1
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Shukla S, Patel H, Chen S, Sun R, Wei L, Chen ZS. Dostarlimab in the treatment of mismatch repair deficient recurrent or advanced endometrial cancer. CANCER PATHOGENESIS AND THERAPY 2024; 2:135-141. [PMID: 39027143 PMCID: PMC11252537 DOI: 10.1016/j.cpt.2023.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 10/05/2023] [Accepted: 10/13/2023] [Indexed: 07/20/2024]
Abstract
Dostarlimab, a programmed death receptor-1 (PD-1)-blocking IgG4 humanized monoclonal antibody, gained accelerated approval from the US Food and Drug Administration (FDA) in April 2021, and received a full approval in February 2023. Dostarlimab was approved for treating adult patients with mismatch repair deficient (dMMR) recurrent or advanced endometrial cancer (EC) that progressed during or after prior treatment who have no other suitable treatment options. Herein, we review the structure-based mechanism of action of dostarlimab and the results of a clinical study (GARNET; NCT02715284) to comprehensively clarify the efficacy and toxicity of the drug. The efficacy and safety of dostarlimab as monotherapy was assessed in a non-randomized, multicenter, open-label, multi-cohort trial that included 209 patients with dMMR recurrent or advanced solid tumors after receiving systemic therapy. Patients received 500 mg of dostarlimab intravenously every three weeks until they were given four doses. Then, patients received 1000 mg dostarlimab intravenously every six weeks until disease progression or unacceptable toxicity. The overall response rate, as determined by shrinkage in tumor size, was 41.6% (95% confidence interval [CI]; 34.9, 48.6), with 34.7 months as the median response duration. In conclusion, dostarlimab is an immunotherapy-based drug that has shown promising results in adult patients with recurrent or advanced dMMR EC. However, its efficacy in other cancer subtypes, the development of resistance to monotherapy, and efficacy and safety in combination with other immunotherapeutic drugs have not yet been studied.
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Affiliation(s)
- Siddhant Shukla
- Institute for Biotechnology, St. John's University, New York, New York 11439, United States
| | - Harsh Patel
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, New York, New York 11439, United States
| | - Shuzhen Chen
- School of Pharmacy, Weifang Medical University, Weifang, Shandong 261053, China
| | - Rainie Sun
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, New York, New York 11439, United States
- Stuyvesant High School, New York, New York 10282, United States
| | - Liuya Wei
- School of Pharmacy, Weifang Medical University, Weifang, Shandong 261053, China
| | - Zhe-Sheng Chen
- Institute for Biotechnology, St. John's University, New York, New York 11439, United States
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, New York, New York 11439, United States
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2
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Huhtinen O, Prince S, Lamminmäki U, Salbo R, Kulmala A. Increased stable integration efficiency in CHO cells through enhanced nuclear localization of Bxb1 serine integrase. BMC Biotechnol 2024; 24:44. [PMID: 38926833 PMCID: PMC11210126 DOI: 10.1186/s12896-024-00871-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 06/20/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND Mammalian display is an appealing technology for therapeutic antibody development. Despite the advantages of mammalian display, such as full-length IgG display with mammalian glycosylation and its inherent ability to select antibodies with good biophysical properties, the restricted library size and large culture volumes remain challenges. Bxb1 serine integrase is commonly used for the stable genomic integration of antibody genes into mammalian cells, but presently lacks the efficiency required for the display of large mammalian display libraries. To increase the Bxb1 integrase-mediated stable integration efficiency, our study investigates factors that potentially affect the nuclear localization of Bxb1 integrase. METHODS In an attempt to enhance Bxb1 serine integrase-mediated integration efficiency, we fused various nuclear localization signals (NLS) to the N- and C-termini of the integrase. Concurrently, we co-expressed multiple proteins associated with nuclear transport to assess their impact on the stable integration efficiency of green fluorescent protein (GFP)-encoding DNA and an antibody display cassette into the genome of Chinese hamster ovary (CHO) cells containing a landing pad for Bxb1 integrase-mediated integration. RESULTS The nucleoplasmin NLS from Xenopus laevis, when fused to the C-terminus of Bxb1 integrase, demonstrated the highest enhancement in stable integration efficiency among the tested NLS fusions, exhibiting over a 6-fold improvement compared to Bxb1 integrase lacking an NLS fusion. Subsequent additions of extra NLS fusions to the Bxb1 integrase revealed an additional 131% enhancement in stable integration efficiency with the inclusion of two copies of C-terminal nucleoplasmin NLS fusions. Further improvement was achieved by co-expressing the Ran GTPase-activating protein (RanGAP). Finally, to validate the applicability of these findings to more complex proteins, the DNA encoding the membrane-bound clinical antibody abrilumab was stably integrated into the genome of CHO cells using Bxb1 integrase with two copies of C-terminal nucleoplasmin NLS fusions and co-expression of RanGAP. This approach demonstrated over 14-fold increase in integration efficiency compared to Bxb1 integrase lacking an NLS fusion. CONCLUSIONS This study demonstrates that optimizing the NLS sequence fusion for Bxb1 integrase significantly enhances the stable genomic integration efficiency. These findings provide a practical approach for constructing larger libraries in mammalian cells through the stable integration of genes into a genomic landing pad.
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Affiliation(s)
- Olli Huhtinen
- Protein & Antibody Engineering, Orion Corporation, Turku, Finland.
- 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
| | - Urpo Lamminmäki
- Department of Life Technologies, University of Turku, Turku, Finland
| | - Rune Salbo
- Protein & Antibody Engineering, Orion Corporation, Turku, Finland
| | - Antti Kulmala
- Protein & Antibody Engineering, Orion Corporation, Turku, Finland.
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3
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Weischedel J, Higgins L, Rogers S, Gramalla-Schmitz A, Wyrzykowska P, Borgoni S, MacCarthy T, Chahwan R. Modular cytosine base editing promotes epigenomic and genomic modifications. Nucleic Acids Res 2024; 52:e8. [PMID: 37994786 PMCID: PMC10810192 DOI: 10.1093/nar/gkad1118] [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: 12/08/2022] [Revised: 10/06/2023] [Accepted: 11/06/2023] [Indexed: 11/24/2023] Open
Abstract
Prokaryotic and eukaryotic adaptive immunity differ considerably. Yet, their fundamental mechanisms of gene editing via Cas9 and activation-induced deaminase (AID), respectively, can be conveniently complimentary. Cas9 is an RNA targeted dual nuclease expressed in several bacterial species. AID is a cytosine deaminase expressed in germinal centre B cells to mediate genomic antibody diversification. AID can also mediate epigenomic reprogramming via active DNA demethylation. It is known that sequence motifs, nucleic acid structures, and associated co-factors affect AID activity. But despite repeated attempts, deciphering AID's intrinsic catalytic activities and harnessing its targeted recruitment to DNA is still intractable. Even recent cytosine base editors are unable to fully recapitulate AID's genomic and epigenomic editing properties. Here, we describe the first instance of a modular AID-based editor that recapitulates the full spectrum of genomic and epigenomic editing activity. Our 'Swiss army knife' toolbox will help better understand AID biology per se as well as improve targeted genomic and epigenomic editing.
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Affiliation(s)
- Julian Weischedel
- Institute of Experimental Immunology, University of Zurich, Zurich 8057, Switzerland
| | - Laurence Higgins
- Living Systems Institute, University of Exeter, Exeter EX4 4QD, UK
| | - Sally Rogers
- Living Systems Institute, University of Exeter, Exeter EX4 4QD, UK
| | - Anna Gramalla-Schmitz
- Institute of Experimental Immunology, University of Zurich, Zurich 8057, Switzerland
| | - Paulina Wyrzykowska
- Institute of Experimental Immunology, University of Zurich, Zurich 8057, Switzerland
| | - Simone Borgoni
- Institute of Experimental Immunology, University of Zurich, Zurich 8057, Switzerland
| | - Thomas MacCarthy
- Department of Applied Mathematics & Statistics, Stony Brook University, NY 11794-3600, USA
| | - Richard Chahwan
- Institute of Experimental Immunology, University of Zurich, Zurich 8057, Switzerland
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4
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Ornelas MY, Cournoyer JE, Bram S, Mehta AP. Evolution and synthetic biology. Curr Opin Microbiol 2023; 76:102394. [PMID: 37801925 PMCID: PMC10842511 DOI: 10.1016/j.mib.2023.102394] [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: 02/19/2023] [Revised: 08/29/2023] [Accepted: 09/08/2023] [Indexed: 10/08/2023]
Abstract
Evolutionary observations have often served as an inspiration for biological design. Decoding of the central dogma of life at a molecular level and understanding of the cellular biochemistry have been elegantly used to engineer various synthetic biology applications, including building genetic circuits in vitro and in cells, building synthetic translational systems, and metabolic engineering in cells to biosynthesize and even bioproduce complex high-value molecules. Here, we review three broad areas of synthetic biology that are inspired by evolutionary observations: (i) combinatorial approaches toward cell-based biomolecular evolution, (ii) engineering interdependencies to establish microbial consortia, and (iii) synthetic immunology. In each of the areas, we will highlight the evolutionary premise that was central toward designing these platforms. These are only a subset of the examples where evolution and natural phenomena directly or indirectly serve as a powerful source of inspiration in shaping synthetic biology and biotechnology.
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Affiliation(s)
- Marya Y Ornelas
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Matthews Avenue, Urbana, IL 61801, United States
| | - Jason E Cournoyer
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Matthews Avenue, Urbana, IL 61801, United States
| | - Stanley Bram
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Matthews Avenue, Urbana, IL 61801, United States
| | - Angad P Mehta
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Matthews Avenue, Urbana, IL 61801, United States; Institute for Genomic Biology, University of Illinois at Urbana, Champaign, United States; Cancer Center at Illinois, University of Illinois at Urbana, Champaign, United States.
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5
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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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6
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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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7
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Rezhdo A, Lessard CT, Islam M, Van Deventer JA. Strategies for enriching and characterizing proteins with inhibitory properties on the yeast surface. Protein Eng Des Sel 2023; 36:gzac017. [PMID: 36648434 PMCID: PMC10365883 DOI: 10.1093/protein/gzac017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 10/20/2022] [Accepted: 11/07/2022] [Indexed: 01/18/2023] Open
Abstract
Display technologies are powerful tools for discovering binding proteins against a broad range of biological targets. However, it remains challenging to adapt display technologies for the discovery of proteins that inhibit the enzymatic activities of targets. Here, we investigate approaches for discovering and characterizing inhibitory antibodies in yeast display format using a well-defined series of constructs and the target matrix metalloproteinase-9. Three previously reported antibodies were used to create model libraries consisting of inhibitory, non-inhibitory, and non-binding constructs. Conditions that preferentially enrich for inhibitory clones were identified for both magnetic bead-based enrichments and fluorescence-activated cell sorting. Half maximal inhibitory concentration (IC50) was obtained through yeast titration assays. The IC50 of the inhibitory antibody obtained in yeast display format falls within the confidence interval of the IC50 value determined in soluble form. Overall, this study identifies strategies for the discovery and characterization of inhibitory clones directly in yeast display format.
