51
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Yan X, Liu X, Zhao C, Chen GQ. Applications of synthetic biology in medical and pharmaceutical fields. Signal Transduct Target Ther 2023; 8:199. [PMID: 37169742 PMCID: PMC10173249 DOI: 10.1038/s41392-023-01440-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 03/15/2023] [Accepted: 03/24/2023] [Indexed: 05/13/2023] Open
Abstract
Synthetic biology aims to design or assemble existing bioparts or bio-components for useful bioproperties. During the past decades, progresses have been made to build delicate biocircuits, standardized biological building blocks and to develop various genomic/metabolic engineering tools and approaches. Medical and pharmaceutical demands have also pushed the development of synthetic biology, including integration of heterologous pathways into designer cells to efficiently produce medical agents, enhanced yields of natural products in cell growth media to equal or higher than that of the extracts from plants or fungi, constructions of novel genetic circuits for tumor targeting, controllable releases of therapeutic agents in response to specific biomarkers to fight diseases such as diabetes and cancers. Besides, new strategies are developed to treat complex immune diseases, infectious diseases and metabolic disorders that are hard to cure via traditional approaches. In general, synthetic biology brings new capabilities to medical and pharmaceutical researches. This review summarizes the timeline of synthetic biology developments, the past and present of synthetic biology for microbial productions of pharmaceutics, engineered cells equipped with synthetic DNA circuits for diagnosis and therapies, live and auto-assemblied biomaterials for medical treatments, cell-free synthetic biology in medical and pharmaceutical fields, and DNA engineering approaches with potentials for biomedical applications.
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Affiliation(s)
- Xu Yan
- School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Xu Liu
- PhaBuilder Biotech Co. Ltd., Shunyi District, Zhaoquan Ying, 101309, Beijing, China
| | - Cuihuan Zhao
- School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Guo-Qiang Chen
- School of Life Sciences, Tsinghua University, 100084, Beijing, China.
- Center for Synthetic and Systems Biology, Tsinghua University, 100084, Beijing, China.
- MOE Key Lab for Industrial Biocatalysis, Dept Chemical Engineering, Tsinghua University, 100084, Beijing, China.
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Kalkan AK, Palaz F, Sofija S, Elmousa N, Ledezma Y, Cachat E, Rios-Solis L. Improving recombinant protein production in CHO cells using the CRISPR-Cas system. Biotechnol Adv 2023; 64:108115. [PMID: 36758652 DOI: 10.1016/j.biotechadv.2023.108115] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 12/28/2022] [Accepted: 02/03/2023] [Indexed: 02/10/2023]
Abstract
Chinese hamster ovary (CHO) cells are among the most widely used mammalian cell lines in the biopharmaceutical industry. Therefore, it is not surprising that significant efforts have been made around the engineering of CHO cells using genetic engineering methods such as the CRISPR-Cas system. In this review, we summarize key recent studies that have used different CRISPR-Cas systems such as Cas9, Cas13 or dCas9 fused with effector domains to improve recombinant protein (r-protein) production in CHO cells. Here, every relevant stage of production was considered, underscoring the advantages and limitations of these systems, as well as discussing their bottlenecks and probable solutions. A special emphasis was given on how these systems could disrupt and/or regulate genes related to glycan composition, which has relevant effects over r-protein properties and in vivo activity. Furthermore, the related promising future applications of CRISPR to achieve a tunable, reversible, or highly stable editing of CHO cells are discussed. Overall, the studies covered in this review show that despite the complexity of mammalian cells, the synthetic biology community has developed many mature strategies to improve r-protein production using CHO cells. In this regard, CRISPR-Cas technology clearly provides efficient and flexible genetic manipulation and allows for the generation of more productive CHO cell lines, leading to more cost-efficient production of biopharmaceuticals, however, there is still a need for many emerging techniques in CRISPR to be reported in CHO cells; therefore, more research in these cells is needed to realize the full potential of this technology.
