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Plaper T, Rihtar E, Železnik Ramuta T, Forstnerič V, Jazbec V, Ivanovski F, Benčina M, Jerala R. The art of designed coiled-coils for the regulation of mammalian cells. Cell Chem Biol 2024; 31:1460-1472. [PMID: 38971158 PMCID: PMC11335187 DOI: 10.1016/j.chembiol.2024.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 05/04/2024] [Accepted: 06/11/2024] [Indexed: 07/08/2024]
Abstract
Synthetic biology aims to engineer complex biological systems using modular elements, with coiled-coil (CC) dimer-forming modules are emerging as highly useful building blocks in the regulation of protein assemblies and biological processes. Those small modules facilitate highly specific and orthogonal protein-protein interactions, offering versatility for the regulation of diverse biological functions. Additionally, their design rules enable precise control and tunability over these interactions, which are crucial for specific applications. Recent advancements showcase their potential for use in innovative therapeutic interventions and biomedical applications. In this review, we discuss the potential of CCs, exploring their diverse applications in mammalian cells, such as synthetic biological circuit design, transcriptional and allosteric regulation, cellular assemblies, chimeric antigen receptor (CAR) T cell regulation, and genome editing and their role in advancing the understanding and regulation of cellular processes.
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Affiliation(s)
- Tjaša Plaper
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Erik Rihtar
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Taja Železnik Ramuta
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Vida Forstnerič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Vid Jazbec
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Filip Ivanovski
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Mojca Benčina
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia; Centre for Technologies of Gene and Cell Therapy, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia; Centre for Technologies of Gene and Cell Therapy, Hajdrihova 19, 1000 Ljubljana, Slovenia.
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2
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Wu RY, Wu CQ, Xie F, Xing X, Xu L. Building RNA-Mediated Artificial Signaling Pathways between Endogenous Genes. Acc Chem Res 2024; 57:1777-1789. [PMID: 38872074 DOI: 10.1021/acs.accounts.4c00070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2024]
Abstract
ConspectusSophisticated genetic networks play a pivotal role in orchestrating cellular responses through intricate signaling pathways across diverse environmental conditions. Beyond the inherent complexity of natural cellular signaling networks, the construction of artificial signaling pathways (ASPs) introduces a vast array of possibilities for reshaping cellular responses, enabling programmable control of living organisms. ASPs can be integrated with existing cellular networks and redirect output responses as desired, allowing seamless communication and coordination with other cellular processes, thereby achieving designable transduction within cells. Among diversified ASPs, establishing connections between originally independent endogenous genes is of particular significance in modifying the genetic networks, so that cells can be endowed with new capabilities to sense and deal with abnormal factors related to differentiated gene expression (i.e., solve the issues of the aberrant gene expression induced by either external or internal stimuli). In a typical scenario, the two genes X and Y in the cell are originally expressed independently. After the introduction of an ASP, changes in the expression of gene X may exert a designed impact on gene Y, subsequently inducing the cellular response related to gene Y. If X represents a disease signal and Y serves as a therapeutic module, the introduction of the ASP empowers cells with a new spontaneous defense system to handle potential risks, which holds great potential for both fundamental and translational studies.In this Account, we primarily review our endeavors in the construction of RNA-mediated ASPs between endogenous genes that can respond to differentiated RNA expression. In contrast to other molecules that may be restricted to specific pathways, synthetic RNA circuits can be easily utilized and expanded as a general platform for constructing ASPs with a high degree of programmability and tunability for diversified functionalities through predictable Watson-Crick base pairing. We first provide an overview of recent advancements in RNA-based genetic circuits, encompassing but not limited to utilization of RNA toehold switches, siRNA and CRISPR systems. Despite notable progress, most reported RNA circuits have to contain at least one exogenous RNA X as input or one engineered RNA Y as a target, which is not suitable for establishing endogenous gene connections. While exogenous RNAs can be engineered and controlled as desired, constructing a general and efficient platform for manipulation of naturally occurring RNAs poses a formidable challenge, especially for the mammalian system. With a focus on this goal, we are devoted to developing efficient strategies to manipulate cell responses by establishing RNA-mediated ASPs between endogenous genes, particularly in mammalian cells. Our step-by-step progress in engineering customized cell signaling circuits, from bacterial cells to mammalian cells, from gene expression regulation to phenotype control, and from small RNA to long mRNA of low abundance and more complex secondary structures, is systematically described. Finally, future perspectives and potential applications of these RNA-mediated ASPs between endogenous genes are also discussed.
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Affiliation(s)
- Ruo-Yue Wu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510006, China
| | - Chao-Qun Wu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510006, China
| | - Fan Xie
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510006, China
| | - Xiwen Xing
- Department of Biotechnology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Liang Xu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510006, China
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3
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Zhou L, Simonian AL. CRISPR/Cas Technology: The Unique Synthetic Biology Genome-Editing Tool Shifting the Paradigm in Viral Diagnostics, Defense, and Therapeutics. Annu Rev Biomed Eng 2024; 26:247-272. [PMID: 38346278 DOI: 10.1146/annurev-bioeng-081723-013033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
The emergence of the COVID-19 pandemic has starkly exposed our significantly limited ability to promptly identify and respond to emergent biological threats. Consequently, there is an urgent need to advance biotechnological methods for addressing both known and unforeseen biological hazards. Recently, the CRISPR/Cas system has revolutionized genetic engineering, enabling precise and efficient synthetic biology applications. Therefore, this review aims to provide a comprehensive introduction to the fundamental principles underlying the CRISPR/Cas system and assess the advantages and limitations of various CRISPR/Cas-based techniques applicable to the detection of, defense against, and treatment of viral infections. These techniques include viral diagnostics, the development of antiviral vaccines, B cell engineering for antibody production, viral activation/interference, and epigenetic modifications. Furthermore, this review delves into the challenges and bioethical considerations associated with use of the CRISPR/Cas system. With the continuous evolution of technology, the CRISPR/Cas system holds considerable promise for addressing both existing and unforeseen biological threats.
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Affiliation(s)
- Lang Zhou
- Department of Materials Engineering, Samuel Ginn College of Engineering, Auburn University, Auburn, Alabama, USA;
| | - Aleksandr L Simonian
- Department of Materials Engineering, Samuel Ginn College of Engineering, Auburn University, Auburn, Alabama, USA;
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4
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Wu CQ, Wu RY, Zhang QL, Wang LL, Wang Y, Dai C, Zhang CX, Xu L. Harnessing Catalytic RNA Circuits for Construction of Artificial Signaling Pathways in Mammalian Cells. Angew Chem Int Ed Engl 2024; 63:e202319309. [PMID: 38298112 DOI: 10.1002/anie.202319309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/21/2024] [Accepted: 01/31/2024] [Indexed: 02/02/2024]
Abstract
Engineering of genetic networks with artificial signaling pathways (ASPs) can reprogram cellular responses and phenotypes under different circumstances for a variety of diagnostic and therapeutic purposes. However, construction of ASPs between originally independent endogenous genes in mammalian cells is highly challenging. Here we report an amplifiable RNA circuit that can theoretically build regulatory connections between any endogenous genes in mammalian cells. We harness the system of catalytic hairpin assembly with combination of controllable CRISPR-Cas9 function to transduce the signals from distinct messenger RNA expression of trigger genes into manipulation of target genes. Through introduction of these RNA-based genetic circuits, mammalian cells are endowed with autonomous capabilities to sense the changes of RNA expression either induced by ligand stimuli or from various cell types and control the cellular responses and fates via apoptosis-related ASPs. Our design provides a generalized platform for construction of ASPs inside the genetic networks of mammalian cells based on differentiated RNA expression.