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Affiliation(s)
- Arlinda Rezhdo
- Chemical and Biological Engineering Department, Tufts University, Medford, MA 02155, USA
| | - Catherine T Lessard
- Chemical and Biological Engineering Department, Tufts University, Medford, MA 02155, USA
| | - Mariha Islam
- Chemical and Biological Engineering Department, Tufts University, Medford, MA 02155, USA
| | - James A Van Deventer
- Chemical and Biological Engineering Department, Tufts University, Medford, MA 02155, USA
- Biomedical Engineering Department, Tufts University, Medford, MA 02155, USA
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8
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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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9
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Luo R, Qu B, An L, Zhao Y, Cao Y, Ren P, Hang H. Simultaneous Maturation of Single Chain Antibody Stability and Affinity by CHO Cell Display. Bioengineering (Basel) 2022; 9:bioengineering9080360. [PMID: 36004885 PMCID: PMC9404881 DOI: 10.3390/bioengineering9080360] [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: 05/29/2022] [Revised: 07/25/2022] [Accepted: 07/25/2022] [Indexed: 11/16/2022] Open
Abstract
Antibody stability and affinity are two important features of its applications in therapy and diagnosis. Antibody display technologies such as yeast and bacterial displays have been successfully used for improving both affinity and stability. Although mammalian cell display has also been utilized for maturing antibody affinity, it has not been applied for improving antibody stability. Previously, we developed a Chinese hamster ovary (CHO) cell display platform in which activation-induced cytidine deaminase (AID) was used to induce antibody mutation, and antibody affinity was successfully matured using the platform. In the current study, we developed thermo-resistant (TR) CHO cells for the purpose of maturing both antibody stability and affinity. We cultured TR CHO cells displaying an antibody mutant library and labeled them at temperatures above 41 °C, enriching cells that displayed antibody mutants with both the highest affinities and the highest display levels. To evaluate our system, we chose three antibodies to improve their affinities and stabilities. We succeeded in simultaneously improving both affinities and stabilities of all three antibodies. Of note, we obtained an anti-TNFα antibody mutant with a Tm (dissolution temperature) value 12 °C higher and affinity 160-fold greater than the parent antibody after two rounds of cell proliferation and flow cytometric sorting. By using CHO cells with its advantages in protein folding, post-translational modifications, and code usage, this procedure is likely to be widely used in maturing antibodies and other proteins in the future.
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Affiliation(s)
- Ruiqi Luo
- Key Laboratory for Protein and Peptide Pharmaceuticals, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; (R.L.); (B.Q.); (L.A.); (Y.Z.)
| | - Baole Qu
- Key Laboratory for Protein and Peptide Pharmaceuticals, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; (R.L.); (B.Q.); (L.A.); (Y.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lili An
- Key Laboratory for Protein and Peptide Pharmaceuticals, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; (R.L.); (B.Q.); (L.A.); (Y.Z.)
| | - Yun Zhao
- Key Laboratory for Protein and Peptide Pharmaceuticals, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; (R.L.); (B.Q.); (L.A.); (Y.Z.)
| | - Yang Cao
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
- Correspondence: (Y.C.); (P.R.); (H.H.)
| | - Peng Ren
- Department of Thoracic Surgery, Peking University Third Hospital, Beijing 100191, China
- Correspondence: (Y.C.); (P.R.); (H.H.)
| | - Haiying Hang
- Key Laboratory for Protein and Peptide Pharmaceuticals, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; (R.L.); (B.Q.); (L.A.); (Y.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (Y.C.); (P.R.); (H.H.)
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10
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Niu Z, Luo Z, Sun P, Ning L, Jin X, Chen G, Guo C, Zhi L, Chang W, Zhu W. In Vitro Nanobody Library Construction by Using Gene Designated-Region Pan-Editing Technology. BIODESIGN RESEARCH 2022; 2022:9823578. [PMID: 37850144 PMCID: PMC10521727 DOI: 10.34133/2022/9823578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 06/09/2022] [Indexed: 10/19/2023] Open
Abstract
Camelid single-domain antibody fragments (nanobodies) are an emerging force in therapeutic biopharmaceuticals and clinical diagnostic reagents in recent years. Nearly all nanobodies available to date have been obtained by animal immunization, a bottleneck restricting the large-scale application of nanobodies. In this study, we developed three kinds of gene designated-region pan-editing (GDP) technologies to introduce multiple mutations in complementarity-determining regions (CDRs) of nanobodies in vitro. Including the integration of G-quadruplex fragments in CDRs, which induces the spontaneous multiple mutations in CDRs; however, these mutant sequences are highly similar, resulting in a lack of sequences diversity in the CDRs. We also used CDR-targeting traditional gRNA-guided base-editors, which effectively diversify the CDRs. And most importantly, we developed the self-assembling gRNAs, which are generated by reprogrammed tracrRNA hijacking of endogenous mRNAs as crRNAs. Using base-editors guided by self-assembling gRNAs, we can realize the iteratively diversify the CDRs. And we believe the last GDP technology is highly promising in immunization-free nanobody library construction, and the full development of this novel nanobody discovery platform can realize the synthetic evolution of nanobodies in vitro.
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Affiliation(s)
- Zhiyuan Niu
- Synthetic Biology Engineering Lab of Henan Province, School of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, 453003 Henan, China
| | - Zhixia Luo
- Synthetic Biology Engineering Lab of Henan Province, School of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, 453003 Henan, China
| | - Pengyang Sun
- Synthetic Biology Engineering Lab of Henan Province, School of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, 453003 Henan, China
| | - Linwei Ning
- Synthetic Biology Engineering Lab of Henan Province, School of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, 453003 Henan, China
| | - Xinru Jin
- Synthetic Biology Engineering Lab of Henan Province, School of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, 453003 Henan, China
| | - Guanxu Chen
- Synthetic Biology Engineering Lab of Henan Province, School of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, 453003 Henan, China
| | - Changjiang Guo
- Synthetic Biology Engineering Lab of Henan Province, School of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, 453003 Henan, China
| | - Lingtong Zhi
- Synthetic Biology Engineering Lab of Henan Province, School of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, 453003 Henan, China
| | - Wei Chang
- Department of Oncology, Xinxiang First People’s Hospital, The Affiliated People’s Hospital of Xinxiang Medical University, Xinxiang 453000China
| | - Wuling Zhu
- Synthetic Biology Engineering Lab of Henan Province, School of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, 453003 Henan, China
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11
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Chocarro L, Blanco E, Arasanz H, Fernández-Rubio L, Bocanegra A, Echaide M, Garnica M, Ramos P, Fernández-Hinojal G, Vera R, Kochan G, Escors D. Clinical landscape of LAG-3-targeted therapy. IMMUNO-ONCOLOGY TECHNOLOGY 2022; 14:100079. [PMID: 35755891 PMCID: PMC9216443 DOI: 10.1016/j.iotech.2022.100079] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Lymphocyte-activated gene 3 (LAG-3) is a cell surface inhibitory receptor and a key regulator of immune homeostasis with multiple biological activities related to T-cell functions. LAG-3 is considered a next-generation immune checkpoint of clinical importance, right next to programmed cell death protein 1 (PD-1) and cytotoxic T-cell lymphocyte antigen-4 (CTLA-4). Indeed, it is the third inhibitory receptor to be exploited in human anticancer immunotherapies. Several LAG-3-antagonistic immunotherapies are being evaluated at various stages of preclinical and clinical development. In addition, combination therapies blocking LAG-3 together with other immune checkpoints are also being evaluated at preclinical and clinical levels. Indeed, the co-blockade of LAG-3 with PD-1 is demonstrating encouraging results. A new generation of bispecific PD-1/LAG-3-blocking agents have also shown strong capacities to specifically target PD-1+ LAG-3+ highly dysfunctional T cells and enhance their proliferation and effector activities. Here we identify and classify preclinical and clinical trials conducted involving LAG-3 as a target through an extensive bibliographic research. The current understanding of LAG-3 clinical applications is summarized, and most of the publically available data up to date regarding LAG-3-targeted therapy preclinical and clinical research and development are reviewed and discussed. LAG-3 is a highly important next-generation immune checkpoint molecule. Ninety-seven clinical trials are evaluating at least 16 LAG-3-targeting molecules. Here we identify preclinical and clinical studies conducted involving LAG-3. Bispecific LAG-3 molecules are being developed, showing strong capacities. LAG-3/PD-1 co-blockade is demonstrating encouraging results.
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Affiliation(s)
- L Chocarro
- Oncoimmunology Research Unit, Navarrabiomed-Fundación Miguel Servet, Universidad Pública de Navarra (UPNA), Hospital Universitario de Navarra (HUN), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
| | - E Blanco
- Oncoimmunology Research Unit, Navarrabiomed-Fundación Miguel Servet, Universidad Pública de Navarra (UPNA), Hospital Universitario de Navarra (HUN), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain.,Division of Gene Therapy and Regulation of Gene Expression, Cima Universidad de Navarra, Instituto de Investigación Sanitaria de Navarra (IdISNA), Pamplona, Spain
| | - H Arasanz
- Oncoimmunology Research Unit, Navarrabiomed-Fundación Miguel Servet, Universidad Pública de Navarra (UPNA), Hospital Universitario de Navarra (HUN), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain.,Medical Oncology Unit, Hospital Universitario de Navarra (HUN), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
| | - L Fernández-Rubio
- Oncoimmunology Research Unit, Navarrabiomed-Fundación Miguel Servet, Universidad Pública de Navarra (UPNA), Hospital Universitario de Navarra (HUN), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
| | - A Bocanegra
- Oncoimmunology Research Unit, Navarrabiomed-Fundación Miguel Servet, Universidad Pública de Navarra (UPNA), Hospital Universitario de Navarra (HUN), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
| | - M Echaide
- Oncoimmunology Research Unit, Navarrabiomed-Fundación Miguel Servet, Universidad Pública de Navarra (UPNA), Hospital Universitario de Navarra (HUN), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
| | - M Garnica
- Oncoimmunology Research Unit, Navarrabiomed-Fundación Miguel Servet, Universidad Pública de Navarra (UPNA), Hospital Universitario de Navarra (HUN), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
| | - P Ramos
- Oncoimmunology Research Unit, Navarrabiomed-Fundación Miguel Servet, Universidad Pública de Navarra (UPNA), Hospital Universitario de Navarra (HUN), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
| | - G Fernández-Hinojal
- Oncoimmunology Research Unit, Navarrabiomed-Fundación Miguel Servet, Universidad Pública de Navarra (UPNA), Hospital Universitario de Navarra (HUN), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain.,Medical Oncology Department, Hospital Clínico San Carlos, Madrid, Spain
| | - R Vera
- Medical Oncology Unit, Hospital Universitario de Navarra (HUN), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
| | - G Kochan
- Oncoimmunology Research Unit, Navarrabiomed-Fundación Miguel Servet, Universidad Pública de Navarra (UPNA), Hospital Universitario de Navarra (HUN), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
| | - D Escors
- Oncoimmunology Research Unit, Navarrabiomed-Fundación Miguel Servet, Universidad Pública de Navarra (UPNA), Hospital Universitario de Navarra (HUN), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
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12
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Zhang MQ, Wang ZG, Fu DD, Zhang JM, Liu HY, Liu SL, Pang DW. Quantum Dots Tracking Endocytosis and Transport of Proteins Displayed by Mammalian Cells. Anal Chem 2022; 94:7567-7575. [PMID: 35581735 DOI: 10.1021/acs.analchem.2c00411] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Mammalian cell display technology uses eukaryotic protein expression system to display proteins on cell surfaces and has become an important method in biological research. Although mammalian cell display technology has many advantages and development potential, certain attributes of the displayed protein remain uncharacterized, such as whether the displayed proteins re-enter the cell and how displayed proteins move into the cell. Here, we present the endocytosis mechanism, motility behavior, and transport kinetics of displayed proteins determined using HaloTag as the displayed protein and quantum dot-based single-particle tracking. The displayed protein enters the cell through clathrin-mediated endocytosis and is transported through the cell in three stages, which is dependent on microfilaments and microtubules. The dynamic information obtained in this study provides answers to questions about endocytosis and postendocytosis transport of displayed proteins and, therefore, is expected to facilitate the development of surface display technology.