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Affiliation(s)
- Ali Kerem Kalkan
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK; Environmental Engineering Department, Gebze Technical University, Turkey
| | - Fahreddin Palaz
- Faculty of Medicine, Hacettepe University, Ankara 06100, Turkey
| | - Semeniuk Sofija
- Centre for Engineering Biology, University of Edinburgh, Edinburgh EH9 3BF, UK; Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Nada Elmousa
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh EH9 3DW, UK
| | - Yuri Ledezma
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh EH9 3DW, UK; Biology Department, Faculty of Pure and Natural Sciences, Universidad Mayor de San Andrés, Bolivia
| | - Elise Cachat
- Centre for Engineering Biology, University of Edinburgh, Edinburgh EH9 3BF, UK; Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences University of Edinburgh, Edinburgh EH9 3BF, UK; UK Centre for Mammalian Synthetic Biology, University of Edinburgh, Edinburgh EH8 9YL, UK
| | - Leonardo Rios-Solis
- Centre for Engineering Biology, University of Edinburgh, Edinburgh EH9 3BF, UK; Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh EH9 3DW, UK; School of Natural and Environmental Sciences, Molecular Biology and Biotechnology Division, Newcastle University, Newcastle Upon Tyne, NE1 7RU, UK.
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53
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Ashe S, Hebrok M. Role of Cell-Based Therapies in T2D. Semin Nephrol 2023; 43:151432. [PMID: 37918206 DOI: 10.1016/j.semnephrol.2023.151432] [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: 11/04/2023]
Abstract
Type 2 diabetes mellitus (T2D) has become a global epidemic affecting the health of millions of people. T2D is a complex and multifactorial metabolic disease, largely characterized by a combination of impaired insulin secretion from β cells residing within the islets of the pancreas and peripheral insulin resistance. In this article, we discuss the current state and risk factors for T2D, conventional treatment options, and upcoming strategies, including progress in the areas of allogeneic and xenogeneic islet transplantation, with a major focus on stem cell-derived β cells and associated technologies.
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Affiliation(s)
- Sudipta Ashe
- Diabetes Center, Department of Medicine, University of California, San Francisco, CA
| | - Matthias Hebrok
- Diabetes Center, Department of Medicine, University of California, San Francisco, CA; TUM School of Medicine, Technical University Munich, Munich, Germany; Center for Organoid Systems, Technical University Munich, Garching, Germany; Institute for Diabetes and Organoid Technology, Helmholtz Diabetes Center, Helmholtz Zentrum München, Neuherberg, Germany; Munich Institute of Biomedical Engineering (MIBE), Technical University Munich, Munich, Germany; German Center for Diabetes Research (DZD), Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany.
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54
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Koukara J, Papadopoulou KK. Advances in plant synthetic biology approaches to control expression of gene circuits. Biochem Biophys Res Commun 2023; 654:55-61. [PMID: 36889035 DOI: 10.1016/j.bbrc.2023.02.061] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 02/22/2023] [Indexed: 03/08/2023]
Abstract
The applications of synthetic biology range from creating simple circuits to monitor an organism's state to complex circuits capable of reconstructing aspects of life. The latter has the potential to be used in plant synthetic biology to address current societal issues by reforming agriculture and enhancing production of molecules of increased demand. For this reason, development of efficient tools to precisely control gene expression of circuits must be prioritized. In this review, we report the latest efforts towards characterization, standardization and assembly of genetic parts into higher-order constructs, as well as available types of inducible systems to modulate their transcription in plant systems. Subsequently, we discuss recent developments in the orthogonal control of gene expression, Boolean logic gates and synthetic genetic toggle-like switches. Finally, we conclude that by combining different means of controlling gene expression, we can create complex circuits capable of reshaping plant life.
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Affiliation(s)
- Jenny Koukara
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Kalliope K Papadopoulou
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece.
