51
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Matsuda T, Ito T, Takemoto C, Katsura K, Ikeda M, Wakiyama M, Kukimoto-Niino M, Yokoyama S, Kurosawa Y, Shirouzu M. Cell-free synthesis of functional antibody fragments to provide a structural basis for antibody-antigen interaction. PLoS One 2018; 13:e0193158. [PMID: 29462206 PMCID: PMC5819829 DOI: 10.1371/journal.pone.0193158] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 02/05/2018] [Indexed: 11/19/2022] Open
Abstract
Growing numbers of therapeutic antibodies offer excellent treatment strategies for many diseases. Elucidation of the interaction between a potential therapeutic antibody and its target protein by structural analysis reveals the mechanism of action and offers useful information for developing rational antibody designs for improved affinity. Here, we developed a rapid, high-yield cell-free system using dialysis mode to synthesize antibody fragments for the structural analysis of antibody–antigen complexes. Optimal synthesis conditions of fragments (Fv and Fab) of the anti-EGFR antibody 059–152 were rapidly determined in a day by using a 30-μl-scale unit. The concentration of supplemented disulfide isomerase, DsbC, was critical to obtaining soluble antibody fragments. The optimal conditions were directly applicable to a 9-ml-scale reaction, with linear scalable yields of more than 1 mg/ml. Analyses of purified 059-152-Fv and Fab showed that the cell-free synthesized antibody fragments were disulfide-bridged, with antigen binding activity comparable to that of clinical antibodies. Examination of the crystal structure of cell-free synthesized 059-152-Fv in complex with the extracellular domain of human EGFR revealed that the epitope of 059-152-Fv broadly covers the EGF binding surface on domain III, including residues that formed critical hydrogen bonds with EGF (Asp355EGFR, Gln384EGFR, H409EGFR, and Lys465EGFR), so that the antibody inhibited EGFR activation. We further demonstrated the application of the cell-free system to site-specific integration of non-natural amino acids for antibody engineering, which would expand the availability of therapeutic antibodies based on structural information and rational design. This cell-free system could be an ideal antibody-fragment production platform for functional and structural analysis of potential therapeutic antibodies and for engineered antibody development.
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Affiliation(s)
- Takayoshi Matsuda
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumiku, Yokohama, Japan
| | - Takuhiro Ito
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumiku, Yokohama, Japan
| | - Chie Takemoto
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumiku, Yokohama, Japan
| | - Kazushige Katsura
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumiku, Yokohama, Japan
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumiku, Yokohama, Japan
| | - Mariko Ikeda
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumiku, Yokohama, Japan
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumiku, Yokohama, Japan
| | - Motoaki Wakiyama
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumiku, Yokohama, Japan
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumiku, Yokohama, Japan
| | - Mutsuko Kukimoto-Niino
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumiku, Yokohama, Japan
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumiku, Yokohama, Japan
| | - Shigeyuki Yokoyama
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumiku, Yokohama, Japan
- RIKEN Structural Biology Laboratory, 1-7-22 Suehiro-cho, Tsurumiku, Yokohama, Japan
| | - Yoshikazu Kurosawa
- Innovation Center for Advanced Medicine, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Mikako Shirouzu
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumiku, Yokohama, Japan
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumiku, Yokohama, Japan
- * E-mail:
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52
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Mori A, Ojima-Kato T, Kojima T, Nakano H. Zipbodyzyme: Development of new antibody-enzyme fusion proteins. J Biosci Bioeng 2018; 125:637-643. [PMID: 29398551 DOI: 10.1016/j.jbiosc.2017.12.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 12/10/2017] [Accepted: 12/23/2017] [Indexed: 12/13/2022]
Abstract
A new antibody-enzyme fusion protein, named Zipbodyzyme, composed of a Fab antibody (i.e., an antigen-binding fragment of an antibody) and an enzyme, has been successfully produced in the cytoplasm of Escherichia coli. Zipbodyzymes have a leucine zipper (LZ) pair at the C-termini of the heavy chain (Hc) and the light chain (Lc) of Fab, to promote the association of the Hc and the Lc in E. coli cytoplasm, adjoining a fused enzyme. A Zipbodyzyme containing mouse-derived anti-E. coli O157 Fab and a luciferase or a green fluorescent protein retained both the antigen-binding and an enzymatic activity/fluorescence. The bifunctional proteins were applicable in direct enzyme-linked immunosorbent assay (ELISA) without the need for a secondary antibody, indicating that the utility of the antibody enzyme bifunctional fusion protein will be expanded.
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Affiliation(s)
- Akihiro Mori
- Laboratory of Molecular Biotechnology, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Teruyo Ojima-Kato
- Laboratory of Molecular Biotechnology, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan; Knowledge Hub Aichi, Aichi Science and Technology Foundation, Yakusa-cho, Toyota 470-0356, Japan
| | - Takaaki Kojima
- Laboratory of Molecular Biotechnology, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Hideo Nakano
- Laboratory of Molecular Biotechnology, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.
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53
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Schoborg JA, Hershewe JM, Stark JC, Kightlinger W, Kath JE, Jaroentomeechai T, Natarajan A, DeLisa MP, Jewett MC. A cell-free platform for rapid synthesis and testing of active oligosaccharyltransferases. Biotechnol Bioeng 2017; 115:739-750. [PMID: 29178580 DOI: 10.1002/bit.26502] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 11/15/2017] [Accepted: 11/20/2017] [Indexed: 12/17/2022]
Abstract
Protein glycosylation, or the attachment of sugar moieties (glycans) to proteins, is important for protein stability, activity, and immunogenicity. However, understanding the roles and regulations of site-specific glycosylation events remains a significant challenge due to several technological limitations. These limitations include a lack of available tools for biochemical characterization of enzymes involved in glycosylation. A particular challenge is the synthesis of oligosaccharyltransferases (OSTs), which catalyze the attachment of glycans to specific amino acid residues in target proteins. The difficulty arises from the fact that canonical OSTs are large (>70 kDa) and possess multiple transmembrane helices, making them difficult to overexpress in living cells. Here, we address this challenge by establishing a bacterial cell-free protein synthesis platform that enables rapid production of a variety of OSTs in their active conformations. Specifically, by using lipid nanodiscs as cellular membrane mimics, we obtained yields of up to 420 μg/ml for the single-subunit OST enzyme, "Protein glycosylation B" (PglB) from Campylobacter jejuni, as well as for three additional PglB homologs from Campylobacter coli, Campylobacter lari, and Desulfovibrio gigas. Importantly, all of these enzymes catalyzed N-glycosylation reactions in vitro with no purification or processing needed. Furthermore, we demonstrate the ability of cell-free synthesized OSTs to glycosylate multiple target proteins with varying N-glycosylation acceptor sequons. We anticipate that this broadly applicable production method will advance glycoengineering efforts by enabling preparative expression of membrane-embedded OSTs from all kingdoms of life.
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Affiliation(s)
- Jennifer A Schoborg
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois.,Chemistry of Life Processes Institute, Evanston, Illinois
| | - Jasmine M Hershewe
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois.,Chemistry of Life Processes Institute, Evanston, Illinois.,Master of Biotechnology Program, Northwestern University, Evanston, Illinois
| | - Jessica C Stark
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois.,Chemistry of Life Processes Institute, Evanston, Illinois
| | - Weston Kightlinger
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois.,Chemistry of Life Processes Institute, Evanston, Illinois
| | - James E Kath
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois.,Chemistry of Life Processes Institute, Evanston, Illinois
| | - Thapakorn Jaroentomeechai
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York
| | | | - Matthew P DeLisa
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York.,Department of Microbiology, Cornell University, Ithaca, New York
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois.,Chemistry of Life Processes Institute, Evanston, Illinois.,Master of Biotechnology Program, Northwestern University, Evanston, Illinois.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois.,Simpson Querrey Institute, Northwestern University, Chicago, Illinois.,Center for Synthetic Biology, Northwestern University, Evanston, Illinois
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54
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Stech M, Nikolaeva O, Thoring L, Stöcklein WFM, Wüstenhagen DA, Hust M, Dübel S, Kubick S. Cell-free synthesis of functional antibodies using a coupled in vitro transcription-translation system based on CHO cell lysates. Sci Rep 2017; 7:12030. [PMID: 28931913 PMCID: PMC5607253 DOI: 10.1038/s41598-017-12364-w] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 09/07/2017] [Indexed: 11/09/2022] Open
Abstract
Antibodies are indispensable tools for basic research as well as diagnostic and therapeutic applications. Consequently, the development of alternative manufacturing strategies which circumvent the hurdles connected to conventional antibody production technologies is of enormous interest. To address this issue, we demonstrate the synthesis of complex antibody formats, in particular immunoglobulin G (IgG) and single-chain variable fragment Fc fusion (scFv-Fc), in a microsome-containing cell-free system based on translationally active chinese hamster ovary (CHO) cell lysates. To mimic the environment for antibody folding and assembly present in living cells, antibody genes were fused to an endoplasmic reticulum (ER)-specific signal sequence. Signal-peptide induced translocation of antibody polypeptide chains into the lumen of ER microsomes was found to be the prerequisite for antibody chain assembly and functionality. In this context, we show the rapid synthesis of antibody molecules in different reaction formats, including batch and continuous-exchange cell-free (CECF) reactions, depending on the amount of protein needed for further analysis. In addition, we demonstrate site-specific and residue-specific labeling of antibodies with fluorescent non-canonical amino acids. In summary, our study describes a novel antibody production platform which combines the highly efficient mammalian protein folding machinery of CHO cells with the benefits of cell-free protein synthesis.
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Affiliation(s)
- M Stech
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany
| | - O Nikolaeva
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany.,Technische Universität Berlin, Institut für Biotechnologie, Medizinische Biotechnologie, Gustav-Meyer-Allee 25, 13355, Berlin, Germany
| | - L Thoring
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany.,Technische Universität Berlin, Institut für Biotechnologie, Medizinische Biotechnologie, Gustav-Meyer-Allee 25, 13355, Berlin, Germany
| | - W F M Stöcklein
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany
| | - D A Wüstenhagen
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany
| | - M Hust
- Technische Universität Braunschweig, Institute for Biochemistry, Biotechnology and Bioinformatics, Department of Biotechnology, Spielmannstr. 7, 38106, Braunschweig, Germany
| | - S Dübel
- Technische Universität Braunschweig, Institute for Biochemistry, Biotechnology and Bioinformatics, Department of Biotechnology, Spielmannstr. 7, 38106, Braunschweig, Germany
| | - S Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany.
