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Teixeira AP, Fussenegger M. Synthetic Gene Circuits for Regulation of Next-Generation Cell-Based Therapeutics. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2309088. [PMID: 38126677 PMCID: PMC10885662 DOI: 10.1002/advs.202309088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Indexed: 12/23/2023]
Abstract
Arming human cells with synthetic gene circuits enables to expand their capacity to execute superior sensing and response actions, offering tremendous potential for innovative cellular therapeutics. This can be achieved by assembling components from an ever-expanding molecular toolkit, incorporating switches based on transcriptional, translational, or post-translational control mechanisms. This review provides examples from the three classes of switches, and discusses their advantages and limitations to regulate the activity of therapeutic cells in vivo. Genetic switches designed to recognize internal disease-associated signals often encode intricate actuation programs that orchestrate a reduction in the sensed signal, establishing a closed-loop architecture. Conversely, switches engineered to detect external molecular or physical cues operate in an open-loop fashion, switching on or off upon signal exposure. The integration of such synthetic gene circuits into the next generation of chimeric antigen receptor T-cells is already enabling precise calibration of immune responses in terms of magnitude and timing, thereby improving the potency and safety of therapeutic cells. Furthermore, pre-clinical engineered cells targeting other chronic diseases are gathering increasing attention, and this review discusses the path forward for achieving clinical success. With synthetic biology at the forefront, cellular therapeutics holds great promise for groundbreaking treatments.
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Affiliation(s)
- Ana P. Teixeira
- Department of Biosystems Science and EngineeringETH ZurichKlingelbergstrasse 48BaselCH‐4056Switzerland
| | - Martin Fussenegger
- Department of Biosystems Science and EngineeringETH ZurichKlingelbergstrasse 48BaselCH‐4056Switzerland
- Faculty of ScienceUniversity of BaselKlingelbergstrasse 48BaselCH‐4056Switzerland
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2
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Bertschi A, Stefanov BA, Xue S, Charpin-El Hamri G, Teixeira AP, Fussenegger M. Controlling therapeutic protein expression via inhalation of a butter flavor molecule. Nucleic Acids Res 2023; 51:e28. [PMID: 36625292 PMCID: PMC10018347 DOI: 10.1093/nar/gkac1256] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 11/29/2022] [Accepted: 12/20/2022] [Indexed: 01/11/2023] Open
Abstract
Precise control of the delivery of therapeutic proteins is critical for gene- and cell-based therapies, and expression should only be switched on in the presence of a specific trigger signal of appropriate magnitude. Focusing on the advantages of delivering the trigger by inhalation, we have developed a mammalian synthetic gene switch that enables regulation of transgene expression by exposure to the semi-volatile small molecule acetoin, a widely used, FDA-approved food flavor additive. The gene switch capitalizes on the bacterial regulatory protein AcoR fused to a mammalian transactivation domain, which binds to promoter regions with specific DNA sequences in the presence of acetoin and dose-dependently activates expression of downstream transgenes. Wild-type mice implanted with alginate-encapsulated cells transgenic for the acetoin gene switch showed a dose-dependent increase in blood levels of reporter protein in response to either administration of acetoin solution via oral gavage or longer exposure to acetoin aerosol generated by a commercial portable inhaler. Intake of typical acetoin-containing foods, such as butter, lychees and cheese, did not activate transgene expression. As a proof of concept, we show that blood glucose levels were normalized by acetoin aerosol inhalation in type-I diabetic mice implanted with acetoin-responsive insulin-producing cells. Delivery of trigger molecules using portable inhalers may facilitate regular administration of therapeutic proteins via next-generation cell-based therapies to treat chronic diseases for which frequent dosing is required.
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Affiliation(s)
- Adrian Bertschi
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Bozhidar-Adrian Stefanov
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Shuai Xue
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Ghislaine Charpin-El Hamri
- Département Génie Biologique, Institut Universitaire de Technologie, Université Claude Bernard, Lyon 1 Villeurbanne Cedex F-69622, France
| | - Ana Palma Teixeira
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Martin Fussenegger
- To whom correspondence should be addressed. Tel: +41 61 387 31 60; Fax: +41 61 387 39 88;
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3
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Bertschi A, Wang P, Galvan S, Teixeira AP, Fussenegger M. Combinatorial protein dimerization enables precise multi-input synthetic computations. Nat Chem Biol 2023; 19:767-777. [PMID: 36894721 DOI: 10.1038/s41589-023-01281-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 02/01/2023] [Indexed: 03/11/2023]
Abstract
Bacterial transcription factors (TFs) with helix-turn-helix (HTH) DNA-binding domains have been widely explored to build orthogonal transcriptional regulation systems in mammalian cells. Here we capitalize on the modular structure of these proteins to build a framework for multi-input logic gates relying on serial combinations of inducible protein-protein interactions. We found that for some TFs, their HTH domain alone is sufficient for DNA binding. By fusing the HTH domain to TFs, we established dimerization dependent rather than DNA-binding-dependent activation. This enabled us to convert gene switches from OFF-type into more widely applicable ON-type systems and to create mammalian gene switches responsive to new inducers. By combining both OFF and ON modes of action, we built a compact, high-performance bandpass filter. Furthermore, we were able to show cytosolic and extracellular dimerization. Cascading up to five pairwise fusion proteins yielded robust multi-input AND logic gates. Combinations of different pairwise fusion proteins afforded a variety of 4-input 1-output AND and OR logic gate configurations.
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Affiliation(s)
- Adrian Bertschi
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Pengli Wang
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Silvia Galvan
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Ana Palma Teixeira
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland. .,University of Basel, Faculty of Science, Basel, Switzerland.