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Affiliation(s)
- Meng-Qian Zhang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Zhi-Gang Wang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin 300071, P. R. China
| | - Dan-Dan Fu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Ju-Mei Zhang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Hao-Yang Liu
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin 300071, P. R. China
| | - Shu-Lin Liu
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin 300071, P. R. China
| | - Dai-Wen Pang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China.,State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin 300071, P. R. China
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13
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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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14
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Engineering Proteins Containing Noncanonical Amino Acids on the Yeast Surface. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2491:491-559. [PMID: 35482204 DOI: 10.1007/978-1-0716-2285-8_23] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Yeast display has been used to advance many critical research areas, including the discovery of unique protein binders and biological therapeutics. In parallel, noncanonical amino acids (ncAAs) have been used to tailor antibody-drug conjugates and enable discovery of therapeutic leads. Together, these two technologies have allowed for generation of synthetic antibody libraries, where the introduction of ncAAs in yeast-displayed proteins allows for library screening for therapeutically relevant targets. The combination of yeast display with genetically encoded ncAAs increases the available chemistry in proteins and advances applications that require high-throughput strategies. In this chapter, we discuss methods for displaying proteins containing ncAAs on the yeast surface, generating and screening libraries of proteins containing ncAAs, preparing bioconjugates on the yeast surface in large scale, generating and screening libraries of aminoacyl-tRNA synthetases (aaRSs) for encoding ncAAs by using reporter constructs, and characterizing ncAA-containing proteins secreted from yeast. The experimental designs laid out in this chapter are generalizable for discovery of protein binders to a variety of targets and aaRS evolution to continue expanding the genetic code beyond what is currently available in yeast.
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15
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Kramer L, Song HW, Mitchell K, Kartik M, Jain R, Escarra VL, Quiros E, Fu H, Singh A, Roy K. Lipid Membrane‐Based Antigen Presentation to B Cells Using a Fully Synthetic Ex Vivo Germinal Center Model. ADVANCED NANOBIOMED RESEARCH 2022; 2. [DOI: 10.1002/anbr.202100137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Liana Kramer
- Wallace H. Coulter Department of Biomedical Engineering Georgia Institute of Technology and Emory University School of Medicine 313 Ferst Dr NW Atlanta GA 30332 USA
| | - Hannah W. Song
- Wallace H. Coulter Department of Biomedical Engineering Georgia Institute of Technology and Emory University School of Medicine 313 Ferst Dr NW Atlanta GA 30332 USA
| | - Kaiya Mitchell
- Wallace H. Coulter Department of Biomedical Engineering Georgia Institute of Technology and Emory University School of Medicine 313 Ferst Dr NW Atlanta GA 30332 USA
| | - Mythili Kartik
- Wallace H. Coulter Department of Biomedical Engineering Georgia Institute of Technology and Emory University School of Medicine 313 Ferst Dr NW Atlanta GA 30332 USA
| | - Ritika Jain
- Wallace H. Coulter Department of Biomedical Engineering Georgia Institute of Technology and Emory University School of Medicine 313 Ferst Dr NW Atlanta GA 30332 USA
| | - Victoria Lozano Escarra
- Wallace H. Coulter Department of Biomedical Engineering Georgia Institute of Technology and Emory University School of Medicine 313 Ferst Dr NW Atlanta GA 30332 USA
| | - Enrique Quiros
- Wallace H. Coulter Department of Biomedical Engineering Georgia Institute of Technology and Emory University School of Medicine 313 Ferst Dr NW Atlanta GA 30332 USA
| | - Harrison Fu
- Wallace H. Coulter Department of Biomedical Engineering Georgia Institute of Technology and Emory University School of Medicine 313 Ferst Dr NW Atlanta GA 30332 USA
| | - Ankur Singh
- Wallace H. Coulter Department of Biomedical Engineering Georgia Institute of Technology and Emory University School of Medicine 313 Ferst Dr NW Atlanta GA 30332 USA
- George W. Woodruff School of Mechanical Engineering Georgia Institute of Technology 313 Ferst Dr NW Atlanta GA 30332 USA
- Parker H. Petit Institute for Bioengineering and Bioscience Georgia Institute of Technology 315 Ferst Dr NW Atlanta GA 30332 USA
| | - Krishnendu Roy
- Wallace H. Coulter Department of Biomedical Engineering Georgia Institute of Technology and Emory University School of Medicine 313 Ferst Dr NW Atlanta GA 30332 USA
- Parker H. Petit Institute for Bioengineering and Bioscience Georgia Institute of Technology 315 Ferst Dr NW Atlanta GA 30332 USA
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16
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Immune Checkpoint Inhibitors (ICI) in Advanced and Recurrent Endometrial Cancer. INDIAN JOURNAL OF GYNECOLOGIC ONCOLOGY 2022. [DOI: 10.1007/s40944-021-00599-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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17
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Masuda H, Sawada A, Hashimoto SI, Tamai K, Lin KY, Harigai N, Kurosawa K, Ohta K, Seo H, Itou H. Fast-tracking antibody maturation using a B cell-based display system. MAbs 2022; 14:2122275. [PMID: 36202784 PMCID: PMC9542628 DOI: 10.1080/19420862.2022.2122275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Affinity maturation, an essential component of antibody engineering, is crucial for developing therapeutic antibodies. Cell display system coupled with somatic hypermutation (SHM) initiated by activation-induced cytidine deaminase (AID) is a commonly used technique for affinity maturation. AID introduces targeted DNA lesions into hotspots of immunoglobulin (Ig) gene loci followed by erroneous DNA repair, leading to biased mutations in the complementary determining regions. However, systems that use an in vivo mimicking mechanism often require several rounds of selection to enrich clones possessing accumulated mutations. We previously described the human ADLib® system, which features autonomous, AID-mediated diversification in Ig gene loci of a chicken B cell line DT40 and streamlines human antibody generation and optimization in one integrated platform. In this study, we further engineered DT40 capable of receiving exogenous antibody genes and examined whether the antibody could be affinity matured. The Ig genes of three representative anti-hVEGF-A antibodies originating from the human ADLib® were introduced; the resulting human IgG1 antibodies had up to 76.4-fold improvement in binding affinities (sub-picomolar KD) within just one round of optimization, owing to efficient accumulation of functional mutations. Moreover, we successfully improved the affinity of a mouse hybridoma-derived anti-hCDCP1 antibody using the engineered DT40, and the observed mutations remained effective in the post-humanized antibody as exhibited by an 8.2-fold increase of in vitro cytotoxicity without compromised physical stability. These results demonstrated the versatility of the novel B cell-based affinity maturation system as an easy-to-use antibody optimization tool regardless of the species of origin.Abbreviations: ADLib®: Autonomously diversifying library, ADLib® KI-AMP: ADLib® knock-in affinity maturation platform, AID: activation-induced cytidine deaminase, CDRs: complementary-determining regions, DIVAC: diversification activator, ECD: extracellular domain, FACS: fluorescence-activated cell sorting, FCM: flow cytometry, HC: heavy chainIg: immunoglobulin, LC: light chain, NGS: next-generation sequencing, PBD: pyrrolobenzodiazepine, SHM: somatic hypermutation, SPR: surface plasmon resonance.
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Affiliation(s)
- Hitomi Masuda
- Research Laboratories, Chiome Bioscience Inc, Tokyo, Japan,CONTACT Hitomi Masuda Research Laboratories, Chiome Bioscience Inc, Sumitomo-Fudosan Nishi-shinjuku bldg. No. 6, 3-12-1 Honmachi, Shibuya-ku, Tokyo151-0071, Japan
| | - Atsushi Sawada
- Research Laboratories, Chiome Bioscience Inc, Tokyo, Japan
| | | | - Kanako Tamai
- Research Laboratories, Chiome Bioscience Inc, Tokyo, Japan
| | - Ke-Yi Lin
- Research Laboratories, Chiome Bioscience Inc, Tokyo, Japan
| | - Naoto Harigai
- Research Laboratories, Chiome Bioscience Inc, Tokyo, Japan
| | - Kohei Kurosawa
- Research Laboratories, Chiome Bioscience Inc, Tokyo, Japan
| | - Kunihiro Ohta
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Hidetaka Seo
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Hiroshi Itou
- Research Laboratories, Chiome Bioscience Inc, Tokyo, Japan,Hiroshi Itou Research Laboratories, Chiome Bioscience Inc, Sumitomo-Fudosan Nishi-shinjuku bldg. No. 6, 3-12-1, Honmachi, Shibuya-ku, Tokyo 151-0071 Japan
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18
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de Brito PM, Saruga A, Cardoso M, Goncalves J. Methods and cell-based strategies to produce antibody libraries: current state. Appl Microbiol Biotechnol 2021; 105:7215-7224. [PMID: 34524471 DOI: 10.1007/s00253-021-11570-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 09/01/2021] [Accepted: 09/02/2021] [Indexed: 11/24/2022]
Abstract
Antibodies are critical components of the adaptive immune system, whose therapeutic applications have been growing exponentially in the last years. Discovery and development of therapeutic antibodies encompasses in vivo immunization, synthetic libraries, and surface display methodologies. To overcome some of their limitations, several platforms in higher eukaryotic cells have been developed. Moreover, these platforms aim to replicate in the bench both primary and secondary antibody diversification mechanisms that occur in vivo. Here, we describe the latest strategies that have been used to mirror both naïve and affinity-maturated antibody repertoire. KEY POINTS: • Therapeutic antibodies are one of the most promising classes of drugs to fight diseases. • Antibodies discovered through hybridoma or display technologies require further engineering. • Innovative antibody discovery platforms in higher eukaryotic cells have been developed.