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55
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Martin RW, Majewska NI, Chen CX, Albanetti TE, Jimenez RBC, Schmelzer AE, Jewett MC, Roy V. Development of a CHO-Based Cell-Free Platform for Synthesis of Active Monoclonal Antibodies. ACS Synth Biol 2017; 6:1370-1379. [PMID: 28350472 DOI: 10.1021/acssynbio.7b00001] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Chinese Hamster Ovary (CHO) cells are routinely optimized to stably express monoclonal antibodies (mAbs) at high titers. At the early stages of lead isolation and optimization, hundreds of sequences for the target protein of interest are screened. Typically, cell-based transient expression technology platforms are used for expression screening, but these can be time- and resource-intensive. Here, we have developed a cell-free protein synthesis (CFPS) platform utilizing a commercially available CHO extract for the rapid in vitro synthesis of active, aglycosylated mAbs. Specifically, we optimized reaction conditions to maximize protein yields, established an oxidizing environment to enable disulfide bond formation, and demonstrated the importance of temporal addition of heavy chain and light chain plasmids for intact mAb production. Using our optimized platform, we demonstrate for the first time to our knowledge the cell-free synthesis of biologically active, intact mAb at >100 mg/L using a eukaryotic-based extract. We then explored the utility of our system as a tool for ranking yields of candidate antibodies. Unlike stable or transient transfection-based screening, which requires a minimum of 7 days for setup and execution, results using our CHO-based CFPS platform are attained within 2 days and it is well-suited for automation. Further development would provide a tool for rapid, high-throughput prediction of mAb expression ranking to accelerate design-build-test cycles required for antibody expression and engineering. Looking forward, the CHO-based CFPS platform could facilitate the synthesis of toxic proteins as well.
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Affiliation(s)
- Rey W. Martin
- Department
of Chemical and Biological Engineering, ‡Chemistry of Life Processes Institute, and §Interdisciplinary
Biological Sciences Program, Northwestern University, Evanston, Illinois 60208, United States
- Cell Culture and Fermentation
Sciences and ⊥Analytical Sciences, MedImmune LLC, Gaithersburg, Maryland 20878, United States
- Member, Robert H. Lurie Comprehensive Cancer Center and ∇Member, Simpson
Querrey Institute, Northwestern University, Chicago, Illinois 60611, United States
| | - Natalia I. Majewska
- Department
of Chemical and Biological Engineering, ‡Chemistry of Life Processes Institute, and §Interdisciplinary
Biological Sciences Program, Northwestern University, Evanston, Illinois 60208, United States
- Cell Culture and Fermentation
Sciences and ⊥Analytical Sciences, MedImmune LLC, Gaithersburg, Maryland 20878, United States
- Member, Robert H. Lurie Comprehensive Cancer Center and ∇Member, Simpson
Querrey Institute, Northwestern University, Chicago, Illinois 60611, United States
| | - Cindy X. Chen
- Department
of Chemical and Biological Engineering, ‡Chemistry of Life Processes Institute, and §Interdisciplinary
Biological Sciences Program, Northwestern University, Evanston, Illinois 60208, United States
- Cell Culture and Fermentation
Sciences and ⊥Analytical Sciences, MedImmune LLC, Gaithersburg, Maryland 20878, United States
- Member, Robert H. Lurie Comprehensive Cancer Center and ∇Member, Simpson
Querrey Institute, Northwestern University, Chicago, Illinois 60611, United States
| | - Thomas E. Albanetti
- Department
of Chemical and Biological Engineering, ‡Chemistry of Life Processes Institute, and §Interdisciplinary
Biological Sciences Program, Northwestern University, Evanston, Illinois 60208, United States
- Cell Culture and Fermentation
Sciences and ⊥Analytical Sciences, MedImmune LLC, Gaithersburg, Maryland 20878, United States
- Member, Robert H. Lurie Comprehensive Cancer Center and ∇Member, Simpson
Querrey Institute, Northwestern University, Chicago, Illinois 60611, United States
| | - Rod Brian C. Jimenez
- Department
of Chemical and Biological Engineering, ‡Chemistry of Life Processes Institute, and §Interdisciplinary
Biological Sciences Program, Northwestern University, Evanston, Illinois 60208, United States
- Cell Culture and Fermentation
Sciences and ⊥Analytical Sciences, MedImmune LLC, Gaithersburg, Maryland 20878, United States
- Member, Robert H. Lurie Comprehensive Cancer Center and ∇Member, Simpson
Querrey Institute, Northwestern University, Chicago, Illinois 60611, United States
| | - Albert E. Schmelzer
- Department
of Chemical and Biological Engineering, ‡Chemistry of Life Processes Institute, and §Interdisciplinary
Biological Sciences Program, Northwestern University, Evanston, Illinois 60208, United States
- Cell Culture and Fermentation
Sciences and ⊥Analytical Sciences, MedImmune LLC, Gaithersburg, Maryland 20878, United States
- Member, Robert H. Lurie Comprehensive Cancer Center and ∇Member, Simpson
Querrey Institute, Northwestern University, Chicago, Illinois 60611, United States
| | - Michael C. Jewett
- Department
of Chemical and Biological Engineering, ‡Chemistry of Life Processes Institute, and §Interdisciplinary
Biological Sciences Program, Northwestern University, Evanston, Illinois 60208, United States
- Cell Culture and Fermentation
Sciences and ⊥Analytical Sciences, MedImmune LLC, Gaithersburg, Maryland 20878, United States
- Member, Robert H. Lurie Comprehensive Cancer Center and ∇Member, Simpson
Querrey Institute, Northwestern University, Chicago, Illinois 60611, United States
| | - Varnika Roy
- Department
of Chemical and Biological Engineering, ‡Chemistry of Life Processes Institute, and §Interdisciplinary
Biological Sciences Program, Northwestern University, Evanston, Illinois 60208, United States
- Cell Culture and Fermentation
Sciences and ⊥Analytical Sciences, MedImmune LLC, Gaithersburg, Maryland 20878, United States
- Member, Robert H. Lurie Comprehensive Cancer Center and ∇Member, Simpson
Querrey Institute, Northwestern University, Chicago, Illinois 60611, United States
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56
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Schinn SM, Bradley W, Groesbeck A, Wu JC, Broadbent A, Bundy BC. Rapid in vitro screening for the location-dependent effects of unnatural amino acids on protein expression and activity. Biotechnol Bioeng 2017; 114:2412-2417. [PMID: 28398594 DOI: 10.1002/bit.26305] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Revised: 02/28/2017] [Accepted: 04/02/2017] [Indexed: 12/25/2022]
Abstract
The incorporation of unnatural amino acids (uAA) can introduce novel functional groups into proteins site-specifically, with important applications in basic sciences and protein engineering. However, uAA incorporation can impact protein expression and functional activity depending on its location within the protein-a process that is not yet completely understood and difficult to predict. Therefore, practical applications often necessitate a time-consuming optimization of uAA location by individual gene cloning, expressions, purification, and evaluations for each location tested. To address this limitation, we introduce a streamlined and versatile in vitro system to rapidly express and screen uAA-containing proteins without cumbersome cell culturing or purification procedures. We utilized this technology to simultaneously screen 24 different t4-lysozyme mutants with different uAA incorporation sites in a matter of hours, compared to weeks-long workflow of conventional methods. Screening data offered a mechanistic explanation to some effects of uAA incorporation on expression and activity. Despite these insights, rational prediction of such effects remained challenging, further confirming the value of a rapid screening approach. Biotechnol. Bioeng. 2017;114: 2412-2417. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Song-Min Schinn
- Department of Chemical Engineering, Brigham Young University, Provo, Utah
| | - William Bradley
- Department of Chemical Engineering, Brigham Young University, Provo, Utah
| | - Ashtyn Groesbeck
- Department of Chemical Engineering, Brigham Young University, Provo, Utah
| | - Jeffrey C Wu
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah
| | - Andrew Broadbent
- Department of Chemical Engineering, Brigham Young University, Provo, Utah
| | - Bradley C Bundy
- Department of Chemical Engineering, Brigham Young University, Provo, Utah
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57
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Yin G, Stephenson HT, Yang J, Li X, Armstrong SM, Heibeck TH, Tran C, Masikat MR, Zhou S, Stafford RL, Yam AY, Lee J, Steiner AR, Gill A, Penta K, Pollitt S, Baliga R, Murray CJ, Thanos CD, McEvoy LM, Sato AK, Hallam TJ. RF1 attenuation enables efficient non-natural amino acid incorporation for production of homogeneous antibody drug conjugates. Sci Rep 2017; 7:3026. [PMID: 28596531 PMCID: PMC5465077 DOI: 10.1038/s41598-017-03192-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 04/27/2017] [Indexed: 11/12/2022] Open
Abstract
Amber codon suppression for the insertion of non-natural amino acids (nnAAs) is limited by competition with release factor 1 (RF1). Here we describe the genome engineering of a RF1 mutant strain that enhances suppression efficiency during cell-free protein synthesis, without significantly impacting cell growth during biomass production. Specifically, an out membrane protease (OmpT) cleavage site was engineered into the switch loop of RF1, which enables its conditional inactivation during cell lysis. This facilitates extract production without additional processing steps, resulting in a scaleable extract production process. The RF1 mutant extract allows nnAA incorporation at previously intractable sites of an IgG1 and at multiple sites in the same polypeptide chain. Conjugation of cytotoxic agents to these nnAAs, yields homogeneous antibody drug conjugates (ADCs) that can be optimized for conjugation site, drug to antibody ratio (DAR) and linker-warheads designed for efficient tumor killing. This platform provides the means to generate therapeutic ADCs inaccessible by other methods that are efficient in their cytotoxin delivery to tumor with reduced dose-limiting toxicities and thus have the potential for better clinical impact.
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Affiliation(s)
- Gang Yin
- Sutro Biopharma Inc, South San Francisco, CA, 94080, USA.
| | | | - Junhao Yang
- Sutro Biopharma Inc, South San Francisco, CA, 94080, USA
| | - Xiaofan Li
- Sutro Biopharma Inc, South San Francisco, CA, 94080, USA
| | | | | | - Cuong Tran
- Sutro Biopharma Inc, South San Francisco, CA, 94080, USA
| | | | - Sihong Zhou
- Sutro Biopharma Inc, South San Francisco, CA, 94080, USA
| | | | - Alice Y Yam
- Sutro Biopharma Inc, South San Francisco, CA, 94080, USA
| | - John Lee
- Sutro Biopharma Inc, South San Francisco, CA, 94080, USA
| | | | - Avinash Gill
- Sutro Biopharma Inc, South San Francisco, CA, 94080, USA
| | - Kalyani Penta
- Sutro Biopharma Inc, South San Francisco, CA, 94080, USA
| | - Sonia Pollitt
- Sutro Biopharma Inc, South San Francisco, CA, 94080, USA
| | - Ramesh Baliga
- Sutro Biopharma Inc, South San Francisco, CA, 94080, USA
| | | | | | | | - Aaron K Sato
- Sutro Biopharma Inc, South San Francisco, CA, 94080, USA
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58
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Lu Y. Cell-free synthetic biology: Engineering in an open world. Synth Syst Biotechnol 2017; 2:23-27. [PMID: 29062958 PMCID: PMC5625795 DOI: 10.1016/j.synbio.2017.02.003] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 02/06/2017] [Indexed: 10/26/2022] Open
Abstract
Cell-free synthetic biology emerges as a powerful and flexible enabling technology that can engineer biological parts and systems for life science applications without using living cells. It provides simpler and faster engineering solutions with an unprecedented freedom of design in an open environment than cell system. This review focuses on recent developments of cell-free synthetic biology on biological engineering fields at molecular and cellular levels, including protein engineering, metabolic engineering, and artificial cell engineering. In cell-free protein engineering, the direct control of reaction conditions in cell-free system allows for easy synthesis of complex proteins, toxic proteins, membrane proteins, and novel proteins with unnatural amino acids. Cell-free systems offer the ability to design metabolic pathways towards the production of desired products. Buildup of artificial cells based on cell-free systems will improve our understanding of life and use them for environmental and biomedical applications.