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Haellman V, Saxena P, Jiang Y, Fussenegger M. Rational design and optimization of synthetic gene switches for controlling cell-fate decisions in pluripotent stem cells. Metab Eng 2021; 65:99-110. [PMID: 33744461 DOI: 10.1016/j.ymben.2021.03.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 02/25/2021] [Accepted: 03/09/2021] [Indexed: 11/26/2022]
Abstract
Advances in synthetic biology have enabled robust control of cell behavior by using tunable genetic circuits to regulate gene expression in a ligand-dependent manner. Such circuits can be used to direct the differentiation of pluripotent stem cells (PSCs) towards desired cell types, but rational design of synthetic gene circuits in PSCs is challenging due to the variable intracellular environment. Here, we provide a framework for implementing synthetic gene switches in PSCs based on combinations of tunable transcriptional, structural, and posttranslational elements that can be engineered as required, using the vanillic acid-controlled transcriptional activator (VanA) as a model system. We further show that the VanA system can be multiplexed with the well-established reverse tetracycline-controlled transcriptional activator (rtTA) system to enable independent control of the expression of different transcription factors in human induced PSCs in order to enhance lineage specification towards early pancreatic progenitors. This work represents a first step towards standardizing the design and construction of synthetic gene switches for building robust gene-regulatory networks to guide stem cell differentiation towards a desired cell fate.
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Affiliation(s)
- Viktor Haellman
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH, 4058, Basel, Switzerland
| | - Pratik Saxena
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH, 4058, Basel, Switzerland
| | - Yanrui Jiang
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH, 4058, Basel, Switzerland
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH, 4058, Basel, Switzerland; Faculty of Science, University of Basel, Mattenstrasse 26, CH, 4058, Basel, Switzerland.
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Kallunki T, Barisic M, Jäättelä M, Liu B. How to Choose the Right Inducible Gene Expression System for Mammalian Studies? Cells 2019; 8:cells8080796. [PMID: 31366153 PMCID: PMC6721553 DOI: 10.3390/cells8080796] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 07/18/2019] [Accepted: 07/26/2019] [Indexed: 12/20/2022] Open
Abstract
Inducible gene expression systems are favored over stable expression systems in a wide variety of basic and applied research areas, including functional genomics, gene therapy, tissue engineering, biopharmaceutical protein production and drug discovery. This is because they are mostly reversible and thus more flexible to use. Furthermore, compared to constitutive expression, they generally exhibit a higher efficiency and have fewer side effects, such as cell death and delayed growth or development. Empowered by decades of development of inducible gene expression systems, researchers can now efficiently activate or suppress any gene, temporarily and quantitively at will, depending on experimental requirements and designs. Here, we review a number of most commonly used mammalian inducible expression systems and provide basic standards and criteria for the selection of the most suitable one.
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Affiliation(s)
- Tuula Kallunki
- Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark
- Department of Drug Design and Pharmacology, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Marin Barisic
- Cell Division and Cytoskeleton, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark
- Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Marja Jäättelä
- Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark
- Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Bin Liu
- Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark.
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Fitz E, Wanka F, Seiboth B. The Promoter Toolbox for Recombinant Gene Expression in Trichoderma reesei. Front Bioeng Biotechnol 2018; 6:135. [PMID: 30364340 PMCID: PMC6193071 DOI: 10.3389/fbioe.2018.00135] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 09/12/2018] [Indexed: 01/05/2023] Open
Abstract
The ascomycete Trichoderma reesei is one of the main fungal producers of cellulases and xylanases based on its high production capacity. Its enzymes are applied in food, feed, and textile industry or in lignocellulose hydrolysis in biofuel and biorefinery industry. Over the last years, the demand to expand the molecular toolbox for T. reesei to facilitate genetic engineering and improve the production of heterologous proteins grew. An important instrument to modify the expression of key genes are promoters to initiate and control their transcription. To date, the most commonly used promoter for T. reesei is the strong inducible promoter of the main cellobiohydrolase cel7a. Beside this one, there is a number of alternative inducible promoters derived from other cellulase- and xylanase encoding genes and a few constitutive promoters. With the advances in genomics and transcriptomics the identification of new constitutive and tunable promoters with different expression strength was simplified. In this review, we will discuss new developments in the field of promoters and compare their advantages and disadvantages. Synthetic expression systems constitute a new option to control gene expression and build up complex gene circuits. Therefore, we will address common structural features of promoters and describe options for promoter engineering and synthetic design of promoters. The availability of well-characterized gene expression control tools is essential for the analysis of gene function, detection of bottlenecks in gene networks and yield increase for biotechnology applications.
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Affiliation(s)
- Elisabeth Fitz
- Research Division Biochemical Technology, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria.,Austrian Centre of Industrial Biotechnology (ACIB) GmbH, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Franziska Wanka
- Austrian Centre of Industrial Biotechnology (ACIB) GmbH, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Bernhard Seiboth
- Research Division Biochemical Technology, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria.,Austrian Centre of Industrial Biotechnology (ACIB) GmbH, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
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7
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Bojar D, Fussenegger M. Programming mammalian gene expression with the antibiotic simocyclinone D8 and the flavonoid luteolin. AIChE J 2018. [DOI: 10.1002/aic.16365] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Daniel Bojar
- Dept. of Biosystems Science and Engineering; ETH Zurich; Basel Switzerland
| | - Martin Fussenegger
- Dept. of Biosystems Science and Engineering; ETH Zurich; Basel Switzerland
- Faculty of Science; University of Basel; Basel Switzerland
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8
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Valdés-Bango Curell R, Barron N. Exploring the Potential Application of Short Non-Coding RNA-Based Genetic Circuits in Chinese Hamster Ovary Cells. Biotechnol J 2018; 13:e1700220. [PMID: 29377624 DOI: 10.1002/biot.201700220] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 01/15/2018] [Indexed: 12/14/2022]
Abstract
The majority of cell engineering for recombinant protein production to date has relied on traditional genetic engineering strategies, such as gene overexpression and gene knock-outs, to substantially improve the production capabilities of Chinese Hamster Ovary (CHO) cells. However, further improvements in cellular productivity or control over product quality is likely to require more sophisticated rational approaches to coordinate and balance cellular pathways. For these strategies to be implemented, novel molecular tools need to be developed to facilitate more refined control of gene expression. Multiple gene control strategies are developed over the last decades in the field of synthetic biology, including DNA and RNA-based systems, which allows tight and timely control over gene expression. microRNAs has received a lot of attention over the last decade in the CHO field and are used to engineer and improve CHO cells. In this review we focus on microRNA-based gene control systems and discuss their potential use as tools rather than targets in order to gain better control over gene expression.