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Affiliation(s)
- Chao-Qun Wu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Ruo-Yue Wu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Qiu-Long Zhang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
- School of Pharmacy and Medical Technology, Key Laboratory of Pharmaceutical Analysis and Laboratory Medicine of Fujian Province, Putian University, Putian, 351100, China
| | - Liang-Liang Wang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Yang Wang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Chu Dai
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Chen-Xi Zhang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Liang Xu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
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5
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Chew YH, Marucci L. Mechanistic Model-Driven Biodesign in Mammalian Synthetic Biology. Methods Mol Biol 2024; 2774:71-84. [PMID: 38441759 DOI: 10.1007/978-1-0716-3718-0_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
Mathematical modeling plays a vital role in mammalian synthetic biology by providing a framework to design and optimize design circuits and engineered bioprocesses, predict their behavior, and guide experimental design. Here, we review recent models used in the literature, considering mathematical frameworks at the molecular, cellular, and system levels. We report key challenges in the field and discuss opportunities for genome-scale models, machine learning, and cybergenetics to expand the capabilities of model-driven mammalian cell biodesign.
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Affiliation(s)
- Yin Hoon Chew
- School of Mathematics, University of Birmingham, Birmingham, UK
| | - Lucia Marucci
- Department of Engineering Mathematics, University of Bristol, Bristol, UK.
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK.
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6
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Makri Pistikou AM, Cremers GAO, Nathalia BL, Meuleman TJ, Bögels BWA, Eijkens BV, de Dreu A, Bezembinder MTH, Stassen OMJA, Bouten CCV, Merkx M, Jerala R, de Greef TFA. Engineering a scalable and orthogonal platform for synthetic communication in mammalian cells. Nat Commun 2023; 14:7001. [PMID: 37919273 PMCID: PMC10622552 DOI: 10.1038/s41467-023-42810-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 10/23/2023] [Indexed: 11/04/2023] Open
Abstract
The rational design and implementation of synthetic mammalian communication systems can unravel fundamental design principles of cell communication circuits and offer a framework for engineering of designer cell consortia with potential applications in cell therapeutics. Here, we develop the foundations of an orthogonal, and scalable mammalian synthetic communication platform that exploits the programmability of synthetic receptors and selective affinity and tunability of diffusing coiled-coil peptides. Leveraging the ability of coiled-coils to exclusively bind to a cognate receptor, we demonstrate orthogonal receptor activation and Boolean logic operations at the receptor level. We show intercellular communication based on synthetic receptors and secreted multidomain coiled-coils and demonstrate a three-cell population system that can perform AND gate logic. Finally, we show CC-GEMS receptor-dependent therapeutic protein expression. Our work provides a modular and scalable framework for the engineering of complex cell consortia, with the potential to expand the aptitude of cell therapeutics and diagnostics.
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Affiliation(s)
- Anna-Maria Makri Pistikou
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Laboratory for Cell and Tissue Engineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Glenn A O Cremers
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Bryan L Nathalia
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Laboratory for Cell and Tissue Engineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Theodorus J Meuleman
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Laboratory for Cell and Tissue Engineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Center for Living Technologies, Eindhoven-Wageningen-Utrecht Alliance, Utrecht, The Netherlands
| | - Bas W A Bögels
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Bruno V Eijkens
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Laboratory for Cell and Tissue Engineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Anne de Dreu
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Maarten T H Bezembinder
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Laboratory for Cell and Tissue Engineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Oscar M J A Stassen
- Laboratory for Cell and Tissue Engineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Carlijn C V Bouten
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Laboratory for Cell and Tissue Engineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Maarten Merkx
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
- EN-FIST Centre of Excellence, Ljubljana, Slovenia
| | - Tom F A de Greef
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.
- Laboratory for Cell and Tissue Engineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.
- Center for Living Technologies, Eindhoven-Wageningen-Utrecht Alliance, Utrecht, The Netherlands.
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands.
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7
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Michaels YS, Durland LJ, Zandstra PW. Engineering T Cell Development for the Next Generation of Stem Cell-Derived Immunotherapies. GEN BIOTECHNOLOGY 2023; 2:106-119. [PMID: 37928777 PMCID: PMC10624212 DOI: 10.1089/genbio.2023.0008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 03/31/2023] [Indexed: 11/07/2023]
Abstract
Engineered T cells are at the leading edge of clinical cell therapy. T cell therapies have had a remarkable impact on patient care for a subset of hematological malignancies. This foundation has motivated the development of off-the-shelf engineered cell therapies for a broad range of devastating indications. Achieving this vision will require cost-effective manufacturing of precision cell products capable of addressing multiple process and clinical-design challenges. Pluripotent stem cell (PSC)-derived engineered T cells are emerging as a solution of choice. To unleash the full potential of PSC-derived T cell therapies, the field will require technologies capable of robustly orchestrating the complex series of time- and dose-dependent signaling events needed to recreate functional T cell development in the laboratory. In this article, we review the current state of allogenic T cell therapies, focusing on strategies to generate engineered lymphoid cells from PSCs. We highlight exciting recent progress in this field and outline timely opportunities for advancement with an emphasis on niche engineering and synthetic biology.
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Affiliation(s)
- Yale S. Michaels
- School of Biomedical Engineering, University of British Columbia, Vancouver, Canada; University of British Columbia, Vancouver, Canada
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Canada; University of British Columbia, Vancouver, Canada
- CancerCare Manitoba Research Institute, CancerCare Manitoba, Winnipeg, Canada; and University of British Columbia, Vancouver, Canada
| | - Lauren J. Durland
- School of Biomedical Engineering, University of British Columbia, Vancouver, Canada; University of British Columbia, Vancouver, Canada
| | - Peter W. Zandstra
- School of Biomedical Engineering, University of British Columbia, Vancouver, Canada; University of British Columbia, Vancouver, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
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8
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Lv X, Hueso-Gil A, Bi X, Wu Y, Liu Y, Liu L, Ledesma-Amaro R. New synthetic biology tools for metabolic control. Curr Opin Biotechnol 2022; 76:102724. [PMID: 35489308 DOI: 10.1016/j.copbio.2022.102724] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 02/28/2022] [Accepted: 03/20/2022] [Indexed: 11/29/2022]
Abstract
In industrial bioprocesses, microbial metabolism dictates the product yields, and therefore, our capacity to control it has an enormous potential to help us move towards a bio-based economy. The rapid development of multiomics data has accelerated our systematic understanding of complex metabolic regulatory mechanisms, which allow us to develop tools to manipulate them. In the last few years, machine learning-based metabolic modeling, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) derived synthetic biology tools, and synthetic genetic circuits have been widely used to control the metabolism of microorganisms, manipulate gene expression, and build synthetic pathways for bioproduction. This review describes the latest developments for metabolic control, and focuses on the trends and challenges of metabolic engineering strategies.
