathology and Laboratory Medicine, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Makoto Kurachi
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Jelena Petrovic
- Department of Pathology and Laboratory Medicine, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Gregory W Schwartz
- Department of Pathology and Laboratory Medicine, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Ethan A Mack
- Department of Pathology and Laboratory Medicine, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Sacha Uljon
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA.,Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA
| | - Winona W Wu
- Department of Pathology and Laboratory Medicine, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Anne G DeHart
- Department of Pathology and Laboratory Medicine, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Susan E McClory
- Divisions of Hematology and Oncology, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Lanwei Xu
- Department of Pathology and Laboratory Medicine, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Phyllis A Gimotty
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Stephen C Blacklow
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA.,Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA
| | - Robert B Faryabi
- Department of Pathology and Laboratory Medicine, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - E John Wherry
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Martha S Jordan
- Department of Pathology and Laboratory Medicine, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Warren S Pear
- Department of Pathology and Laboratory Medicine, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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4
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Bozovičar K, Bratkovič T. Evolving a Peptide: Library Platforms and Diversification Strategies. Int J Mol Sci 2019; 21:E215. [PMID: 31892275 PMCID: PMC6981544 DOI: 10.3390/ijms21010215] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 12/22/2019] [Accepted: 12/25/2019] [Indexed: 12/22/2022] Open
Abstract
Peptides are widely used in pharmaceutical industry as active pharmaceutical ingredients, versatile tools in drug discovery, and for drug delivery. They find themselves at the crossroads of small molecules and proteins, possessing favorable tissue penetration and the capability to engage into specific and high-affinity interactions with endogenous receptors. One of the commonly employed approaches in peptide discovery and design is to screen combinatorial libraries, comprising a myriad of peptide variants of either chemical or biological origin. In this review, we focus mainly on recombinant peptide libraries, discussing different platforms for their display or expression, and various diversification strategies for library design. We take a look at well-established technologies as well as new developments and future directions.
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Affiliation(s)
| | - Tomaž Bratkovič
- Department of Pharmaceutical Biology, Faculty of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, SI-1000 Ljubljana, Slovenia;
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5
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Liu R, Li X, Xiao W, Lam KS. Tumor-targeting peptides from combinatorial libraries. Adv Drug Deliv Rev 2017; 110-111:13-37. [PMID: 27210583 DOI: 10.1016/j.addr.2016.05.009] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Revised: 05/10/2016] [Accepted: 05/11/2016] [Indexed: 02/07/2023]
Abstract
Cancer is one of the major and leading causes of death worldwide. Two of the greatest challenges in fighting cancer are early detection and effective treatments with no or minimum side effects. Widespread use of targeted therapies and molecular imaging in clinics requires high affinity, tumor-specific agents as effective targeting vehicles to deliver therapeutics and imaging probes to the primary or metastatic tumor sites. Combinatorial libraries such as phage-display and one-bead one-compound (OBOC) peptide libraries are powerful approaches in discovering tumor-targeting peptides. This review gives an overview of different combinatorial library technologies that have been used for the discovery of tumor-targeting peptides. Examples of tumor-targeting peptides identified from each combinatorial library method will be discussed. Published tumor-targeting peptide ligands and their applications will also be summarized by the combinatorial library methods and their corresponding binding receptors.
