1
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Chen C, Wang Z, Kang M, Lee KB, Ge X. High-fidelity large-diversity monoclonal mammalian cell libraries by cell cycle arrested recombinase-mediated cassette exchange. Nucleic Acids Res 2023; 51:e113. [PMID: 37941133 PMCID: PMC10711435 DOI: 10.1093/nar/gkad1001] [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: 02/08/2023] [Revised: 09/26/2023] [Accepted: 10/18/2023] [Indexed: 11/10/2023] Open
Abstract
Mammalian cells carrying defined genetic variations have shown great potentials in both fundamental research and therapeutic development. However, their full use was limited by lack of a robust method to construct large monoclonal high-quality combinatorial libraries. This study developed cell cycle arrested recombinase-mediated cassette exchange (aRMCE), able to provide monoclonality, precise genomic integration and uniform transgene expression. Via optimized nocodazole-mediated mitotic arrest, 20% target gene replacement efficiency was achieved without antibiotic selection, and the improved aRMCE efficiency was applicable to a variety of tested cell clones, transgene targets and transfection methods. As a demonstration of this versatile method, we performed directed evolution of fragment crystallizable (Fc), for which error-prone libraries of over 107 variants were constructed and displayed as IgG on surface of CHO cells. Diversities of constructed libraries were validated by deep sequencing, and panels of novel Fc mutants were identified showing improved binding towards specific Fc gamma receptors and enhanced effector functions. Due to its large cargo capacity and compatibility with different mutagenesis approaches, we expect this mammalian cell platform technology has broad applications for directed evolution, multiplex genetic assays, cell line development and stem cell engineering.
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Affiliation(s)
- Chuan Chen
- Department of Chemical and Environmental Engineering, University of California Riverside, Riverside, CA 92521, USA
| | - Zening Wang
- Department of Chemical and Environmental Engineering, University of California Riverside, Riverside, CA 92521, USA
- Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Minhyo Kang
- Department of Chemical and Environmental Engineering, University of California Riverside, Riverside, CA 92521, USA
| | - Ki Baek Lee
- Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Xin Ge
- Department of Chemical and Environmental Engineering, University of California Riverside, Riverside, CA 92521, USA
- Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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2
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Gaa R, Kumari K, Mayer HM, Yanakieva D, Tsai SP, Joshi S, Guenther R, Doerner A. An integrated mammalian library approach for optimization and enhanced microfluidics-assisted antibody hit discovery. ARTIFICIAL CELLS, NANOMEDICINE, AND BIOTECHNOLOGY 2023; 51:74-82. [PMID: 36762883 DOI: 10.1080/21691401.2023.2173219] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Recent years have seen the development of a variety of mammalian library approaches for display and secretion mode. Advantages include library approaches for engineering, preservation of precious immune repertoires and their repeated interrogation, as well as screening in final therapeutic format and host. Mammalian display approaches for antibody optimization exploit these advantages, necessitating the generation of large libraries but in turn enabling early screening for both manufacturability and target specificity. For suitable libraries, high antibody integration rates and resulting monoclonality need to be balanced - we present a solution for sufficient transmutability and acceptable monoclonality by applying an optimized ratio of coding to non-coding lentivirus. The recent advent of microfluidic-assisted hit discovery represents a perfect match to mammalian libraries in secretion mode, as the lower throughput fits well with the facile generation of libraries comprising a few million functional clones. In the presented work, Chinese Hamster Ovary cells were engineered to both express the target of interest and secrete antibodies in relevant formats, and specific clones were strongly enriched by high throughput screening for autocrine cellular binding. The powerful combination of mammalian secretion libraries and microfluidics-assisted hit discovery could reduce attrition rates and increase the probability to identify the best possible therapeutic antibody hits faster.
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Affiliation(s)
- Ramona Gaa
- Protein Engineering and Antibody Technologies, Merck KGaA, Darmstadt, Germany
| | - Kavita Kumari
- Discovery Biology, Syngene International, Phase-IV, Bangalore, India
| | - Hannah Melina Mayer
- Protein Engineering and Antibody Technologies, Merck KGaA, Darmstadt, Germany
| | - Desislava Yanakieva
- Protein Engineering and Antibody Technologies, Merck KGaA, Darmstadt, Germany
| | - Shang-Pu Tsai
- Protein Engineering and Antibody Technologies, EMD Serono, Billerica, MA, USA
| | - Saurabh Joshi
- Discovery Biology, Syngene International, Phase-IV, Bangalore, India
| | - Ralf Guenther
- Protein Engineering and Antibody Technologies, Merck KGaA, Darmstadt, Germany
| | - Achim Doerner
- Protein Engineering and Antibody Technologies, Merck KGaA, Darmstadt, Germany
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3
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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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4
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Chang J, Rader C, Peng H. A mammalian cell display platform based on scFab transposition. Antib Ther 2023; 6:157-169. [PMID: 37492588 PMCID: PMC10365156 DOI: 10.1093/abt/tbad009] [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: 12/27/2022] [Revised: 05/03/2023] [Accepted: 05/07/2023] [Indexed: 07/27/2023] Open
Abstract
In vitro display technologies have been successfully utilized for the discovery and evolution of monoclonal antibodies (mAbs) for diagnostic and therapeutic applications, with phage display and yeast display being the most commonly used platforms due to their simplicity and high efficiency. As their prokaryotic or lower eukaryotic host organisms typically have no or different post-translational modifications, several mammalian cell-based display and screening technologies for isolation and optimization of mAbs have emerged and are being developed. We report here a novel and useful mammalian cell display platform based on the PiggyBac transposon system to display mAbs in a single-chain Fab (scFab) format on the surface of HEK293F cells. Immune rabbit antibody libraries encompassing ~7 × 107 independent clones were generated in an all-in-one transposon vector, stably delivered into HEK293F cells and displayed as an scFab with rabbit variable and human constant domains. After one round of magnetic activated cell sorting and two rounds of fluorescence activated cell sorting, mAbs with high affinity in the subnanomolar range and cross-reactivity to the corresponding human and mouse antigens were identified, demonstrating the power of this platform for antibody discovery. We developed a highly efficient mammalian cell display platform based on the PiggyBac transposon system for antibody discovery, which could be further utilized for humanization as well as affinity and specificity maturation.