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Affiliation(s)
- Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Angeles Hueso-Gil
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London SW72AZ, UK
| | - Xinyu Bi
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Yaokang Wu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Yanfeng Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China.
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London SW72AZ, UK.
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9
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Occhipinti A, Hamadi Y, Kugler H, Wintersteiger CM, Yordanov B, Angione C. Discovering Essential Multiple Gene Effects Through Large Scale Optimization: An Application to Human Cancer Metabolism. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021; 18:2339-2352. [PMID: 32248120 DOI: 10.1109/tcbb.2020.2973386] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Computational modelling of metabolic processes has proven to be a useful approach to formulate our knowledge and improve our understanding of core biochemical systems that are crucial to maintaining cellular functions. Towards understanding the broader role of metabolism on cellular decision-making in health and disease conditions, it is important to integrate the study of metabolism with other core regulatory systems and omics within the cell, including gene expression patterns. After quantitatively integrating gene expression profiles with a genome-scale reconstruction of human metabolism, we propose a set of combinatorial methods to reverse engineer gene expression profiles and to find pairs and higher-order combinations of genetic modifications that simultaneously optimize multi-objective cellular goals. This enables us to suggest classes of transcriptomic profiles that are most suitable to achieve given metabolic phenotypes. We demonstrate how our techniques are able to compute beneficial, neutral or "toxic" combinations of gene expression levels. We test our methods on nine tissue-specific cancer models, comparing our outcomes with the corresponding normal cells, identifying genes as targets for potential therapies. Our methods open the way to a broad class of applications that require an understanding of the interplay among genotype, metabolism, and cellular behaviour, at scale.
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10
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Schibeci Natoli Scialli N, Colitti B, Bertolotti L, Pezzoni G, Martignani E, Melega M, Brocchi E, Rosati S. Genome editing of a hybridoma cell line via the CRISPR/Cas9 system: A new approach for constitutive high-level expression of heterologous proteins in eukaryotic system. Vet Immunol Immunopathol 2021; 238:110286. [PMID: 34171554 DOI: 10.1016/j.vetimm.2021.110286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 05/22/2021] [Accepted: 06/14/2021] [Indexed: 11/20/2022]
Abstract
The power of the CRISPR/Cas9 system has revolutionized genome editing in many fields of biology. These applications have expanded exponentially over recent years, including those regarding protein expression technologies. The CRISPR/Cas9 system avoids random integration of the gene of interest and due to this characteristic can be exploited to obtain a stable cell line for the high-yield expression of recombinant proteins. Here we propose a method to edit a hybridoma cell line for the constitutive expression of proteins of interest using the CRISPR/Cas9 system. First, with the scope of optimizing the method, we replaced part of the light chain of immunoglobulin with the Green Fluorescent Protein (GFP) gene, obtaining a precise knock-in in the hybridoma genome. We confirmed the expression and secretion of GFP into the culture medium via fluorimetric analysis, as well as correct genome editing by RNA sequencing. Then, using the same approach, we included the gene encoding a protein of diagnostic interest, the Bovine Herpesvirus 1 glycoprotein E, in the donor DNA. We obtained a stable clone able to secrete gE protein in fusion with GFP into the culture medium. This result was confirmed by ELISA and Western Blot analysis. This study confirms the suitability of this cell line for the production of proteins of diagnostic interest by stable gene expression in a mammalian system. These experiments will enable the technique to be developed from its proof of concept to more specific applications in the field of infectious disease diagnostics.
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Affiliation(s)
| | - Barbara Colitti
- Department of Veterinary Science, University of Turin, Largo Braccini 2, 10095, Grugliasco, TO, Italy
| | - Luigi Bertolotti
- Department of Veterinary Science, University of Turin, Largo Braccini 2, 10095, Grugliasco, TO, Italy
| | - Giulia Pezzoni
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Via Bianchi 7, 25124, Brescia, Italy
| | - Eugenio Martignani
- Department of Veterinary Science, University of Turin, Largo Braccini 2, 10095, Grugliasco, TO, Italy
| | - Maverick Melega
- Department of Veterinary Science, University of Turin, Largo Braccini 2, 10095, Grugliasco, TO, Italy
| | - Emiliana Brocchi
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Via Bianchi 7, 25124, Brescia, Italy
| | - Sergio Rosati
- Department of Veterinary Science, University of Turin, Largo Braccini 2, 10095, Grugliasco, TO, Italy.
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11
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Shakiba N, Jones RD, Weiss R, Del Vecchio D. Context-aware synthetic biology by controller design: Engineering the mammalian cell. Cell Syst 2021; 12:561-592. [PMID: 34139166 PMCID: PMC8261833 DOI: 10.1016/j.cels.2021.05.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 04/19/2021] [Accepted: 05/14/2021] [Indexed: 12/25/2022]
Abstract
The rise of systems biology has ushered a new paradigm: the view of the cell as a system that processes environmental inputs to drive phenotypic outputs. Synthetic biology provides a complementary approach, allowing us to program cell behavior through the addition of synthetic genetic devices into the cellular processor. These devices, and the complex genetic circuits they compose, are engineered using a design-prototype-test cycle, allowing for predictable device performance to be achieved in a context-dependent manner. Within mammalian cells, context effects impact device performance at multiple scales, including the genetic, cellular, and extracellular levels. In order for synthetic genetic devices to achieve predictable behaviors, approaches to overcome context dependence are necessary. Here, we describe control systems approaches for achieving context-aware devices that are robust to context effects. We then consider cell fate programing as a case study to explore the potential impact of context-aware devices for regenerative medicine applications.
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Affiliation(s)
- Nika Shakiba
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Ross D Jones
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Ron Weiss
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Domitilla Del Vecchio
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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12
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Zimak J, Wagoner ZW, Nelson N, Waechtler B, Schlosser H, Kopecky M, Wu J, Zhao W. Epigenetic silencing directs expression heterogeneity of stably integrated multi-transcript unit genetic circuits. Sci Rep 2021; 11:2424. [PMID: 33510302 PMCID: PMC7844226 DOI: 10.1038/s41598-021-81975-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 01/08/2021] [Indexed: 12/19/2022] Open
Abstract
We report that epigenetic silencing causes the loss of function of multi-transcript unit constructs that are integrated using CRISPR-Cas9. Using a modular two color reporter system flanked by selection markers, we demonstrate that expression heterogeneity does not correlate with sequence alteration but instead correlates with chromosomal accessibility. We partially reverse this epigenetic silencing via small-molecule inhibitors of methylation and histone deacetylation. We then correlate each heterogeneously-expressing phenotype with its expected epigenetic state by employing ATAC-seq. The stability of each expression phenotype is reinforced by selective pressure, which indicates that ongoing epigenetic remodeling can occur for over one month after integration. Collectively, our data suggests that epigenetic silencing limits the utility of multi-transcript unit constructs that are integrated via double-strand repair pathways. Our research implies that mammalian synthetic biologists should consider localized epigenetic outcomes when designing complex genetic circuits.