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Affiliation(s)
- Paula Matos de Brito
- Faculty of Pharmacy, iMed.ULisboa - Research Institute for Medicines, University of Lisbon, Av. Professor Gama Pinto, 1649-019, Lisbon, Portugal
| | - Andreia Saruga
- Faculty of Pharmacy, iMed.ULisboa - Research Institute for Medicines, University of Lisbon, Av. Professor Gama Pinto, 1649-019, Lisbon, Portugal.,INESC MN - Instituto de Engenharia de Sistemas e Computadores - Microsystems and Nanotecnologies, R. Alves Redol 9, 1000-029, Lisbon, Portugal
| | - Miguel Cardoso
- Faculty of Pharmacy, iMed.ULisboa - Research Institute for Medicines, University of Lisbon, Av. Professor Gama Pinto, 1649-019, Lisbon, Portugal
| | - Joao Goncalves
- Faculty of Pharmacy, iMed.ULisboa - Research Institute for Medicines, University of Lisbon, Av. Professor Gama Pinto, 1649-019, Lisbon, Portugal.
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19
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Furtmann N, Schneider M, Spindler N, Steinmann B, Li Z, Focken I, Meyer J, Dimova D, Kroll K, Leuschner WD, Debeaumont A, Mathieu M, Lange C, Dittrich W, Kruip J, Schmidt T, Birkenfeld J. An end-to-end automated platform process for high-throughput engineering of next-generation multi-specific antibody therapeutics. MAbs 2021; 13:1955433. [PMID: 34382900 PMCID: PMC8366542 DOI: 10.1080/19420862.2021.1955433] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Next-generation multi-specific antibody therapeutics (MSATs) are engineered to combine several functional activities into one molecule to provide higher efficacy compared to conventional, mono-specific antibody therapeutics. However, highly engineered MSATs frequently display poor yields and less favorable drug-like properties (DLPs), which can adversely affect their development. Systematic screening of a large panel of MSAT variants in very high throughput (HT) is thus critical to identify potent molecule candidates with good yield and DLPs early in the discovery process. Here we report on the establishment of a novel, format-agnostic platform process for the fast generation and multiparametric screening of tens of thousands of MSAT variants. To this end, we have introduced full automation across the entire value chain for MSAT engineering. Specifically, we have automated the in-silico design of very large MSAT panels such that it reflects precisely the wet-lab processes for MSAT DNA library generation. This includes mass saturation mutagenesis or bulk modular cloning technologies while, concomitantly, enabling library deconvolution approaches using HT Sanger DNA sequencing. These DNA workflows are tightly linked to fully automated downstream processes for compartmentalized mammalian cell transfection expression, and screening of multiple parameters. All sub-processes are seamlessly integrated with tailored workflow supporting bioinformatics. As described here, we used this platform to perform multifactor optimization of a next-generation bispecific, cross-over dual variable domain-Ig (CODV-Ig). Screening of more than 25,000 individual protein variants in mono- and bispecific format led to the identification of CODV-Ig variants with over 1,000-fold increased potency and significantly optimized production titers, demonstrating the power and versatility of the platform.
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Affiliation(s)
- Norbert Furtmann
- R&D Large Molecules Research Platform Germany, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Frankfurt Am Main, Germany
| | - Marion Schneider
- R&D Large Molecules Research Platform Germany, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Frankfurt Am Main, Germany
| | - Nadja Spindler
- R&D Large Molecules Research Platform Germany, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Frankfurt Am Main, Germany
| | - Bjoern Steinmann
- R&D Large Molecules Research Platform Germany, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Frankfurt Am Main, Germany
| | - Ziyu Li
- R&D Integrated Drug Discovery Germany, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Frankfurt Am Main, Germany
| | - Ingo Focken
- R&D Large Molecules Research Platform Germany, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Frankfurt Am Main, Germany
| | - Joachim Meyer
- Digital R&D, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Frankfurt Am Main, Germany
| | - Dilyana Dimova
- R&D Large Molecules Research Platform Germany, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Frankfurt Am Main, Germany
| | - Katja Kroll
- R&D Large Molecules Research Platform Germany, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Frankfurt Am Main, Germany
| | - Wulf Dirk Leuschner
- R&D Large Molecules Research Platform Germany, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Frankfurt Am Main, Germany
| | - Audrey Debeaumont
- R&D Large Molecules Research Platform Germany, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Frankfurt Am Main, Germany
| | - Magali Mathieu
- R&D Integrated Drug Discovery France, Sanofi, Vitry Sur Seine Cedex, France
| | - Christian Lange
- R&D Large Molecules Research Platform Germany, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Frankfurt Am Main, Germany
| | - Werner Dittrich
- R&D Large Molecules Research Platform Germany, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Frankfurt Am Main, Germany
| | - Jochen Kruip
- IA Specialty Care Digital Innovation Biologics, Sanofi-Aventis Deutschland GmbH, Frankfurt Am Main, Germany
| | - Thorsten Schmidt
- R&D Large Molecules Research Platform Germany, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Frankfurt Am Main, Germany
| | - Joerg Birkenfeld
- R&D Large Molecules Research Platform Germany, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Frankfurt Am Main, Germany
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20
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Kumar S, Ghosh S, Sharma G, Wang Z, Kehry MR, Marino MH, Neben TY, Lu S, Luo S, Roberts S, Ramaswamy S, Danaee H, Jenkins D. Preclinical characterization of dostarlimab, a therapeutic anti-PD-1 antibody with potent activity to enhance immune function in in vitro cellular assays and in vivo animal models. MAbs 2021; 13:1954136. [PMID: 34313545 PMCID: PMC8317941 DOI: 10.1080/19420862.2021.1954136] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Inhibitors of programmed cell death protein 1 (PD-1) and its ligand (PD-L1) have dramatically changed the treatment landscape for patients with cancer. Clinical activity of anti-PD-(L)1 antibodies has resulted in increased median overall survival and durable responses in patients across selected tumor types. To date, 6 PD-1 and PD-L1, here collectively referred to as PD-(L)1, pathway inhibitors are approved by the US Food and Drug Administration for clinical use. The availability of multiple anti-PD-(L)1 antibodies provides treatment and dosing regimen choice for patients with cancer. Here, we describe the nonclinical characterization of dostarlimab (TSR-042), a humanized anti-PD-1 antibody, which binds with high affinity to human PD-1 and effectively inhibits its interaction with its ligands, PD-L1 and PD-L2. Dostarlimab enhanced effector T-cell functions, including cytokine production, in vitro. Since dostarlimab does not bind mouse PD-1, its single-agent antitumor activity was evaluated using humanized mouse models. In this model system, dostarlimab demonstrated antitumor activity as assessed by tumor growth inhibition, which was associated with increased infiltration of immune cells. Single-dose and 4-week repeat-dose toxicology studies in cynomolgus monkeys indicated that dostarlimab was well tolerated. In a clinical setting, based on data from the GARNET trial, dostarlimab (Jemperli) was approved for the treatment of adult patients with mismatch repair–deficient recurrent or advanced endometrial cancer that had progressed on or following prior treatment with a platinum-containing regimen. Taken together, these data demonstrate that dostarlimab is a potent anti-PD-1 receptor antagonist, with properties that support its continued clinical investigation in patients with cancer.
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Affiliation(s)
- Sujatha Kumar
- Translational Research, Immuno-Oncology, Checkmate Pharmaceuticals, Cambridge, MA, USA
| | - Srimoyee Ghosh
- Oncology Experimental Medicine Unit, GlaxoSmithKline, Waltham, MA, USA
| | - Geeta Sharma
- Synthetic Lethal Research Unit, Oncolog, GlaxoSmithKline, Waltham, MA, USA
| | - Zebin Wang
- Translational Strategy & Research, GlaxoSmithKline,Waltham, MA, USA
| | | | | | | | - Sharon Lu
- Clinical Pharmacology, Scholar Rock, Cambridge, MA, USA
| | - Shouqi Luo
- Toxicology, Atea Pharmaceuticals, Boston, MA, USA
| | - Simon Roberts
- Nonclinical Development, Research In Vivo/In Vitro Translation, GlaxoSmithKline, Waltham, MA, USA
| | | | - Hadi Danaee
- Translational Medicine, Blue Print Medicines, Cambridge, MA, USA
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21
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Yin Y, Quinlan BD, Ou T, Guo Y, He W, Farzan M. In vitro affinity maturation of broader and more-potent variants of the HIV-1-neutralizing antibody CAP256-VRC26.25. Proc Natl Acad Sci U S A 2021; 118:e2106203118. [PMID: 34261793 PMCID: PMC8307357 DOI: 10.1073/pnas.2106203118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Three variable 2 (V2) loops of HIV-1 envelope glycoprotein (Env) trimer converge at the Env apex to form the epitope of an important classes of HIV-1 broadly neutralizing antibodies (bNAbs). These V2-glycan/apex antibodies are exceptionally potent but less broad (∼60 to 75%) than many other bNAbs. Their CDRH3 regions are typically long, acidic, and tyrosine sulfated. Tyrosine sulfation complicates efforts to improve these antibodies through techniques such as phage or yeast display. To improve the breadth of CAP256-VRC26.25 (VRC26.25), a very potent apex antibody, we adapted and extended a B cell display approach. Specifically, we used CRISPR/Cas12a to introduce VRC26.25 heavy- and light-chain genes into their respective loci in a B cell line, ensuring that each cell expresses a single VRC26.25 variant. We then diversified these loci through activation-induced cytidine deaminase-mediated hypermutation and homology-directed repair using randomized CDRH3 sequences as templates. Iterative sorting with soluble Env trimers and further randomization selected VRC26.25 variants with successively improving affinities. Three mutations in the CDRH3 region largely accounted for this improved affinity, and VRC26.25 modified with these mutations exhibited greater breadth and potency than the original antibody. Our data describe a broader and more-potent form of VRC26.25 as well as an approach useful for improving the breadth and potency of antibodies with functionally important posttranslational modifications.