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Affiliation(s)
- Jing Chang
- Department of Immunology and Microbiology, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL 33458, USA
| | - Christoph Rader
- Department of Immunology and Microbiology, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL 33458, USA
| | - Haiyong Peng
- Department of Immunology and Microbiology, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL 33458, USA
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5
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Huhtinen O, Salbo R, Lamminmäki U, Prince S. Selection of biophysically favorable antibody variants using a modified Flp-In CHO mammalian display platform. Front Bioeng Biotechnol 2023; 11:1170081. [PMID: 37229492 PMCID: PMC10203562 DOI: 10.3389/fbioe.2023.1170081] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 04/17/2023] [Indexed: 05/27/2023] Open
Abstract
Mammalian display enables the selection of biophysically favorable antibodies from a large IgG antibody library displayed on the plasma membrane of mammalian cells. We constructed and validated a novel mammalian display platform utilizing the commercially available Flp-In CHO cell line as a starting point. We introduced a single copy of a landing pad for Bxb1 integrase-driven recombinase-mediated cassette exchange into the FRT site of the Flp-In CHO line to facilitate the efficient single-copy integration of an antibody display cassette into the genome of the cell line. We then proceeded to demonstrate the ability of our platform to select biophysically favorable antibodies from a library of 1 × 106 displayed antibodies designed to improve the biophysical properties of bococizumab via randomization of problematic hydrophobic surface residues of the antibody. Enrichment of bococizumab variants via fluorescence-activated cell sorting selections was followed by next generation sequencing and thorough characterization of biophysical properties of 10 bococizumab variants that subsequently allowed attribution of the mutations to the biophysical properties of the antibody variants. The mammalian displayed variants exhibited reduced aggregation propensity and polyreactivity, while critically retaining its target binding thereby demonstrating the utility of this valuable tool.
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Affiliation(s)
- Olli Huhtinen
- Protein and Antibody Engineering, Orion Corporation, Turku, Finland
- Department of Life Technologies, University of Turku, Turku, Finland
| | - Rune Salbo
- Protein and Antibody Engineering, Orion Corporation, Turku, Finland
| | - Urpo Lamminmäki
- Department of Life Technologies, University of Turku, Turku, Finland
| | - Stuart Prince
- MediCity Research Laboratory, University of Turku, Turku, Finland
- Institute of Biomedicine, University of Turku, Turku, Finland
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6
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Su W, Wang Y, Zou S, Zhao Y, Li Y, Zhang C, Guo X, Li S. Construction of Peptide Library in Mammalian Cells by dsDNA-Based Strategy. ACS OMEGA 2023; 8:1037-1046. [PMID: 36643544 PMCID: PMC9835800 DOI: 10.1021/acsomega.2c06402] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 12/19/2022] [Indexed: 06/16/2023]
Abstract
While different display technologies, represented by phage display, have been widely used in drug discovery, they still can hardly achieve function-based peptide screening, which in most cases is performed in mammalian cells. And most attempts to screen functional peptides with mammalian platforms utilized plasmids to store coding information. Our previous work established double-stranded DNAs (dsDNAs) as innovative biological parts to implement AND-gate genetic circuits in mammalian cells. In the current study, we employ dsDNAs with terminal NNK degenerate codons to implement AND-gate genetic circuits and generate peptide libraries in mammalian cells. This dsDNA-based AND-gate (DBAG) peptide library construction strategy is easy to perform, requiring only PCR reaction and cell transfection. High-throughput sequencing (HTS) and single-cell sequencing results revealed both peptide length and amino acid sequence diversity of DBAG peptide libraries. Moreover, as a feasibility test of this strategy, we identified an MDM2-interacting peptide by applying the DBAG peptide library to a mammalian cell-based two-hybrid system. Our work establishes dsDNAs with terminal degenerate codons as biological parts to build peptide libraries in mammalian cells, which may have great application potential in the future.
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Affiliation(s)
- Weijun Su
- School
of Medicine, Nankai University, Tianjin 300071, China
| | - Yi Wang
- Department
of Breast Cancer Pathology and Research Laboratory, Tianjin Medical
University Cancer Institute & 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
| | - Siqi Zou
- School
of Medicine, Nankai University, Tianjin 300071, China
| | - Yanjie Zhao
- Department
of Breast Cancer Pathology and Research Laboratory, Tianjin Medical
University Cancer Institute & 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 & 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
| | - Chunze Zhang
- Department
of Colorectal Surgery, Tianjin Union Medical
Center, Tianjin 300121, China
| | - Xiaojing Guo
- Department
of Breast Cancer Pathology and Research Laboratory, Tianjin Medical
University Cancer Institute & 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
| | - Shuai Li
- Department
of Breast Cancer Pathology and Research Laboratory, Tianjin Medical
University Cancer Institute & 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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7
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Gaa R, Mayer HM, Noack D, Doerner A. Efficient Microfluidic Downstream Processes for Rapid Antibody Hit Confirmation. Methods Mol Biol 2023; 2681:327-341. [PMID: 37405656 DOI: 10.1007/978-1-0716-3279-6_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2023]
Abstract
Microfluidics has been recently applied to better understand the spatial and temporal progression of the immune response in several species, for tool and biotherapeutic production cell line development and rapid antibody hit discovery. Several technologies have emerged that allow interrogation of large diversities of antibody-secreting cells in defined compartments such as picoliter droplets or nanopens. Mostly primary cells of immunized rodents but also recombinant mammalian libraries are screened for specific binding or directly for the desired function. While post-microfluidic downstream processes appear as standard steps, they represent considerable and interdependent challenges that can lead to high attrition rates even if original selections had been successful. In addition to next-generation sequencing recently described in depth elsewhere, this report aims at in detail explanations of exemplary droplet-based sorting followed by single-cell antibody gene PCR recovery and reproduction or single-cell sub-cultivation for crude supernatant confirmatory studies.