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Affiliation(s)
| | - Niall Barron
- The National Institute for Bioprocessing Research and Training, Fosters Avenue, Blackrock, Dublin, Ireland.,University College Dublin, Dublin, Ireland
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Huang Z, Lee DY, Yoon S. Quantitative intracellular flux modeling and applications in biotherapeutic development and production using CHO cell cultures. Biotechnol Bioeng 2017; 114:2717-2728. [DOI: 10.1002/bit.26384] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 06/07/2017] [Accepted: 07/12/2017] [Indexed: 12/23/2022]
Affiliation(s)
- Zhuangrong Huang
- Department of Chemical Engineering, University of Massachusetts Lowell; One University Avenue; Lowell Massachusetts
| | - Dong-Yup Lee
- Department of Chemical and Biomolecular Engineering; National University of Singapore; Singapore Singapore
- Bioprocessing Technology Institute; Agency for Science, Technology and Research (A*STAR); Singapore Singapore
| | - Seongkyu Yoon
- Department of Chemical Engineering, University of Massachusetts Lowell; One University Avenue; Lowell Massachusetts
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Teixeira AP, Fussenegger M. Synthetic biology-inspired therapies for metabolic diseases. Curr Opin Biotechnol 2017; 47:59-66. [PMID: 28662442 DOI: 10.1016/j.copbio.2017.06.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 06/13/2017] [Indexed: 12/15/2022]
Abstract
Our ability to engineer mammalian cells with effective therapeutic behaviors has brought new hope for treating metabolic diseases. Synthetic gene networks have been customized to interface with the host metabolism, discriminate between healthy and diseased states, and respond by producing an adjusted dose of the therapeutic molecule. Such devices have the potential to treat a range of dysfunctions that are simply not addressable using conventional therapies. Recently, the repurposing of native signaling pathways has formed the basis of autonomous therapeutic programs genetically installed in mammalian cells and has greatly expanded the possibilities to effectively tackle metabolic disorders. Here, we outline network topologies that have been successfully validated in animal models of metabolic diseases and discuss future developments that will be important for bringing this technology closer to clinical application.
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Affiliation(s)
- Ana Palma Teixeira
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland; Instituto de Tecnologia Química e Biológica António Xavier, ITQB-NOVA, Avenida da República, 2780-157 Oeiras, Portugal; IBET, Instituto de Biologia Experimental e Tecnológica, Avenida da República, 2781-157 Oeiras, Portugal
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland; University of Basel, Faculty of Science, Mattenstrasse 26, CH-4058 Basel, Switzerland.
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Ausländer S, Ausländer D, Fussenegger M. Synthetische Biologie - die Synthese der Biologie. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201609229] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Simon Ausländer
- Department of Biosystems Science and Engineering; ETH Zürich; Mattenstrasse 26 4058 Basel Schweiz
| | - David Ausländer
- Department of Biosystems Science and Engineering; ETH Zürich; Mattenstrasse 26 4058 Basel Schweiz
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering; ETH Zürich; Mattenstrasse 26 4058 Basel Schweiz
- Faculty of Science; Universität Basel; Mattenstrasse 26 4058 Basel Schweiz
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12
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Ausländer S, Ausländer D, Fussenegger M. Synthetic Biology-The Synthesis of Biology. Angew Chem Int Ed Engl 2017; 56:6396-6419. [PMID: 27943572 DOI: 10.1002/anie.201609229] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 11/17/2016] [Indexed: 01/01/2023]
Abstract
Synthetic biology concerns the engineering of man-made living biomachines from standardized components that can perform predefined functions in a (self-)controlled manner. Different research strategies and interdisciplinary efforts are pursued to implement engineering principles to biology. The "top-down" strategy exploits nature's incredible diversity of existing, natural parts to construct synthetic compositions of genetic, metabolic, or signaling networks with predictable and controllable properties. This mainly application-driven approach results in living factories that produce drugs, biofuels, biomaterials, and fine chemicals, and results in living pills that are based on engineered cells with the capacity to autonomously detect and treat disease states in vivo. In contrast, the "bottom-up" strategy seeks to be independent of existing living systems by designing biological systems from scratch and synthesizing artificial biological entities not found in nature. This more knowledge-driven approach investigates the reconstruction of minimal biological systems that are capable of performing basic biological phenomena, such as self-organization, self-replication, and self-sustainability. Moreover, the syntheses of artificial biological units, such as synthetic nucleotides or amino acids, and their implementation into polymers inside living cells currently set the boundaries between natural and artificial biological systems. In particular, the in vitro design, synthesis, and transfer of complete genomes into host cells point to the future of synthetic biology: the creation of designer cells with tailored desirable properties for biomedicine and biotechnology.
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Affiliation(s)
- Simon Ausländer
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - David Ausländer
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland.,Faculty of Science, University of Basel, Mattenstrasse 26, 4058, Basel, Switzerland
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Schwarz KA, Leonard JN. Engineering cell-based therapies to interface robustly with host physiology. Adv Drug Deliv Rev 2016; 105:55-65. [PMID: 27266446 DOI: 10.1016/j.addr.2016.05.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 05/10/2016] [Accepted: 05/24/2016] [Indexed: 12/21/2022]
Abstract
Engineered cell-based therapies comprise a rapidly growing clinical technology for treating disease by leveraging the natural capabilities of cells, including migration, information transduction, and biosynthesis and secretion. There now exists a substantial portfolio of intracellular and extracellular sensors that enable bioengineers to program cells to execute defined responses to specific changes in state or environmental cues. As our capability to construct more sophisticated cellular programs increases, assessing and improving the degree to which cell-based therapies perform as desired in vivo will become an increasingly important consideration and opportunity for technological advancement. In this review, we seek to describe both current capabilities and potential needs for building cell-based therapies that interface with host physiology in a manner that is robust - a phrase we use in this context to describe the achievement of therapeutic efficacy across a range of patients and implementations. We first review the portfolio of sensors and outputs currently available for use in cell-based therapies by highlighting key advancements and current gaps. Then, we propose a conceptual framework for evaluating and pursuing robust clinical performance of engineered cell-based therapies.