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Affiliation(s)
- Yiming Yin
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458
| | - Brian D Quinlan
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458
| | - Tianling Ou
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458
| | - Yan Guo
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458
| | - Wenhui He
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458
| | - Michael Farzan
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458
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22
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Hendel SJ, Shoulders MD. Directed evolution in mammalian cells. Nat Methods 2021; 18:346-357. [PMID: 33828274 DOI: 10.1038/s41592-021-01090-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 02/01/2021] [Accepted: 02/09/2021] [Indexed: 02/06/2023]
Abstract
Directed evolution experiments are typically carried out using in vitro systems, bacteria, or yeast-even when the goal is to probe or modulate mammalian biology. Performing directed evolution in systems that do not match the intended mammalian environment severely constrains the scope and functionality of the targets that can be evolved. We review new platforms that are now making it possible to use the mammalian cell itself as the setting for directed evolution and present an overview of frontier challenges and high-impact targets for this approach.
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Affiliation(s)
- Samuel J Hendel
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Matthew D Shoulders
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.
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23
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Griesbeck O. CRISPR/Cas9-based directed evolution in mammalian cells. Curr Opin Struct Biol 2021; 69:35-40. [PMID: 33784525 DOI: 10.1016/j.sbi.2021.02.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 02/13/2021] [Accepted: 02/15/2021] [Indexed: 11/25/2022]
Abstract
An increasingly powerful set of new CRISPR/Cas-based methods is becoming available for directed evolution of proteins in mammalian cells. Although in vitro techniques or microbial expression systems have been dominating directed evolution, there are now promising approaches to diversify proteins in mammalian cells in situ. This can be achieved by simple indel mutagenesis or more sophisticated homology repair mechanisms for cassette mutagenesis of coding sequences. Cas9 variant fusions to base editors and other effectors pose another promising way to introduce diversity into proteins. CRISPR/Cas9-based directed evolution in mammalian cells opens a new exciting era of discovery for the many classes of proteins for which a mammalian cellular context is preferable.
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Affiliation(s)
- Oliver Griesbeck
- Max-Planck-Institut für Neurobiologie, Am Klopferspitz 18, 82152, Martinsried, Germany.
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24
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Affinity maturation: highlights in the application of in vitro strategies for the directed evolution of antibodies. Emerg Top Life Sci 2021; 5:601-608. [PMID: 33660765 PMCID: PMC8726058 DOI: 10.1042/etls20200331] [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] [Received: 12/08/2020] [Revised: 02/16/2021] [Accepted: 02/23/2021] [Indexed: 01/04/2023]
Abstract
Affinity maturation is a key technique in protein engineering which is used to improve affinity and binding interactions in vitro, a process often required to fulfil the therapeutic potential of antibodies. There are many available display technologies and maturation methods developed over the years, which have been instrumental in the production of therapeutic antibodies. However, due to the inherent limitations in display capacity of these technologies, accommodation of expansive and complex library builds is still a challenge. In this article, we discuss our recent efforts in the affinity maturation of a difficult antibody lineage using an unbiased approach, which sought to explore a larger sequence space through the application of DNA recombination and shuffling techniques across the entire antibody region and selections using ribosome display. We also highlight the key features of several display technologies and diversification methods, and discuss the strategies devised by different groups in response to different challenges. Particular attention is drawn to examples which are aimed at the expansion of sequence, structural or experimental diversity through different means and approaches. Here, we provide our perspectives on these methodologies and the considerations involved in the design of effective strategies for the directed evolution of antibodies.
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25
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Ricca E, Baccigalupi L, Isticato R. Spore-adsorption: Mechanism and applications of a non-recombinant display system. Biotechnol Adv 2020; 47:107693. [PMID: 33387640 DOI: 10.1016/j.biotechadv.2020.107693] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/22/2020] [Accepted: 12/23/2020] [Indexed: 12/18/2022]
Abstract
Surface display systems have been developed to express target molecules on almost all types of biological entities from viruses to mammalian cells and on a variety of synthetic particles. Various approaches have been developed to achieve the display of many different target molecules, aiming at several technological and biomedical applications. Screening of libraries, delivery of drugs or antigens, bio-catalysis, sensing of pollutants and bioremediation are commonly considered as fields of potential application for surface display systems. In this review, the non-recombinant approach to display antigens and enzymes on the surface of bacterial spores is discussed. Examples of molecules displayed on the spore surface and their potential applications are summarized and a mechanism of display is proposed.
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Affiliation(s)
- Ezio Ricca
- Department of Biology, Federico II University of Naples, Italy.
| | - Loredana Baccigalupi
- Department of Molecular Medicine and Medical Biotechnology, Federico II University of Naples, Italy
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26
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Kasherman L, Ahrari S, Lheureux S. Dostarlimab in the treatment of recurrent or primary advanced endometrial cancer. Future Oncol 2020; 17:877-892. [PMID: 33251877 DOI: 10.2217/fon-2020-0655] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Immune checkpoint inhibitors have demonstrated significant clinical activity across various tumor subtypes; however, their utility in gynecologic malignancies has thus far proven modest. Since the identification of a molecular subclassification system for endometrial cancer (EC), research in immune checkpoint inhibitor therapies has been focusing on certain subgroups predictive for response, particularly microsatellite instability hypermutated/DNA mismatch repair-deficient subtype. Dostarlimab, a PD-1 inhibitor, has demonstrated preliminary evidence of clinical activity and acceptable safety profile in patients with across recurrent EC, particularly microsatellite instability-hypermutated/DNA mismatch repair-deficient EC. This review outlines existing data for the efficacy and safety of dostarlimab in recurrent or advanced-stage EC.
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Affiliation(s)
- Lawrence Kasherman
- Division of Medical Oncology & Hematology, Bras Family Drug Development Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON M5G 2M9, Canada
| | - Soha Ahrari
- Department of Pharmacy, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON M5G 2M9, Canada
| | - Stephanie Lheureux
- Division of Medical Oncology & Hematology, Bras Family Drug Development Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON M5G 2M9, Canada
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27
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In vitro evolution of antibody affinity via insertional scanning mutagenesis of an entire antibody variable region. Proc Natl Acad Sci U S A 2020; 117:27307-27318. [PMID: 33067389 DOI: 10.1073/pnas.2002954117] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
We report a systematic combinatorial exploration of affinity enhancement of antibodies by insertions and deletions (InDels). Transposon-based introduction of InDels via the method TRIAD (transposition-based random insertion and deletion mutagenesis) was used to generate large libraries with random in-frame InDels across the entire single-chain variable fragment gene that were further recombined and screened by ribosome display. Knowledge of potential insertion points from TRIAD libraries formed the basis of exploration of length and sequence diversity of novel insertions by insertional-scanning mutagenesis (InScaM). An overall 256-fold affinity improvement of an anti-IL-13 antibody BAK1 as a result of InDel mutagenesis and combination with known point mutations validates this approach, and suggests that the results of this InDel mutagenesis and conventional exploration of point mutations can synergize to generate antibodies with higher affinity.
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28
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Streamlined human antibody generation and optimization by exploiting designed immunoglobulin loci in a B cell line. Cell Mol Immunol 2020; 18:1545-1561. [PMID: 32457406 PMCID: PMC8166883 DOI: 10.1038/s41423-020-0440-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 04/06/2020] [Accepted: 04/07/2020] [Indexed: 01/30/2023] Open
Abstract
Monoclonal antibodies (mAbs) are widely utilized as therapeutic drugs for various diseases, such as cancer, autoimmune diseases, and infectious diseases. Using the avian-derived B cell line DT40, we previously developed an antibody display technology, namely, the ADLib system, which rapidly generates antigen-specific mAbs. Here, we report the development of a human version of the ADLib system and showcase the streamlined generation and optimization of functional human mAbs. Tailored libraries were first constructed by replacing endogenous immunoglobulin genes with designed human counterparts. From these libraries, clones producing full-length human IgGs against distinct antigens can be isolated, as exemplified by the selection of antagonistic mAbs. Taking advantage of avian biology, effective affinity maturation was achieved in a straightforward manner by seamless diversification of the parental clones into secondary libraries followed by single-cell sorting, quickly affording mAbs with improved affinities and functionalities. Collectively, we demonstrate that the human ADLib system could serve as an integrative platform with unique diversity for rapid de novo generation and optimization of therapeutic or diagnostic antibody leads. Furthermore, our results suggest that libraries can be constructed by introducing exogenous genes into DT40 cells, indicating that the ADLib system has the potential to be applied for the rapid and effective directed evolution and optimization of proteins in various fields beyond biomedicine.
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29
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Luo R, Zhao Y, Fan Y, An L, Jiang T, Ma S, Hang H. High efficiency CHO cell display-based antibody maturation. Sci Rep 2020; 10:8102. [PMID: 32415149 PMCID: PMC7229201 DOI: 10.1038/s41598-020-65044-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 04/21/2020] [Indexed: 11/09/2022] Open
Abstract
Previously, we developed a CHO cell display-based antibody maturation procedure in which an antibody (or other protein) gene of interest was induced to mutate by activation-induced cytidine deaminase (AID) and then form a library by simply proliferating the CHO cells in culture. In this study, we further improved the efficiency of this maturation system by reengineering AID, and optimizing the nucleic acid sequence of the target antibody gene and AID gene as well as the protocol for AID gene transfection. These changes have increased both the mutation rate and the number of mutation type of antibody genes by more than 10 fold, and greatly improved the maturation efficiency of antibody/other proteins.
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Affiliation(s)
- Ruiqi Luo
- 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, 100039, China
| | - Yun Zhao
- Key Laboratory for Protein and Peptide Pharmaceuticals, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yingjun Fan
- 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, 100039, China
| | - Lili An
- Key Laboratory for Protein and Peptide Pharmaceuticals, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Tao Jiang
- University of Chinese Academy of Sciences, Beijing, 100039, China.,National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shaohua Ma
- Department of Thoracic Surgery, Peking University Third Hospital, Beijing, 100191, 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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30
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Stimple SD, Smith MD, Tessier PM. Directed evolution methods for overcoming trade-offs between protein activity and stability. AIChE J 2020; 66. [PMID: 32719568 DOI: 10.1002/aic.16814] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Engineered proteins are being widely developed and employed in applications ranging from enzyme catalysts to therapeutic antibodies. Directed evolution, an iterative experimental process composed of mutagenesis and library screening, is a powerful technique for enhancing existing protein activities and generating entirely new ones not observed in nature. However, the process of accumulating mutations for enhanced protein activity requires chemical and structural changes that are often destabilizing, and low protein stability is a significant barrier to achieving large enhancements in activity during multiple rounds of directed evolution. Here we highlight advances in understanding the origins of protein activity/stability trade-offs for two important classes of proteins (enzymes and antibodies) as well as innovative experimental and computational methods for overcoming such trade-offs. These advances hold great potential for improving the generation of highly active and stable proteins that are needed to address key challenges related to human health, energy and the environment.