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Affiliation(s)
- Ramona Gaa
- Protein Engineering and Antibody Technologies, Merck Healthcare KGaA, Darmstadt, Germany
| | - Hannah Melina Mayer
- Protein Engineering and Antibody Technologies, Merck Healthcare KGaA, Darmstadt, Germany
| | - Daniela Noack
- Protein Engineering and Antibody Technologies, Merck Healthcare KGaA, Darmstadt, Germany
| | - Achim Doerner
- Protein Engineering and Antibody Technologies, Merck Healthcare KGaA, Darmstadt, Germany.
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8
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Gaa R, Mayer HM, Noack D, Kumari K, Guenther R, Tsai SP, Ji Q, Doerner A. Mammalian display to secretion switchable libraries for antibody preselection and high throughput functional screening. MAbs 2023; 15:2251190. [PMID: 37646089 PMCID: PMC10469430 DOI: 10.1080/19420862.2023.2251190] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 08/10/2023] [Accepted: 08/20/2023] [Indexed: 09/01/2023] Open
Abstract
Recently, there has been a co-evolution of mammalian libraries and diverse microfluidic approaches for therapeutic antibody hit discovery. Mammalian libraries enable the preservation of full immune repertoires, produce hit candidates in final format and facilitate broad combinatorial bispecific antibody screening, while several available microfluidic methodologies offer opportunities for rapid high-content screens. Here, we report proof-of-concept studies exploring the potential of combining microfluidic technologies with mammalian libraries for antibody discovery. First, antibody secretion, target co-expression and integration of appropriate reporter cell lines enabled the selection of in-trans acting agonistic bispecific antibodies. Second, a functional screen for internalization was established and comparison of autocrine versus co-encapsulation setups highlighted the advantages of an autocrine one cell approach. Third, synchronization of antibody-secreting cells prior to microfluidic screens reduced assay variability. Furthermore, a display to secretion switchable system was developed and applied for pre-enrichment of antibody clones with high manufacturability in conjunction with subsequent screening for functional properties. These case studies demonstrate the system's feasibility and may serve as basis for further development of integrated workflows combining manufacturability sorting and functional screens for the identification of optimal therapeutic antibody candidates.
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Affiliation(s)
- Ramona Gaa
- NBE Technologies, Merck KGaA, Darmstadt, Germany
| | | | | | - Kavita Kumari
- Discovery Biology, Syngene International, Bangalore, India
| | | | | | - Qingyong Ji
- NBE Technologies, EMD Serono, Billerica, MA, USA
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9
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Edelstein J, Fritz M, Lai SK. Challenges and opportunities in gene editing of B cells. Biochem Pharmacol 2022; 206:115285. [PMID: 36241097 DOI: 10.1016/j.bcp.2022.115285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/28/2022] [Accepted: 09/30/2022] [Indexed: 01/29/2023]
Abstract
B cells have long been an underutilized target in immune cell engineering, despite a number of unique attributes that could address longstanding challenges in medicine. Notably, B cells evolved to secrete large quantities of antibodies for prolonged periods, making them suitable platforms for long-term protein delivery. Recent advances in gene editing technologies, such as CRISPR-Cas, have improved the precision and efficiency of engineering and expanded potential applications of engineered B cells. While most work on B cell editing has focused on ex vivo modification, a body of recent work has also advanced the possibility of in vivo editing applications. In this review, we will discuss both past and current approaches to B cell engineering, and its promising applications in immunology research and therapeutic gene editing.
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Affiliation(s)
- Jasmine Edelstein
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Marshall Fritz
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Samuel K Lai
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA; Department of Biomedical Engineering, University of North Carolina, Chapel Hill, NC, USA; Department of Immunology and Microbiology, University of North Carolina, Chapel Hill, NC, USA.
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10
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Kleinboehl E, Laoharawee K, Moriarity B. Primary B cell engineering for therapeutic research. Trends Mol Med 2022; 28:528-529. [PMID: 35430120 PMCID: PMC9936666 DOI: 10.1016/j.molmed.2022.03.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/17/2022] [Accepted: 03/21/2022] [Indexed: 01/13/2023]
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11
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Mammalian Display Platform for the Maturation of Bispecific TCR-Based Molecules. Antibodies (Basel) 2022; 11:antib11020034. [PMID: 35645207 PMCID: PMC9150015 DOI: 10.3390/antib11020034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 04/22/2022] [Accepted: 04/29/2022] [Indexed: 02/06/2023] Open
Abstract
Bispecific T cell receptor (TCR)-based molecules capable of redirecting and activating T cells towards tumor cells represent a novel and promising class of biotherapeutics for the treatment of cancer. Usage of TCRs allows for targeting of intracellularly expressed and highly selective cancer antigens, but also requires a complex maturation process to increase the naturally low affinity and stability of TCRs. Even though TCR domains can be matured via phage and yeast display, these techniques share the disadvantages of non-human glycosylation patterns and the need for a later reformatting into the final bispecific format. Here, we describe the development and application of a Chinese Hamster Ovary (CHO) display for affinity engineering of TCRs in the context of the final bispecific TCR format. The recombinase-mediated cassette exchange (RCME)-based system allows for stable, single-copy integration of bispecific TCR molecules with high efficiency into a defined genetic locus of CHO cells. We used the system to isolate affinity-increased variants of bispecific T cell engaging receptor (TCER) molecules from a library encoding different CDR variants of a model TCR targeting preferentially expressed antigen in melanoma (PRAME). When expressed as a soluble protein, the selected TCER molecules exhibited strong reactivity against PRAME-positive tumor cells associated with a pronounced cytokine release from activated T cells. The obtained data support the usage of the CHO display-based maturation system for TCR affinity maturation in the context of the final bispecific TCER format.