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55
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Zhou J, Ge Q, Wang D, Guo Q, Tao Y. Engineering a modular double-transmembrane synthetic receptor system for customizing cellular programs. Cell Rep 2023; 42:112385. [PMID: 37043348 DOI: 10.1016/j.celrep.2023.112385] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 02/21/2023] [Accepted: 03/28/2023] [Indexed: 04/13/2023] Open
Abstract
Implementation of designer receptors in engineered cells confers them to sense a particular physiological or disease state and respond with user-defined programs. To expand the therapeutic application scope of engineered cells, synthetic receptors realized through different strategies are in great demand. Here, we develop a synthetic receptor system that exerts dual control by incorporating two transmembrane helices for the signal chain. Together with a sensor-actuator device with minimal background signals and a positive loop circuit, this receptor system can sensitively respond to extracellular protein signals. We demonstrate that this synthetic receptor system can be readily adapted to respond to various inputs, such as interleukin-1 (IL-1), programmed death ligand 1 (PD-L1), and HER2, and release customized outputs, including fluorescence signals and the therapeutic molecule IL-2. The robust signaling ability and generality of this receptor system promise it to be a useful tool in the field of cell engineering for fundamental research and translational applications.
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Affiliation(s)
- Jingru Zhou
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Center for Cross-disciplinary Sciences, Biomedical Sciences and Health Laboratory of Anhui Province, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, P.R. China
| | - Qiangqiang Ge
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Center for Cross-disciplinary Sciences, Biomedical Sciences and Health Laboratory of Anhui Province, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, P.R. China
| | - Dandan Wang
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Center for Cross-disciplinary Sciences, Biomedical Sciences and Health Laboratory of Anhui Province, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, P.R. China
| | - Qiong Guo
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Center for Cross-disciplinary Sciences, Biomedical Sciences and Health Laboratory of Anhui Province, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, P.R. China.
| | - Yuyong Tao
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Center for Cross-disciplinary Sciences, Biomedical Sciences and Health Laboratory of Anhui Province, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, P.R. China.
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56
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Xing Y, Zhou M, Si Y, Yang CY, Feng LW, Wu Q, Wang F, Wang X, Huang W, Cheng Y, Zhang R, Duan X, Liu J, Song P, Sun H, Wang H, Zhang J, Jiang S, Zhu M, Wang G. Integrated opposite charge grafting induced ionic-junction fiber. Nat Commun 2023; 14:2355. [PMID: 37095082 PMCID: PMC10126126 DOI: 10.1038/s41467-023-37884-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 04/03/2023] [Indexed: 04/26/2023] Open
Abstract
The emergence of ionic-junction devices has attracted growing interests due to the potential of serving as signal transmission and translation media between electronic devices and biological systems using ions. Among them, fiber-shaped iontronics possesses a great advantage in implantable applications owing to the unique one-dimensional geometry. However, fabricating stable ionic-junction on curved surfaces remains a challenge. Here, we developed a polyelectrolyte based ionic-junction fiber via an integrated opposite charge grafting method capable of large-scale continuous fabrication. The ionic-junction fibers can be integrated into functions such as ionic diodes and ionic bipolar junction transistors, where rectification and switching of input signals are implemented. Moreover, synaptic functionality has also been demonstrated by utilizing the fiber memory capacitance. The connection between the ionic-junction fiber and sciatic nerves of the mouse simulating end-to-side anastomosis is further performed to realize effective nerve signal conduction, verifying the capability for next-generation artificial neural pathways in implantable bioelectronics.