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Affiliation(s)
- Samuel D. Stimple
- Department of Pharmaceutical Sciences Biointerfaces Institute, University of Michigan Ann Arbor Michigan
- Department of Chemical Engineering Biointerfaces Institute, University of Michigan Ann Arbor Michigan
| | - Matthew D. Smith
- Department of Chemical Engineering Biointerfaces Institute, University of Michigan Ann Arbor Michigan
| | - Peter M. Tessier
- Department of Pharmaceutical Sciences Biointerfaces Institute, University of Michigan Ann Arbor Michigan
- Department of Chemical Engineering Biointerfaces Institute, University of Michigan Ann Arbor Michigan
- Department of Biomedical Engineering Biointerfaces Institute, University of Michigan Ann Arbor Michigan
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31
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Fan Y, Jiang W, Ran F, Luo R, An L, Hang H. An Efficient Exogenous Gene Insertion Site in CHO Cells with High Transcription Level to Enhance AID-Induced Mutation. Biotechnol J 2020; 15:e1900313. [PMID: 31975519 DOI: 10.1002/biot.201900313] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 12/18/2019] [Indexed: 11/10/2022]
Abstract
Antibodies have been extensively used for the purpose of scientific research, clinical diagnosis, and therapy. Combination of in vitro somatic hypermutation and mammalian cell surface display has been an efficient technology for antibody or other proteins optimization, in which the efficiency of activation-induced cytidine deaminase (AID) mutations in genes is one of the most important key factors. Gene transcriptional level has been found to be positively proportional to AID-induced mutation frequency. Thus, construction of the cell clone bearing a gene of interest (GOI) with high transcription level can increase AID-induced mutations. In this study, a retargetable gene cassette is inserted onto predetermined chromosome site (ywhae gene site) which is among the genes with the highest as well as stable transcription, and is found that one subsite is suitable to be retargeted for efficient protein display in Chinese hamster ovary (CHO) cells. The resultant cell clone (T31) has higher and more stable transcription/expression than CHO-puro clone which was previously established through the strategy of random insertion followed by a high-throughput selection. It also possesses a significantly higher mutation frequency to GOI than CHO-puro cells; thus, it is a better clone for the in vitro improvement of antibody affinity, and probably other properties.
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Affiliation(s)
- Yingjun Fan
- Key Laboratory of Protein and Peptide Drugs, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei Jiang
- Key Laboratory of Protein and Peptide Drugs, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fanlei Ran
- Key Laboratory of Protein and Peptide Drugs, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ruiqi Luo
- Key Laboratory of Protein and Peptide Drugs, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lili An
- Key Laboratory of Protein and Peptide Drugs, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Haiying Hang
- Key Laboratory of Protein and Peptide Drugs, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
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32
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Abstract
While antibody libraries are traditionally screened in phage, bacterial, or yeast display formats, they are produced in large scale for pharmaceutical and commercial use in mammalian cell lines. The simpler organisms used for screening have significantly different folding and glycosylation machinery than mammalian cells; consequently, clones resulting from these libraries may require further optimization for mammalian cell expression. To streamline the antibody discovery process, we developed a Chinese hamster ovary (CHO) cell-based selection system that allows for long-term display of antibody Fab fragments. This system is facilitated by a semi-stable Epi-CHO episomal platform to maintain antibody expression for up to 2 months and is compatible with standard PCR-based mutagenesis strategies. This protocol describes the simple and accessible use of CHO display coupled with flow cytometry to enrich for antibody variants with increased ligand-binding affinity from large libraries of ~106 variants, using HER2-binding antibodies as an example.
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Affiliation(s)
- Annalee W Nguyen
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA.
| | - Kevin Le
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Jennifer A Maynard
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
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33
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Crook ZR, Sevilla GP, Mhyre AJ, Olson JM. Mammalian Surface Display Screening of Diverse Cystine-Dense Peptide Libraries for Difficult-to-Drug Targets. Methods Mol Biol 2020; 2070:363-396. [PMID: 31625107 DOI: 10.1007/978-1-4939-9853-1_21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Many diseases are mediated by targets that are not amenable to conventional small-molecule drug approaches. While antibody-based drugs have undeniable utility, peptides of the 1-9 kDa size range (10-80 amino acids) have drawn interest as alternate drug scaffolds This is born of a desire to identify compounds with the advantages of antibody-based therapeutics (affinity, potency, specificity, and ability to disrupt protein:protein interactions) without all of their liabilities (large size, expensive manufacturing, and necessity of humanization). Of these alternate scaffolds, cystine-dense peptides (CDPs) have several specific benefits. Due to their stable intra-chain disulfide bridges, CDPs often demonstrate resistance to heat and proteolysis, along with low immunogenicity. These properties do not require chemical modifications, permitting CDP screening by conventional genetic means. The cystine topology of a typical CDP requires an oxidative environment, and we have found that the mammalian secretory pathway is most effective at allowing diverse CDPs to achieve a stable fold. As such, high-diversity screens to identify CDPs that interact with targets of interest can be efficiently conducted using mammalian surface display. In this protocol, we present the theory and tools to conduct a mammalian surface display screen for CDPs that bind with targets of interest, including the steps to validate binding and mature the affinity of preliminary candidates. With these methods, CDPs of all kinds can be brought to bear against targets that would benefit from a peptide-based intervention.
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Affiliation(s)
- Zachary R Crook
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Gregory P Sevilla
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Andrew J Mhyre
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - James M Olson
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
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34
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Hu FJ, Lundqvist M, Uhlén M, Rockberg J. SAMURAI (Solid-phase Assisted Mutagenesis by Uracil Restriction for Accurate Integration) for antibody affinity maturation and paratope mapping. Nucleic Acids Res 2019; 47:e34. [PMID: 30715449 PMCID: PMC6451119 DOI: 10.1093/nar/gkz050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 01/08/2019] [Accepted: 01/24/2019] [Indexed: 12/31/2022] Open
Abstract
Mutagenesis libraries are essential for combinatorial protein engineering. Despite improvements in gene synthesis and directed mutagenesis, current methodologies still have limitations regarding the synthesis of complete antibody single-chain variable fragment (scFv) genes and simultaneous diversification of all six CDRs. Here, we describe the generation of mutagenesis libraries for antibody affinity maturation using a cell-free solid-phase technique for annealing of single-strand mutagenic oligonucleotides. The procedure consists of PCR-based incorporation of uracil into a wild-type template, bead-based capture, elution of single-strand DNA, and in vitro uracil excision enzyme based degradation of the template DNA. Our approach enabled rapid (8 hours) mutagenesis and automated cloning of 50 position-specific alanine mutants for mapping of a scFv antibody paratope. We further exemplify our method by generating affinity maturation libraries with diversity introduced in critical, nonessential, or all CDR positions randomly. Assessment with Illumina deep sequencing showed less than 1% wild-type in two libraries and the ability to diversify all CDR positions simultaneously. Selections of the libraries with bacterial display and deep sequencing evaluation of the selection output showed that diversity introduced in non-essential positions allowed for a more effective enrichment of improved binders compared to the other two diversification strategies.
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Affiliation(s)
- Francis Jingxin Hu
- KTH - Royal Institute of Technology, Department of Protein Science, 106 91 Stockholm, Sweden
| | - Magnus Lundqvist
- KTH - Royal Institute of Technology, Department of Protein Science, 106 91 Stockholm, Sweden
| | - Mathias Uhlén
- KTH - Royal Institute of Technology, Department of Protein Science, 106 91 Stockholm, Sweden.,KTH - Royal Institute of Technology, Science for Life Laboratory, Solna 171 65, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2970 Hørsholm, Denmark
| | - Johan Rockberg
- KTH - Royal Institute of Technology, Department of Protein Science, 106 91 Stockholm, Sweden
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35
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Devilder MC, Moyon M, Gautreau-Rolland L, Navet B, Perroteau J, Delbos F, Gesnel MC, Breathnach R, Saulquin X. Ex vivo evolution of human antibodies by CRISPR-X: from a naive B cell repertoire to affinity matured antibodies. BMC Biotechnol 2019; 19:14. [PMID: 30777060 PMCID: PMC6378725 DOI: 10.1186/s12896-019-0504-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 02/05/2019] [Indexed: 12/13/2022] Open
Affiliation(s)
- Marie-Claire Devilder
- CRCINA, INSERM, CNRS, Université d'Angers, Université de Nantes, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology", Nantes, France.,Centre Hospitalier Universitaire Hôtel-Dieu, Nantes, France
| | - Melinda Moyon
- CRCINA, INSERM, CNRS, Université d'Angers, Université de Nantes, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology", Nantes, France
| | - Laetitia Gautreau-Rolland
- CRCINA, INSERM, CNRS, Université d'Angers, Université de Nantes, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology", Nantes, France
| | - Benjamin Navet
- CRCINA, INSERM, CNRS, Université d'Angers, Université de Nantes, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology", Nantes, France
| | - Jeanne Perroteau
- CRCINA, INSERM, CNRS, Université d'Angers, Université de Nantes, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology", Nantes, France
| | - Florent Delbos
- HLA Laboratory, EFS Centre Pays de la Loire, Nantes, France
| | - Marie-Claude Gesnel
- CRCINA, INSERM, CNRS, Université d'Angers, Université de Nantes, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology", Nantes, France.,Centre Hospitalier Universitaire Hôtel-Dieu, Nantes, France
| | - Richard Breathnach
- CRCINA, INSERM, CNRS, Université d'Angers, Université de Nantes, Nantes, France. .,LabEx IGO "Immunotherapy, Graft, Oncology", Nantes, France.
| | - Xavier Saulquin
- CRCINA, INSERM, CNRS, Université d'Angers, Université de Nantes, Nantes, France. .,LabEx IGO "Immunotherapy, Graft, Oncology", Nantes, France.
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36
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Yeap LS, Meng FL. Cis- and trans-factors affecting AID targeting and mutagenic outcomes in antibody diversification. Adv Immunol 2019; 141:51-103. [PMID: 30904133 DOI: 10.1016/bs.ai.2019.01.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Antigen receptor diversification is a hallmark of adaptive immunity which allows specificity of the receptor to particular antigen. B cell receptor (BCR) or its secreted form, antibody, is diversified through antigen-independent and antigen-dependent mechanisms. During B cell development in bone marrow, BCR is diversified via V(D)J recombination mediated by RAG endonuclease. Upon stimulation by antigen, B cell undergo somatic hypermutation (SHM) to allow affinity maturation and class switch recombination (CSR) to change the effector function of the antibody. Both SHM and CSR are initiated by activation-induced cytidine deaminase (AID). Repair of AID-initiated lesions through different DNA repair pathways results in diverse mutagenic outcomes. Here, we focus on discussing cis- and trans-factors that target AID to its substrates and factors that affect different outcomes of AID-initiated lesions. The knowledge of mechanisms that govern AID targeting and outcomes could be harnessed to elicit rare functional antibodies and develop ex vivo antibody diversification approaches with diversifying base editors.
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Affiliation(s)
- Leng-Siew Yeap
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Fei-Long Meng
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.