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12
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Hanning KR, Minot M, Warrender AK, Kelton W, Reddy ST. Deep mutational scanning for therapeutic antibody engineering. Trends Pharmacol Sci 2021; 43:123-135. [PMID: 34895944 DOI: 10.1016/j.tips.2021.11.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/02/2021] [Accepted: 11/10/2021] [Indexed: 12/24/2022]
Abstract
The biophysical and functional properties of monoclonal antibody (mAb) drug candidates are often improved by protein engineering methods to increase the probability of clinical efficacy. One emerging method is deep mutational scanning (DMS) which combines the power of exhaustive protein mutagenesis and functional screening with deep sequencing and bioinformatics. The application of DMS has yielded significant improvements to the affinity, specificity, and stability of several preclinical antibodies alongside novel applications such as introducing multi-specific binding properties. DMS has also been applied directly on target antigens to precisely map antibody-binding epitopes and notably to profile the mutational escape potential of viral targets (e.g., SARS-CoV-2 variants). Finally, DMS combined with machine learning is enabling advances in the computational screening and engineering of therapeutic antibodies.
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Affiliation(s)
- Kyrin R Hanning
- Te Huataki Waiora School of Health, University of Waikato, Hamilton 3240, New Zealand
| | - Mason Minot
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, Basel 4058, Switzerland
| | - Annmaree K Warrender
- Te Huataki Waiora School of Health, University of Waikato, Hamilton 3240, New Zealand
| | - William Kelton
- Te Huataki Waiora School of Health, University of Waikato, Hamilton 3240, New Zealand.
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, Basel 4058, Switzerland.
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13
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Dyson MR, Masters E, Pazeraitis D, Perera RL, Syrjanen JL, Surade S, Thorsteinson N, Parthiban K, Jones PC, Sattar M, Wozniak-Knopp G, Rueker F, Leah R, McCafferty J. Beyond affinity: selection of antibody variants with optimal biophysical properties and reduced immunogenicity from mammalian display libraries. MAbs 2021; 12:1829335. [PMID: 33103593 PMCID: PMC7592150 DOI: 10.1080/19420862.2020.1829335] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The early phase of protein drug development has traditionally focused on target binding properties leading to a desired mode of therapeutic action. As more protein therapeutics pass through the development pipeline; however, it is clear that non-optimal biophysical properties can emerge, particularly as proteins are formulated at high concentrations, causing aggregation or polyreactivity. Such late-stage "developability" problems can lead to delay or failure in traversing the development process. Aggregation propensity is also correlated with increased immunogenicity, resulting in expensive, late-stage clinical failures. Using nucleases-directed integration, we have constructed large mammalian display libraries where each cell contains a single antibody gene/cell inserted at a single locus, thereby achieving transcriptional normalization. We show a strong correlation between poor biophysical properties and display level achieved in mammalian cells, which is not replicated by yeast display. Using two well-documented examples of antibodies with poor biophysical characteristics (MEDI-1912 and bococizumab), a library of variants was created based on surface hydrophobic and positive charge patches. Mammalian display was used to select for antibodies that retained target binding and permitted increased display level. The resultant variants exhibited reduced polyreactivity and reduced aggregation propensity. Furthermore, we show in the case of bococizumab that biophysically improved variants are less immunogenic than the parental molecule. Thus, mammalian display helps to address multiple developability issues during the earliest stages of lead discovery, thereby significantly de-risking the future development of protein drugs.
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Affiliation(s)
| | | | | | | | - Johanna L Syrjanen
- WM Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory , NY, USA
| | | | | | | | | | | | - Gordana Wozniak-Knopp
- Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences , Vienna, Austria
| | - Florian Rueker
- Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences , Vienna, Austria
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14
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Valldorf B, Hinz SC, Russo G, Pekar L, Mohr L, Klemm J, Doerner A, Krah S, Hust M, Zielonka S. Antibody display technologies: selecting the cream of the crop. Biol Chem 2021; 403:455-477. [PMID: 33759431 DOI: 10.1515/hsz-2020-0377] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 03/05/2021] [Indexed: 02/07/2023]
Abstract
Antibody display technologies enable the successful isolation of antigen-specific antibodies with therapeutic potential. The key feature that facilitates the selection of an antibody with prescribed properties is the coupling of the protein variant to its genetic information and is referred to as genotype phenotype coupling. There are several different platform technologies based on prokaryotic organisms as well as strategies employing higher eukaryotes. Among those, phage display is the most established system with more than a dozen of therapeutic antibodies approved for therapy that have been discovered or engineered using this approach. In recent years several other technologies gained a certain level of maturity, most strikingly mammalian display. In this review, we delineate the most important selection systems with respect to antibody generation with an emphasis on recent developments.