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14
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Ausländer S, Fussenegger M. Engineering Gene Circuits for Mammalian Cell-Based Applications. Cold Spring Harb Perspect Biol 2016; 8:cshperspect.a023895. [PMID: 27194045 DOI: 10.1101/cshperspect.a023895] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Synthetic gene switches are basic building blocks for the construction of complex gene circuits that transform mammalian cells into useful cell-based machines for next-generation biotechnological and biomedical applications. Ligand-responsive gene switches are cellular sensors that are able to process specific signals to generate gene product responses. Their involvement in complex gene circuits results in sophisticated circuit topologies that are reminiscent of electronics and that are capable of providing engineered cells with the ability to memorize events, oscillate protein production, and perform complex information-processing tasks. Microencapsulated mammalian cells that are engineered with closed-loop gene networks can be implanted into mice to sense disease-related input signals and to process this information to produce a custom, fine-tuned therapeutic response that rebalances animal metabolism. Progress in gene circuit design, in combination with recent breakthroughs in genome engineering, may result in tailored engineered mammalian cells with great potential for future cell-based therapies.
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Affiliation(s)
- Simon Ausländer
- Department of Biosystems Science and Engineering, ETH Zurich, CH-4058 Basel, Switzerland
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, CH-4058 Basel, Switzerland Faculty of Science, University of Basel, CH-4058 Basel, Switzerland
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15
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Kis Z, Pereira HS, Homma T, Pedrigi RM, Krams R. Mammalian synthetic biology: emerging medical applications. J R Soc Interface 2016; 12:rsif.2014.1000. [PMID: 25808341 DOI: 10.1098/rsif.2014.1000] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
In this review, we discuss new emerging medical applications of the rapidly evolving field of mammalian synthetic biology. We start with simple mammalian synthetic biological components and move towards more complex and therapy-oriented gene circuits. A comprehensive list of ON-OFF switches, categorized into transcriptional, post-transcriptional, translational and post-translational, is presented in the first sections. Subsequently, Boolean logic gates, synthetic mammalian oscillators and toggle switches will be described. Several synthetic gene networks are further reviewed in the medical applications section, including cancer therapy gene circuits, immuno-regulatory networks, among others. The final sections focus on the applicability of synthetic gene networks to drug discovery, drug delivery, receptor-activating gene circuits and mammalian biomanufacturing processes.
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Affiliation(s)
- Zoltán Kis
- Department of Bioengineering, Imperial College London, London, UK
| | | | - Takayuki Homma
- Department of Bioengineering, Imperial College London, London, UK
| | - Ryan M Pedrigi
- Department of Bioengineering, Imperial College London, London, UK
| | - Rob Krams
- Department of Bioengineering, Imperial College London, London, UK
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16
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Chen X, Li T, Wang X, Du Z, Liu R, Yang Y. Synthetic dual-input mammalian genetic circuits enable tunable and stringent transcription control by chemical and light. Nucleic Acids Res 2015; 44:2677-90. [PMID: 26673714 PMCID: PMC4824083 DOI: 10.1093/nar/gkv1343] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 11/18/2015] [Indexed: 12/21/2022] Open
Abstract
Programmable transcription factors can enable precise control of gene expression triggered by a chemical inducer or light. To obtain versatile transgene system with combined benefits of a chemical inducer and light inducer, we created various chimeric promoters through the assembly of different copies of the tet operator and Gal4 operator module, which simultaneously responded to a tetracycline-responsive transcription factor and a light-switchable transactivator. The activities of these chimeric promoters can be regulated by tetracycline and blue light synergistically or antagonistically. Further studies of the antagonistic genetic circuit exhibited high spatiotemporal resolution and extremely low leaky expression, which therefore could be used to spatially and stringently control the expression of highly toxic protein Diphtheria toxin A for light regulated gene therapy. When transferring plasmids engineered for the gene switch-driven expression of a firefly luciferase (Fluc) into mice, the Fluc expression levels of the treated animals directly correlated with the tetracycline and light input program. We suggest that dual-input genetic circuits using TET and light that serve as triggers to achieve expression profiles may enable the design of robust therapeutic gene circuits for gene- and cell-based therapies.
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Affiliation(s)
- Xianjun Chen
- Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China Optogenetics & Molecular Imaging Interdisciplinary Research Center, CAS Center for Excellence in Brain Science, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China
| | - Ting Li
- Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China Optogenetics & Molecular Imaging Interdisciplinary Research Center, CAS Center for Excellence in Brain Science, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China
| | - Xue Wang
- Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China
| | - Zengmin Du
- Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China Optogenetics & Molecular Imaging Interdisciplinary Research Center, CAS Center for Excellence in Brain Science, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China
| | - Renmei Liu
- Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China Optogenetics & Molecular Imaging Interdisciplinary Research Center, CAS Center for Excellence in Brain Science, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China
| | - Yi Yang
- Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China Optogenetics & Molecular Imaging Interdisciplinary Research Center, CAS Center for Excellence in Brain Science, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China Collaborative Innovation Center of Genetics and Development, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China
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17
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Wang H, Ye H, Xie M, Daoud El-Baba M, Fussenegger M. Cosmetics-triggered percutaneous remote control of transgene expression in mice. Nucleic Acids Res 2015; 43:e91. [PMID: 25943548 PMCID: PMC4538802 DOI: 10.1093/nar/gkv326] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 03/31/2015] [Indexed: 12/24/2022] Open
Abstract
Synthetic biology has significantly advanced the rational design of trigger-inducible gene switches that program cellular behavior in a reliable and predictable manner. Capitalizing on genetic componentry, including the repressor PmeR and its cognate operator OPmeR, that has evolved in Pseudomonas syringae pathovar tomato DC3000 to sense and resist plant-defence metabolites of the paraben class, we have designed a set of inducible and repressible mammalian transcription-control devices that could dose-dependently fine-tune transgene expression in mammalian cells and mice in response to paraben derivatives. With an over 60-years track record as licensed preservatives in the cosmetics industry, paraben derivatives have become a commonplace ingredient of most skin-care products including shower gels, cleansing toners and hand creams. As parabens can rapidly reach the bloodstream of mice following topical application, we used this feature to percutaneously program transgene expression of subcutaneous designer cell implants using off-the-shelf commercial paraben-containing skin-care cosmetics. The combination of non-invasive, transdermal and orthogonal trigger-inducible remote control of transgene expression may provide novel opportunities for dynamic interventions in future gene and cell-based therapies.