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Affiliation(s)
- Jan Zimak
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, 92697, USA.,Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Zachary W Wagoner
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, 92697, USA.,Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Nellie Nelson
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, 92697, USA.,Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Brooke Waechtler
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, 92697, USA.,Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Hana Schlosser
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, 92697, USA.,Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Morgan Kopecky
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, 92697, USA.,Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Jie Wu
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA, 92697, USA.,Department of Biological Chemistry, University of California, Irvine, Irvine, CA, 92697, USA
| | - Weian Zhao
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, 92697, USA. .,Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA. .,Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA, 92697, USA. .,Edwards Life Sciences Center for Advanced Cardiovascular Technology, University of California, Irvine, Irvine, CA, 92697, USA. .,Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, 92697, USA. .,Department of Biological Chemistry, University of California, Irvine, Irvine, CA, 92697, USA.
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13
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Young R, Haines M, Storch M, Freemont PS. Combinatorial metabolic pathway assembly approaches and toolkits for modular assembly. Metab Eng 2020; 63:81-101. [PMID: 33301873 DOI: 10.1016/j.ymben.2020.12.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 11/16/2020] [Accepted: 12/03/2020] [Indexed: 12/18/2022]
Abstract
Synthetic Biology is a rapidly growing interdisciplinary field that is primarily built upon foundational advances in molecular biology combined with engineering design principles such as modularity and interoperability. The field considers living systems as programmable at the genetic level and has been defined by the development of new platform technologies and methodological advances. A key concept driving the field is the Design-Build-Test-Learn cycle which provides a systematic framework for building new biological systems. One major application area for synthetic biology is biosynthetic pathway engineering that requires the modular assembly of different genetic regulatory elements and biosynthetic enzymes. In this review we provide an overview of modular DNA assembly and describe and compare the plethora of in vitro and in vivo assembly methods for combinatorial pathway engineering. Considerations for part design and methods for enzyme balancing are also presented, and we briefly discuss alternatives to intracellular pathway assembly including microbial consortia and cell-free systems for biosynthesis. Finally, we describe computational tools and automation for pathway design and assembly and argue that a deeper understanding of the many different variables of genetic design, pathway regulation and cellular metabolism will allow more predictive pathway design and engineering.
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Affiliation(s)
- Rosanna Young
- Department of Infectious Disease, Sir Alexander Fleming Building, South Kensington Campus, Imperial College London, SW7 2AZ, UK
| | - Matthew Haines
- Department of Infectious Disease, Sir Alexander Fleming Building, South Kensington Campus, Imperial College London, SW7 2AZ, UK
| | - Marko Storch
- Department of Infectious Disease, Sir Alexander Fleming Building, South Kensington Campus, Imperial College London, SW7 2AZ, UK; London Biofoundry, Imperial College Translation & Innovation Hub, London, W12 0BZ, UK
| | - Paul S Freemont
- Department of Infectious Disease, Sir Alexander Fleming Building, South Kensington Campus, Imperial College London, SW7 2AZ, UK; London Biofoundry, Imperial College Translation & Innovation Hub, London, W12 0BZ, UK; UK DRI Care Research and Technology Centre, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 0NN, UK.
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14
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Toda S. Synthetic tissue engineering: Programming multicellular self-organization by designing customized cell-cell communication. Biophys Physicobiol 2020; 17:42-50. [PMID: 33173713 PMCID: PMC7593132 DOI: 10.2142/biophysico.bsj-2020002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 05/27/2020] [Indexed: 12/02/2022] Open
Abstract
Cells communicate with each other to organize multicellular collective systems and assemble complex, elaborate tissue structures by themselves during development. Despite intensive biological studies, what kind of cell-cell communication can sufficiently drive self-organization of specific tissue architectures remain unclear. Thanks to recent advances on genetic engineering technologies, synthetic biologists start to build customized cell-cell communication with user-defined signal input and gene expression output to program multicellular behaviors using mammalian systems. This review article introduces how we can design and engineer customized cell-cell communication to program synthetic self-organizing multicellular structures. Creating tissue formation processes with synthetic genetic programs will help understanding of fundamental principles of how genetic programs drive tissue self-organization and provide new capabilities on tissue engineering for cell-based regenerative therapy applications.
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Affiliation(s)
- Satoshi Toda
- WPI Nano Life Science Institute, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
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15
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Doshi A, Sadeghi F, Varadarajan N, Cirino PC. Small-molecule inducible transcriptional control in mammalian cells. Crit Rev Biotechnol 2020; 40:1131-1150. [PMID: 32862714 DOI: 10.1080/07388551.2020.1808583] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Tools for tuning transcription in mammalian cells have broad applications, from basic biological discovery to human gene therapy. While precise control over target gene transcription via dosing with small molecules (drugs) is highly sought, the design of such inducible systems that meets required performance metrics poses a great challenge in mammalian cell synthetic biology. Important characteristics include tight and tunable gene expression with a low background, minimal drug toxicity, and orthogonality. Here, we review small-molecule-inducible transcriptional control devices that have demonstrated success in mammalian cells and mouse models. Most of these systems employ natural or designed ligand-binding protein domains to directly or indirectly communicate with transcription machinery at a target sequence, via carefully constructed fusions. Example fusions include those to transcription activator-like effectors (TALEs), DNA-targeting proteins (e.g. dCas systems) fused to transactivating domains, and recombinases. Similar to the architecture of Type I nuclear receptors, many of the systems are designed such that the transcriptional controller is excluded from the nucleus in the absence of an inducer. Techniques that use ligand-induced proteolysis and antibody-based chemically induced dimerizers are also described. Collectively, these transcriptional control devices take advantage of a variety of recently developed molecular biology tools and cell biology insights and represent both proof of concept (e.g. targeting reporter gene expression) and disease-targeting studies.