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Affiliation(s)
- Bernhard Valldorf
- Chemical and Pharmaceutical Development, Merck KGaA, Frankfurter Strasse 250, D-64293Darmstadt, Germany
| | - Steffen C Hinz
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, D-64287Darmstadt, Germany
| | - Giulio Russo
- Abcalis GmbH, Inhoffenstrasse 7, D-38124Braunschweig, Germany.,Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106Braunschweig, Germany
| | - Lukas Pekar
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, D-64293Darmstadt, Germany
| | - Laura Mohr
- Institute of Cell Biology and Neuroscience and Buchmann Institute for Molecular Life Sciences, University of Frankfurt, Max-von-Laue-Strasse 13, D-60438Frankfurt am Main, Germany
| | - Janina Klemm
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, D-64287Darmstadt, Germany
| | - Achim Doerner
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, D-64293Darmstadt, Germany
| | - Simon Krah
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, D-64293Darmstadt, Germany
| | - Michael Hust
- Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106Braunschweig, Germany
| | - Stefan Zielonka
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, D-64293Darmstadt, Germany
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15
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Aebischer-Gumy C, Moretti P, Ollier R, Ries Fecourt C, Rousseau F, Bertschinger M. SPLICELECT™: an adaptable cell surface display technology based on alternative splicing allowing the qualitative and quantitative prediction of secreted product at a single-cell level. MAbs 2021; 12:1709333. [PMID: 31955651 PMCID: PMC6973322 DOI: 10.1080/19420862.2019.1709333] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
We describe a mammalian expression construct (SPLICELECT™) that allows the redirection of a proportion of a secreted protein onto the cell surface using alternative splicing: whereas the majority of the RNA is spliced into a transcript encoding a secreted protein, a weak splice donor site yields a secondary transcript encoding, in addition, a C-terminal transmembrane domain. The different sequence elements can be modified in order to modulate the level of cell surface display and of secretion in an independent manner. In this work, we demonstrated that the cell surface display of stable cell lines is correlated with the level of the secreted protein of interest, but also with the level of heterodimerization in the case of a bispecific antibody. It was also shown that this construct may be useful for rapid screening of multiple antibody candidates in binding assays following transient transfection. Thus, the correlation of product quantity and quality of the secreted and of membrane-displayed product in combination with the flexibility of the construct with regards to cell surface display/secretion levels make SPLICELECT™ a valuable tool with many potential applications, not limited to industrial cell line development or antibody engineering.
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Affiliation(s)
- Christel Aebischer-Gumy
- Cell Sciences, Ichnos Sciences SA (formerly Glenmark Pharmaceuticals SA), La Chaux-de-Fonds, Switzerland
| | - Pierre Moretti
- Cell Sciences, Ichnos Sciences SA (formerly Glenmark Pharmaceuticals SA), La Chaux-de-Fonds, Switzerland
| | - Romain Ollier
- Antibody Engineering, Ichnos Sciences SA (formerly Glenmark Pharmaceuticals SA), La Chaux-de-Fonds, Switzerland
| | - Christelle Ries Fecourt
- Antibody Engineering, Ichnos Sciences SA (formerly Glenmark Pharmaceuticals SA), La Chaux-de-Fonds, Switzerland
| | - François Rousseau
- Antibody Engineering, Ichnos Sciences SA (formerly Glenmark Pharmaceuticals SA), La Chaux-de-Fonds, Switzerland
| | - Martin Bertschinger
- Cell Sciences, Ichnos Sciences SA (formerly Glenmark Pharmaceuticals SA), La Chaux-de-Fonds, Switzerland
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16
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Ministro JH, Oliveira SS, Oliveira JG, Cardoso M, Aires-da-Silva F, Corte-Real S, Goncalves J. Synthetic antibody discovery against native antigens by CRISPR/Cas9-library generation and endoplasmic reticulum screening. Appl Microbiol Biotechnol 2020; 104:2501-2512. [PMID: 32020276 DOI: 10.1007/s00253-020-10423-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 01/18/2020] [Accepted: 01/26/2020] [Indexed: 01/03/2023]
Abstract
Despite the significant advances of antibodies as therapeutic agents, there is still much room for improvement concerning the discovery of these macromolecules. Here, we present a new synthetic cell-based strategy that takes advantage of eukaryotic cell biology to produce highly diverse antibody libraries and, simultaneously, link them to a high-throughput selection mechanism, replicating B cell diversification mechanisms. The interference of site-specific recognition by CRISPR/Cas9 with error-prone DNA repair mechanisms was explored for the generation of diversity, in a cell population containing a gene for a light chain antibody fragment. We achieved up to 93% of cells containing a mutated antibody gene after diversification mechanisms, specifically inside one of the antigen-binding sites. This targeted variability strategy was then integrated into an intracellular selection mechanism. By fusing the antibody with a KDEL retention signal, the interaction of antibodies and native membrane antigens occurs inside the endoplasmic reticulum during the process of protein secretion, enabling the detection of high-quality leads for expression and affinity by flow cytometry. We successfully obtained antibody lead candidates against CD3 as proof of concept. In summary, we developed a novel antibody discovery platform against native antigens by endoplasmic synthetic library generation using CRISPR/Cas9, which will contribute to a faster discovery of new biotherapeutic molecules, reducing the time-to-market.