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Affiliation(s)
- Yuan Lu
- Key Lab of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China.,Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
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59
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Shukla AA, Wolfe LS, Mostafa SS, Norman C. Evolving trends in mAb production processes. Bioeng Transl Med 2017; 2:58-69. [PMID: 29313024 PMCID: PMC5689530 DOI: 10.1002/btm2.10061] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 02/24/2017] [Accepted: 03/06/2017] [Indexed: 12/30/2022] Open
Abstract
Monoclonal antibodies (mAbs) have established themselves as the leading biopharmaceutical therapeutic modality. The establishment of robust manufacturing platforms are key for antibody drug discovery efforts to seamlessly translate into clinical and commercial successes. Several drivers are influencing the design of mAb manufacturing processes. The advent of biosimilars is driving a desire to achieve lower cost of goods and globalize biologics manufacturing. High titers are now routinely achieved for mAbs in mammalian cell culture. These drivers have resulted in significant evolution in process platform approaches. Additionally, several new trends in bioprocessing have arisen in keeping with these needs. These include the consideration of alternative expression systems, continuous biomanufacturing and non-chromatographic separation formats. This paper discusses these drivers in the context of the kinds of changes they are driving in mAb production processes.
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Affiliation(s)
| | - Leslie S. Wolfe
- Process Development & ManufacturingKBI Biopharma Inc.DurhamNC27704
| | - Sigma S. Mostafa
- Process Development & ManufacturingKBI Biopharma Inc.DurhamNC27704
| | - Carnley Norman
- Process Development & ManufacturingKBI Biopharma Inc.DurhamNC27704
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60
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61
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Legastelois I, Buffin S, Peubez I, Mignon C, Sodoyer R, Werle B. Non-conventional expression systems for the production of vaccine proteins and immunotherapeutic molecules. Hum Vaccin Immunother 2016; 13:947-961. [PMID: 27905833 DOI: 10.1080/21645515.2016.1260795] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The increasing demand for recombinant vaccine antigens or immunotherapeutic molecules calls into question the universality of current protein expression systems. Vaccine production can require relatively low amounts of expressed materials, but represents an extremely diverse category consisting of different target antigens with marked structural differences. In contrast, monoclonal antibodies, by definition share key molecular characteristics and require a production system capable of very large outputs, which drives the quest for highly efficient and cost-effective systems. In discussing expression systems, the primary assumption is that a universal production platform for vaccines and immunotherapeutics will unlikely exist. This review provides an overview of the evolution of traditional expression systems, including mammalian cells, yeast and E.coli, but also alternative systems such as other bacteria than E. coli, transgenic animals, insect cells, plants and microalgae, Tetrahymena thermophila, Leishmania tarentolae, filamentous fungi, cell free systems, and the incorporation of non-natural amino acids.
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Affiliation(s)
| | - Sophie Buffin
- a Research and Development, Sanofi Pasteur , Marcy L'Etoile , France
| | - Isabelle Peubez
- a Research and Development, Sanofi Pasteur , Marcy L'Etoile , France
| | | | - Régis Sodoyer
- b Technology Research Institute Bioaster , Lyon , France
| | - Bettina Werle
- b Technology Research Institute Bioaster , Lyon , France
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62
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Perez JG, Stark JC, Jewett MC. Cell-Free Synthetic Biology: Engineering Beyond the Cell. Cold Spring Harb Perspect Biol 2016; 8:cshperspect.a023853. [PMID: 27742731 DOI: 10.1101/cshperspect.a023853] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cell-free protein synthesis (CFPS) technologies have enabled inexpensive and rapid recombinant protein expression. Numerous highly active CFPS platforms are now available and have recently been used for synthetic biology applications. In this review, we focus on the ability of CFPS to expand our understanding of biological systems and its applications in the synthetic biology field. First, we outline a variety of CFPS platforms that provide alternative and complementary methods for expressing proteins from different organisms, compared with in vivo approaches. Next, we review the types of proteins, protein complexes, and protein modifications that have been achieved using CFPS systems. Finally, we introduce recent work on genetic networks in cell-free systems and the use of cell-free systems for rapid prototyping of in vivo networks. Given the flexibility of cell-free systems, CFPS holds promise to be a powerful tool for synthetic biology as well as a protein production technology in years to come.
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Affiliation(s)
- Jessica G Perez
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208-3120.,Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208-3120
| | - Jessica C Stark
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208-3120.,Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208-3120
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208-3120.,Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208-3120.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois 60611-3068.,Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, Illinois 60611-2875
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63
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64
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Gupta SK, Shukla P. Microbial platform technology for recombinant antibody fragment production: A review. Crit Rev Microbiol 2016; 43:31-42. [PMID: 27387055 DOI: 10.3109/1040841x.2016.1150959] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Recombinant antibody fragments are being used for the last few years as an important therapeutic protein to cure various critical and life threatening human diseases. Several expression platforms now days employed for the production of these recombinant fragments, out of which bacterial system has emerged a promising host for higher expression. Since, a small antibody fragment unlike full antibody does not require human-like post-translational modification therefore it is potentially expressed in prokaryotic production system. Recently, small antibody fragments such as scFvs (single-chain variable fragments) and Fabs (antibody fragments) which does not require glycosylation are successfully produced in bacteria and have commercially launched for therapeutic use as these fragments shows better tissue penetration and less immunogenic to human body compared to full-size antibody. Recently developed Wacker's ESETEC secretion technology is an efficient technology for the expression and secretion of the antibody fragment (Fab) exceeded up to 4.0 g/L while scFv up to 3.5 g/L into the fermentation broth. The Pfenex system and pOP prokaryotic expression vector are another platform used for the considerably good amount of antibody fragment production successfully. In this review, we summarize the recent progress on various expression platforms and cloning approaches for the production of different forms of antibody fragments in E. coli.
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Affiliation(s)
- Sanjeev Kumar Gupta
- a Advanced Biotech Lab, Ipca Laboratories Ltd., Kandivli Industrial Estate, Kandivli (west) , Mumbai , Mahrashtra , India
| | - Pratyoosh Shukla
- b Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology , Maharshi Dayanand University , Rohtak , Haryana , India
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65
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Xu Y, Jiang G, Tran C, Li X, Heibeck TH, Masikat MR, Cai Q, Steiner AR, Sato AK, Hallam TJ, Yin G. RP-HPLC DAR Characterization of Site-Specific Antibody Drug Conjugates Produced in a Cell-Free Expression System. Org Process Res Dev 2016. [DOI: 10.1021/acs.oprd.6b00072] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Yiren Xu
- Sutro Biopharma, Inc. 310 Utah Avenue, Suite 150, South San Francisco, California 94080, United States
| | - Guifeng Jiang
- Sutro Biopharma, Inc. 310 Utah Avenue, Suite 150, South San Francisco, California 94080, United States
| | - Cuong Tran
- Sutro Biopharma, Inc. 310 Utah Avenue, Suite 150, South San Francisco, California 94080, United States
| | - Xiaofan Li
- Sutro Biopharma, Inc. 310 Utah Avenue, Suite 150, South San Francisco, California 94080, United States
| | - Tyler H. Heibeck
- Sutro Biopharma, Inc. 310 Utah Avenue, Suite 150, South San Francisco, California 94080, United States
| | - Mary Rose Masikat
- Sutro Biopharma, Inc. 310 Utah Avenue, Suite 150, South San Francisco, California 94080, United States
| | - Qi Cai
- Sutro Biopharma, Inc. 310 Utah Avenue, Suite 150, South San Francisco, California 94080, United States
| | - Alexander R. Steiner
- Sutro Biopharma, Inc. 310 Utah Avenue, Suite 150, South San Francisco, California 94080, United States
| | - Aaron K. Sato
- Sutro Biopharma, Inc. 310 Utah Avenue, Suite 150, South San Francisco, California 94080, United States
| | - Trevor J. Hallam
- Sutro Biopharma, Inc. 310 Utah Avenue, Suite 150, South San Francisco, California 94080, United States
| | - Gang Yin
- Sutro Biopharma, Inc. 310 Utah Avenue, Suite 150, South San Francisco, California 94080, United States
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66
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Gong Q, Hazen M, Marshall B, Crowell SR, Ou Q, Wong AW, Phung W, Vernes JM, Meng YG, Tejada M, Andersen D, Kelley RF. Increased in vivo effector function of human IgG4 isotype antibodies through afucosylation. MAbs 2016; 8:1098-106. [PMID: 27216702 DOI: 10.1080/19420862.2016.1189049] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
For some antibodies intended for use as human therapeutics, reduced effector function is desired to avoid toxicities that might be associated with depletion of target cells. Since effector function(s), including antibody-dependent cell-mediated cytotoxicity (ADCC), require the Fc portion to be glycosylated, reduced ADCC activity antibodies can be obtained through aglycosylation of the human IgG1 isotype. An alternative is to switch to an IgG4 isotype in which the glycosylated antibody is known to have reduced effector function relative to glycosylated IgG1 antibody. ADCC activity of glycosylated IgG1 antibodies is sensitive to the fucosylation status of the Fc glycan, with both in vitro and in vivo ADCC activity increased upon fucose removal ("afucosylation"). The effect of afucosylation on activity of IgG4 antibodies is less well characterized, but it has been shown to increase the in vitro ADCC activity of an anti-CD20 antibody. Here, we show that both in vitro and in vivo activity of anti-CD20 IgG4 isotype antibodies is increased via afucosylation. Using blends of material made in Chinese hamster ovary (CHO) and Fut8KO-CHO cells, we show that ADCC activity of an IgG4 version of an anti-human CD20 antibody is directly proportional to the fucose content. In mice transgenic for human FcγRIIIa, afucosylation of an IgG4 anti-mouse CD20 antibody increases the B cell depletion activity to a level approaching that of the mIgG2a antibody.
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Affiliation(s)
- Qian Gong
- a Department of Immunology , Genentech Inc. , South San Francisco , CA , USA
| | - Meredith Hazen
- b Department of Antibody Engineering , Genentech Inc. , South San Francisco , CA , USA
| | - Brett Marshall
- c Department of Biological Technologies , Genentech Inc. , South San Francisco , CA , USA
| | - Susan R Crowell
- d Department of Preclinical and Translational Pharmacokinetics , Genentech Inc. , South San Francisco , CA , USA
| | - Qinglin Ou
- a Department of Immunology , Genentech Inc. , South San Francisco , CA , USA
| | - Athena W Wong
- e Department of Early Stage Cell Culture , Genentech Inc. , South San Francisco , CA , USA
| | - Wilson Phung
- f Department of Protein Chemistry , Genentech Inc. , South San Francisco CA , USA
| | - Jean-Michel Vernes
- g Department of Biochemical and Cellular Pharmacology , Genentech Inc. , South San Francisco , CA , USA
| | - Y Gloria Meng
- g Department of Biochemical and Cellular Pharmacology , Genentech Inc. , South San Francisco , CA , USA
| | - Max Tejada
- c Department of Biological Technologies , Genentech Inc. , South San Francisco , CA , USA
| | - Dana Andersen
- h Department of Pharmaceutical Development , Genentech Inc. , South San Francisco , CA , USA
| | - Robert F Kelley
- i Department of Drug Delivery , Genentech Inc. , South San Francisco , CA , USA
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Schinn SM, Broadbent A, Bradley WT, Bundy BC. Protein synthesis directly from PCR: progress and applications of cell-free protein synthesis with linear DNA. N Biotechnol 2016; 33:480-7. [PMID: 27085957 DOI: 10.1016/j.nbt.2016.04.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 03/30/2016] [Accepted: 04/07/2016] [Indexed: 11/18/2022]
Abstract
A rapid, versatile method of protein expression and screening can greatly facilitate the future development of therapeutic biologics, proteomic drug targets and biocatalysts. An attractive candidate is cell-free protein synthesis (CFPS), a cell-lysate-based in vitro expression system, which can utilize linear DNA as expression templates, bypassing time-consuming cloning steps of plasmid-based methods. Traditionally, such linear DNA expression templates (LET) have been vulnerable to degradation by nucleases present in the cell lysate, leading to lower yields. This challenge has been significantly addressed in the recent past, propelling LET-based CFPS as a useful tool for studying, screening and engineering proteins in a high-throughput manner. Currently, LET-based CFPS has promise in fields such as functional proteomics, protein microarrays, and the optimization of complex biological systems.