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Affiliation(s)
- Aarti Doshi
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Fatemeh Sadeghi
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Navin Varadarajan
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Patrick C Cirino
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA.,Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
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16
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Direct Readout of Neural Stem Cell Transgenesis with an Integration-Coupled Gene Expression Switch. Neuron 2020; 107:617-630.e6. [PMID: 32559415 PMCID: PMC7447981 DOI: 10.1016/j.neuron.2020.05.038] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 04/22/2020] [Accepted: 05/26/2020] [Indexed: 12/29/2022]
Abstract
Stable genomic integration of exogenous transgenes is essential in neurodevelopmental and stem cell studies. Despite tools driving increasingly efficient genomic insertion with DNA vectors, transgenesis remains fundamentally hindered by the impossibility of distinguishing integrated from episomal transgenes. Here, we introduce an integration-coupled On genetic switch, iOn, which triggers gene expression upon incorporation into the host genome through transposition, thus enabling rapid and accurate identification of integration events following transfection with naked plasmids. In vitro, iOn permits rapid drug-free stable transgenesis of mouse and human pluripotent stem cells with multiple vectors. In vivo, we demonstrate faithful cell lineage tracing, assessment of regulatory elements, and mosaic analysis of gene function in somatic transgenesis experiments that reveal neural progenitor potentialities and interaction. These results establish iOn as a universally applicable strategy to accelerate and simplify genetic engineering in cultured systems and model organisms by conditioning transgene activation to genomic integration. A gene expression switch powered by genomic integration Accelerated readout of additive transgenesis with one or multiple vectors Faithful lineage tracing and mosaic analysis by somatic transfection Near-universal applicability in cultured cells and animal models
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17
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A reversible RNA on-switch that controls gene expression of AAV-delivered therapeutics in vivo. Nat Biotechnol 2019; 38:169-175. [PMID: 31873216 PMCID: PMC7008088 DOI: 10.1038/s41587-019-0357-y] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Accepted: 11/11/2019] [Indexed: 11/08/2022]
Abstract
Widespread use of gene therapy technologies is limited in part by the lack of small genetic switches with wide dynamic ranges that control transgene expression without the requirement of additional protein components1-5. In this study, we engineered a class of type III hammerhead ribozymes to develop RNA switches that are highly efficient at cis-cleaving mammalian mRNAs and showed that they can be tightly regulated by a steric-blocking antisense oligonucleotide. Our variant ribozymes enabled in vivo regulation of adeno-associated virus (AAV)-delivered transgenes, allowing dose-dependent and up to 223-fold regulation of protein expression over at least 43 weeks. To test the potential of these reversible on-switches in gene therapy for anemia of chronic kidney disease6, we demonstrated regulated expression of physiological levels of erythropoietin with a well-tolerated dose of the inducer oligonucleotide. These small, modular and efficient RNA switches may improve the safety and efficacy of gene therapies and broaden their use.
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18
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Pagan-Diaz GJ, Ramos-Cruz KP, Sam R, Kandel ME, Aydin O, Saif MTA, Popescu G, Bashir R. Engineering geometrical 3-dimensional untethered in vitro neural tissue mimic. Proc Natl Acad Sci U S A 2019; 116:25932-25940. [PMID: 31796592 PMCID: PMC6926042 DOI: 10.1073/pnas.1916138116] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Formation of tissue models in 3 dimensions is more effective in recapitulating structure and function compared to their 2-dimensional (2D) counterparts. Formation of 3D engineered tissue to control shape and size can have important implications in biomedical research and in engineering applications such as biological soft robotics. While neural spheroids routinely are created during differentiation processes, further geometric control of in vitro neural models has not been demonstrated. Here, we present an approach to form functional in vitro neural tissue mimic (NTM) of different shapes using stem cells, a fibrin matrix, and 3D printed molds. We used murine-derived embryonic stem cells for optimizing cell-seeding protocols, characterization of the resulting internal structure of the construct, and remodeling of the extracellular matrix, as well as validation of electrophysiological activity. Then, we used these findings to biofabricate these constructs using neurons derived from human embryonic stem cells. This method can provide a large degree of design flexibility for development of in vitro functional neural tissue models of varying forms for therapeutic biomedical research, drug discovery, and disease modeling, and engineering applications.
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Affiliation(s)
- Gelson J Pagan-Diaz
- Department of Bioengineering, University of Illinois, Urbana-Champaign, Urbana, IL 61801
| | - Karla P Ramos-Cruz
- Department of Bioengineering, University of Illinois, Urbana-Champaign, Urbana, IL 61801
| | - Richard Sam
- School of Molecular and Cellular Biology, University of Illinois, Urbana-Champaign, Urbana, IL 61801
| | - Mikhail E Kandel
- Department of Electrical and Computer Engineering, University of Illinois, Urbana-Champaign, Urbana, IL 61801
| | - Onur Aydin
- Department of Mechanical Science and Engineering, University of Illinois, Urbana-Champaign, Urbana, IL 61801
| | - M Taher A Saif
- Department of Mechanical Science and Engineering, University of Illinois, Urbana-Champaign, Urbana, IL 61801
| | - Gabriel Popescu
- Department of Bioengineering, University of Illinois, Urbana-Champaign, Urbana, IL 61801
- Department of Electrical and Computer Engineering, University of Illinois, Urbana-Champaign, Urbana, IL 61801
| | - Rashid Bashir
- Department of Bioengineering, University of Illinois, Urbana-Champaign, Urbana, IL 61801;
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19
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Sarsaiya S, Shi J, Chen J. Bioengineering tools for the production of pharmaceuticals: current perspective and future outlook. Bioengineered 2019; 10:469-492. [PMID: 31656120 PMCID: PMC6844412 DOI: 10.1080/21655979.2019.1682108] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 09/08/2019] [Accepted: 10/11/2019] [Indexed: 01/18/2023] Open
Abstract
The bioengineering tools have significant advantages through less time-consuming and utilized as a promising stage for the production of pharmaceutical bioproducts under the single platform. This review highlighted the advantages and current improvement in the plant, animal and microbial bioengineering tools and outlines feasible approaches by biological and process's bioengineering levels for advancing the economic feasibility of pharmaceutical's production. The critical analysis results revealed that system biology and synthetic biology along with advanced bioengineering tools like transcriptome, proteome, metabolome and nano bioengineering tools have shown a promising impact on the development of pharmaceutical's bioproducts. Tools to overcome and resolve the accompanying encounters of pharmaceutical's production that include nano bioengineering tools are also discussed. As a summary and prospect, it also gives new insight into the challenges and possible breakthrough of the development of pharmaceutical's bioproducts through bioengineering tools.
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Affiliation(s)
- Surendra Sarsaiya
- Key Laboratory of Basic Pharmacology and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China
- Bioresource Institute for Healthy Utilization, Zunyi Medical University, Zunyi, China
| | - Jingshan Shi
- Key Laboratory of Basic Pharmacology and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China
| | - Jishuang Chen
- Bioresource Institute for Healthy Utilization, Zunyi Medical University, Zunyi, China
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
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20
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Synthetic biology for improving cell fate decisions and tissue engineering outcomes. Emerg Top Life Sci 2019; 3:631-643. [PMID: 33523179 DOI: 10.1042/etls20190091] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 10/02/2019] [Accepted: 10/07/2019] [Indexed: 02/07/2023]
Abstract
Synthetic biology is a relatively new field of science that combines aspects of biology and engineering to create novel tools for the construction of biological systems. Using tools within synthetic biology, stem cells can then be reprogrammed and differentiated into a specified cell type. Stem cells have already proven to be largely beneficial in many different therapies and have paved the way for tissue engineering and regenerative medicine. Although scientists have made great strides in tissue engineering, there still remain many questions to be answered in regard to regeneration. Presented here is an overview of synthetic biology, common tools built within synthetic biology, and the way these tools are being used in stem cells. Specifically, this review focuses on how synthetic biologists engineer genetic circuits to dynamically control gene expression while also introducing emerging topics such as genome engineering and synthetic transcription factors. The findings mentioned in this review show the diverse use of stem cells within synthetic biology and provide a foundation for future research in tissue engineering with the use of synthetic biology tools. Overall, the work done using synthetic biology in stem cells is in its early stages, however, this early work is leading to new approaches for repairing diseased and damaged tissues and organs, and further expanding the field of tissue engineering.