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Affiliation(s)
- Joana H Ministro
- iMed.ULisboa - Research Institute for Medicines, Faculty of Pharmacy, University of Lisbon, Av. Professor Gama Pinto, 1649-019, Lisbon, Portugal.,Technophage SA, Av. Prof. Egas Moniz, Edifício Egas Moniz, 1649-028, Lisbon, Portugal
| | - Soraia S Oliveira
- iMed.ULisboa - Research Institute for Medicines, Faculty of Pharmacy, University of Lisbon, Av. Professor Gama Pinto, 1649-019, Lisbon, Portugal.,Technophage SA, Av. Prof. Egas Moniz, Edifício Egas Moniz, 1649-028, Lisbon, Portugal
| | - Joana G Oliveira
- iMed.ULisboa - Research Institute for Medicines, Faculty of Pharmacy, University of Lisbon, Av. Professor Gama Pinto, 1649-019, Lisbon, Portugal.,Technophage SA, Av. Prof. Egas Moniz, Edifício Egas Moniz, 1649-028, Lisbon, Portugal
| | - Miguel Cardoso
- iMed.ULisboa - Research Institute for Medicines, Faculty of Pharmacy, University of Lisbon, Av. Professor Gama Pinto, 1649-019, Lisbon, Portugal
| | - Frederico Aires-da-Silva
- CIISA - Faculdade de Medicina Veterinária, Universidade de Lisboa, Av. da Universidade Técnica, 1300-477, Lisbon, Portugal
| | - Sofia Corte-Real
- iMed.ULisboa - Research Institute for Medicines, Faculty of Pharmacy, University of Lisbon, Av. Professor Gama Pinto, 1649-019, Lisbon, Portugal.,Technophage SA, Av. Prof. Egas Moniz, Edifício Egas Moniz, 1649-028, Lisbon, Portugal
| | - Joao Goncalves
- iMed.ULisboa - Research Institute for Medicines, Faculty of Pharmacy, University of Lisbon, Av. Professor Gama Pinto, 1649-019, Lisbon, Portugal.
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17
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Parthiban K, Perera RL, Sattar M, Huang Y, Mayle S, Masters E, Griffiths D, Surade S, Leah R, Dyson MR, McCafferty J. A comprehensive search of functional sequence space using large mammalian display libraries created by gene editing. MAbs 2019; 11:884-898. [PMID: 31107136 PMCID: PMC6601556 DOI: 10.1080/19420862.2019.1618673] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The construction of large libraries in mammalian cells allows the direct screening of millions of molecular variants for binding properties in a cell type relevant for screening or production. We have created mammalian cell libraries of up to 10 million clones displaying a repertoire of IgG-formatted antibodies on the cell surface. TALE nucleases or CRISPR/Cas9 were used to direct the integration of the antibody genes into a single genomic locus, thereby rapidly achieving stable expression and transcriptional normalization. The utility of the system is illustrated by the affinity maturation of a PD-1-blocking antibody through the systematic mutation and functional survey of 4-mer variants within a 16 amino acid paratope region. Mutating VH CDR3 only, we identified a dominant "solution" involving substitution of a central tyrosine to histidine. This appears to be a local affinity maximum, and this variant was surpassed by a lysine substitution when light chain variants were introduced. We achieve this comprehensive and quantitative interrogation of sequence space by combining high-throughput oligonucleotide synthesis with mammalian display and flow cytometry operating at the multi-million scale.
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18
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D'Amico L, Menzel U, Prummer M, Müller P, Buchi M, Kashyap A, Haessler U, Yermanos A, Gébleux R, Briendl M, Hell T, Wolter FI, Beerli RR, Truxova I, Radek Š, Vlajnic T, Grawunder U, Reddy S, Zippelius A. A novel anti-HER2 anthracycline-based antibody-drug conjugate induces adaptive anti-tumor immunity and potentiates PD-1 blockade in breast cancer. J Immunother Cancer 2019; 7:16. [PMID: 30665463 PMCID: PMC6341578 DOI: 10.1186/s40425-018-0464-1] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 11/23/2018] [Indexed: 12/31/2022] Open
Abstract
Increasing evidence suggests that antibody-drug conjugates (ADCs) can enhance anti-tumor immunity and improve clinical outcome. Here, we elucidate the therapeutic efficacy and immune-mediated mechanisms of a novel HER2-targeting ADC bearing a potent anthracycline derivate as payload (T-PNU) in a human HER2-expressing syngeneic breast cancer model resistant to trastuzumab and ado-trastuzumab emtansine. Mechanistically, the anthracycline component of the novel ADC induced immunogenic cell death leading to exposure and secretion of danger-associated molecular signals. RNA sequencing derived immunogenomic signatures and TCRβ clonotype analysis of tumor-infiltrating lymphocytes revealed a prominent role of the adaptive immune system in the regulation of T-PNU mediated anti-cancer activity. Depletion of CD8 T cells severely reduced T-PNU efficacy, thus confirming the role of cytotoxic T cells as drivers of the T-PNU mediated anti-tumor immune response. Furthermore, T-PNU therapy promoted immunological memory formation in tumor-bearing animals protecting those from tumor rechallenge. Finally, the combination of T-PNU and checkpoint inhibition, such as α-PD1, significantly enhanced tumor eradication following the treatment. In summary, a novel PNU-armed, HER2-targeting ADC elicited long-lasting immune protection in a murine orthotopic breast cancer model resistant to other HER2-directed therapies. Our findings delineate the therapeutic potential of this novel ADC payload and support its clinical development for breast cancer patients and potentially other HER2 expressing malignancies.