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Affiliation(s)
- Song-Min Schinn
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - Andrew Broadbent
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - William T Bradley
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - Bradley C Bundy
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA.
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68
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Xiao X, Chen Y, Varkey R, Kallewaard N, Koksal AC, Zhu Q, Wu H, Chowdhury PS, Dall'Acqua WF. A novel antibody discovery platform identifies anti-influenza A broadly neutralizing antibodies from human memory B cells. MAbs 2016; 8:916-27. [PMID: 27049174 DOI: 10.1080/19420862.2016.1170263] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Monoclonal antibody isolation directly from circulating human B cells is a powerful tool to delineate humoral responses to pathological conditions and discover antibody therapeutics. We have developed a platform aimed at improving the efficiencies of B cell selection and V gene recovery. Here, memory B cells are activated and amplified using Epstein-Barr virus infection, co-cultured with CHO-muCD40L cells, and then assessed by functional screenings. An in vitro transcription and translation (IVTT) approach was used to analyze variable (V) genes recovered from each B cell sample and identify the relevant heavy/light chain pair(s). We achieved efficient amplification and activation of memory B cells, and eliminated the need to: 1) seed B cells at clonal level (≤1 cell/well) or perform limited dilution cloning; 2) immortalize B cells; or 3) assemble V genes into an IgG expression vector to confirm the relevant heavy/light chain pairing. Cross-reactive antibodies targeting a conserved epitope on influenza A hemagglutinin were successfully isolated from a healthy donor. In-depth analysis of the isolated antibodies suggested their potential uses as anti-influenza A antibody therapeutics and uncovered a distinct affinity maturation pathway. Importantly, our results showed that cognate heavy/light chain pairings contributed to both the expression level and binding abilities of our newly isolated VH1-69 family, influenza A neutralizing antibodies, contrasting with previous observations that light chains do not significantly contribute to the function of this group of antibodies. Our results further suggest the potential use of the IVTT as a powerful antibody developability assessment tool.
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Affiliation(s)
- Xiaodong Xiao
- a Department of Antibody Discovery and Protein Engineering , MedImmune , Gaithersburg , MD , USA
| | - Yan Chen
- a Department of Antibody Discovery and Protein Engineering , MedImmune , Gaithersburg , MD , USA
| | - Reena Varkey
- a Department of Antibody Discovery and Protein Engineering , MedImmune , Gaithersburg , MD , USA
| | - Nicole Kallewaard
- b Department of Infectious Diseases and Vaccines , MedImmune , Gaithersburg , MD , USA
| | - Adem C Koksal
- a Department of Antibody Discovery and Protein Engineering , MedImmune , Gaithersburg , MD , USA
| | - Qing Zhu
- b Department of Infectious Diseases and Vaccines , MedImmune , Gaithersburg , MD , USA
| | - Herren Wu
- a Department of Antibody Discovery and Protein Engineering , MedImmune , Gaithersburg , MD , USA
| | - Partha S Chowdhury
- a Department of Antibody Discovery and Protein Engineering , MedImmune , Gaithersburg , MD , USA
| | - William F Dall'Acqua
- a Department of Antibody Discovery and Protein Engineering , MedImmune , Gaithersburg , MD , USA
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69
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Schoborg JA, Clark LG, Choudhury A, Hodgman CE, Jewett MC. Yeast knockout library allows for efficient testing of genomic mutations for cell-free protein synthesis. Synth Syst Biotechnol 2016; 1:2-6. [PMID: 29062921 PMCID: PMC5640588 DOI: 10.1016/j.synbio.2016.02.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 01/27/2016] [Accepted: 02/12/2016] [Indexed: 12/31/2022] Open
Abstract
Cell-free protein synthesis (CFPS) systems from crude lysates have benefitted from modifications to their enzyme composition. For example, functionally deleting enzymes in the source strain that are deleterious to CFPS can improve protein synthesis yields. However, making such modifications can take substantial time. As a proof-of-concept to accelerate prototyping capabilities, we assessed the feasibility of using the yeast knockout collection to identify negative effectors in a Saccharomyces cerevisiae CFPS platform. We analyzed extracts made from six deletion strains that targeted the single deletion of potentially negative effectors (e.g., nucleases). We found a statistically significant increase in luciferase yields upon loss of function of GCN3, PEP4, PPT1, NGL3, and XRN1 with a maximum increase of over 6-fold as compared to the wild type. Our work has implications for yeast CFPS and for rapidly prototyping strains to enable cell-free synthetic biology applications.
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Key Words
- ANOVA, analysis of variance
- ATP, adenosine triphosphate
- CFPS, cell-free protein synthesis
- CRISPR, clustered regularly interspaced short palindromic repeats
- Cell-free biology
- Cell-free protein synthesis
- In vitro translation
- NTP, nucleoside triphosphate
- OD, optical density
- Protein expression
- SC, synthetic complete media
- Saccharomyces cerevisiae
- Synthetic biology
- YKO, yeast knockout
- cAMP, cyclic adenosine monophosphate
- eIF, eukaryotic initiation factor
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Affiliation(s)
- Jennifer A. Schoborg
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3120, USA
- Chemistry of Life Processes Institute, 2170 Campus Drive, Evanston, IL 60208-3120, USA
| | - Lauren G. Clark
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3120, USA
- Chemistry of Life Processes Institute, 2170 Campus Drive, Evanston, IL 60208-3120, USA
| | - Alaksh Choudhury
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3120, USA
- Chemistry of Life Processes Institute, 2170 Campus Drive, Evanston, IL 60208-3120, USA
- Masters in Biotechnology Program, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3120, USA
| | - C. Eric Hodgman
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3120, USA
- Chemistry of Life Processes Institute, 2170 Campus Drive, Evanston, IL 60208-3120, USA
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3120, USA
- Chemistry of Life Processes Institute, 2170 Campus Drive, Evanston, IL 60208-3120, USA
- Masters in Biotechnology Program, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3120, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, 676 N. St Clair St, Suite 1200, Chicago, IL 60611-3068, USA
- Simpson Querrey Institute, Northwestern University, 303 E. Superior St, Suite 11-131, Chicago, IL 60611-2875, USA
- Corresponding author. 2145 Sheridan Road, Tech E-136, Evanston, IL 60208-3120, USA.2145 Sheridan RoadTech E-136EvanstonIL60208-3120USA
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70
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Karim AS, Jewett MC. A cell-free framework for rapid biosynthetic pathway prototyping and enzyme discovery. Metab Eng 2016; 36:116-126. [PMID: 26996382 DOI: 10.1016/j.ymben.2016.03.002] [Citation(s) in RCA: 149] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 02/12/2016] [Accepted: 03/10/2016] [Indexed: 10/22/2022]
Abstract
Speeding up design-build-test (DBT) cycles is a fundamental challenge facing biochemical engineering. To address this challenge, we report a new cell-free protein synthesis driven metabolic engineering (CFPS-ME) framework for rapid biosynthetic pathway prototyping. In our framework, cell-free cocktails for synthesizing target small molecules are assembled in a mix-and-match fashion from crude cell lysates either containing selectively enriched pathway enzymes from heterologous overexpression or directly producing pathway enzymes in lysates by CFPS. As a model, we apply our approach to n-butanol biosynthesis showing that Escherichia coli lysates support a highly active 17-step CoA-dependent n-butanol pathway in vitro. The elevated degree of flexibility in the cell-free environment allows us to manipulate physiochemical conditions, access enzymatic nodes, discover new enzymes, and prototype enzyme sets with linear DNA templates to study pathway performance. We anticipate that CFPS-ME will facilitate efforts to define, manipulate, and understand metabolic pathways for accelerated DBT cycles without the need to reengineer organisms.
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Affiliation(s)
- Ashty S Karim
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Tech E-136, Evanston, IL 60208, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Tech E-136, Evanston, IL 60208, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA; Simpson Querrey Institute, Northwestern University, Chicago, IL 60611, USA.
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71
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Morgado G, Gerngross D, Roberts TM, Panke S. Synthetic Biology for Cell-Free Biosynthesis: Fundamentals of Designing Novel In Vitro Multi-Enzyme Reaction Networks. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 162:117-146. [PMID: 27757475 DOI: 10.1007/10_2016_13] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cell-free biosynthesis in the form of in vitro multi-enzyme reaction networks or enzyme cascade reactions emerges as a promising tool to carry out complex catalysis in one-step, one-vessel settings. It combines the advantages of well-established in vitro biocatalysis with the power of multi-step in vivo pathways. Such cascades have been successfully applied to the synthesis of fine and bulk chemicals, monomers and complex polymers of chemical importance, and energy molecules from renewable resources as well as electricity. The scale of these initial attempts remains small, suggesting that more robust control of such systems and more efficient optimization are currently major bottlenecks. To this end, the very nature of enzyme cascade reactions as multi-membered systems requires novel approaches for implementation and optimization, some of which can be obtained from in vivo disciplines (such as pathway refactoring and DNA assembly), and some of which can be built on the unique, cell-free properties of cascade reactions (such as easy analytical access to all system intermediates to facilitate modeling).
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Affiliation(s)
- Gaspar Morgado
- Bioprocess Laboratory, Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Daniel Gerngross
- Bioprocess Laboratory, Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Tania M Roberts
- Bioprocess Laboratory, Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Sven Panke
- Bioprocess Laboratory, Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland.
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72
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A cell‐free expression and purification process for rapid production of protein biologics. Biotechnol J 2015; 11:238-48. [DOI: 10.1002/biot.201500214] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 08/14/2015] [Accepted: 09/28/2015] [Indexed: 01/08/2023]
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73
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Lysate of engineered Escherichia coli supports high-level conversion of glucose to 2,3-butanediol. Metab Eng 2015; 32:133-142. [PMID: 26428449 DOI: 10.1016/j.ymben.2015.09.015] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 08/19/2015] [Accepted: 09/18/2015] [Indexed: 01/04/2023]
Abstract
Cell-free metabolic engineering (CFME) is emerging as a powerful approach for the production of target molecules and pathway debugging. Unfortunately, high cofactor costs, limited cofactor and energy regeneration, and low volumetric productivities hamper the widespread use and practical implementation of CFME technology. To address these challenges, we have developed a cell-free system that harnesses ensembles of catalytic proteins prepared from crude lysates, or extracts, of cells to fuel highly active heterologous metabolic conversions. As a model pathway, we selected conversion of glucose to 2,3-butanediol (2,3-BD), a medium level commodity chemical with many industrial applications. Specifically, we engineered a single strain of Escherichia coli to express three pathway enzymes necessary to make meso-2,3-BD (m2,3-BD). We then demonstrated that lysates from this strain, with addition of glucose and catalytic amounts of cofactors NAD+ and ATP, can produce m2,3-BD. Endogenous glycolytic enzymes convert glucose to pyruvate, the starting intermediate for m2,3-BD synthesis. Strikingly, with no strain optimization, we observed a maximal synthesis rate of m2,3-BD of 11.3 ± 0.1 g/L/h with a theoretical yield of 71% (0.36 g m2,3-BD/g glucose) in batch reactions. Titers reached 82 ± 8 g/L m2,3-BD in a 30 h fed-batch reaction. Our results highlight the ability for high-level co-factor regeneration in cell-free lysates. Further, they suggest exciting opportunities to use lysate-based systems to rapidly prototype metabolic pathways and carry out molecular transformations when bioconversion yields (g product/L), productivities (g product/L/h), or cellular toxicity limit commercial feasibility of whole-cell fermentation.