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21
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Santorelli M, Lam C, Morsut L. Synthetic development: building mammalian multicellular structures with artificial genetic programs. Curr Opin Biotechnol 2019; 59:130-140. [PMID: 31128430 PMCID: PMC6778502 DOI: 10.1016/j.copbio.2019.03.016] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 03/08/2019] [Accepted: 03/24/2019] [Indexed: 12/28/2022]
Abstract
Synthetic biology efforts began in simple single-cell systems, which were relatively easy to manipulate genetically (Cameron et al., 2014). The field grew exponentially in the last two decades, and one of the latest frontiers are synthetic developmental programs for multicellular mammalian systems (Black et al., 2017; Wieland and Fussenegger, 2012) to genetically control features such as patterning or morphogenesis. These programs rely on engineered cell-cell communications, multicellular gene regulatory networks and effector genes. Here, we contextualize the first of these synthetic developmental programs, examine molecular and computational tools that can be used to generate next generation versions, and present the general logic that underpins these approaches. These advances are exciting as they represent a novel way to address both control and understanding in the field of developmental biology and tissue development (Elowitz and Lim, 2010; Velazquez et al., 2018; White et al., 2018; Morsut, 2017). This field is just at the beginning, and it promises to be of major interest in the upcoming years of biomedical research.
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Affiliation(s)
- Marco Santorelli
- The Eli and Edythe Broad CIRM Center, Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, United States
| | - Calvin Lam
- The Eli and Edythe Broad CIRM Center, Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, United States
| | - Leonardo Morsut
- The Eli and Edythe Broad CIRM Center, Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, United States; Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, United States.
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22
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Parola C, Neumeier D, Friedensohn S, Csepregi L, Di Tacchio M, Mason DM, Reddy ST. Antibody discovery and engineering by enhanced CRISPR-Cas9 integration of variable gene cassette libraries in mammalian cells. MAbs 2019; 11:1367-1380. [PMID: 31478465 PMCID: PMC6816377 DOI: 10.1080/19420862.2019.1662691] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Antibody engineering in mammalian cells offers the important advantage of expression and screening of libraries in their native conformation, increasing the likelihood of generating candidates with more favorable molecular properties. Major advances in cellular engineering enabled by CRISPR-Cas9 genome editing have made it possible to expand the use of mammalian cells in biotechnological applications. Here, we describe an antibody engineering and screening approach where complete variable light (VL) and heavy (VH) chain cassette libraries are stably integrated into the genome of hybridoma cells by enhanced Cas9-driven homology-directed repair (HDR), resulting in their surface display and secretion. By developing an improved HDR donor format that utilizes in situ linearization, we are able to achieve >15-fold improvement of genomic integration, resulting in a screening workflow that only requires a simple plasmid electroporation. This proved suitable for different applications in antibody discovery and engineering. By integrating and screening an immune library obtained from the variable gene repertoire of an immunized mouse, we could isolate a diverse panel of >40 unique antigen-binding variants. Additionally, we successfully performed affinity maturation by directed evolution screening of an antibody library based on random mutagenesis, leading to the isolation of several clones with affinities in the picomolar range.
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Affiliation(s)
- Cristina Parola
- Department of Biosystems Science and Engineering, ETH Zürich , Basel , Switzerland
| | - Daniel Neumeier
- Department of Biosystems Science and Engineering, ETH Zürich , Basel , Switzerland
| | - Simon Friedensohn
- Department of Biosystems Science and Engineering, ETH Zürich , Basel , Switzerland
| | - Lucia Csepregi
- Department of Biosystems Science and Engineering, ETH Zürich , Basel , Switzerland
| | | | - Derek M Mason
- Department of Biosystems Science and Engineering, ETH Zürich , Basel , Switzerland
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zürich , Basel , Switzerland
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23
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Bressan RB, Pollard SM. Genome Editing in Human Neural Stem and Progenitor Cells. Results Probl Cell Differ 2019; 66:163-182. [PMID: 30209659 DOI: 10.1007/978-3-319-93485-3_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2024]
Abstract
Experimental tools for precise manipulation of mammalian genomes enable reverse genetic approaches to explore biology and disease. Powerful genome editing technologies built upon designer nucleases, such as CRISPR/Cas9, have recently emerged. Parallel progress has been made in methodologies for the expansion and differentiation of human pluripotent and tissue stem cells. Together these innovations provide a remarkable new toolbox for human cellular genetics and are opening up vast opportunities for discoveries and applications across the breadth of life sciences research. In this chapter, we review the emergence of genome editing technologies and how these are being deployed in studies of human neurobiology, neurological disease, and neuro-oncology. We focus our discussion on CRISPR/Cas9 and its application in studies of human neural stem and progenitor cells.
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Affiliation(s)
- Raul Bardini Bressan
- MRC Centre for Regenerative Medicine and Edinburgh Cancer Research Centre, University of Edinburgh, Edinburgh, UK
| | - Steven M Pollard
- MRC Centre for Regenerative Medicine and Edinburgh Cancer Research Centre, University of Edinburgh, Edinburgh, UK.
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24
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Supramaniam P, Ces O, Salehi-Reyhani A. Microfluidics for Artificial Life: Techniques for Bottom-Up Synthetic Biology. MICROMACHINES 2019; 10:E299. [PMID: 31052344 PMCID: PMC6562628 DOI: 10.3390/mi10050299] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/24/2019] [Accepted: 04/26/2019] [Indexed: 01/08/2023]
Abstract
Synthetic biology is a rapidly growing multidisciplinary branch of science that exploits the advancement of molecular and cellular biology. Conventional modification of pre-existing cells is referred to as the top-down approach. Bottom-up synthetic biology is an emerging complementary branch that seeks to construct artificial cells from natural or synthetic components. One of the aims in bottom-up synthetic biology is to construct or mimic the complex pathways present in living cells. The recent, and rapidly growing, application of microfluidics in the field is driven by the central tenet of the bottom-up approach-the pursuit of controllably generating artificial cells with precisely defined parameters, in terms of molecular and geometrical composition. In this review we survey conventional methods of artificial cell synthesis and their limitations. We proceed to show how microfluidic approaches have been pivotal in overcoming these limitations and ushering in a new generation of complexity that may be imbued in artificial cells and the milieu of applications that result.
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Affiliation(s)
- Pashiini Supramaniam
- Department of Chemistry, White City Campus, Imperial College London, London SW7 2AZ, UK.
| | - Oscar Ces
- Department of Chemistry, White City Campus, Imperial College London, London SW7 2AZ, UK.
- FabriCELL, Imperial College London, London SW7 2AZ, UK.
| | - Ali Salehi-Reyhani
- FabriCELL, Imperial College London, London SW7 2AZ, UK.
- Department of Chemistry, King's College London, Britannia House, London SE1 1DB, UK.