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Affiliation(s)
- Lucia D'Amico
- Cancer Immunology, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Ulrike Menzel
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Michael Prummer
- NEXUS Personalized Health Technologies, ETH Zürich, Switzerland and Swiss Institute of Bioinformatics, Zürich, Switzerland
| | - Philipp Müller
- Cancer Immunology, Department of Biomedicine, University of Basel, Basel, Switzerland.,Department of Cancer Immunology and Immune Modulation, Boehringer Ingelheim Pharma GmbH and Co. KG, Birkendorfer Str. 65, 88400, Biberach an der Riss, Germany
| | - Mélanie Buchi
- Cancer Immunology, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Abhishek Kashyap
- Cancer Immunology, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Ulrike Haessler
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Alexander Yermanos
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Rémy Gébleux
- NBE-Therapeutics Ltd, Hochbergerstrasse 60C, 4057, Basel, Switzerland
| | - Manfred Briendl
- NBE-Therapeutics Ltd, Hochbergerstrasse 60C, 4057, Basel, Switzerland
| | - Tamara Hell
- NBE-Therapeutics Ltd, Hochbergerstrasse 60C, 4057, Basel, Switzerland
| | - Fabian I Wolter
- NBE-Therapeutics Ltd, Hochbergerstrasse 60C, 4057, Basel, Switzerland.,Celonic AG, Eulerstrasse 55, 4051, Basel, Switzerland
| | - Roger R Beerli
- NBE-Therapeutics Ltd, Hochbergerstrasse 60C, 4057, Basel, Switzerland
| | - Iva Truxova
- Sotio s.a, Jankovcova 1518/2, 170 00, Prague 7, Czech Republic
| | - Špíšek Radek
- Sotio s.a, Jankovcova 1518/2, 170 00, Prague 7, Czech Republic
| | - Tatjana Vlajnic
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Ulf Grawunder
- NBE-Therapeutics Ltd, Hochbergerstrasse 60C, 4057, Basel, Switzerland
| | - Sai Reddy
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Alfred Zippelius
- Cancer Immunology, Department of Biomedicine, University of Basel, Basel, Switzerland.
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19
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Hellmann I, Waldmeier L, Bannwarth-Escher MC, Maslova K, Wolter FI, Grawunder U, Beerli RR. Novel Antibody Drug Conjugates Targeting Tumor-Associated Receptor Tyrosine Kinase ROR2 by Functional Screening of Fully Human Antibody Libraries Using Transpo-mAb Display on Progenitor B Cells. Front Immunol 2018; 9:2490. [PMID: 30450096 PMCID: PMC6224377 DOI: 10.3389/fimmu.2018.02490] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Accepted: 10/09/2018] [Indexed: 12/14/2022] Open
Abstract
Receptor tyrosine kinase-like orphan receptor 2 (ROR2) has been identified as a highly relevant tumor-associated antigen in a variety of cancer indications of high unmet medical need, including renal cell carcinoma and osteosarcoma, making it an attractive target for targeted cancer therapy. Here, we describe the de novo discovery of fully human ROR2-specific antibodies and potent antibody drug conjugates (ADCs) derived thereof by combining antibody discovery from immune libraries of human immunoglobulin transgenic animals using the Transpo-mAb mammalian cell-based IgG display platform with functional screening for internalizing antibodies using a secondary ADC assay. The discovery strategy entailed immunization of transgenic mice with the cancer antigen ROR2, harboring transgenic IgH and IgL chain gene loci with limited number of fully human V, D, and J gene segments. This was followed by recovering antibody repertoires from the immunized animals, expressing and screening them as full-length human IgG libraries by transposon-mediated display in progenitor B lymphocytes ("Transpo-mAb Display") for ROR2 binding. Individual cellular "Transpo-mAb" clones isolated by single cell sorting and capable of expressing membrane-bound as well as secreted human IgG were directly screened during antibody discovery, not only for high affinity binding to human ROR2, but also functionally as ADCs using a cytotoxicity assay with a secondary anti-human IgG-toxin-conjugate. Using this strategy, we identified and validated 12 fully human, monoclonal anti-human ROR2 antibodies with nanomolar affinities that are highly potent as ADCs and could be promising candidates for the therapy of human cancer. The screening for functional and internalizing antibodies during the early phase of antibody discovery demonstrates the utility of the mammalian cell-based Transpo-mAb Display platform to select for functional binders and as a powerful tool to improve the efficiency for the development of therapeutically relevant ADCs.
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20
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Mason DM, Weber CR, Parola C, Meng SM, Greiff V, Kelton WJ, Reddy ST. High-throughput antibody engineering in mammalian cells by CRISPR/Cas9-mediated homology-directed mutagenesis. Nucleic Acids Res 2018; 46:7436-7449. [PMID: 29931269 PMCID: PMC6101513 DOI: 10.1093/nar/gky550] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 06/04/2018] [Accepted: 06/06/2018] [Indexed: 12/26/2022] Open
Abstract
Antibody engineering is often performed to improve therapeutic properties by directed evolution, usually by high-throughput screening of phage or yeast display libraries. Engineering antibodies in mammalian cells offer advantages associated with expression in their final therapeutic format (full-length glycosylated IgG); however, the inability to express large and diverse libraries severely limits their potential throughput. To address this limitation, we have developed homology-directed mutagenesis (HDM), a novel method which extends the concept of CRISPR/Cas9-mediated homology-directed repair (HDR). HDM leverages oligonucleotides with degenerate codons to generate site-directed mutagenesis libraries in mammalian cells. By improving HDR to a robust efficiency of 15-35% and combining mammalian display screening with next-generation sequencing, we validated this approach can be used for key applications in antibody engineering at high-throughput: rational library construction, novel variant discovery, affinity maturation and deep mutational scanning (DMS). We anticipate that HDM will be a valuable tool for engineering and optimizing antibodies in mammalian cells, and eventually enable directed evolution of other complex proteins and cellular therapeutics.