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74
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Xu Y, Lee J, Tran C, Heibeck TH, Wang WD, Yang J, Stafford RL, Steiner AR, Sato AK, Hallam TJ, Yin G. Production of bispecific antibodies in "knobs-into-holes" using a cell-free expression system. MAbs 2015; 7:231-42. [PMID: 25427258 PMCID: PMC4623329 DOI: 10.4161/19420862.2015.989013] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Bispecific antibodies have emerged in recent years as a promising field of research for therapies in oncology, inflammable diseases, and infectious diseases. Their capability of dual target recognition allows for novel therapeutic hypothesis to be tested, where traditional mono-specific antibodies would lack the needed mode of target engagement. Among extremely diverse architectures of bispecific antibodies, knobs-into-holes (KIHs) technology, which involves engineering CH3 domains to create either a “knob” or a “hole” in each heavy chain to promote heterodimerization, has been widely applied. Here, we describe the use of a cell-free expression system (Xpress CF) to produce KIH bispecific antibodies in multiple scaffolds, including 2-armed heterodimeric scFv-KIH and one-armed asymmetric BiTE-KIH with tandem scFv. Efficient KIH production can be achieved by manipulating the plasmid ratio between knob and hole, and further improved by addition of prefabricated knob or hole. These studies demonstrate the versatility of Xpress CF in KIH production and provide valuable insights into KIH construct design for better assembly and expression titer.
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Key Words
- BiTE, bispecific T-cell engager
- BiTE-KIH
- CHO, Chinese hamster ovary
- ELISA, enzyme-linked immunosorbent assay
- EpCAM, epithelial cell adhesion molecule
- FACS, fluorescence-activated cell sorting
- Fab, antigen-binding fragment
- Fc, fragment crystallizable
- FcR, Fc receptor
- HC, immunoglobulin heavy chain
- HER2, human epidermal growth factor receptor 2
- IgG, immunoglobulin G
- KIH, knob-into-hole
- LC, immunoglobulin light chain
- LC-MS, liquid chromatography-mass spectrometry
- PK, pharmacokinetics
- bispecific antibody
- cell-free protein expression
- knob-into-hole
- prefabrication
- scFv, single-chain fragment variable
- scFv-KIH
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Affiliation(s)
- Yiren Xu
- a Sutro Biopharma, Inc. ; South San Francisco , CA USA
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75
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Li J, Lawton TJ, Kostecki JS, Nisthal A, Fang J, Mayo SL, Rosenzweig AC, Jewett MC. Cell‐free protein synthesis enables high yielding synthesis of an active multicopper oxidase. Biotechnol J 2015; 11:212-8. [DOI: 10.1002/biot.201500030] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 06/26/2015] [Accepted: 07/31/2015] [Indexed: 12/22/2022]
Affiliation(s)
- Jian Li
- Department of Chemical and Biological Engineering Northwestern University Evanston IL USA
- Chemistry of Life Processes Institute Northwestern University Evanston IL USA
- Robert H. Lurie Comprehensive Cancer Center Northwestern University Chicago IL USA
- Simpson Querrey Institute for BioNanotechnology in Medicine Northwestern University Chicago IL USA
| | - Thomas J. Lawton
- Department of Molecular Biosciences Northwestern University Evanston IL USA
| | - Jan S. Kostecki
- Division of Biological Sciences California Institute of Technology Pasadena CA USA
| | - Alex Nisthal
- Division of Biological Sciences California Institute of Technology Pasadena CA USA
| | - Jia Fang
- Department of Molecular Biosciences Northwestern University Evanston IL USA
| | - Stephen L. Mayo
- Division of Biological Sciences California Institute of Technology Pasadena CA USA
| | - Amy C. Rosenzweig
- Robert H. Lurie Comprehensive Cancer Center Northwestern University Chicago IL USA
- Department of Molecular Biosciences Northwestern University Evanston IL USA
- Department of Chemistry Northwestern University Evanston IL USA
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering Northwestern University Evanston IL USA
- Chemistry of Life Processes Institute Northwestern University Evanston IL USA
- Robert H. Lurie Comprehensive Cancer Center Northwestern University Chicago IL USA
- Simpson Querrey Institute for BioNanotechnology in Medicine Northwestern University Chicago IL USA
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76
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Robust production of recombinant phosphoproteins using cell-free protein synthesis. Nat Commun 2015; 6:8168. [PMID: 26350765 PMCID: PMC4566161 DOI: 10.1038/ncomms9168] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 07/25/2015] [Indexed: 01/18/2023] Open
Abstract
Understanding the functional and structural consequences of site-specific protein phosphorylation has remained limited by our inability to produce phosphoproteins at high yields. Here we address this limitation by developing a cell-free protein synthesis (CFPS) platform that employs crude extracts from a genomically recoded strain of Escherichia coli for site-specific, co-translational incorporation of phosphoserine into proteins. We apply this system to the robust production of up to milligram quantities of human MEK1 kinase. Then, we recapitulate a physiological signalling cascade in vitro to evaluate the contributions of site-specific phosphorylation of mono- and doubly phosphorylated forms on MEK1 activity. We discover that only one phosphorylation event is necessary and sufficient for MEK1 activity. Our work sets the stage for using CFPS as a rapid high-throughput technology platform for direct expression of programmable phosphoproteins containing multiple phosphorylated residues. This work will facilitate study of phosphorylation-dependent structure–function relationships, kinase signalling networks and kinase inhibitor drugs. The inability to produce recombinant phosphoproteins has hindered research into their structure and function. Here the authors develop a cell-free protein synthesis platform to site-specifically incorporate phosphoserine into proteins at high yields, and recapitulate a MEK1 kinase signalling cascade.
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77
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Efficient expression of full-length antibodies in the cytoplasm of engineered bacteria. Nat Commun 2015; 6:8072. [PMID: 26311203 PMCID: PMC4560801 DOI: 10.1038/ncomms9072] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 07/15/2015] [Indexed: 02/06/2023] Open
Abstract
Current methods for producing immunoglobulin G (IgG) antibodies in engineered cells often require refolding steps or secretion across one or more biological membranes. Here, we describe a robust expression platform for biosynthesis of full-length IgG antibodies in the Escherichia coli cytoplasm. Synthetic heavy and light chains, both lacking canonical export signals, are expressed in specially engineered E. coli strains that permit formation of stable disulfide bonds within the cytoplasm. IgGs with clinically relevant antigen- and effector-binding activities are readily produced in the E. coli cytoplasm by grafting antigen-specific variable heavy and light domains into a cytoplasmically stable framework and remodelling the fragment crystallizable domain with amino-acid substitutions that promote binding to Fcγ receptors. The resulting cytoplasmic IgGs—named ‘cyclonals'—effectively bypass the potentially rate-limiting steps of membrane translocation and glycosylation. Current methods for production of monoclonal antibodies often require refolding steps or secretion across biological membranes. Here, Robinson et al. describe engineered E. coli strains for efficient production of functional immunoglobulin G antibodies in the bacterial cytoplasm.
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78
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Hornsby M, Paduch M, Miersch S, Sääf A, Matsuguchi T, Lee B, Wypisniak K, Doak A, King D, Usatyuk S, Perry K, Lu V, Thomas W, Luke J, Goodman J, Hoey RJ, Lai D, Griffin C, Li Z, Vizeacoumar FJ, Dong D, Campbell E, Anderson S, Zhong N, Gräslund S, Koide S, Moffat J, Sidhu S, Kossiakoff A, Wells J. A High Through-put Platform for Recombinant Antibodies to Folded Proteins. Mol Cell Proteomics 2015; 14:2833-47. [PMID: 26290498 PMCID: PMC4597156 DOI: 10.1074/mcp.o115.052209] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Indexed: 01/09/2023] Open
Abstract
Antibodies are key reagents in biology and medicine, but commercial sources are rarely recombinant and thus do not provide a permanent and renewable resource. Here, we describe an industrialized platform to generate antigens and validated recombinant antibodies for 346 transcription factors (TFs) and 211 epigenetic antigens. We describe an optimized automated phage display and antigen expression pipeline that in aggregate produced about 3000 sequenced Fragment antigen-binding domain that had high affinity (typically EC50<20 nm), high stability (Tm∼80 °C), good expression in E. coli (∼5 mg/L), and ability to bind antigen in complex cell lysates. We evaluated a subset of Fabs generated to homologous SCAN domains for binding specificities. These Fragment antigen-binding domains were monospecific to their target SCAN antigen except in rare cases where they cross-reacted with a few highly related antigens. Remarkably, immunofluorescence experiments in six cell lines for 270 of the TF antigens, each having multiple antibodies, show that ∼70% stain predominantly in the cytosol and ∼20% stain in the nucleus which reinforces the dominant role that translocation plays in TF biology. These cloned antibody reagents are being made available to the academic community through our web site recombinant-antibodies.org to allow a more system-wide analysis of TF and chromatin biology. We believe these platforms, infrastructure, and automated approaches will facilitate the next generation of renewable antibody reagents to the human proteome in the coming decade.