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25
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Grenci G, Bertocchi C, Ravasio A. Integrating Microfabrication into Biological Investigations: the Benefits of Interdisciplinarity. MICROMACHINES 2019; 10:E252. [PMID: 30995747 PMCID: PMC6523848 DOI: 10.3390/mi10040252] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 04/08/2019] [Accepted: 04/13/2019] [Indexed: 12/14/2022]
Abstract
The advent of micro and nanotechnologies, such as microfabrication, have impacted scientific research and contributed to meaningful real-world applications, to a degree seen during historic technological revolutions. Some key areas benefitting from the invention and advancement of microfabrication platforms are those of biological and biomedical sciences. Modern therapeutic approaches, involving point-of-care, precision or personalized medicine, are transitioning from the experimental phase to becoming the standard of care. At the same time, biological research benefits from the contribution of microfluidics at every level from single cell to tissue engineering and organoids studies. The aim of this commentary is to describe, through proven examples, the interdisciplinary process used to develop novel biological technologies and to emphasize the role of technical knowledge in empowering researchers who are specialized in a niche area to look beyond and innovate.
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Affiliation(s)
- Gianluca Grenci
- Mechanobiology Institute (MBI), National University of Singapore, Singapore 117411, Singapore.
- Biomedical Engineering Department, National University of Singapore, Singapore 117583, Singapore.
| | - Cristina Bertocchi
- Department of Physiology, School of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 8330025, Chile.
| | - Andrea Ravasio
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile.
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26
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Grath A, Dai G. Direct cell reprogramming for tissue engineering and regenerative medicine. J Biol Eng 2019; 13:14. [PMID: 30805026 PMCID: PMC6373087 DOI: 10.1186/s13036-019-0144-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 01/27/2019] [Indexed: 02/06/2023] Open
Abstract
Direct cell reprogramming, also called transdifferentiation, allows for the reprogramming of one somatic cell type directly into another, without the need to transition through an induced pluripotent state. Thus, it is an attractive approach to develop novel tissue engineering applications to treat diseases and injuries where there is a shortage of proliferating cells for tissue repair. In certain tissue damage, terminally differentiated somatic cells lose their ability to proliferate, as a result, damaged tissues cannot heal by themselves. Examples of these scenarios include myocardial infarctions, neurodegenerative diseases, and cartilage injuries. Transdifferentiation is capable of reprogramming cells that are abundant in the body into desired cell phenotypes that are able to restore tissue function in damaged areas. Therefore, direct cell reprogramming is a promising direction in the cell and tissue engineering and regenerative medicine fields. In recent years, several methods for transdifferentiation have been developed, ranging from the overexpression of transcription factors via viral vectors, to small molecules, to clustered regularly interspaced short palindromic repeats (CRISPR) and its associated protein (Cas9) for both genetic and epigenetic reprogramming. Overexpressing transcription factors by use of a lentivirus is currently the most prevalent technique, however it lacks high reprogramming efficiencies and can pose problems when transitioning to human subjects and clinical trials. CRISPR/Cas9, fused with proteins that modulate transcription, has been shown to improve efficiencies greatly. Transdifferentiation has successfully generated many cell phenotypes, including endothelial cells, skeletal myocytes, neuronal cells, and more. These cells have been shown to emulate mature adult cells such that they are able to mimic major functions, and some are capable of promoting regeneration of damaged tissue in vivo. While transdifferentiated cells have not yet seen clinical use, they have had promise in mice models, showing success in treating liver disease and several brain-related diseases, while also being utilized as a cell source for tissue engineered vascular grafts to treat damaged blood vessels. Recently, localized transdifferentiated cells have been generated in situ, allowing for treatments without invasive surgeries and more complete transdifferentiation. In this review, we summarized the recent development in various cell reprogramming techniques, their applications in converting various somatic cells, their uses in tissue regeneration, and the challenges of transitioning to a clinical setting, accompanied with potential solutions.
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Affiliation(s)
- Alexander Grath
- Department of Bioengineering, Northeastern University, Lake Hall 214A, 360 Huntington Avenue, Boston, MA 02115 USA
| | - Guohao Dai
- Department of Bioengineering, Northeastern University, Lake Hall 214A, 360 Huntington Avenue, Boston, MA 02115 USA
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Lauersen KJ. Eukaryotic microalgae as hosts for light-driven heterologous isoprenoid production. PLANTA 2019; 249:155-180. [PMID: 30467629 DOI: 10.1007/s00425-018-3048-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 11/14/2018] [Indexed: 05/21/2023]
Abstract
Eukaryotic microalgae hold incredible metabolic potential for the sustainable production of heterologous isoprenoid products. Recent advances in algal engineering have enabled the demonstration of prominent examples of heterologous isoprenoid production. Isoprenoids, also known as terpenes or terpenoids, are the largest class of natural chemicals, with a vast diversity of structures and biological roles. Some have high-value in human-use applications, although may be found in their native contexts in low abundance or be difficult to extract and purify. Heterologous production of isoprenoid compounds in heterotrophic microbial hosts such as bacteria or yeasts has been an active area of research for some time and is now a mature technology. Eukaryotic microalgae represent sustainable alternatives to these hosts for biotechnological production processes as their cultivation can be driven by light and freely available CO2 as a carbon source. Their photosynthetic lifestyles require metabolic architectures structured towards the generation of associated isoprenoids (carotenoids, phytol) which participate in photon capture, energy dissipation, and electron transfer. Eukaryotic microalgae should, therefore, contain inherently high capacities for the generation of heterologous isoprenoid products. Although engineering strategies in eukaryotic microalgae have lagged behind the more genetically tractable bacteria and yeasts, recent advances in algal engineering concepts have demonstrated prominent examples of light-driven heterologous isoprenoid production from these photosynthetic hosts. This work seeks to provide practical insights into the choice of eukaryotic microalgae as biotechnological chassis. Recent reports of advances in algal engineering for heterologous isoprenoid production are highlighted as encouraging examples that promote their expanded use as sustainable green-cell factories. Current state of the art, limitations, and future challenges are also discussed.
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Affiliation(s)
- Kyle J Lauersen
- Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615, Bielefeld, Germany.
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Mason DM, Weber CR, Parola C, Meng SM, Greiff V, Kelton WJ, Reddy ST. High-throughput antibody engineering in mammalian cells by CRISPR/Cas9-mediated homology-directed mutagenesis. Nucleic Acids Res 2018; 46:7436-7449. [PMID: 29931269 PMCID: PMC6101513 DOI: 10.1093/nar/gky550] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 06/04/2018] [Accepted: 06/06/2018] [Indexed: 12/26/2022] Open
Abstract
Antibody engineering is often performed to improve therapeutic properties by directed evolution, usually by high-throughput screening of phage or yeast display libraries. Engineering antibodies in mammalian cells offer advantages associated with expression in their final therapeutic format (full-length glycosylated IgG); however, the inability to express large and diverse libraries severely limits their potential throughput. To address this limitation, we have developed homology-directed mutagenesis (HDM), a novel method which extends the concept of CRISPR/Cas9-mediated homology-directed repair (HDR). HDM leverages oligonucleotides with degenerate codons to generate site-directed mutagenesis libraries in mammalian cells. By improving HDR to a robust efficiency of 15-35% and combining mammalian display screening with next-generation sequencing, we validated this approach can be used for key applications in antibody engineering at high-throughput: rational library construction, novel variant discovery, affinity maturation and deep mutational scanning (DMS). We anticipate that HDM will be a valuable tool for engineering and optimizing antibodies in mammalian cells, and eventually enable directed evolution of other complex proteins and cellular therapeutics.