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Affiliation(s)
- Derek M Mason
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
| | - Cédric R Weber
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
| | - Cristina Parola
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
- Life Science Graduate School, Systems Biology, ETH Zürich, University of Zurich, Zurich 8057, Switzerland
| | - Simon M Meng
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
| | - Victor Greiff
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
| | - William J Kelton
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
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21
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Potent and selective antitumor activity of a T cell-engaging bispecific antibody targeting a membrane-proximal epitope of ROR1. Proc Natl Acad Sci U S A 2018; 115:E5467-E5476. [PMID: 29844189 DOI: 10.1073/pnas.1719905115] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
T cell-engaging bispecific antibodies (biAbs) present a promising strategy for cancer immunotherapy, and numerous bispecific formats have been developed for retargeting cytolytic T cells toward tumor cells. To explore the therapeutic utility of T cell-engaging biAbs targeting the receptor tyrosine kinase ROR1, which is expressed by tumor cells of various hematologic and solid malignancies, we used a bispecific ROR1 × CD3 scFv-Fc format based on a heterodimeric and aglycosylated Fc domain designed for extended circulatory t1/2 and diminished systemic T cell activation. A diverse panel of ROR1-targeting scFv derived from immune and naïve rabbit antibody repertoires was compared in this bispecific format for target-dependent T cell recruitment and activation. An ROR1-targeting scFv with a membrane-proximal epitope, R11, revealed potent and selective antitumor activity in vitro, in vivo, and ex vivo and emerged as a prime candidate for further preclinical and clinical studies. To elucidate the precise location and engagement of this membrane-proximal epitope, which is conserved between human and mouse ROR1, the 3D structure of scFv R11 in complex with the kringle domain of ROR1 was determined by X-ray crystallography at 1.6-Å resolution.
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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: 49] [Impact Index Per Article: 8.2] [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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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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24
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Klose D, Woitok M, Niesen J, Beerli RR, Grawunder U, Fischer R, Barth S, Fendel R, Nachreiner T. Generation of an artificial human B cell line test system using Transpo-mAbTM technology to evaluate the therapeutic efficacy of novel antigen-specific fusion proteins. PLoS One 2017; 12:e0180305. [PMID: 28704435 PMCID: PMC5509223 DOI: 10.1371/journal.pone.0180305] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Accepted: 06/13/2017] [Indexed: 12/21/2022] Open
Abstract
The antigen-specific targeting of autoreactive B cells via their unique B cell receptors (BCRs) is a novel and promising alternative to the systemic suppression of humoral immunity. We generated and characterized cytolytic fusion proteins based on an existing immunotoxin comprising tetanus toxoid fragment C (TTC) as the targeting component and the modified Pseudomonas aeruginosa exotoxin A (ETA') as the cytotoxic component. The immunotoxin was reconfigured to replace ETA' with either the granzyme B mutant R201K or MAPTau as human effector domains. The novel cytolytic fusion proteins were characterized with a recombinant human lymphocytic cell line developed using Transpo-mAb™ technology. Genes encoding a chimeric TTC-reactive immunoglobulin G were successfully integrated into the genome of the precursor B cell line REH so that the cells could present TTC-reactive BCRs on their surface. These cells were used to investigate the specific cytotoxicity of GrB(R201K)-TTC and TTC-MAPTau, revealing that the serpin proteinase inhibitor 9-resistant granzyme B R201K mutant induced apoptosis specifically in the lymphocytic cell line. Our data confirm that antigen-based fusion proteins containing granzyme B (R201K) are suitable candidates for the depletion of autoreactive B cells.
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Affiliation(s)
- Diana Klose
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
- Department of Experimental Medicine and Immunotherapy, Institute for Applied Medical Engineering, University Hospital RWTH Aachen, Aachen, Germany
| | - Mira Woitok
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
- Institute of Molecular Biotechnology (Biology VII), RWTH Aachen University, Aachen, Germany
| | - Judith Niesen
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
| | | | | | - Rainer Fischer
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
- Institute of Molecular Biotechnology (Biology VII), RWTH Aachen University, Aachen, Germany
| | - Stefan Barth
- Department of Experimental Medicine and Immunotherapy, Institute for Applied Medical Engineering, University Hospital RWTH Aachen, Aachen, Germany
- South African Research Chair in Cancer Biotechnology, Institute of Infectious Disease and Molecular Medicine (IDM), Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Rolf Fendel
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
- * E-mail:
| | - Thomas Nachreiner
- Department of Experimental Medicine and Immunotherapy, Institute for Applied Medical Engineering, University Hospital RWTH Aachen, Aachen, Germany
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25
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Weber J, Peng H, Rader C. From rabbit antibody repertoires to rabbit monoclonal antibodies. Exp Mol Med 2017; 49:e305. [PMID: 28336958 PMCID: PMC5382564 DOI: 10.1038/emm.2017.23] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 12/22/2016] [Indexed: 12/11/2022] Open
Abstract
In this review, we explain why and how rabbit monoclonal antibodies have become outstanding reagents for laboratory research and increasingly for diagnostic and therapeutic applications. Starting with the unique ontogeny of rabbit B cells that affords highly distinctive antibody repertoires rich in in vivo pruned binders of high diversity, affinity and specificity, we describe the generation of rabbit monoclonal antibodies by hybridoma technology, phage display and alternative methods, along with an account of successful humanization strategies.
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Affiliation(s)
- Justus Weber
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA
| | - Haiyong Peng
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA
| | - Christoph Rader
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA
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26
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Stefan N, Gébleux R, Waldmeier L, Hell T, Escher M, Wolter FI, Grawunder U, Beerli RR. Highly Potent, Anthracycline-based Antibody–Drug Conjugates Generated by Enzymatic, Site-specific Conjugation. Mol Cancer Ther 2017; 16:879-892. [DOI: 10.1158/1535-7163.mct-16-0688] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 10/14/2016] [Accepted: 02/02/2017] [Indexed: 11/16/2022]
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