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Affiliation(s)
- Ruiwu Liu
- Department of Biochemistry and Molecular Medicine, University of California Davis, Sacramento, CA 95817, USA; University of California Davis Comprehensive Cancer Center, Sacramento, CA 95817, USA
| | - Xiaocen Li
- Department of Biochemistry and Molecular Medicine, University of California Davis, Sacramento, CA 95817, USA; University of California Davis Comprehensive Cancer Center, Sacramento, CA 95817, USA
| | - Wenwu Xiao
- Department of Biochemistry and Molecular Medicine, University of California Davis, Sacramento, CA 95817, USA; University of California Davis Comprehensive Cancer Center, Sacramento, CA 95817, USA
| | - Kit S Lam
- Department of Biochemistry and Molecular Medicine, University of California Davis, Sacramento, CA 95817, USA; University of California Davis Comprehensive Cancer Center, Sacramento, CA 95817, USA; Division of Hematology & Oncology, Department of Internal Medicine, University of California Davis, Sacramento, CA 95817, USA
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6
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Efficacy and toxicity management of CAR-T-cell immunotherapy: a matter of responsiveness control or tumour-specificity? Biochem Soc Trans 2016; 44:406-11. [PMID: 27068947 DOI: 10.1042/bst20150286] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Indexed: 02/05/2023]
Abstract
Chimaeric antigen receptor (CAR)-expressing T-cells have demonstrated potent clinical efficacy in patients with haematological malignancies. However, the use of CAR-T-cells targeting solid tumour-associated antigens (TAAs) has been limited by organ toxicities related to activation of T-cell effector functions through the CAR. Most existing CARs recognize TAAs, which are also found in normal tissues. CAR-T-cell-mediated destruction of normal tissues constitutes a major roadblock to CAR-T-cell therapy, and must be avoided or mitigated. There is a broad range of strategies for modulating antigen responsiveness of CAR-T-cells, with varying degrees of complexity. Some of them might ameliorate the acute and chronic toxicities associated with current CAR constructs. However, further embellishments to CAR therapy may complicate clinical implementation and possibly create new immunogenicity issues. In contrast, the development of CARs targeting truly tumour-specific antigens might circumvent on-target/off-tumour toxicities without adding additional complexity to CAR-T-cell therapies, but these antigens have been elusive and may require novel selection strategies for their discovery.
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7
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In Vitro Selection of Cancer Cell-Specific Molecular Recognition Elements from Amino Acid Libraries. J Immunol Res 2015; 2015:186586. [PMID: 26436100 PMCID: PMC4576012 DOI: 10.1155/2015/186586] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 08/17/2015] [Accepted: 08/23/2015] [Indexed: 11/27/2022] Open
Abstract
Differential cell systematic evolution of ligands by exponential enrichment (SELEX) is an in vitro selection method for obtaining molecular recognition elements (MREs) that specifically bind to individual cell types with high affinity. MREs are selected from initial large libraries of different nucleic or amino acids. This review outlines the construction of peptide and antibody fragment libraries as well as their different host types. Common methods of selection are also reviewed. Additionally, examples of cancer cell MREs are discussed, as well as their potential applications.
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8
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Chen C, Li N, Zhao Y, Hang H. Coupling recombinase-mediated cassette exchange with somatic hypermutation for antibody affinity maturation in CHO cells. Biotechnol Bioeng 2015; 113:39-51. [PMID: 26235363 DOI: 10.1002/bit.25541] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 10/07/2014] [Accepted: 11/17/2014] [Indexed: 02/06/2023]
Abstract
Heterologous expression of activation-induced cytidine deaminase (AID) can induce somatic hypermutation (SHM) for genes of interest in various cells, and several research groups (including ours) have successfully improved antibody affinity in mammalian or chicken cells using AID-induced SHM. These affinity maturation systems are time-consuming and inefficient. In this study, we developed an antibody affinity maturation platform in Chinese hamster ovary (CHO) cells by coupling recombinase-mediated cassette exchange (RMCE) with SHM. Stable CHO cell clones containing a single copy puromycin resistance gene (PuroR) expression cassette flanked by recombination target sequences (FRT and loxP) being able to highly express a gene of interest placed in the cassette were developed. The PuroR gene was replaced with an antibody gene by RMCE, and the antibody was displayed on the cell surface. Cells displaying antibodies on their membrane were transfected with the AID gene, and mutations of the antibody gene were accumulated by AID-mediated hypermutation during cell proliferation followed by flow cytometric cell sorting for cells bearing antibody mutants with improved affinity. Affinity improvements were detected after only one round of cell sorting and proliferation, mutant clones with 15-fold affinity improvement were isolated within five rounds of maturation (within 2 months). CHO cells are fast growing, stress-resistant and produce antibody with glycosylations suitable for therapy. Our antibody-evolution platform based on CHO cells makes antibody-affinity maturation more efficient and is especially convenient for therapeutic antibody affinity improvement.