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Affiliation(s)
- Yi Xing
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, 201620, Shanghai, China
| | - Mingjie Zhou
- Department of Hand Surgery, Center for the Reconstruction of Limb Function, National Clinical Research Center for Aging and Medicine, Huashan Hospital; Department of Hand and Upper Extremity Surgery, Jing'an District Central Hospital; NHC Key Laboratory of Hand Reconstruction, Shanghai Key Laboratory of Peripheral Nerve and Microsurgery, Institute of Hand Surgery, Fudan University, 200040, Shanghai, China
| | - Yueguang Si
- State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institute of Brain Science, Department of Ophthalmology, Zhongshan Hospital, Fudan University, 200032, Shanghai, China
| | - Chi-Yuan Yang
- Laboratory of Organic Electronics, Department of Science and Technology, Linköping University, SE-601 74, Norrköping, Sweden
| | - Liang-Wen Feng
- College of Chemistry, Sichuan University, 610064, Chengdu, China
| | - Qilin Wu
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, 201620, Shanghai, China
| | - Fei Wang
- Department of Hand Surgery, Center for the Reconstruction of Limb Function, National Clinical Research Center for Aging and Medicine, Huashan Hospital; Department of Hand and Upper Extremity Surgery, Jing'an District Central Hospital; NHC Key Laboratory of Hand Reconstruction, Shanghai Key Laboratory of Peripheral Nerve and Microsurgery, Institute of Hand Surgery, Fudan University, 200040, Shanghai, China
| | - Xiaomin Wang
- Department of Hand Surgery, Center for the Reconstruction of Limb Function, National Clinical Research Center for Aging and Medicine, Huashan Hospital; Department of Hand and Upper Extremity Surgery, Jing'an District Central Hospital; NHC Key Laboratory of Hand Reconstruction, Shanghai Key Laboratory of Peripheral Nerve and Microsurgery, Institute of Hand Surgery, Fudan University, 200040, Shanghai, China
| | - Wei Huang
- School of Automation Engineering, University of Electronic Science and Technology of China, 611731, Chengdu, China
| | - Yuhua Cheng
- School of Automation Engineering, University of Electronic Science and Technology of China, 611731, Chengdu, China
| | - Ruilin Zhang
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 130022, Changchun, Jilin, China
| | - Xiaozheng Duan
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 130022, Changchun, Jilin, China
| | - Jun Liu
- National Key Laboratory on Electromagnetic Environmental Effects and Eletro-optical Engineering, 210007, Nanjing, China
| | - Ping Song
- National Key Laboratory on Electromagnetic Environmental Effects and Eletro-optical Engineering, 210007, Nanjing, China
| | - Hengda Sun
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, 201620, Shanghai, China
| | - Hongzhi Wang
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, 201620, Shanghai, China
| | - Jiayi Zhang
- State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institute of Brain Science, Department of Ophthalmology, Zhongshan Hospital, Fudan University, 200032, Shanghai, China
| | - Su Jiang
- Department of Hand Surgery, Center for the Reconstruction of Limb Function, National Clinical Research Center for Aging and Medicine, Huashan Hospital; Department of Hand and Upper Extremity Surgery, Jing'an District Central Hospital; NHC Key Laboratory of Hand Reconstruction, Shanghai Key Laboratory of Peripheral Nerve and Microsurgery, Institute of Hand Surgery, Fudan University, 200040, Shanghai, China
| | - Meifang Zhu
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, 201620, Shanghai, China
| | - Gang Wang
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, 201620, Shanghai, China.
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57
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Ding Y, Tous C, Choi J, Chen J, Wong WW. Orthogonal inducible control of Cas13 circuits enables programmable RNA regulation in mammalian cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.20.533499. [PMID: 36993327 PMCID: PMC10055290 DOI: 10.1101/2023.03.20.533499] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
RNA plays an indispensable role in mammalian cell functions. Cas13, a class of RNA-guided ribonuclease, is a flexible tool for modifying and regulating coding and non-coding RNAs, with enormous potential for creating new cell functions. However, the lack of control over Cas13 activity has limited its cell engineering capability. Here, we present the CRISTAL ( C ontrol of R NA with Inducible S pli T C A s13 Orthologs and Exogenous L igands) platform. CRISTAL is powered by a collection (10 total) of orthogonal split inducible Cas13s that can be turned ON or OFF via small molecules in multiple cell types, providing precise temporal control. Also, we engineered Cas13 logic circuits that can respond to endogenous signaling and exogenous small molecule inputs. Furthermore, the orthogonality, low leakiness, and high dynamic range of our inducible Cas13d and Cas13b enable the design and construction of a robust incoherent feedforward loop, leading to near-perfect and tunable adaptation response. Finally, using our inducible Cas13s, we achieve simultaneous multiplexed control of multiple genes in vitro and in mice. Together, our CRISTAL design represents a powerful platform for precisely regulating RNA dynamics to advance cell engineering and elucidate RNA biology.