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Affiliation(s)
- Hui Wang
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Haifeng Ye
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, 200241 Shanghai, China
| | - Mingqi Xie
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Marie Daoud El-Baba
- Département Génie Biologique, Institut Universitaire de Technologie, F-69622 Villeurbanne Cedex, France
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland Faculty of Science, University of Basel, CH-4058 Basel, Switzerland
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18
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Daringer N, Dudek RM, Schwarz KA, Leonard JN. Modular extracellular sensor architecture for engineering mammalian cell-based devices. ACS Synth Biol 2014; 3:892-902. [PMID: 24611683 PMCID: PMC4161666 DOI: 10.1021/sb400128g] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Indexed: 12/31/2022]
Abstract
Engineering mammalian cell-based devices that monitor and therapeutically modulate human physiology is a promising and emerging frontier in clinical synthetic biology. However, realizing this vision will require new technologies enabling engineered circuitry to sense and respond to physiologically relevant cues. No existing technology enables an engineered cell to sense exclusively extracellular ligands, including proteins and pathogens, without relying upon native cellular receptors or signal transduction pathways that may be subject to crosstalk with native cellular components. To address this need, we here report a technology we term a Modular Extracellular Sensor Architecture (MESA). This self-contained receptor and signal transduction platform is maximally orthogonal to native cellular processes and comprises independent, tunable protein modules that enable performance optimization and straightforward engineering of novel MESA that recognize novel ligands. We demonstrate ligand-inducible activation of MESA signaling, optimization of receptor performance using design-based approaches, and generation of MESA biosensors that produce outputs in the form of either transcriptional regulation or transcription-independent reconstitution of enzymatic activity. This systematic, quantitative platform characterization provides a framework for engineering MESA to recognize novel ligands and for integrating these sensors into diverse mammalian synthetic biology applications.
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Affiliation(s)
- Nichole
M. Daringer
- Department
of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Rachel M. Dudek
- Department
of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Kelly A. Schwarz
- Department
of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Joshua N. Leonard
- Department
of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry
of Life Processes Institute, Northwestern
University, Evanston, Illinois 60208, United
States
- Member, Robert H.
Lurie Comprehensive Cancer Center, Northwestern University, Evanston, Illinois 60208, United States
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19
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Stanton BC, Siciliano V, Ghodasara A, Wroblewska L, Clancy K, Trefzer AC, Chesnut JD, Weiss R, Voigt CA. Systematic transfer of prokaryotic sensors and circuits to mammalian cells. ACS Synth Biol 2014; 3:880-91. [PMID: 25360681 PMCID: PMC4277766 DOI: 10.1021/sb5002856] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Prokaryotic regulatory proteins respond to diverse signals and represent a rich resource for building synthetic sensors and circuits. The TetR family contains >10(5) members that use a simple mechanism to respond to stimuli and bind distinct DNA operators. We present a platform that enables the transfer of these regulators to mammalian cells, which is demonstrated using human embryonic kidney (HEK293) and Chinese hamster ovary (CHO) cells. The repressors are modified to include nuclear localization signals (NLS) and responsive promoters are built by incorporating multiple operators. Activators are also constructed by modifying the protein to include a VP16 domain. Together, this approach yields 15 new regulators that demonstrate 19- to 551-fold induction and retain both the low levels of crosstalk in DNA binding specificity observed between the parent regulators in Escherichia coli, as well as their dynamic range of activity. By taking advantage of the DAPG small molecule sensing mediated by the PhlF repressor, we introduce a new inducible system with 50-fold induction and a threshold of 0.9 μM DAPG, which is comparable to the classic Dox-induced TetR system. A set of NOT gates is constructed from the new repressors and their response function quantified. Finally, the Dox- and DAPG- inducible systems and two new activators are used to build a synthetic enhancer (fuzzy AND gate), requiring the coordination of 5 transcription factors organized into two layers. This work introduces a generic approach for the development of mammalian genetic sensors and circuits to populate a toolbox that can be applied to diverse applications from biomanufacturing to living therapeutics.
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Affiliation(s)
- Brynne C. Stanton
- Synthetic
Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Velia Siciliano
- Synthetic
Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Amar Ghodasara
- Synthetic
Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Liliana Wroblewska
- Synthetic
Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Kevin Clancy
- Synthetic Biology R&D, Life Science Solutions Group, Thermo Fisher Scientific, Carlsbad, California 92008, United States
| | - Axel C. Trefzer
- Synthetic Biology R&D, Life Science Solutions Group, Thermo Fisher Scientific, Carlsbad, California 92008, United States
| | - Jonathan D. Chesnut
- Synthetic Biology R&D, Life Science Solutions Group, Thermo Fisher Scientific, Carlsbad, California 92008, United States
| | - Ron Weiss
- Synthetic
Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Christopher A. Voigt
- Synthetic
Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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20
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Xie M, Ye H, Hamri GCE, Fussenegger M. Antagonistic control of a dual-input mammalian gene switch by food additives. Nucleic Acids Res 2014; 42:e116. [PMID: 25030908 PMCID: PMC4132709 DOI: 10.1093/nar/gku545] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Synthetic biology has significantly advanced the design of mammalian trigger-inducible transgene-control devices that are able to programme complex cellular behaviour. Fruit-based benzoate derivatives licensed as food additives, such as flavours (e.g. vanillate) and preservatives (e.g. benzoate), are a particularly attractive class of trigger compounds for orthogonal mammalian transgene control devices because of their innocuousness, physiological compatibility and simple oral administration. Capitalizing on the genetic componentry of the soil bacterium Comamonas testosteroni, which has evolved to catabolize a variety of aromatic compounds, we have designed different mammalian gene expression systems that could be induced and repressed by the food additives benzoate and vanillate. When implanting designer cells engineered for gene switch-driven expression of the human placental secreted alkaline phosphatase (SEAP) into mice, blood SEAP levels of treated animals directly correlated with a benzoate-enriched drinking programme. Additionally, the benzoate-/vanillate-responsive device was compatible with other transgene control systems and could be assembled into higher-order control networks providing expression dynamics reminiscent of a lap-timing stopwatch. Designer gene switches using licensed food additives as trigger compounds to achieve antagonistic dual-input expression profiles and provide novel control topologies and regulation dynamics may advance future gene- and cell-based therapies.
