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Liu Z, Kim D, Kang S, Jung JU. A Detailed Protocol for Constructing a Human Single-Chain Variable Fragment (scFv) Library and Downstream Screening via Phage Display. Methods Protoc 2024; 7:13. [PMID: 38392687 PMCID: PMC10893473 DOI: 10.3390/mps7010013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/23/2024] [Accepted: 01/30/2024] [Indexed: 02/24/2024] Open
Abstract
The development of monoclonal antibodies (mAbs) represents a significant milestone in both basic research and clinical applications due to their target specificity and versatility in therapeutic and diagnostic applications. The innovative strategy of mAb screening, utilizing phage display, facilitates the in vitro screening of antibodies with high affinity to target antigens. The single-chain variable fragment (scFv) is a subset of mAb derivatives, known for its high binding affinity and smaller size-just one-third of that of human IgG. This report outlines a detailed and comprehensive procedure for constructing a scFv phagemid library derived from human patients, followed by screening via phage display affinity selection. The protocol utilizes 348 primer combinations spanning the entire human antibody repertoire to minimize sequence bias and maintain library diversity during polymerase chain reaction (PCR) for scFv generation, resulting in a library size greater than 1 × 108. Furthermore, we describe a high-throughput phage display screening protocol using enzyme-linked immunosorbent assay (ELISA) to evaluate more than 1200 scFv candidates. The generation of a highly diverse scFv library, coupled with the implementation of a phage display screening methodology, is expected to provide a valuable resource for researchers in pursuit of scFvs with high affinity for target antigens, thus advancing both research and clinical endeavors.
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Affiliation(s)
- Ziyi Liu
- Cancer Biology Department, Infection Biology Program, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; (Z.L.); (D.K.); (S.K.)
- Global Center for Pathogen Research and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Dokyun Kim
- Cancer Biology Department, Infection Biology Program, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; (Z.L.); (D.K.); (S.K.)
- Global Center for Pathogen Research and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Seokmin Kang
- Cancer Biology Department, Infection Biology Program, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; (Z.L.); (D.K.); (S.K.)
- Global Center for Pathogen Research and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Jae U. Jung
- Cancer Biology Department, Infection Biology Program, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; (Z.L.); (D.K.); (S.K.)
- Global Center for Pathogen Research and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
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Chockalingam K, Peng Z, Vuong CN, Berghman LR, Chen Z. Golden Gate assembly with a bi-directional promoter (GBid): A simple, scalable method for phage display Fab library creation. Sci Rep 2020; 10:2888. [PMID: 32076016 PMCID: PMC7031318 DOI: 10.1038/s41598-020-59745-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 02/03/2020] [Indexed: 11/09/2022] Open
Abstract
Fabs offer an attractive platform for monoclonal antibody discovery/engineering, but library construction can be cumbersome. We report a simple method – Golden Gate assembly with a bi-directional promoter (GBid) – for constructing phage display Fab libraries. In GBid, the constant domains of the Fabs are located in the backbone of the phagemid vector and the library insert comprises only the variable regions of the antibodies and a central bi-directional promoter. This vector design reduces the process of Fab library construction to “scFv-like” simplicity and the double promoter ensures robust expression of both constituent chains. To maximize the library size, the 3 fragments comprising the insert – two variable chains and one bi-directional promoter – are assembled via a 3-fragment overlap extension PCR and the insert is incorporated into the vector via a high-efficiency one-fragment, one-pot Golden Gate assembly. The reaction setup requires minimal preparatory work and enzyme quantities, making GBid highly scalable. Using GBid, we constructed a chimeric chicken-human Fab phage display library comprising 1010 variants targeting the multi-transmembrane protein human CD20 (hCD20). Selection/counter-selection on transfected whole cells yielded hCD20-specific antibodies in four rounds of panning. The simplicity and scalability of GBid makes it a powerful tool for the discovery/engineering of Fabs and IgGs.
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Affiliation(s)
- Karuppiah Chockalingam
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, College Station, Texas, 77843, USA
| | - Zeyu Peng
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, College Station, Texas, 77843, USA.,Biosion, Inc., Nanjing, 210061, China
| | - Christine N Vuong
- Department of Poultry Science, Texas A&M University, College Station, Texas, 77843, USA.,Department of Poultry Science, University of Arkansas, Fayetteville, Arkansas, 72703, USA
| | - Luc R Berghman
- Department of Poultry Science, Texas A&M University, College Station, Texas, 77843, USA
| | - Zhilei Chen
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, College Station, Texas, 77843, USA.