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Affiliation(s)
- Michael Hornsby
- From the ‡Department of Pharmaceutical Chemistry University of California, San Francisco, California 94158
| | - Marcin Paduch
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Shane Miersch
- ¶Donnelly Center for Cellular and Biomolecular Research, Department of Molecular Genetics, University of Toronto, Toronto, MG5 1L6, Canada
| | - Annika Sääf
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Tet Matsuguchi
- From the ‡Department of Pharmaceutical Chemistry University of California, San Francisco, California 94158
| | - Brian Lee
- From the ‡Department of Pharmaceutical Chemistry University of California, San Francisco, California 94158
| | - Karolina Wypisniak
- From the ‡Department of Pharmaceutical Chemistry University of California, San Francisco, California 94158
| | - Allison Doak
- From the ‡Department of Pharmaceutical Chemistry University of California, San Francisco, California 94158
| | - Daniel King
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Svitlana Usatyuk
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Kimberly Perry
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Vince Lu
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - William Thomas
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Judy Luke
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Jay Goodman
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Robert J Hoey
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Darson Lai
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Carly Griffin
- ¶Donnelly Center for Cellular and Biomolecular Research, Department of Molecular Genetics, University of Toronto, Toronto, MG5 1L6, Canada
| | - Zhijian Li
- ¶Donnelly Center for Cellular and Biomolecular Research, Department of Molecular Genetics, University of Toronto, Toronto, MG5 1L6, Canada
| | - Franco J Vizeacoumar
- **Saskatchewan Cancer Agency, University of Saskatchewan, Saskatoon, S7N 4H4, Canada
| | - Debbie Dong
- ¶Donnelly Center for Cellular and Biomolecular Research, Department of Molecular Genetics, University of Toronto, Toronto, MG5 1L6, Canada
| | - Elliot Campbell
- ‖Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854
| | - Stephen Anderson
- ‖Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854
| | - Nan Zhong
- ‡‡Structural Genomics Consortium, Toronto, M5G Il7, Canada
| | | | - Shohei Koide
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Jason Moffat
- ¶Donnelly Center for Cellular and Biomolecular Research, Department of Molecular Genetics, University of Toronto, Toronto, MG5 1L6, Canada
| | - Sachdev Sidhu
- ¶Donnelly Center for Cellular and Biomolecular Research, Department of Molecular Genetics, University of Toronto, Toronto, MG5 1L6, Canada;
| | - Anthony Kossiakoff
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637;
| | - James Wells
- From the ‡Department of Pharmaceutical Chemistry University of California, San Francisco, California 94158;
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79
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80
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Malpiedi LP, Nerli BB, Taqueda ME, Abdalla DS, Pessoa A. Optimized extraction of a single-chain variable fragment of antibody by using aqueous micellar two-phase systems. Protein Expr Purif 2015; 111:53-60. [DOI: 10.1016/j.pep.2015.03.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2015] [Revised: 03/24/2015] [Accepted: 03/25/2015] [Indexed: 01/06/2023]
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81
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Anderson MJ, Stark JC, Hodgman CE, Jewett MC. Energizing eukaryotic cell-free protein synthesis with glucose metabolism. FEBS Lett 2015; 589:1723-1727. [PMID: 26054976 DOI: 10.1016/j.febslet.2015.05.045] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Revised: 05/14/2015] [Accepted: 05/16/2015] [Indexed: 11/18/2022]
Abstract
Eukaryotic cell-free protein synthesis (CFPS) is limited by the dependence on costly high-energy phosphate compounds and exogenous enzymes to power protein synthesis (e.g., creatine phosphate and creatine kinase, CrP/CrK). Here, we report the ability to use glucose as a secondary energy substrate to regenerate ATP in a Saccharomyces cerevisiae crude extract CFPS platform. We observed synthesis of 3.64±0.35 μg mL(-1) active luciferase in batch reactions with 16 mM glucose and 25 mM phosphate, resulting in a 16% increase in relative protein yield (μg protein/$ reagents) compared to the CrP/CrK system. Our demonstration provides the foundation for development of cost-effective eukaryotic CFPS platforms.
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Affiliation(s)
- Mark J Anderson
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Rd Technological Institute E136, Evanston, IL USA, 60208-3120
- Chemistry of Life Processes Institute, Northwestern University, 2170 Campus Drive, Evanston, IL USA, 60208-3120
| | - Jessica C Stark
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Rd Technological Institute E136, Evanston, IL USA, 60208-3120
- Chemistry of Life Processes Institute, Northwestern University, 2170 Campus Drive, Evanston, IL USA, 60208-3120
| | - C Eric Hodgman
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Rd Technological Institute E136, Evanston, IL USA, 60208-3120
- Chemistry of Life Processes Institute, Northwestern University, 2170 Campus Drive, Evanston, IL USA, 60208-3120
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Rd Technological Institute E136, Evanston, IL USA, 60208-3120
- Chemistry of Life Processes Institute, Northwestern University, 2170 Campus Drive, Evanston, IL USA, 60208-3120
- Member, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, 676 N. St Clair St, Suite 1200, Chicago, IL, USA, 60611-3068
- Simpson Querrey Institute, 303 E. Superior St, Suite 11-131 Chicago, IL USA, 60611-2875
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82
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Abstract
Antibody conjugates are important in many areas of medicine and biological research, and antibody-drug conjugates (ADCs) are becoming an important next generation class of therapeutics for cancer treatment. Early conjugation technologies relied upon random conjugation to multiple amino acid side chains, resulting in heterogeneous mixtures of labeled antibody. Recent studies, however, strongly support the notion that site-specific conjugation produces a homogeneous population of antibody conjugates with improved pharmacologic properties over randomly coupled molecules. Genetically incorporated unnatural amino acids (uAAs) allow unique orthogonal coupling strategies compared to those used for the 20 naturally occurring amino acids. Thus, uAAs provide a novel paradigm for creation of next generation ADCs. Additionally, uAA-based site-specific conjugation could also empower creation of additional multifunctional conjugates important as biopharmaceuticals, diagnostics, or reagents.
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Affiliation(s)
- Trevor J Hallam
- †Sutro Biopharma, 310 Utah Avenue, Suite 150, South San Francisco, California 94080, United States
| | - Erik Wold
- ‡The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Alan Wahl
- §Ambrx, Inc. 10975 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Vaughn V Smider
- ‡The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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83
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Abstract
Antibody-drug conjugates are an important and emerging drug class for the treatment of cancer. Recent evidence strongly suggests that site-specific drug conjugation results in a homogenous population of molecules with more favorable activity and pharmacokinetic properties than randomly conjugated antibodies. Unnatural amino acids (uAAs) can be incorporated in recombinant proteins to enable unique orthogonal chemistries in comparison to the side chains of the natural 20 amino acids. Thus, uAAs present a novel platform for which to create next-generation antibody-drug conjugates. Furthermore, site-specific conjugation through uAAs can also enpower unique small molecule, bispecific, multispecific and other conjugates that could be important constructs for therapeutics, diagnostics and research reagents. Here, we review the progress in uAA incorporation and conjugate construction through both cell-based and -free approaches.
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84
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Cai Q, Hanson JA, Steiner AR, Tran C, Masikat MR, Chen R, Zawada JF, Sato AK, Hallam TJ, Yin G. A simplified and robust protocol for immunoglobulin expression in Escherichia coli cell-free protein synthesis systems. Biotechnol Prog 2015; 31:823-31. [PMID: 25826247 PMCID: PMC5029582 DOI: 10.1002/btpr.2082] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 02/18/2015] [Indexed: 11/29/2022]
Abstract
Cell‐free protein synthesis (CFPS) systems allow for robust protein expression with easy manipulation of conditions to improve protein yield and folding. Recent technological developments have significantly increased the productivity and reduced the operating costs of CFPS systems, such that they can compete with conventional in vivo protein production platforms, while also offering new routes for the discovery and production of biotherapeutics. As cell‐free systems have evolved, productivity increases have commonly been obtained by addition of components to previously designed reaction mixtures without careful re‐examination of the essentiality of reagents from previous generations. Here we present a systematic sensitivity analysis of the components in a conventional Escherichia coli CFPS reaction mixture to evaluate their optimal concentrations for production of the immunoglobulin G trastuzumab. We identify eight changes to the system, which result in optimal expression of trastuzumab. We find that doubling the potassium glutamate concentration, while entirely eliminating pyruvate, coenzyme A, NAD, total tRNA, folinic acid, putrescine and ammonium glutamate, results in a highly productive cell‐free system with a 95% reduction in reagent costs (excluding cell‐extract, plasmid, and T7 RNA polymerase made in‐house). A larger panel of other proteins was also tested and all show equivalent or improved yields with our simplified system. Furthermore, we demonstrate that all of the reagents for CFPS can be combined in a single freeze‐thaw stable master mix to improve reliability and ease of use. These improvements are important for the application of the CFPS system in fields such as protein engineering, high‐throughput screening, and biotherapeutics. © 2015 American Institute of Chemical Engineers Biotechnol. Prog., 31:823–831, 2015
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Affiliation(s)
- Qi Cai
- Sutro Biopharma, Inc., South San Francisco, CA, 94080
| | | | | | - Cuong Tran
- Sutro Biopharma, Inc., South San Francisco, CA, 94080
| | | | - Rishard Chen
- Sutro Biopharma, Inc., South San Francisco, CA, 94080
| | | | - Aaron K Sato
- Sutro Biopharma, Inc., South San Francisco, CA, 94080
| | | | - Gang Yin
- Sutro Biopharma, Inc., South San Francisco, CA, 94080
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85
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Kwon YC, Jewett MC. High-throughput preparation methods of crude extract for robust cell-free protein synthesis. Sci Rep 2015; 5:8663. [PMID: 25727242 PMCID: PMC4345344 DOI: 10.1038/srep08663] [Citation(s) in RCA: 223] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 01/15/2015] [Indexed: 12/24/2022] Open
Abstract
Crude extract based cell-free protein synthesis (CFPS) has emerged as a powerful technology platform for high-throughput protein production and genetic part characterization. Unfortunately, robust preparation of highly active extracts generally requires specialized and costly equipment and can be labor and time intensive. Moreover, cell lysis procedures can be hard to standardize, leading to different extract performance across laboratories. These challenges limit new entrants to the field and new applications, such as comprehensive genome engineering programs to improve extract performance. To address these challenges, we developed a generalizable and easily accessible high-throughput crude extract preparation method for CFPS based on sonication. To validate our approach, we investigated two Escherichia coli strains: BL21 Star™ (DE3) and a K12 MG1655 variant, achieving similar productivity (defined as CFPS yield in g/L) by varying only a few parameters. In addition, we observed identical productivity of cell extracts generated from culture volumes spanning three orders of magnitude (10 mL culture tubes to 10 L fermentation). We anticipate that our rapid and robust extract preparation method will speed-up screening of genomically engineered strains for CFPS applications, make possible highly active extracts from non-model organisms, and promote a more general use of CFPS in synthetic biology and biotechnology.
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Affiliation(s)
- Yong-Chan Kwon
- 1] Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA [2] Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
| | - Michael C Jewett
- 1] Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA [2] Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA [3] Robert H. Lurie Comprehensive Cancer Center, Medicine Northwestern University, Chicago, IL 60611, USA [4] Institute of Bionanotechnology in Medicine Northwestern University, Chicago, IL 60611, USA
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86
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Deyev SM, Lebedenko EN, Petrovskaya LE, Dolgikh DA, Gabibov AG, Kirpichnikov MP. Man-made antibodies and immunoconjugates with desired properties: function optimization using structural engineering. RUSSIAN CHEMICAL REVIEWS 2015. [DOI: 10.1070/rcr4459] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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87
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88
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Dudley QM, Karim AS, Jewett MC. Cell-free metabolic engineering: biomanufacturing beyond the cell. Biotechnol J 2015; 10:69-82. [PMID: 25319678 PMCID: PMC4314355 DOI: 10.1002/biot.201400330] [Citation(s) in RCA: 217] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 07/24/2014] [Accepted: 08/22/2014] [Indexed: 12/20/2022]
Abstract
Industrial biotechnology and microbial metabolic engineering are poised to help meet the growing demand for sustainable, low-cost commodity chemicals and natural products, yet the fraction of biochemicals amenable to commercial production remains limited. Common problems afflicting the current state-of-the-art include low volumetric productivities, build-up of toxic intermediates or products, and byproduct losses via competing pathways. To overcome these limitations, cell-free metabolic engineering (CFME) is expanding the scope of the traditional bioengineering model by using in vitro ensembles of catalytic proteins prepared from purified enzymes or crude lysates of cells for the production of target products. In recent years, the unprecedented level of control and freedom of design, relative to in vivo systems, has inspired the development of engineering foundations for cell-free systems. These efforts have led to activation of long enzymatic pathways (>8 enzymes), near theoretical conversion yields, productivities greater than 100 mg L(-1) h(-1) , reaction scales of >100 L, and new directions in protein purification, spatial organization, and enzyme stability. In the coming years, CFME will offer exciting opportunities to: (i) debug and optimize biosynthetic pathways; (ii) carry out design-build-test iterations without re-engineering organisms; and (iii) perform molecular transformations when bioconversion yields, productivities, or cellular toxicity limit commercial feasibility.