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Affiliation(s)
- Mingqi Xie
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Haifeng Ye
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | | | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland Faculty of Science, University of Basel, CH-4058 Basel, Switzerland
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21
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Liu SP, Liu RX, Xiao MR, Zhang L, Ding ZY, Gu ZH, Shi GY. A systems level engineered E. coli capable of efficiently producing L-phenylalanine. Process Biochem 2014. [DOI: 10.1016/j.procbio.2014.01.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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22
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Lee EJ, Tabor JJ, Mikos AG. Leveraging synthetic biology for tissue engineering applications. Inflamm Regen 2014. [DOI: 10.2492/inflammregen.34.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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23
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Immune signal transduction in leishmaniasis from natural to artificial systems: Role of feedback loop insertion. Biochim Biophys Acta Gen Subj 2014; 1840:71-9. [DOI: 10.1016/j.bbagen.2013.08.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 07/31/2013] [Accepted: 08/23/2013] [Indexed: 12/17/2022]
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24
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Rössger K, Charpin-El-Hamri G, Fussenegger M. Bile acid-controlled transgene expression in mammalian cells and mice. Metab Eng 2013; 21:81-90. [PMID: 24280297 DOI: 10.1016/j.ymben.2013.11.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 10/08/2013] [Accepted: 11/11/2013] [Indexed: 12/27/2022]
Abstract
In recent years, using trigger-inducible mammalian gene switches to design sophisticated transcription-control networks has become standard practice in synthetic biology. These switches provide unprecedented precision, complexity and reliability when programming novel mammalian cell functions. Metabolite-responsive repressors of human-pathogenic bacteria are particularly attractive for use in these orthogonal synthetic mammalian gene switches because the trigger compound sensitivity often matches the human physiological range. We have designed both a bile acid-repressible (BEAROFF) as well as a bile-acid-inducible (BEARON) gene switch by capitalizing on components that have evolved to manage bile acid resistance in Campylobacter jejuni, the leading causative agent of human food-borne enteritis. We have shown that both of these switches enable bile acid-adjustable transgene expression in different mammalian cell lines as well as in mice. For the BEAROFF device, the C. jejuni repressor CmeR was fused to the VP16 transactivation domain to create a synthetic transactivator that activates minimal promoters containing tandem operator modules (Ocme) in a bile acid-repressible manner. Fusion of CmeR to a transsilencing domain resulted in an artificial transsilencer that binds and represses a constitutive Ocme-containing promoter until it is released by addition of bile acid (BEARON). A tailored multi-step tuning program for the inducible gene switch, which included the optimization of individual component performance, control of their relative abundances, the choice of the cell line and trigger compound, resulted in a BEARON device with significantly improved bile acid-responsive control characteristics. Synthetic metabolite-triggered gene switches that are able to interface with host metabolism may foster advances in future gene and cell-based therapies.
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Affiliation(s)
- Katrin Rössger
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Ghislaine Charpin-El-Hamri
- Département Génie Biologique, Institut Universitaire de Technologie (IUTA), F-69622 Villeurbanne Cedex, France
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland; Faculty of Science, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland.
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25
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Ausländer S, Fussenegger M. From gene switches to mammalian designer cells: present and future prospects. Trends Biotechnol 2013; 31:155-68. [DOI: 10.1016/j.tibtech.2012.11.006] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Revised: 11/14/2012] [Accepted: 11/14/2012] [Indexed: 10/27/2022]
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26
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Lanza AM, Cheng JK, Alper HS. Emerging synthetic biology tools for engineering mammalian cell systems and expediting cell line development. Curr Opin Chem Eng 2012. [DOI: 10.1016/j.coche.2012.09.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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27
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Synthetic signaling networks for therapeutic applications. Curr Opin Biotechnol 2012; 23:773-9. [DOI: 10.1016/j.copbio.2012.01.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Revised: 01/03/2012] [Accepted: 01/08/2012] [Indexed: 01/02/2023]
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28
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Genetically switched d-lactate production in Escherichia coli. Metab Eng 2012; 14:560-8. [DOI: 10.1016/j.ymben.2012.05.004] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2011] [Revised: 05/03/2012] [Accepted: 05/11/2012] [Indexed: 11/15/2022]
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29
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Wieland M, Fussenegger M. Engineering Molecular Circuits Using Synthetic Biology in Mammalian Cells. Annu Rev Chem Biomol Eng 2012; 3:209-34. [DOI: 10.1146/annurev-chembioeng-061010-114145] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Markus Wieland
- Department of Biosystems Science and Bioengineering, ETH Zurich, CH-4058 Basel, Switzerland; ,
| | - Martin Fussenegger
- Department of Biosystems Science and Bioengineering, ETH Zurich, CH-4058 Basel, Switzerland; ,
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30
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A novel reporter system for bacterial and mammalian cells based on the non-ribosomal peptide indigoidine. Metab Eng 2012; 14:325-35. [DOI: 10.1016/j.ymben.2012.04.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2011] [Revised: 03/19/2012] [Accepted: 04/13/2012] [Indexed: 12/16/2022]
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31
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Chen YY, Smolke CD. From DNA to targeted therapeutics: bringing synthetic biology to the clinic. Sci Transl Med 2012; 3:106ps42. [PMID: 22030748 DOI: 10.1126/scitranslmed.3002944] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Synthetic biology aims to make biological engineering more scalable and predictable, lowering the cost and facilitating the translation of synthetic biological systems to practical applications. Increasingly sophisticated, rationally designed synthetic systems that are capable of complex functions pave the way to translational applications, including disease diagnostics and targeted therapeutics. Here, we provide an overview of recent developments in synthetic biology in the context of translational research and discuss challenges at the interface between synthetic biology and clinical medicine.