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Affiliation(s)
- Chuan Chen
- Key Laboratory for Protein and Peptide Pharmaceuticals, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Nan Li
- Key Laboratory for Protein and Peptide Pharmaceuticals, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yun Zhao
- Key Laboratory for Protein and Peptide Pharmaceuticals, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Haiying Hang
- Key Laboratory for Protein and Peptide Pharmaceuticals, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
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9
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Breous-Nystrom E, Schultze K, Meier M, Flueck L, Holzer C, Boll M, Seibert V, Schuster A, Blanusa M, Schaefer V, Grawunder U, Martin-Parras L, van Dijk MA. Retrocyte Display® technology: Generation and screening of a high diversity cellular antibody library. Methods 2014; 65:57-67. [DOI: 10.1016/j.ymeth.2013.09.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 08/13/2013] [Accepted: 09/03/2013] [Indexed: 10/26/2022] Open
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10
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Lin YC, Chen BM, Lu WC, Su CI, Prijovich ZM, Chung WC, Wu PY, Chen KC, Lee IC, Juan TY, Roffler SR. The B7-1 cytoplasmic tail enhances intracellular transport and mammalian cell surface display of chimeric proteins in the absence of a linear ER export motif. PLoS One 2013; 8:e75084. [PMID: 24073236 PMCID: PMC3779271 DOI: 10.1371/journal.pone.0075084] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 08/12/2013] [Indexed: 11/18/2022] Open
Abstract
Membrane-tethered proteins (mammalian surface display) are increasingly being used for novel therapeutic and biotechnology applications. Maximizing surface expression of chimeric proteins on mammalian cells is important for these applications. We show that the cytoplasmic domain from the B7-1 antigen, a commonly used element for mammalian surface display, can enhance the intracellular transport and surface display of chimeric proteins in a Sar1 and Rab1 dependent fashion. However, mutational, alanine scanning and deletion analysis demonstrate the absence of linear ER export motifs in the B7 cytoplasmic domain. Rather, efficient intracellular transport correlated with the presence of predicted secondary structure in the cytoplasmic tail. Examination of the cytoplasmic domains of 984 human and 782 mouse type I transmembrane proteins revealed that many previously identified ER export motifs are rarely found in the cytoplasmic tail of type I transmembrane proteins. Our results suggest that efficient intracellular transport of B7 chimeric proteins is associated with the structure rather than to the presence of a linear ER export motif in the cytoplasmic tail, and indicate that short (less than ~ 10-20 amino acids) and unstructured cytoplasmic tails should be avoided to express high levels of chimeric proteins on mammalian cells.
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Affiliation(s)
- Yi-Chieh Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Bing-Mae Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Wei-Cheng Lu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Chien-I Su
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | | | - Wen-Chuan Chung
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Pei-Yu Wu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Kai-Chuan Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - I-Chiao Lee
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Ting-Yi Juan
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Steve R. Roffler
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
- * E-mail:
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11
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Stolp ZD, Stotland A, Diaz S, Hilton BJ, Burford W, Wolkowicz R. A Novel Two-Tag System for Monitoring Transport and Cleavage through the Classical Secretory Pathway - Adaptation to HIV Envelope Processing. PLoS One 2013; 8:e68835. [PMID: 23840860 PMCID: PMC3686725 DOI: 10.1371/journal.pone.0068835] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 06/03/2013] [Indexed: 11/19/2022] Open
Abstract
The classical secretory pathway is essential for the transport of a host of proteins to the cell surface and/or extracellular matrix. While the pathway is well-established, many factors still remain to be elucidated. One of the most relevant biological processes that occur during transport involves the cleavage of pro-proteins by enzymes residing in the endoplasmic reticulum/Golgi/TransGolgi Network compartment. Teasing out the requirements involved in the classical secretory pathway and cleavage during transport would shed new light into mis-regulation leading to disease. Current methodologies fail to link transport and cleavage at the single cell level. Here, we describe a cell-based assay that relies on an engineered protein scaffold that can discriminate between transport to the cell surface, in the absence or presence of cleavage. Our novel two-tag system works in a robust and quantitative manner and distinguishes between cleaved and non-cleaved events based on cell surface expression of one or two epitope tags, respectively. Here, we have used the HIV-1 envelope as a substrate, which is cleaved during transport, as proof of principle. Importantly, this assay can be easily coupled to existing siRNA-based screens to identify novel regulators and effectors involved in transport and/or cleavage of cell surface proteins. In addition, unlike other in vivo based assays, the assay described here can also be easily adapted to drug discovery purposes.