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37
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Nguyen AW, Le KC, Maynard JA. Identification of high affinity HER2 binding antibodies using CHO Fab surface display. Protein Eng Des Sel 2019; 31:91-101. [PMID: 29566240 DOI: 10.1093/protein/gzy004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 02/02/2018] [Indexed: 12/27/2022] Open
Abstract
Discovery of monoclonal antibodies is most commonly performed using phage or yeast display but mammalian cells are used for production because of the complex antibody structure, including the multiple disulfide bonds and glycosylation, required for function. As this transition between host organisms is often accompanied by impaired binding, folding or expression, development pipelines include laborious plate-based screening or engineering strategies to adapt an antibody to mammalian expression. To circumvent these problems, we developed a plasmid-based Fab screening platform on Chinese hamster ovary (CHO) cells which allows for antibody selection in the production host and in the presence of the same post-translational modifications as the manufactured product. A hu4D5 variant with low affinity for the human epidermal growth factor receptor (HER2) growth factor receptor was mutagenized and this library of ~10(6) unique clones was screened to identify variants with up to 400-fold enhanced HER2 binding. After two rounds of fluorescence activated cell sorting (FACS), four unique clones exhibited improved antigen binding when expressed on the CHO surface or as purified human IgG. Three of the four clones contained free cysteines in third complementarity determining region of the antibody heavy chain, which did not impair expression or cause aggregation. The improved clones had similar yields and stabilities as hu4D5 and similar sub-nanomolar affinities as measured by equilibrium binding to target cells. The limited size of mammalian libraries restricts the utility of this approach for naïve antibody library screening, but it is a powerful approach for antibody affinity maturation or specificity enhancement and is readily generalizable to engineering other surface receptors, including T-cell receptors and chimeric antigen receptors.
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Affiliation(s)
- Annalee W Nguyen
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| | - Kevin C Le
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| | - Jennifer A Maynard
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
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Ghosh S, Sharma G, Travers J, Kumar S, Choi J, Jun HT, Kehry M, Ramaswamy S, Jenkins D. TSR-033, a Novel Therapeutic Antibody Targeting LAG-3, Enhances T-Cell Function and the Activity of PD-1 Blockade In Vitro and In Vivo. Mol Cancer Ther 2018; 18:632-641. [PMID: 30587557 DOI: 10.1158/1535-7163.mct-18-0836] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/25/2018] [Accepted: 12/18/2018] [Indexed: 11/16/2022]
Abstract
Progressive upregulation of checkpoints on tumor-infiltrating lymphocytes promotes an immunosuppressive tumor microenvironment, severely compromising tumor immunity. Lymphocyte activation gene-3 (LAG-3) is a coinhibitory receptor associated with impaired T-cell function and is frequently coexpressed with programmed cell death protein-1 (PD-1) in the context of human cancers. Targeting LAG-3 in conjunction with PD-1 thus represents a strategy to amplify and broaden the therapeutic impact of PD-1 blockade alone. We have generated a high affinity and selective humanized monoclonal IgG4 antibody, TSR-033, which binds human LAG-3 and serves as a functional antagonist, enhancing in vitro T-cell activation both in mixed lymphocyte reactions and staphylococcal enterotoxin B-driven stimulation assays. In a humanized mouse non-small cell lung carcinoma model, TSR-033 boosted the antitumor efficacy of PD-1 monotherapy, with a concomitant increase in immune activation. Analogous studies in a murine syngeneic tumor model using surrogate antibodies demonstrated significant synergy between LAG-3 and PD-1 blockade-combination treatment led to a marked improvement in therapeutic efficacy, increased T-cell proliferation, IFNγ production, and elicited durable immunologic memory upon tumor rechallenge. Taken together, the pharmacologic activity of TSR-033 demonstrates that it is a potent anti-LAG-3 therapeutic antibody and supports its clinical investigation in cancer patients.
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Enhancers Improve the AID-Induced Hypermutation in Episomal Vector for Antibody Affinity Maturation in Mammalian Cell Display. Antibodies (Basel) 2018; 7:antib7040042. [PMID: 31544892 PMCID: PMC6698961 DOI: 10.3390/antib7040042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 12/10/2018] [Accepted: 12/11/2018] [Indexed: 12/03/2022] Open
Abstract
The induction of somatic hypermutation (SHM) in various cell lines by activation-induced cytidine deaminase (AID) has been used in protein-directed selection, especially in antibody affinity maturation. Several antibody affinity maturation systems based on mammalian cells have been developed in recent years, i.e., 293T, H1299, Raji and CHO cells. However, the efficiency of in vitro AID-induced hypermutation is low, restricting the application of such systems. In this study, we examined the role of Ig and Ek enhancers in enhancing SHM in the episomal vector pCEP4 that expresses an anti-high mobility group box 1 (HMGB1) full-length antibody. The plasmid containing the two enhancers exhibited two-fold improvement of mutation rate over pCEP4 in an AID expression H1299 cell line (H1299-AID). With the engineered episomal vector, we improved the affinity of this antibody in H1299-AID cells by 20-fold.
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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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Transient AID expression for in situ mutagenesis with improved cellular fitness. Sci Rep 2018; 8:9413. [PMID: 29925928 PMCID: PMC6010430 DOI: 10.1038/s41598-018-27717-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 06/07/2018] [Indexed: 12/13/2022] Open
Abstract
Activation induced cytidine deaminase (AID) in germinal center B cells introduces somatic DNA mutations in transcribed immunoglobulin genes to increase antibody diversity. Ectopic expression of AID coupled with selection has been successfully employed to develop proteins with desirable properties. However, this process is laborious and time consuming because many rounds of selection are typically required to isolate the target proteins. AID expression can also adversely affect cell viability due to off target mutagenesis. Here we compared stable and transient expression of AID mutants with different catalytic activities to determine conditions for maximum accumulation of mutations with minimal toxicity. We find that transient (3–5 days) expression of an AID upmutant in the presence of selection pressure could induce a high rate of mutagenesis in reporter genes without affecting cells growth and expansion. Our findings may help improve protein evolution by ectopic expression of AID and other enzymes that can induce DNA mutations.
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42
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Heredia JD, Park J, Brubaker RJ, Szymanski SK, Gill KS, Procko E. Mapping Interaction Sites on Human Chemokine Receptors by Deep Mutational Scanning. THE JOURNAL OF IMMUNOLOGY 2018; 200:3825-3839. [PMID: 29678950 DOI: 10.4049/jimmunol.1800343] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 03/30/2018] [Indexed: 02/02/2023]
Abstract
Chemokine receptors CXCR4 and CCR5 regulate WBC trafficking and are engaged by the HIV-1 envelope glycoprotein gp120 during infection. We combine a selection of human CXCR4 and CCR5 libraries comprising nearly all of ∼7000 single amino acid substitutions with deep sequencing to define sequence-activity landscapes for surface expression and ligand interactions. After consideration of sequence constraints for surface expression, known interaction sites with HIV-1-blocking Abs were appropriately identified as conserved residues following library sorting for Ab binding, validating the use of deep mutational scanning to map functional interaction sites in G protein-coupled receptors. Chemokine CXCL12 was found to interact with residues extending asymmetrically into the CXCR4 ligand-binding cavity, similar to the binding surface of CXCR4 recognized by an antagonistic viral chemokine previously observed crystallographically. CXCR4 mutations distal from the chemokine binding site were identified that enhance chemokine recognition. This included disruptive mutations in the G protein-coupling site that diminished calcium mobilization, as well as conservative mutations to a membrane-exposed site (CXCR4 residues H792.45 and W1614.50) that increased ligand binding without loss of signaling. Compared with CXCR4-CXCL12 interactions, CCR5 residues conserved for gp120 (HIV-1 BaL strain) interactions map to a more expansive surface, mimicking how the cognate chemokine CCL5 makes contacts across the entire CCR5 binding cavity. Acidic substitutions in the CCR5 N terminus and extracellular loops enhanced gp120 binding. This study demonstrates how comprehensive mutational scanning can define functional interaction sites on receptors, and novel mutations that enhance receptor activities can be found simultaneously.
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Affiliation(s)
- Jeremiah D Heredia
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Jihye Park
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Riley J Brubaker
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Steven K Szymanski
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Kevin S Gill
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Erik Procko
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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Abstract
Antibodies have been used for over a century prophylactically and, less often, therapeutically against viruses. 'Super-antibodies' — a new generation of highly potent and/or broadly cross-reactive human monoclonal antibodies — offer new opportunities for prophylaxis and therapy of viral infections. Super-antibodies are typically generated infrequently and/or in a limited number of individuals during natural infections. Isolation of these antibodies has primarily been achieved by large-scale screening for suitable donors and new single B cell approaches to human monoclonal antibody generation. Super-antibodies may offer the possibility of treating multiple viruses of a given family with a single reagent. They are also valuable templates for rational vaccine design. The great potency of super-antibodies has many advantages for practical development as therapeutic reagents. These advantages can be enhanced by a variety of antibody engineering technologies.
So-called super-antibodies are highly potent, broadly reactive antiviral antibodies that offer promise for the treatment of various chronic and emerging viruses. This Review describes how recent technological advances led to their isolation from rare, infected individuals and their development for the prevention and treatment of various viral infections. Antibodies have been used for more than 100 years in the therapy of infectious diseases, but a new generation of highly potent and/or broadly cross-reactive human monoclonal antibodies (sometimes referred to as 'super-antibodies') offers new opportunities for intervention. The isolation of these antibodies, most of which are rarely induced in human infections, has primarily been achieved by large-scale screening for suitable donors and new single B cell approaches to human monoclonal antibody generation. Engineering the antibodies to improve half-life and effector functions has further augmented their in vivo activity in some cases. Super-antibodies offer promise for the prophylaxis and therapy of infections with a range of viruses, including those that are highly antigenically variable and those that are newly emerging or that have pandemic potential. The next few years will be decisive in the realization of the promise of super-antibodies.
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Bowers PM, Boyle WJ, Damoiseaux R. The Use of Somatic Hypermutation for the Affinity Maturation of Therapeutic Antibodies. Methods Mol Biol 2018; 1827:479-489. [PMID: 30196512 DOI: 10.1007/978-1-4939-8648-4_24] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The engineering of antibodies and antibody fragments for affinity maturation, stability, and other biophysical characteristics is a common aspect of therapeutic development. Maturation of antibodies in B cells during the adaptive immune response is the result of a process called somatic hypermutation (SHM), in which the activation-induced cytidine deaminase (AID) acts to introduce mutations into immunoglobulin (Ig) genes. Iterative selection and clonal expansion of B cells containing affinity-enhancing mutations drive an increase in the overall affinity of antibodies. Here we describe the use of SHM coupled with mammalian cell surface display for the maturation of antibodies in vitro and the complementarity of these methods with the mining of immune lineages using next-generation sequencing (NGS).