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Wilson HD, Li X, Peng H, Rader C. A Sortase A Programmable Phage Display Format for Improved Panning of Fab Antibody Libraries. J Mol Biol 2018; 430:4387-4400. [PMID: 30213726 DOI: 10.1016/j.jmb.2018.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 09/01/2018] [Accepted: 09/05/2018] [Indexed: 11/26/2022]
Abstract
Phage display of combinatorial antibody libraries is a versatile tool in the field of antibody engineering, with diverse applications including monoclonal antibody (mAb) discovery, affinity maturation, and humanization. To improve the selection efficiency of antibody libraries, we developed a new phagemid display system that addresses the complication of bald phage propagation. The phagemid facilitates the biotinylation of fragment of antigen binding (Fab) antibody fragments displayed on phage via Sortase A catalysis and the subsequent enrichment of Fab-displaying phage during selections. In multiple contexts, this selection approach improved the enrichment of target-reactive mAbs by depleting background phage. Panels of cancer cell line-reactive mAbs with high diversity and specificity were isolated from a naïve chimeric rabbit/human Fab library using this approach, highlighting its potential to accelerate antibody engineering efforts and to empower concerted antibody drug and target discovery.
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Affiliation(s)
- Henry D Wilson
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Xiuling Li
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Haiyong Peng
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Christoph Rader
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA.
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Peng H, Nerreter T, Chang J, Qi J, Li X, Karunadharma P, Martinez GJ, Fallahi M, Soden J, Freeth J, Beerli RR, Grawunder U, Hudecek M, Rader C. Mining Naïve Rabbit Antibody Repertoires by Phage Display for Monoclonal Antibodies of Therapeutic Utility. J Mol Biol 2017; 429:2954-2973. [PMID: 28818634 DOI: 10.1016/j.jmb.2017.08.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Revised: 08/01/2017] [Accepted: 08/06/2017] [Indexed: 01/25/2023]
Abstract
Owing to their high affinities and specificities, rabbit monoclonal antibodies (mAbs) have demonstrated value and potential primarily as basic research and diagnostic reagents, but, in some cases, also as therapeutics. To accelerate access to rabbit mAbs bypassing immunization, we generated a large naïve rabbit antibody repertoire represented by a phage display library encompassing >10 billion independent antibodies in chimeric rabbit/human Fab format and validated it by next-generation sequencing. Panels of rabbit mAbs selected from this library against two emerging cancer targets, ROR1 and ROR2, revealed high diversity, affinity, and specificity. Moreover, ROR1- and ROR2-targeting rabbit mAbs demonstrated therapeutic utility as components of chimeric antigen receptor-engineered T cells, further corroborating the value of the naïve rabbit antibody library as a rich and virtually unlimited source of rabbit mAbs.
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Affiliation(s)
- Haiyong Peng
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Thomas Nerreter
- Medizinische Klinik und Poliklinik II, Universitätsklinikum Würzburg, 97080 Würzburg, Germany
| | - Jing Chang
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Junpeng Qi
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Xiuling Li
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | | | | | - Mohammad Fallahi
- Informatics Core, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Jo Soden
- Retrogenix Ltd, Whaley Bridge, High Peak, SK23 7LY, United Kingdom
| | - Jim Freeth
- Retrogenix Ltd, Whaley Bridge, High Peak, SK23 7LY, United Kingdom
| | | | | | - Michael Hudecek
- Medizinische Klinik und Poliklinik II, Universitätsklinikum Würzburg, 97080 Würzburg, Germany
| | - Christoph Rader
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA.
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Bishehsari F, Gach JS, Akagi N, Webber MK, Bauer J, Jung BH. Anti-p21 autoantibodies detected in colorectal cancer patients: A proof of concept study. Oncoimmunology 2014; 3:e952202. [PMID: 25960931 DOI: 10.4161/21624011.2014.952202] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Accepted: 06/04/2014] [Indexed: 12/29/2022] Open
Abstract
Whereas the presence of autoantibodies in cancer patients has been acknowledged, their diagnostic or therapeutic significance has yet to be established. This is due, at least in part, to the lack of robust screening techniques to detect and characterize such antibodies for further assessment. In this study, we screened colorectal cancer (CRC) patient sera for antibodies specifically targeting the key cell cycle inhibitory factor p21 encoded by the cyclin-dependent kinase inhibitor 1A (CDKN1A). Anti-p21 antibody titers were higher in CRC patient samples versus controls, correlating with a more advanced disease stage and lymph node involvement. Further, we isolated for the first time a specific human antibody fragment against p21, which could potentially be useful as a tool to study tumorigenicity in CRC patients.