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Affiliation(s)
| | | | - Michael C. Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
- Member, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA
- Member, Institute for Bionanotechnology in Medicine, Northwestern University, Chicago, IL, USA
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89
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Kline T, Steiner AR, Penta K, Sato AK, Hallam TJ, Yin G. Methods to Make Homogenous Antibody Drug Conjugates. Pharm Res 2014; 32:3480-93. [PMID: 25511917 PMCID: PMC4596908 DOI: 10.1007/s11095-014-1596-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 12/03/2014] [Indexed: 02/06/2023]
Abstract
Antibody drug conjugates (ADCs) have progressed from hypothesis to approved therapeutics in less than 30 years, and the technologies available to modify both the antibodies and the cytotoxic drugs are expanding rapidly. For reasons well reviewed previously, the field is trending strongly toward homogeneous, defined antibody conjugation. In this review we present the antibody and small molecule chemistries that are currently used and being explored to develop specific, homogenous ADCs.
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Affiliation(s)
- Toni Kline
- Sutro Biopharma, Inc, 310 Utah Ave Ste 150, South San Francisco, California, 94080, USA
| | - Alexander R Steiner
- Sutro Biopharma, Inc, 310 Utah Ave Ste 150, South San Francisco, California, 94080, USA
| | - Kalyani Penta
- Sutro Biopharma, Inc, 310 Utah Ave Ste 150, South San Francisco, California, 94080, USA
| | - Aaron K Sato
- Sutro Biopharma, Inc, 310 Utah Ave Ste 150, South San Francisco, California, 94080, USA
| | - Trevor J Hallam
- Sutro Biopharma, Inc, 310 Utah Ave Ste 150, South San Francisco, California, 94080, USA
| | - Gang Yin
- Sutro Biopharma, Inc, 310 Utah Ave Ste 150, South San Francisco, California, 94080, USA.
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90
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Koerber JT, Hornsby MJ, Wells JA. An improved single-chain Fab platform for efficient display and recombinant expression. J Mol Biol 2014; 427:576-86. [PMID: 25481745 DOI: 10.1016/j.jmb.2014.11.017] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 11/17/2014] [Accepted: 11/25/2014] [Indexed: 12/13/2022]
Abstract
Antibody phage display libraries combined with high-throughput selections have recently demonstrated tremendous promise to create the next generation of renewable, recombinant antibodies to study proteins and their many post-translational modification states; however, many challenges still remain, such as optimized antibody scaffolds. Recently, a single-chain fragment antigen binding (Fab) (scFab) format, in which the carboxy-terminus of the light chain is linked to the amino-terminus of the heavy chain, was described to potentially combine the high display levels of a single-chain fragment variable with the high stability of purified Fabs. However, this format required removal of the interchain disulfide bond to achieve modest display levels and subsequent bacterial expression resulted in high levels of aggregated scFab, hindering further use of scFabs. Here, we developed an improved scFab format that retains the interchain disulfide bond by increasing the linker length between the light and heavy chains to improve display and bacterial expression levels to 1-3 mg/L. Furthermore, rerouting of the scFab to the co-translational signal recognition particle pathway combined with reengineering of the signal peptide sequence results in display levels 24-fold above the original scFab format and 3-fold above parent Fab levels. This optimized scFab scaffold can be easily reformatted in a single step for expression in a bacterial or mammalian host to produce stable (Tm of 81 °C), predominantly monomeric (>90%) antibodies at a high yield. Ultimately, this new scFab format will advance high-throughput antibody generation platforms to discover the next generation of research and therapeutic antibodies.
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Affiliation(s)
- James T Koerber
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, 94158, USA; Recombinant Antibody Network, University of California, San Francisco, CA, 94158, USA
| | - Michael J Hornsby
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, 94158, USA; Recombinant Antibody Network, University of California, San Francisco, CA, 94158, USA
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, 94158, USA; Recombinant Antibody Network, University of California, San Francisco, CA, 94158, USA.
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91
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Panowski S, Bhakta S, Raab H, Polakis P, Junutula JR. Site-specific antibody drug conjugates for cancer therapy. MAbs 2014; 6:34-45. [PMID: 24423619 PMCID: PMC3929453 DOI: 10.4161/mabs.27022] [Citation(s) in RCA: 476] [Impact Index Per Article: 47.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Antibody therapeutics have revolutionized the treatment of cancer over the past two decades. Antibodies that specifically bind tumor surface antigens can be effective therapeutics; however, many unmodified antibodies lack therapeutic activity. These antibodies can instead be applied successfully as guided missiles to deliver potent cytotoxic drugs in the form of antibody drug conjugates (ADCs). The success of ADCs is dependent on four factors—target antigen, antibody, linker, and payload. The field has made great progress in these areas, marked by the recent approval by the US Food and Drug Administration of two ADCs, brentuximab vedotin (Adcetris®) and ado-trastuzumab emtansine (Kadcyla®). However, the therapeutic window for many ADCs that are currently in pre-clinical or clinical development remains narrow and further improvements may be required to enhance the therapeutic potential of these ADCs. Production of ADCs is an area where improvement is needed because current methods yield heterogeneous mixtures that may include 0–8 drug species per antibody molecule. Site-specific conjugation has been recently shown to eliminate heterogeneity, improve conjugate stability, and increase the therapeutic window. Here, we review and describe various site-specific conjugation strategies that are currently used for the production of ADCs, including use of engineered cysteine residues, unnatural amino acids, and enzymatic conjugation through glycotransferases and transglutaminases. In addition, we also summarize differences among these methods and highlight critical considerations when building next-generation ADC therapeutics.
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Affiliation(s)
| | | | - Helga Raab
- Genentech, Inc; South San Francisco, CA USA
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92
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Ju MS, Jung ST. Aglycosylated full-length IgG antibodies: steps toward next-generation immunotherapeutics. Curr Opin Biotechnol 2014; 30:128-39. [PMID: 25035939 DOI: 10.1016/j.copbio.2014.06.013] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Revised: 05/17/2014] [Accepted: 06/15/2014] [Indexed: 12/17/2022]
Abstract
Albeit the removal of Asn297 glycans of IgG perturbs the overall conformation and flexibility of the IgG CH2 domain, resulting in the loss of Fc-ligand interactions and therapeutically critical immune effector functions, aglycosylated full-length IgG antibodies are nearly identical to the glycosylated counterparts in terms of antigen binding, stability at physiological or low temperature conditions, pharmacokinetics, and biodistribution. To bypass the drawbacks of glycosylated antibodies that include glycan heterogeneity and requirement of high capital investment for biomanufacturing, aglycosylated antibodies have been developed and several are under clinical trials. Comprehensive cellular and bioprocess engineering has enabled to produce highly complex aglycosylated IgGs in a simple bacterial cultivation with comparable production level as that of mammalian cells. Moreover, extensive engineering of aglycosylated Fc has converted the aglycosylated IgG antibodies into a new class of effector functional human immunotherapeutics.
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Affiliation(s)
- Man-Seok Ju
- Department of Bio and Nano Chemistry, Kookmin University, Seoul 136-702, Republic of Korea
| | - Sang Taek Jung
- Department of Bio and Nano Chemistry, Kookmin University, Seoul 136-702, Republic of Korea.
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93
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Stech M, Hust M, Schulze C, Dübel S, Kubick S. Cell-free eukaryotic systems for the production, engineering, and modification of scFv antibody fragments. Eng Life Sci 2014; 14:387-398. [PMID: 25821419 PMCID: PMC4374706 DOI: 10.1002/elsc.201400036] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 05/06/2014] [Accepted: 05/08/2014] [Indexed: 01/27/2023] Open
Abstract
Open cell-free translation systems based on Escherichia coli cell lysates have successfully been used to produce antibodies and antibody fragments. In this study, we demonstrate the cell-free expression of functional single-chain antibody variable fragments (scFvs) in a eukaryotic and endotoxin-free in vitro translation system based on Spodoptera frugiperda (Sf21) insect cell extracts. Three scFv candidates with different specificities were chosen as models. The first scFv candidate SH527-IIA4 specifically discriminates between its phosphorylated (SMAD2-P) and nonphosphorylated antigens (SMAD2) (where SMAD is mothers against decapentaplegic homolog 2), whereas the second scFv candidate SH527-IIC10 recognizes both, SMAD2-P and SMAD2. The third scFv candidate SH855-C11 binds specifically to a linear epitope of the CXC chemokine receptor type 5. The translocation of antibody fragments into the lumen of endogenous microsomal vesicles, which are contained in the lysate, was facilitated by fusion of scFv genes to the insect cell specific signal sequence of honeybee melittin. We compared the binding capabilities of scFv fragments with and without melittin signal peptide and detected that translocated scFv fragments were highly functional, whereas scFvs synthesized in the cytosol of the cell extract showed strongly decreased binding capabilities. Additionally, we describe a cell-free protein synthesis method for the incorporation of noncanonical amino acids into scFv molecules in eukaryotic cell lysates. We demonstrate the successful cotranslational labeling of de novo synthesized scFv molecules with fluorescent amino acids, using residue-specific as well as site-specific labeling.
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Affiliation(s)
- Marlitt Stech
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses Potsdam-Golm Potsdam, Germany
| | - Michael Hust
- Department of Biotechnology, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig Braunschweig, Germany
| | - Corina Schulze
- Department of Life Sciences and Technology, Beuth Hochschule für Technik Berlin, University of Applied Sciences Berlin, Germany
| | - Stefan Dübel
- Department of Biotechnology, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig Braunschweig, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses Potsdam-Golm Potsdam, Germany
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94
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Smith MT, Wilding KM, Hunt JM, Bennett AM, Bundy BC. The emerging age of cell-free synthetic biology. FEBS Lett 2014; 588:2755-61. [PMID: 24931378 DOI: 10.1016/j.febslet.2014.05.062] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 05/29/2014] [Accepted: 05/30/2014] [Indexed: 01/16/2023]
Abstract
The engineering of and mastery over biological parts has catalyzed the emergence of synthetic biology. This field has grown exponentially in the past decade. As increasingly more applications of synthetic biology are pursued, more challenges are encountered, such as delivering genetic material into cells and optimizing genetic circuits in vivo. An in vitro or cell-free approach to synthetic biology simplifies and avoids many of the pitfalls of in vivo synthetic biology. In this review, we describe some of the innate features that make cell-free systems compelling platforms for synthetic biology and discuss emerging improvements of cell-free technologies. We also select and highlight recent and emerging applications of cell-free synthetic biology.
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Affiliation(s)
- Mark Thomas Smith
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - Kristen M Wilding
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - Jeremy M Hunt
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - Anthony M Bennett
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - Bradley C Bundy
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA.