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Affiliation(s)
- Zachary D. Stolp
- Department of Biology, San Diego State University, San Diego, California, United States of America
| | - Aleksandr Stotland
- Department of Biology, San Diego State University, San Diego, California, United States of America
| | - Samantha Diaz
- Department of Biology, San Diego State University, San Diego, California, United States of America
| | - Brett J. Hilton
- Department of Biology, San Diego State University, San Diego, California, United States of America
| | - Wesley Burford
- Department of Biology, San Diego State University, San Diego, California, United States of America
| | - Roland Wolkowicz
- Department of Biology, San Diego State University, San Diego, California, United States of America
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12
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Alonso-Camino V, Sánchez-Martín D, Compte M, Nuñez-Prado N, Diaz RM, Vile R, Alvarez-Vallina L. CARbodies: Human Antibodies Against Cell Surface Tumor Antigens Selected From Repertoires Displayed on T Cell Chimeric Antigen Receptors. MOLECULAR THERAPY. NUCLEIC ACIDS 2013; 2:e93. [PMID: 23695536 PMCID: PMC4817937 DOI: 10.1038/mtna.2013.19] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
A human single-chain variable fragment (scFv) antibody library was expressed on the surface of human T cells after transduction with lentiviral vectors (LVs). The repertoire was fused to a first-generation T cell receptor ζ (TCRζ)-based chimeric antigen receptor (CAR). We used this library to isolate antibodies termed CARbodies that recognize antigens expressed on the tumor cell surface in a proof-of-principle system. After three rounds of activation-selection there was a clear repertoire restriction, with the emergence dominant clones. The CARbodies were purified from bacterial cultures as soluble and active proteins. Furthermore, to validate its potential application for adoptive cell therapy, human T cells were transduced with a LV encoding a second-generation costimulatory CAR (CARv2) bearing the selected CARbodies. Transduced human primary T cells expressed significant levels of the CARbodies-based CARv2 fusion protein on the cell surface, and importantly could be specifically activated, after stimulation with tumor cells. This approach is a promising tool for the generation of antibodies fully adapted to the display format (CAR) and the selection context (cell synapse), which could extend the scope of current adoptive cell therapy strategies with CAR-redirected T cells.
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Affiliation(s)
- Vanesa Alonso-Camino
- 1] Molecular Immunology Unit, Hospital Universitario Puerta de Hierro, Madrid, Spain [2] Current addresses: Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, USA
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13
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Abstract
Display technology has been developed and widely used in antibody screening and selecting. While phage can only display antibody fragments, mammalian cells can display not only fragments but full-length antibodies. Here we described the display of full length antibody on the surface of 293 cells. Both heavy chain and light chain genes were cloned in a single mammalian expression vector containing dual mammalian expression cassettes. While transfected into 293 cells of the vector, both heavy and light chains were expressed. With the help of transmembrane domain of platelet-derived growth factor receptor (PDGFR-TM) fused at the 3'-end of heavy chain in frame, expressed full-length antibodies were displayed on the cell surface and can be easily detected and analyzed by flow cytometry.