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Key Words
- CDKN1A, cyclin-dependent kinase inhibitor 1
- CRC, colorectal cancer
- ELISA, enzyme-linked immunosorbent assay
- Fab, fragment antigen-binding
- HER2/ERBB2, v-erb-b2 avian erythroblastic leukemia viral oncogene homologue 2
- Ni-NTA, nickel-charged nitrilotriacetic acid
- OD50, half-maximum binding titer
- TAAs, tumor-associated antigens
- TP53, tumor protein p53.
- aAbs, autoantibodies
- autoantibody
- immunofluorescence assay
- olorectal cancer
- p21
- p21/CIP1, CDKN1A protein
- phage display
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Affiliation(s)
- Faraz Bishehsari
- Division of Gastroenterology; Northwestern University ; Chicago, IL USA
| | - Johannes S Gach
- Division of Infectious Diseases; University of California Irvine ; Irvine, CA USA
| | - Naomi Akagi
- Division of Gastroenterology and Hepatology; University of Illinois at Chicago ; Chicago, IL USA
| | - Molly K Webber
- School of Medicine; University of Pittsburgh ; Pittsburgh, PA USA
| | - Jessica Bauer
- Division of Gastroenterology and Hepatology; University of Illinois at Chicago ; Chicago, IL USA
| | - Barbara H Jung
- Division of Gastroenterology and Hepatology; University of Illinois at Chicago ; Chicago, IL USA
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Grönwall C, Charles ED, Dustin LB, Rader C, Silverman GJ. Selection of apoptotic cell specific human antibodies from adult bone marrow. PLoS One 2014; 9:e95999. [PMID: 24760047 PMCID: PMC3997490 DOI: 10.1371/journal.pone.0095999] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 04/02/2014] [Indexed: 11/18/2022] Open
Abstract
Autoreactive antibodies that recognize neo-determinants on apoptotic cells in mice have been proposed to have protective, homeostatic and immunoregulatory properties, although our knowledge about the equivalent antibodies in humans has been much more limited. In the current study, human monoclonal antibodies with binding specificity for apoptotic cells were isolated from the bone marrow of healthy adults using phage display technology. These antibodies were shown to recognize phosphorylcholine (PC)-associated neo-determinants. Interestingly, three of the four identified apoptotic cell-specific antibody clones were encoded by VH3 region rearrangements with germline or nearly germline configuration without evidence of somatic hypermutation. Importantly, the different identified antibody clones had diverse heavy chain CDR3 and deduced binding surfaces as suggested by structure modeling. This may suggest a potentially great heterogeneity in human antibodies recognizing PC-related epitopes on apoptotic cells. To re-construct the postulated structural format of the parental anti-PC antibody, the dominant clone was also expressed as a recombinant human polymeric IgM, which revealed a substantially increased binding reactivity, with dose-dependent and antigen-inhibitable binding of apoptotic cells. Our findings may have implication for improved prognostic testing and therapeutic interventions in human inflammatory disease.
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Affiliation(s)
- Caroline Grönwall
- School of Medicine, New York University, New York, New York, United States of America
| | - Edgar D. Charles
- Laboratory of Virology and Infectious Disease, Rockefeller University, New York, New York, United States of America
| | | | - Christoph Rader
- Department of Cancer Biology and Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, Florida, United States of America
| | - Gregg J. Silverman
- School of Medicine, New York University, New York, New York, United States of America
- * E-mail:
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Tay MYF, Lee CC, Vasudevan SG, Moreland NJ. Identification of dengue-specific human antibody fragments using phage display. Methods Mol Biol 2014; 1138:161-73. [PMID: 24696337 DOI: 10.1007/978-1-4939-0348-1_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
High-affinity antibodies are valuable tools for dengue research. A method for the selection of dengue-specific, human antibody fragments using naïve repertoires displayed on M13 filamentous bacteriophage is described. Naïve repertoires are unbiased, thus enabling the identification of antibodies to dengue structural and nonstructural proteins from the same library. Dengue-specific clones are enriched by binding to an immobilized dengue antigen, followed by washing, elution, and amplification of phage for subsequent rounds of selection. Dengue virus has four antigenically related serotypes, and the serotype of the antigen can be kept constant or alternated during the selection process depending on whether serotype-specific or cross-reactive antibodies are required. After the selection process, clones are screened, and specific clones are identified by phage ELISA and Western blot.
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Affiliation(s)
- Moon Y F Tay
- Emerging Infectious Diseases Program, Duke-NUS Graduate Medical School, Singapore, Singapore
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