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Affiliation(s)
- Peter M Bowers
- Clinical and Translational Science Institute, UCLA David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
| | - William J Boyle
- Clinical and Translational Science Institute, UCLA David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Robert Damoiseaux
- Department of Molecular and Medical Pharmacology, California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA, USA
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45
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Kennedy PJ, Oliveira C, Granja PL, Sarmento B. Monoclonal antibodies: technologies for early discovery and engineering. Crit Rev Biotechnol 2017; 38:394-408. [PMID: 28789584 DOI: 10.1080/07388551.2017.1357002] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Antibodies are essential in modern life sciences biotechnology. Their architecture and diversity allow for high specificity and affinity to a wide array of biochemicals. Combining monoclonal antibody (mAb) technology with recombinant DNA and protein expression links antibody genotype with phenotype. Yet, the ability to select and screen for high affinity binders from recombinantly-displayed, combinatorial libraries unleashes the true power of mAbs and a flood of clinical applications. The identification of novel antibodies can be accomplished by a myriad of in vitro display technologies from the proven (e.g. phage) to the emerging (e.g. mammalian cell and cell-free) based on affinity binding as well as function. Lead candidates can be further engineered for increased affinity and half-life, reduced immunogenicity and/or enhanced manufacturing, and storage capabilities. This review begins with antibody biology and how the structure and genetic machinery relate to function, diversity, and in vivo affinity maturation and follows with the general requirements of (therapeutic) antibody discovery and engineering with an emphasis on in vitro display technologies. Throughout, we highlight where antibody biology inspires technology development and where high-throughput, "big data" and in silico strategies are playing an increasing role. Antibodies dominate the growing class of targeted therapeutics, alone or as bioconjugates. However, their versatility extends to research, diagnostics, and beyond.
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Affiliation(s)
- Patrick J Kennedy
- a i3S - Instituto de Investigação e Inovação em Saúde , Universidade do Porto , Porto , Portugal.,b INEB - Instituto de Engenharia Biomédica , Universidade do Porto , Porto , Portugal.,c IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto , Porto , Portugal.,d ICBAS - Instituto de Ciências Biomédicas Abel Salazar , Universidade do Porto , Porto , Portugal
| | - Carla Oliveira
- a i3S - Instituto de Investigação e Inovação em Saúde , Universidade do Porto , Porto , Portugal.,c IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto , Porto , Portugal
| | - Pedro L Granja
- a i3S - Instituto de Investigação e Inovação em Saúde , Universidade do Porto , Porto , Portugal.,b INEB - Instituto de Engenharia Biomédica , Universidade do Porto , Porto , Portugal.,d ICBAS - Instituto de Ciências Biomédicas Abel Salazar , Universidade do Porto , Porto , Portugal.,e Departmento de Engenharia Metalúrgica e de Materiais , FEUP - Faculdade de Engenharia da Universidade do Porto , Porto , Portugal
| | - Bruno Sarmento
- a i3S - Instituto de Investigação e Inovação em Saúde , Universidade do Porto , Porto , Portugal.,b INEB - Instituto de Engenharia Biomédica , Universidade do Porto , Porto , Portugal.,f CESPU , Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde & Instituto Universitário de Ciências da Saúde , Gandra , Portugal
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46
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Sun Z, Lu S, Yang Z, Li J, Zhang MY. Construction of a recombinant full-length membrane associated IgG library. Virus Res 2017; 238:156-163. [DOI: 10.1016/j.virusres.2017.06.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 06/22/2017] [Accepted: 06/22/2017] [Indexed: 01/12/2023]
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47
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Nagamune T. Biomolecular engineering for nanobio/bionanotechnology. NANO CONVERGENCE 2017; 4:9. [PMID: 28491487 PMCID: PMC5401866 DOI: 10.1186/s40580-017-0103-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 03/29/2017] [Indexed: 05/02/2023]
Abstract
Biomolecular engineering can be used to purposefully manipulate biomolecules, such as peptides, proteins, nucleic acids and lipids, within the framework of the relations among their structures, functions and properties, as well as their applicability to such areas as developing novel biomaterials, biosensing, bioimaging, and clinical diagnostics and therapeutics. Nanotechnology can also be used to design and tune the sizes, shapes, properties and functionality of nanomaterials. As such, there are considerable overlaps between nanotechnology and biomolecular engineering, in that both are concerned with the structure and behavior of materials on the nanometer scale or smaller. Therefore, in combination with nanotechnology, biomolecular engineering is expected to open up new fields of nanobio/bionanotechnology and to contribute to the development of novel nanobiomaterials, nanobiodevices and nanobiosystems. This review highlights recent studies using engineered biological molecules (e.g., oligonucleotides, peptides, proteins, enzymes, polysaccharides, lipids, biological cofactors and ligands) combined with functional nanomaterials in nanobio/bionanotechnology applications, including therapeutics, diagnostics, biosensing, bioanalysis and biocatalysts. Furthermore, this review focuses on five areas of recent advances in biomolecular engineering: (a) nucleic acid engineering, (b) gene engineering, (c) protein engineering, (d) chemical and enzymatic conjugation technologies, and (e) linker engineering. Precisely engineered nanobiomaterials, nanobiodevices and nanobiosystems are anticipated to emerge as next-generation platforms for bioelectronics, biosensors, biocatalysts, molecular imaging modalities, biological actuators, and biomedical applications.
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Affiliation(s)
- Teruyuki Nagamune
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
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48
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Julian MC, Li L, Garde S, Wilen R, Tessier PM. Efficient affinity maturation of antibody variable domains requires co-selection of compensatory mutations to maintain thermodynamic stability. Sci Rep 2017; 7:45259. [PMID: 28349921 PMCID: PMC5368667 DOI: 10.1038/srep45259] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 02/27/2017] [Indexed: 12/31/2022] Open
Abstract
The ability of antibodies to accumulate affinity-enhancing mutations in their complementarity-determining regions (CDRs) without compromising thermodynamic stability is critical to their natural function. However, it is unclear if affinity mutations in the hypervariable CDRs generally impact antibody stability and to what extent additional compensatory mutations are required to maintain stability during affinity maturation. Here we have experimentally and computationally evaluated the functional contributions of mutations acquired by a human variable (VH) domain that was evolved using strong selections for enhanced stability and affinity for the Alzheimer’s Aβ42 peptide. Interestingly, half of the key affinity mutations in the CDRs were destabilizing. Moreover, the destabilizing effects of these mutations were compensated for by a subset of the affinity mutations that were also stabilizing. Our findings demonstrate that the accumulation of both affinity and stability mutations is necessary to maintain thermodynamic stability during extensive mutagenesis and affinity maturation in vitro, which is similar to findings for natural antibodies that are subjected to somatic hypermutation in vivo. These findings for diverse antibodies and antibody fragments specific for unrelated antigens suggest that the formation of the antigen-binding site is generally a destabilizing process and that co-enrichment for compensatory mutations is critical for maintaining thermodynamic stability.
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Affiliation(s)
- Mark C Julian
- Center for Biotechnology &Interdisciplinary Studies, Isermann Dept. of Chemical &Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Lijuan Li
- Center for Biotechnology &Interdisciplinary Studies, Isermann Dept. of Chemical &Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Shekhar Garde
- Center for Biotechnology &Interdisciplinary Studies, Isermann Dept. of Chemical &Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Rebecca Wilen
- Center for Biotechnology &Interdisciplinary Studies, Isermann Dept. of Chemical &Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Peter M Tessier
- Center for Biotechnology &Interdisciplinary Studies, Isermann Dept. of Chemical &Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
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49
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Hess GT, Frésard L, Han K, Lee CH, Li A, Cimprich KA, Montgomery SB, Bassik MC. Directed evolution using dCas9-targeted somatic hypermutation in mammalian cells. Nat Methods 2016; 13:1036-1042. [PMID: 27798611 PMCID: PMC5557288 DOI: 10.1038/nmeth.4038] [Citation(s) in RCA: 323] [Impact Index Per Article: 40.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 09/27/2016] [Indexed: 12/23/2022]
Abstract
Engineering and study of protein function by directed evolution has been limited by the technical requirement to use global mutagenesis or introduce DNA libraries. Here, we develop CRISPR-X, a strategy to repurpose the somatic hypermutation machinery for protein engineering in situ. Using catalytically inactive dCas9 to recruit variants of cytidine deaminase (AID) with MS2-modified sgRNAs, we can specifically mutagenize endogenous targets with limited off-target damage. This generates diverse libraries of localized point mutations and can target multiple genomic locations simultaneously. We mutagenize GFP and select for spectrum-shifted variants, including EGFP. Additionally, we mutate the target of the cancer therapeutic bortezomib, PSMB5, and identify known and novel mutations that confer bortezomib resistance. Finally, using a hyperactive AID variant, we mutagenize loci both upstream and downstream of transcriptional start sites. These experiments illustrate a powerful approach to create complex libraries of genetic variants in native context, which is broadly applicable to investigate and improve protein function.
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Affiliation(s)
- Gaelen T Hess
- Department of Genetics, Stanford University, Stanford, California, USA
| | - Laure Frésard
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Kyuho Han
- Department of Genetics, Stanford University, Stanford, California, USA
| | - Cameron H Lee
- Department of Genetics, Stanford University, Stanford, California, USA
| | - Amy Li
- Department of Genetics, Stanford University, Stanford, California, USA
| | - Karlene A Cimprich
- Department of Chemical and Systems Biology, Stanford University, Stanford, California, USA
| | - Stephen B Montgomery
- Department of Genetics, Stanford University, Stanford, California, USA
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Michael C Bassik
- Department of Genetics, Stanford University, Stanford, California, USA
- Stanford University Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford, California, USA
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50
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Heesters BA, van der Poel CE, Das A, Carroll MC. Antigen Presentation to B Cells. Trends Immunol 2016; 37:844-854. [PMID: 27793570 DOI: 10.1016/j.it.2016.10.003] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Revised: 10/06/2016] [Accepted: 10/06/2016] [Indexed: 12/20/2022]
Abstract
Unlike T cells that recognize digested peptides, B cells recognize their cognate antigen in its native form. The B cell receptor used in recognition can also be secreted to bind to antigens and initiate multiple effector functions such as phagocytosis, complement activation, or neutralization of receptors. While B cells can interact with soluble antigens, it is now clear that the presentation of membrane-bound antigen plays a crucial role in B cell activation, and in particular during affinity-maturation, the process during which high-affinity B cells are selected. In this review we discuss how native antigen is presented to B cells and its impact at several stages of B cell responses.
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Affiliation(s)
- Balthasar A Heesters
- Program in Cellular and Molecular Medicine, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Current address: Department of Cell Biology and Histology, Academic Medical Center, Amsterdam, 1105 AZ, The Netherlands
| | - Cees E van der Poel
- Program in Cellular and Molecular Medicine, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Abhishek Das
- Program in Cellular and Molecular Medicine, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Michael C Carroll
- Program in Cellular and Molecular Medicine, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.
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