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Affiliation(s)
- Derek M Mason
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
| | - Cédric R Weber
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
| | - Cristina Parola
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
- Life Science Graduate School, Systems Biology, ETH Zürich, University of Zurich, Zurich 8057, Switzerland
| | - Simon M Meng
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
| | - Victor Greiff
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
| | - William J Kelton
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
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Weisenberger MS, Deans TL. Bottom-up approaches in synthetic biology and biomaterials for tissue engineering applications. J Ind Microbiol Biotechnol 2018; 45:599-614. [PMID: 29552703 PMCID: PMC6041164 DOI: 10.1007/s10295-018-2027-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Accepted: 03/11/2018] [Indexed: 12/30/2022]
Abstract
Synthetic biologists use engineering principles to design and construct genetic circuits for programming cells with novel functions. A bottom-up approach is commonly used to design and construct genetic circuits by piecing together functional modules that are capable of reprogramming cells with novel behavior. While genetic circuits control cell operations through the tight regulation of gene expression, a diverse array of environmental factors within the extracellular space also has a significant impact on cell behavior. This extracellular space offers an addition route for synthetic biologists to apply their engineering principles to program cell-responsive modules within the extracellular space using biomaterials. In this review, we discuss how taking a bottom-up approach to build genetic circuits using DNA modules can be applied to biomaterials for controlling cell behavior from the extracellular milieu. We suggest that, by collectively controlling intrinsic and extrinsic signals in synthetic biology and biomaterials, tissue engineering outcomes can be improved.
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Affiliation(s)
| | - Tara L Deans
- Department of Bioengineering, University of Utah, Salt Lake City, UT, 84112, USA.
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Dangi AK, Sinha R, Dwivedi S, Gupta SK, Shukla P. Cell Line Techniques and Gene Editing Tools for Antibody Production: A Review. Front Pharmacol 2018; 9:630. [PMID: 29946262 PMCID: PMC6006397 DOI: 10.3389/fphar.2018.00630] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 05/25/2018] [Indexed: 12/16/2022] Open
Abstract
The present day modern formulation practices for drugs are based on newer tools and techniques toward effective utilization. The methods of antibody formulations are to be revolutionized based on techniques of cell engineering and gene editing. In the present review, we have discussed innovations in cell engineering toward production of novel antibodies for therapeutic applications. Moreover, this review deciphers the use of RNAi, ribozyme engineering, CRISPR-Cas-based techniques for better strategies for antibody production. Overall, this review describes the multidisciplinary aspects of the production of therapeutic proteins that has gained more attention due to its increasing demand.
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Affiliation(s)
- Arun K. Dangi
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | | | - Shailja Dwivedi
- Advanced Biotech Lab, Ipca Laboratories Limited, Mumbai, India
| | | | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
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31
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Boldt J. Machine metaphors and ethics in synthetic biology. LIFE SCIENCES, SOCIETY AND POLICY 2018; 14:12. [PMID: 29862436 PMCID: PMC5985241 DOI: 10.1186/s40504-018-0077-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 05/16/2018] [Indexed: 06/08/2023]
Abstract
The extent to which machine metaphors are used in synthetic biology is striking. These metaphors contain a specific perspective on organisms as well as on scientific and technological progress. Expressions such as "genetically engineered machine", "genetic circuit", and "platform organism", taken from the realms of electronic engineering, car manufacturing, and information technology, highlight specific aspects of the functioning of living beings while at the same time hiding others, such as evolutionary change and interdependencies in ecosystems. Since these latter aspects are relevant for, for example, risk evaluation of uncontained uses of synthetic organisms, it is ethically imperative to resist the thrust of machine metaphors in this respect. In addition, from the perspective of the machine metaphor viewing an entity as a moral agent or patient becomes dubious. If one were to regard living beings, including humans, as machines, it becomes difficult to justify ascriptions of moral status. Finally, the machine metaphor reinforces beliefs in the potential of synthetic biology to play a decisive role in solving societal problems, and downplays the role of alternative technological, and social and political measures.
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Affiliation(s)
- Joachim Boldt
- Department of Medical Ethics and the History of Medicine, University of Freiburg, Freiburg, Germany.
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Bittihn P, Din MO, Tsimring LS, Hasty J. Rational engineering of synthetic microbial systems: from single cells to consortia. Curr Opin Microbiol 2018; 45:92-99. [PMID: 29574330 DOI: 10.1016/j.mib.2018.02.009] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 02/06/2018] [Accepted: 02/19/2018] [Indexed: 12/11/2022]
Abstract
One promise of synthetic biology is to provide solutions for biomedical and industrial problems by rational design of added functionality in living systems. Microbes are at the forefront of this biological engineering endeavor due to their general ease of handling and their relevance in many potential applications from fermentation to therapeutics. In recent years, the field has witnessed an explosion of novel regulatory tools, from synthetic orthogonal transcription factors to posttranslational mechanisms for increased control over the behavior of synthetic circuits. Tool development has been paralleled by the discovery of principles that enable increased modularity and the management of host-circuit interactions. Engineered cell-to-cell communication bridges the scales from intracellular to population-level coordination. These developments facilitate the translation of more than a decade of circuit design into applications.
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Affiliation(s)
- Philip Bittihn
- BioCircuits Institute, University of California, San Diego, La Jolla, CA 92093, USA
| | - M Omar Din
- BioCircuits Institute, University of California, San Diego, La Jolla, CA 92093, USA
| | - Lev S Tsimring
- BioCircuits Institute, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jeff Hasty
- BioCircuits Institute, University of California, San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Molecular Biology Section, Division of Biological Science, University of California, San Diego, La Jolla, CA 92093, USA.
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33
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Tycko J, Van MV, Elowitz MB, Bintu L. Advancing towards a global mammalian gene regulation model through single-cell analysis and synthetic biology. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2017. [DOI: 10.1016/j.cobme.2017.10.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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34
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Editorial Overview: Synthetic biology and biomedical engineering. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2017. [DOI: 10.1016/j.cobme.2017.12.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Muldoon JJ, Donahue PS, Dolberg TB, Leonard JN. Building with intent: technologies and principles for engineering mammalian cell-based therapies to sense and respond. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2017; 4:127-133. [PMID: 29450405 DOI: 10.1016/j.cobme.2017.10.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The engineering of cells as programmable devices has enabled therapeutic strategies that could not otherwise be achieved. Such strategies include recapitulating and enhancing native cellular functions and composing novel functions. These novel functions may be composed using both natural and engineered biological components, with the latter exemplified by the development of synthetic receptor and signal transduction systems. Recent advances in implementing these approaches include the treatment of cancer, where the most clinical progress has been made to date, and the treatment of diabetes. Principles for engineering cell-based therapies that are safe and effective are increasingly needed and beginning to emerge, and will be essential in the development of this new class of therapeutics.
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Affiliation(s)
- Joseph J Muldoon
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States.,Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois 60208, United States
| | - Patrick S Donahue
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States.,Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois 60208, United States.,Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Taylor B Dolberg
- 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.,Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois 60208, United States.,Center for Synthetic Biology, 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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