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Affiliation(s)
- Yvonne Y Chen
- Society of Fellows, Harvard University, 78 Mount Auburn Street, Cambridge, MA 02138, USA
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32
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Ausländer S, Wieland M, Fussenegger M. Smart medication through combination of synthetic biology and cell microencapsulation. Metab Eng 2012; 14:252-60. [DOI: 10.1016/j.ymben.2011.06.003] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Revised: 05/11/2011] [Accepted: 06/09/2011] [Indexed: 01/05/2023]
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33
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Kämpf MM, Engesser R, Busacker M, Hörner M, Karlsson M, Zurbriggen MD, Fussenegger M, Timmer J, Weber W. Rewiring and dosing of systems modules as a design approach for synthetic mammalian signaling networks. MOLECULAR BIOSYSTEMS 2012; 8:1824-32. [PMID: 22532387 DOI: 10.1039/c2mb05509k] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Modularly structured signaling networks coordinate the fate and function of complex biological systems. Each component in the network performs a discrete computational operation, but when connected to each other intricate functionality emerges. Here we study such an architecture by connecting auxin signaling modules and inducible protein biotinylation systems with transcriptional control systems to construct synthetic mammalian high-detect, low-detect and band-detect networks that translate overlapping gradients of inducer molecules into distinct gene expression patterns. Guided by a mathematical model we apply fundamental computational operations like conjunction or addition to rewire individual building blocks to qualitatively and quantitatively program the way the overall network interprets graded input signals. The design principles described in this study might serve as a conceptual blueprint for the development of next-generation mammalian synthetic gene networks in fundamental and translational research.
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Affiliation(s)
- Michael M Kämpf
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
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34
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Oldham P, Hall S, Burton G. Synthetic biology: mapping the scientific landscape. PLoS One 2012; 7:e34368. [PMID: 22539946 PMCID: PMC3335118 DOI: 10.1371/journal.pone.0034368] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2011] [Accepted: 02/27/2012] [Indexed: 12/18/2022] Open
Abstract
This article uses data from Thomson Reuters Web of Science to map and analyse the scientific landscape for synthetic biology. The article draws on recent advances in data visualisation and analytics with the aim of informing upcoming international policy debates on the governance of synthetic biology by the Subsidiary Body on Scientific, Technical and Technological Advice (SBSTTA) of the United Nations Convention on Biological Diversity. We use mapping techniques to identify how synthetic biology can best be understood and the range of institutions, researchers and funding agencies involved. Debates under the Convention are likely to focus on a possible moratorium on the field release of synthetic organisms, cells or genomes. Based on the empirical evidence we propose that guidance could be provided to funding agencies to respect the letter and spirit of the Convention on Biological Diversity in making research investments. Building on the recommendations of the United States Presidential Commission for the Study of Bioethical Issues we demonstrate that it is possible to promote independent and transparent monitoring of developments in synthetic biology using modern information tools. In particular, public and policy understanding and engagement with synthetic biology can be enhanced through the use of online interactive tools. As a step forward in this process we make existing data on the scientific literature on synthetic biology available in an online interactive workbook so that researchers, policy makers and civil society can explore the data and draw conclusions for themselves.
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Affiliation(s)
- Paul Oldham
- ESRC Centre for Economic and Social Aspects of Genomics, Lancaster University, Lancaster, United Kingdom.
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35
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Hörner M, Weber W. Molecular switches in animal cells. FEBS Lett 2012; 586:2084-96. [DOI: 10.1016/j.febslet.2012.02.032] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Revised: 02/17/2012] [Accepted: 02/20/2012] [Indexed: 12/11/2022]
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36
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Botezatu L, Sievers S, Gama-Norton L, Schucht R, Hauser H, Wirth D. Genetic aspects of cell line development from a synthetic biology perspective. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2012; 127:251-284. [PMID: 22068842 DOI: 10.1007/10_2011_117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Animal cells can be regarded as factories for the production of relevant proteins. The advances described in this chapter towards the development of cell lines with higher productivity capacities, certain metabolic and proliferation properties, reduced apoptosis and other features must be regarded in an integrative perspective. The systematic application of systems biology approaches in combination with a synthetic arsenal for targeted modification of endogenous networks are proposed to lead towards the achievement of a predictable and technologically advanced cell system with high biotechnological impact.
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Affiliation(s)
- L Botezatu
- Helmholtz Centre for Infection Research, Braunschweig, Germany
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37
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Karlsson M, Weber W, Fussenegger M. Design and construction of synthetic gene networks in mammalian cells. Methods Mol Biol 2012; 813:359-76. [PMID: 22083754 DOI: 10.1007/978-1-61779-412-4_22] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Advances in the development of molecular tools for the inducible control of transcription, translation, and protein degradation are the basis for the rapidly emerging design and construction of synthetic gene networks in mammalian cells.In this chapter, we describe such tools and how they can be integrated into a synthetic gene network with desired functionality. The network design and construction process is illustrated in the form of a detailed protocol for the implementation of a logic NOR gate based on an inducible promoter combined with an inducible protein degradation system.