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Affiliation(s)
- Chen Zhou
- Antivirus Research Center, School of Pharmaceutical Science, Southern Medical University, Guangzhou, China
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14
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Zhou C, Jacobsen FW, Cai L, Chen Q, Shen WD. Development of a novel mammalian cell surface antibody display platform. MAbs 2010; 2:508-18. [PMID: 20716968 DOI: 10.4161/mabs.2.5.12970] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Antibody display systems have been successfully applied to screen, select and characterize antibody fragments. These systems typically use prokaryotic organisms such as phage and bacteria or lower eukaryotic organisms, such as yeast. These organisms possess either no or different post-translational modification functions from mammalian cells and prefer to display small antibody fragments instead of full-length IgGs. We report here a novel mammalian cell-based antibody display platform that displays full-length functional antibodies on the surface of mammalian cells. Through recombinase-mediated DNA integration, each host cell contains one copy of the gene of interest in the genome. Utilizing a hot-spot integration site, the expression levels of the gene of interest are high and comparable between clones, ensuring a high signal to noise ratio. Coupled with fluorescence-activated cell sorting (FACS) technology, our platform is high throughput and can distinguish antibodies with very high antigen binding affinities directly on the cell surface. Single-round FACS can enrich high affinity antibodies by more than 500 fold. Antibodies with significantly improved neutralizing activity have been identified from a randomly mutagenized library, demonstrating the power of this platform in screening and selecting antibody therapeutics.
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Affiliation(s)
- Chen Zhou
- Protein Science, Amgen Inc., Thousand Oaks, CA, USA
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Puthenveetil S, Liu DS, White KA, Thompson S, Ting AY. Yeast display evolution of a kinetically efficient 13-amino acid substrate for lipoic acid ligase. J Am Chem Soc 2010; 131:16430-8. [PMID: 19863063 DOI: 10.1021/ja904596f] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Escherichia coli lipoic acid ligase (LplA) catalyzes ATP-dependent covalent ligation of lipoic acid onto specific lysine side chains of three acceptor proteins involved in oxidative metabolism. Our lab has shown that LplA and engineered mutants can ligate useful small-molecule probes such as alkyl azides ( Nat. Biotechnol. 2007 , 25 , 1483 - 1487 ) and photo-cross-linkers ( Angew. Chem., Int. Ed. 2008 , 47 , 7018 - 7021 ) in place of lipoic acid, facilitating imaging and proteomic studies. Both to further our understanding of lipoic acid metabolism, and to improve LplA's utility as a biotechnological platform, we have engineered a novel 13-amino acid peptide substrate for LplA. LplA's natural protein substrates have a conserved beta-hairpin structure, a conformation that is difficult to recapitulate in a peptide, and thus we performed in vitro evolution to engineer the LplA peptide substrate, called "LplA Acceptor Peptide" (LAP). A approximately 10(7) library of LAP variants was displayed on the surface of yeast cells, labeled by LplA with either lipoic acid or bromoalkanoic acid, and the most efficiently labeled LAP clones were isolated by fluorescence activated cell sorting. Four rounds of evolution followed by additional rational mutagenesis produced a "LAP2" sequence with a k(cat)/K(m) of 0.99 muM(-1) min(-1), >70-fold better than our previous rationally designed 22-amino acid LAP1 sequence (Nat. Biotechnol. 2007, 25, 1483-1487), and only 8-fold worse than the k(cat)/K(m) values of natural lipoate and biotin acceptor proteins. The kinetic improvement over LAP1 allowed us to rapidly label cell surface peptide-fused receptors with quantum dots.
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Affiliation(s)
- Sujiet Puthenveetil
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
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Alonso-Camino V, Sánchez-Martín D, Compte M, Álvarez-Vallina LSL. Lymphocyte display: a novel antibody selection platform based on T cell activation. PLoS One 2009; 4:e7174. [PMID: 19777065 PMCID: PMC2747005 DOI: 10.1371/journal.pone.0007174] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2009] [Accepted: 08/30/2009] [Indexed: 12/02/2022] Open
Abstract
Since their onset, display technologies have proven useful for the selection of antibodies against a variety of targets; however, most of the antibodies selected with the currently available platforms need to be further modified for their use in humans, and are restricted to accessible antigens. Furthermore, these platforms are not well suited for in vivo selections. We present here a novel cell based antibody display platform, which takes advantage of the functional capabilities of T lymphocytes. The display of antibodies on the surface of T lymphocytes, as a part of a chimeric-immune receptor (CIR) mediating signaling, may ideally link the antigen-antibody interaction to a demonstrable change in T cell phenotype, due to subsequent expression of the early T cell activation marker CD69. In this proof-of-concept, an in vitro selection was carried out using a human T cell line lentiviral-transduced to express a tumor-specific CIR on the surface, against a human tumor cell line expressing the carcinoembryonic antigen. Based on an effective interaction between the CIR and the tumor antigen, we demonstrated that combining CIR-mediated activation with FACS sorting of CD69+ T cells, it is possible to isolate binders to tumor specific cell surface antigen, with an enrichment factor of at least 103-fold after two rounds, resulting in a homogeneous population of T cells expressing tumor-specific CIRs.