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95
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Stafford RL, Matsumoto ML, Yin G, Cai Q, Fung JJ, Stephenson H, Gill A, You M, Lin SH, Wang WD, Masikat MR, Li X, Penta K, Steiner AR, Baliga R, Murray CJ, Thanos CD, Hallam TJ, Sato AK. In vitro Fab display: a cell-free system for IgG discovery. Protein Eng Des Sel 2014; 27:97-109. [PMID: 24586053 PMCID: PMC3966677 DOI: 10.1093/protein/gzu002] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Selection technologies such as ribosome display enable the rapid discovery of novel antibody fragments entirely in vitro. It has been assumed that the open nature of the cell-free reactions used in these technologies limits selections to single-chain protein fragments. We present a simple approach for the selection of multi-chain proteins, such as antibody Fab fragments, using ribosome display. Specifically, we show that a two-chain trastuzumab (Herceptin) Fab domain can be displayed in a format which tethers either the heavy or light chain to the ribosome while retaining functional antigen binding. Then, we constructed synthetic Fab HC and LC libraries and performed test selections against carcinoembryonic antigen (CEA) and vascular endothelial growth factor (VEGF). The Fab selection output was reformatted into full-length immunoglobulin Gs (IgGs) and directly expressed at high levels in an optimized cell-free system for immediate screening, purification and characterization. Several novel IgGs were identified using this cell-free platform that bind to purified CEA, CEA positive cells and VEGF.
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Affiliation(s)
- Ryan L Stafford
- Sutro Biopharma, Inc., 310 Utah Ave Suite 150, South San Francisco, CA 94080, USA
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96
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Groff D, Armstrong S, Rivers PJ, Zhang J, Yang J, Green E, Rozzelle J, Liang S, Kittle JD, Steiner AR, Baliga R, Thanos CD, Hallam TJ, Sato AK, Yam AY. Engineering toward a bacterial "endoplasmic reticulum" for the rapid expression of immunoglobulin proteins. MAbs 2014; 6:671-8. [PMID: 24517929 DOI: 10.4161/mabs.28172] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Antibodies are well-established as therapeutics, and the preclinical and clinical pipeline of these important biologics is growing rapidly. Consequently, there is considerable interest in technologies to engineer and manufacture them. Mammalian cell culture is commonly used for production because eukaryotic expression systems have evolved complex and efficient chaperone systems for the folding of antibodies. However, given the ease and manipulability of bacteria, antibody discovery efforts often employ bacterial expression systems despite their limitations in generating high titers of functional antibody. Open-Cell Free Synthesis (OCFS) is a coupled transcription-translation system that has the advantages of prokaryotic systems while achieving high titers of antibody expression. Due to the open nature of OCFS, it is easily modified by chemical or protein additives to improve the folding of select proteins. As such, we undertook a protein additive screen to identify chaperone proteins that improve the folding and assembly of trastuzumab in OCFS. From the screen, we identified the disulfide isomerase DsbC and the prolyl isomerase FkpA as important positive effectors of IgG folding. These periplasmic chaperones function synergistically for the folding and assembly of IgG, and, when present in sufficient quantities, gram per liter IgG titers can be produced. This technological advancement allows the rapid development and manufacturing of immunoglobulin proteins and pushes OCFS to the forefront of production technologies for biologics.
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Affiliation(s)
- Dan Groff
- Sutro Biopharma; South San Francisco, CA USA
| | | | | | - Juan Zhang
- Sutro Biopharma; South San Francisco, CA USA
| | - Junhao Yang
- Sutro Biopharma; South San Francisco, CA USA
| | - Evan Green
- Sutro Biopharma; South San Francisco, CA USA
| | | | - Shengwen Liang
- Molecular Technologies Laboratories LLC; Ohio University Innovation Center; Athens, OH USA
| | - Joseph D Kittle
- Molecular Technologies Laboratories LLC; Ohio University Innovation Center; Athens, OH USA
| | | | | | | | | | | | - Alice Y Yam
- Sutro Biopharma; South San Francisco, CA USA
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97
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Zimmerman ES, Heibeck TH, Gill A, Li X, Murray CJ, Madlansacay MR, Tran C, Uter NT, Yin G, Rivers PJ, Yam AY, Wang WD, Steiner AR, Bajad SU, Penta K, Yang W, Hallam TJ, Thanos CD, Sato AK. Production of site-specific antibody-drug conjugates using optimized non-natural amino acids in a cell-free expression system. Bioconjug Chem 2014; 25:351-61. [PMID: 24437342 DOI: 10.1021/bc400490z] [Citation(s) in RCA: 256] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Antibody-drug conjugates (ADCs) are a targeted chemotherapeutic currently at the cutting edge of oncology medicine. These hybrid molecules consist of a tumor antigen-specific antibody coupled to a chemotherapeutic small molecule. Through targeted delivery of potent cytotoxins, ADCs exhibit improved therapeutic index and enhanced efficacy relative to traditional chemotherapies and monoclonal antibody therapies. The currently FDA-approved ADCs, Kadcyla (Immunogen/Roche) and Adcetris (Seattle Genetics), are produced by conjugation to surface-exposed lysines, or partial disulfide reduction and conjugation to free cysteines, respectively. These stochastic modes of conjugation lead to heterogeneous drug products with varied numbers of drugs conjugated across several possible sites. As a consequence, the field has limited understanding of the relationships between the site and extent of drug loading and ADC attributes such as efficacy, safety, pharmacokinetics, and immunogenicity. A robust platform for rapid production of ADCs with defined and uniform sites of drug conjugation would enable such studies. We have established a cell-free protein expression system for production of antibody drug conjugates through site-specific incorporation of the optimized non-natural amino acid, para-azidomethyl-l-phenylalanine (pAMF). By using our cell-free protein synthesis platform to directly screen a library of aaRS variants, we have discovered a novel variant of the Methanococcus jannaschii tyrosyl tRNA synthetase (TyrRS), with a high activity and specificity toward pAMF. We demonstrate that site-specific incorporation of pAMF facilitates near complete conjugation of a DBCO-PEG-monomethyl auristatin (DBCO-PEG-MMAF) drug to the tumor-specific, Her2-binding IgG Trastuzumab using strain-promoted azide-alkyne cycloaddition (SPAAC) copper-free click chemistry. The resultant ADCs proved highly potent in in vitro cell cytotoxicity assays.
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Affiliation(s)
- Erik S Zimmerman
- Sutro Biopharma, Inc. 310 Utah Ave Suite 150 South San Francisco, California 94080, United States
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98
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Production and stabilization of the trimeric influenza hemagglutinin stem domain for potentially broadly protective influenza vaccines. Proc Natl Acad Sci U S A 2013; 111:125-30. [PMID: 24344259 DOI: 10.1073/pnas.1308701110] [Citation(s) in RCA: 156] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The rapid dissemination of the 2009 pandemic H1N1 influenza virus emphasizes the need for universal influenza vaccines that would broadly protect against multiple mutated strains. Recent efforts have focused on the highly conserved hemagglutinin (HA) stem domain, which must undergo a significant conformational change for effective viral infection. Although the production of isolated domains of multimeric ectodomain proteins has proven difficult, we report a method to rapidly produce the properly folded HA stem domain protein from influenza virus A/California/05/2009 (H1N1) by using Escherichia coli-based cell-free protein synthesis and a simple refolding protocol. The T4 bacteriophage fibritin foldon placed at the C terminus of the HA stem domain induces trimer formation. Placing emphasis on newly exposed protein surfaces, several hydrophobic residues were mutated, two polypeptide segments were deleted, and the number of disulfide bonds in each monomer was reduced from four to two. High pH and Brij 35 detergent emerged as the most beneficial factors for improving the refolding yield. To stabilize the trimer of the HA stem-foldon fusion, new intermolecular disulfide bonds were finally introduced between foldon monomers and between stem domain monomers. The correct immunogenic conformation of the stabilized HA stem domain trimer was confirmed by using antibodies CR6261, C179, and FI6 that block influenza infection by binding to the HA stem domain trimer. These results suggest great promise for a broadly protective vaccine and also demonstrate a unique approach for producing individual domains of complex multimeric proteins.
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99
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Perez HL, Cardarelli PM, Deshpande S, Gangwar S, Schroeder GM, Vite GD, Borzilleri RM. Antibody-drug conjugates: current status and future directions. Drug Discov Today 2013; 19:869-81. [PMID: 24239727 DOI: 10.1016/j.drudis.2013.11.004] [Citation(s) in RCA: 315] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 09/27/2013] [Accepted: 11/04/2013] [Indexed: 01/25/2023]
Abstract
Antibody-drug conjugates (ADCs) aim to take advantage of the specificity of monoclonal antibodies (mAbs) to deliver potent cytotoxic drugs selectively to antigen-expressing tumor cells. Despite the simple concept, various parameters must be considered when designing optimal ADCs, such as selection of the appropriate antigen target and conjugation method. Each component of the ADC (the antibody, linker and drug) must also be optimized to fully realize the goal of a targeted therapy with improved efficacy and tolerability. Advancements over the past several decades have led to a new generation of ADCs comprising non-immunogenic mAbs, linkers with balanced stability and highly potent cytotoxic agents. Although challenges remain, recent clinical success has generated intense interest in this therapeutic class.
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Affiliation(s)
- Heidi L Perez
- Bristol-Myers Squibb Research & Development, Princeton, NJ 08543, USA
| | - Pina M Cardarelli
- Bristol-Myers Squibb Research & Development, Redwood City, CA 94063, USA
| | - Shrikant Deshpande
- Bristol-Myers Squibb Research & Development, Redwood City, CA 94063, USA
| | - Sanjeev Gangwar
- Bristol-Myers Squibb Research & Development, Redwood City, CA 94063, USA
| | | | - Gregory D Vite
- Bristol-Myers Squibb Research & Development, Princeton, NJ 08543, USA
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100
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Hristodorov D, Fischer R, Linden L. With or without sugar? (A)glycosylation of therapeutic antibodies. Mol Biotechnol 2013; 54:1056-68. [PMID: 23097175 DOI: 10.1007/s12033-012-9612-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Antibodies and antibody-based drugs are currently the fastest-growing class of therapeutics. Over the last three decades, more than 30 therapeutic monoclonal antibodies and derivatives thereof have been approved for and successfully applied in diverse indication areas including cancer, organ transplants, autoimmune/inflammatory disorders, and cardiovascular disease. The isotype of choice for antibody therapeutics is human IgG, whose Fc region contains a ubiquitous asparagine residue (N297) that acts as an acceptor site for N-linked glycans. The nature of these glycans can decisively influence the therapeutic performance of a recombinant antibody, and their absence or modification can lead to the loss of Fc effector functions, greater immunogenicity, and unfavorable pharmacokinetic profiles. However, recent studies have shown that aglycosylated antibodies can be genetically engineered to display novel or enhanced effector functions and that favorable pharmacokinetic properties can be preserved. Furthermore, the ability to produce aglycosylated antibodies in lower eukaryotes and bacteria offers the potential to broaden and simplify the production platforms and avoid the problem of antibody heterogeneity, which occurs when mammalian cells are used for production. In this review, we discuss the importance of Fc glycosylation focusing on the use of aglycosylated and glyco-engineered antibodies as therapeutic proteins.
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Affiliation(s)
- Dmitrij Hristodorov
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Forckenbeckstrasse 6, 52074 Aachen, Germany
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