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Affiliation(s)
- Maria Karlsson
- Faculty of Biology, BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
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38
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Gitzinger M, Kemmer C, Fluri DA, El-Baba MD, Weber W, Fussenegger M. The food additive vanillic acid controls transgene expression in mammalian cells and mice. Nucleic Acids Res 2011; 40:e37. [PMID: 22187155 PMCID: PMC3300003 DOI: 10.1093/nar/gkr1251] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Trigger-inducible transcription-control devices that reversibly fine-tune transgene expression in response to molecular cues have significantly advanced the rational reprogramming of mammalian cells. When designed for use in future gene- and cell-based therapies the trigger molecules have to be carefully chosen in order to provide maximum specificity, minimal side-effects and optimal pharmacokinetics in a mammalian organism. Capitalizing on control components that enable Caulobacter crescentus to metabolize vanillic acid originating from lignin degradation that occurs in its oligotrophic freshwater habitat, we have designed synthetic devices that specifically adjust transgene expression in mammalian cells when exposed to vanillic acid. Even in mice transgene expression was robust, precise and tunable in response to vanillic acid. As a licensed food additive that is regularly consumed by humans via flavoured convenience food and specific fresh vegetable and fruits, vanillic acid can be considered as a safe trigger molecule that could be used for diet-controlled transgene expression in future gene- and cell-based therapies.
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Affiliation(s)
- Marc Gitzinger
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
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39
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Karlsson M, Weber W, Fussenegger M. De novo design and construction of an inducible gene expression system in mammalian cells. Methods Enzymol 2011; 497:239-53. [PMID: 21601090 DOI: 10.1016/b978-0-12-385075-1.00011-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Inducible expression systems represent the founding technology for the emergence of synthetic biology in mammalian cells. The core molecules in these systems are bacterial regulator proteins that bind to or dissociate from a cognate DNA operator sequence in response to an exogenous stimulus like a small-molecule inducer. In this chapter, we describe a generic protocol of how bacterial regulator proteins can be applied to the design, construction, and optimization of an inducible expression system in mammalian cells. By choosing regulator proteins with an appropriate small-molecule inducer, this protocol provides a straightforward approach for establishing biosensors, cell-to-cell communication systems, or tools to control gene expression in vivo.
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Affiliation(s)
- Maria Karlsson
- Faculty of Biology, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
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Fungal gene expression on demand: an inducible, tunable, and metabolism-independent expression system for Aspergillus niger. Appl Environ Microbiol 2011; 77:2975-83. [PMID: 21378046 DOI: 10.1128/aem.02740-10] [Citation(s) in RCA: 135] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Filamentous fungi are the cause of serious human and plant diseases but are also exploited in biotechnology as production platforms. Comparative genomics has documented their genetic diversity, and functional genomics and systems biology approaches are under way to understand the functions and interaction of fungal genes and proteins. In these approaches, gene functions are usually inferred from deletion or overexpression mutants. However, studies at these extreme points give only limited information. Moreover, many overexpression studies use metabolism-dependent promoters, often causing pleiotropic effects and thus limitations in their significance. We therefore established and systematically evaluated a tunable expression system for Aspergillus niger that is independent of carbon and nitrogen metabolism and silent under noninduced conditions. The system consists of two expression modules jointly targeted to a defined genomic locus. One module ensures constitutive expression of the tetracycline-dependent transactivator rtTA2(S)-M2, and one module harbors the rtTA2(S)-M2-dependent promoter that controls expression of the gene of interest (the Tet-on system). We show here that the system is tight, responds within minutes after inducer addition, and allows fine-tuning based on the inducer concentration or gene copy number up to expression levels higher than the expression levels of the gpdA promoter. We also validate the Tet-on system for the generation of conditional overexpression mutants and demonstrate its power when combined with a gene deletion approach. Finally, we show that the system is especially suitable when the functions of essential genes must be examined.
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Synthetic biology: tools to design, build, and optimize cellular processes. J Biomed Biotechnol 2010; 2010:130781. [PMID: 20150964 PMCID: PMC2817555 DOI: 10.1155/2010/130781] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2009] [Accepted: 10/28/2009] [Indexed: 11/17/2022] Open
Abstract
The general central
dogma frames the emergent properties of life,
which make biology both necessary and difficult
to engineer. In a process engineering paradigm,
each biological process stream and process unit
is heavily influenced by regulatory interactions
and interactions with the surrounding
environment. Synthetic biology is developing the
tools and methods that will increase control
over these interactions, eventually resulting in
an integrative synthetic biology that will allow
ground-up cellular optimization. In this review,
we attempt to contextualize the areas of
synthetic biology into three tiers: (1) the
process units and associated streams of the
central dogma, (2) the intrinsic regulatory
mechanisms, and (3) the extrinsic physical and
chemical environment. Efforts at each of these
three tiers attempt to control cellular systems
and take advantage of emerging tools and
approaches. Ultimately, it will be possible to
integrate these approaches and realize the
vision of integrative synthetic biology when
cells are completely rewired for
biotechnological goals. This review will
highlight progress towards this goal as well as
areas requiring further research.
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Weber W, Lienhart C, Daoud-El Baba M, Grass RN, Kohler T, Müller R, Stark WJ, Fussenegger M. Magnet-guided transduction of mammalian cells and mice using engineered magnetic lentiviral particles. J Biotechnol 2009; 141:118-22. [PMID: 19433214 DOI: 10.1016/j.jbiotec.2009.02.023] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2009] [Revised: 02/16/2009] [Accepted: 02/26/2009] [Indexed: 02/08/2023]
Abstract
Targeted delivery of therapeutic transgenes into specific cells remains a highly relevant challenge for tissue engineering and future gene-based therapies. We have designed streptavidin-pseudotyped lentiviral particles which upon coupling with biotinylated magnetic carbon-coated cobalt nanoparticles could be guided by magnetic fields to site-specifically transduce desired target cells in culture as well as in mice. Magnetic patterns projected onto monolayer cultures were replicated by fluorescent cells following targeted transduction by magnetic lentiviral particles engineered for constitutive expression of the green fluorescent protein (GFP). Even after intravenous injection into mice magnetic GFP-transgenic lentiviral particles could be guided to a preferred transduction site in the animal using a magnetic field. Magnet-guided transgene delivery producing desired patterns of transduced cell populations may enable the design of defined tissue topologies and provide site-specific transduction of therapeutic transgenes for cell-specific interventions in future gene and cancer therapies.
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Affiliation(s)
- Wilfried Weber
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
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