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Affiliation(s)
- Vanesa Alonso-Camino
- Molecular Immunology Unit, Hospital Universitario Puerta de Hierro, Madrid, Spain
| | - David Sánchez-Martín
- Molecular Immunology Unit, Hospital Universitario Puerta de Hierro, Madrid, Spain
| | - Marta Compte
- Molecular Immunology Unit, Hospital Universitario Puerta de Hierro, Madrid, Spain
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Mersich C, Jungbauer A. Generation of bioactive peptides by biological libraries. J Chromatogr B Analyt Technol Biomed Life Sci 2008; 861:160-70. [PMID: 17644452 DOI: 10.1016/j.jchromb.2007.06.031] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2007] [Revised: 06/13/2007] [Accepted: 06/23/2007] [Indexed: 11/19/2022]
Abstract
Biological libraries are powerful tools for discovery of new ligands as well as for identification of cellular interaction partners. Since the first development of the first biological libraries in form of phage displays, numerous biological libraries have been developed. For the development of new ligands, the usage of synthetic oligonucleotides is the method of choice. Generation of random oligonucleotides has been refined and various strategies for random oligonucleotide design were developed. We trace the progress and design of new strategies for the generation of random oligonucleotides, and include a look at arising diversity biases. On the other hand, genomic libraries are widely employed for investigation of cellular protein-protein interactions and targeted search of proteomic binding partners. Expression of random peptides and proteins in a linear form or integrated in a scaffold can be facilitated both in vitro and in vivo. A typical in vitro system, ribosome display, provides the largest available library size. In vivo methods comprise smaller libraries, the size of which depends on their transformation efficiency. Libraries in different hosts such as phage, bacteria, yeast, insect cells, mammalian cells exhibit higher biosynthetic capabilities. The latest library systems are compared and their strengths and limitations are reviewed.
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Affiliation(s)
- Christa Mersich
- Department of Biotechnology, University of Natural Resources and Applied Life Sciences Vienna, Muthgasse 18, Vienna, Austria
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Ho M, Nagata S, Pastan I. Isolation of anti-CD22 Fv with high affinity by Fv display on human cells. Proc Natl Acad Sci U S A 2006; 103:9637-42. [PMID: 16763048 PMCID: PMC1480459 DOI: 10.1073/pnas.0603653103] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In vitro antibody affinity maturation has generally been achieved by display of mouse or human antibodies on the surface of microorganisms (phage, bacteria, and yeast). However, problems with protein folding, posttranslational modification, and codon usage still limit the number of improved antibodies that can be obtained. An ideal system would select and improve antibodies in a mammalian cell environment where they are naturally made. Here we show that human embryonic kidney 293T cells that are widely used for transient protein expression can be used for cell surface display of single-chain Fv antibodies for affinity maturation. In a proof-of-concept experiment, cells expressing a rare mutant antibody with higher affinity were enriched 240-fold by a single-pass cell sorting from a large excess of cells expressing WT antibody with a slightly lower affinity. Furthermore, we successfully obtained a highly enriched mutant with increased binding affinity for CD22 after a single selection of a combinatory library randomizing an intrinsic antibody hotspot. Important features are that one display selection cycle requires only 1 week, and transfection of cells in a single 100-mm dish produces 10(7) individual clones so that a repertoire of 10(9) is feasible under current experimental conditions.
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Affiliation(s)
- Mitchell Ho
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4264
| | - Satoshi Nagata
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4264
| | - Ira Pastan
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4264
- *To whom correspondence should be addressed. E-mail:
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Mammalian cells put on a display. Nat Methods 2005. [DOI: 10.1038/nmeth0305-160a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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