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58
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Luo J, Chen J, Huang Y, You L, Dai Z. Engineering living materials by synthetic biology. BIOPHYSICS REVIEWS 2023; 4:011305. [PMID: 38505813 PMCID: PMC10903423 DOI: 10.1063/5.0115645] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 11/18/2022] [Indexed: 03/21/2024]
Abstract
Natural biological materials are programmed by genetic information and able to self-organize, respond to environmental stimulus, and couple with inorganic matter. Inspired by the natural system and to mimic their complex and delicate fabrication process and functions, the field of engineered living materials emerges at the interface of synthetic biology and materials science. Here, we review the recent efforts and discuss the challenges and future opportunities.
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Affiliation(s)
- Jiren Luo
- Materials Synthetic Biology Center, CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Jiangfeng Chen
- Materials Synthetic Biology Center, CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yaoge Huang
- Materials Synthetic Biology Center, CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, 27708, USA
| | - Zhuojun Dai
- Materials Synthetic Biology Center, CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
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59
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Contreras‐Llano LE, Liu Y, Henson T, Meyer CC, Baghdasaryan O, Khan S, Lin C, Wang A, Hu CJ, Tan C. Engineering Cyborg Bacteria Through Intracellular Hydrogelation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2204175. [PMID: 36628538 PMCID: PMC10037956 DOI: 10.1002/advs.202204175] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 11/18/2022] [Indexed: 05/06/2023]
Abstract
Natural and artificial cells are two common chassis in synthetic biology. Natural cells can perform complex tasks through synthetic genetic constructs, but their autonomous replication often causes safety concerns for biomedical applications. In contrast, artificial cells based on nonreplicating materials, albeit possessing reduced biochemical complexity, provide more defined and controllable functions. Here, for the first time, the authors create hybrid material-cell entities termed Cyborg Cells. To create Cyborg Cells, a synthetic polymer network is assembled inside each bacterium, rendering them incapable of dividing. Cyborg Cells preserve essential functions, including cellular metabolism, motility, protein synthesis, and compatibility with genetic circuits. Cyborg Cells also acquire new abilities to resist stressors that otherwise kill natural cells. Finally, the authors demonstrate the therapeutic potential by showing invasion into cancer cells. This work establishes a new paradigm in cellular bioengineering by exploiting a combination of intracellular man-made polymers and their interaction with the protein networks of living cells.
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Affiliation(s)
| | - Yu‐Han Liu
- Institute of Biomedical SciencesAcademia SinicaTaipei11529Taiwan
| | - Tanner Henson
- Department of Biomedical EngineeringUniversity of CaliforniaDavisCA95616USA
- Department of SurgeryUniversity of CaliforniaDavis School of MedicineSacramentoCA95817USA
| | - Conary C. Meyer
- Department of Biomedical EngineeringUniversity of CaliforniaDavisCA95616USA
| | | | - Shahid Khan
- Department of Biomedical EngineeringUniversity of CaliforniaDavisCA95616USA
| | - Chi‐Long Lin
- Institute of Biomedical SciencesAcademia SinicaTaipei11529Taiwan
| | - Aijun Wang
- Department of Biomedical EngineeringUniversity of CaliforniaDavisCA95616USA
- Department of SurgeryUniversity of CaliforniaDavis School of MedicineSacramentoCA95817USA
| | - Che‐Ming J. Hu
- Institute of Biomedical SciencesAcademia SinicaTaipei11529Taiwan
| | - Cheemeng Tan
- Department of Biomedical EngineeringUniversity of CaliforniaDavisCA95616USA
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60
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Ding Q, Ye C. Microbial cell factories based on filamentous bacteria, yeasts, and fungi. Microb Cell Fact 2023; 22:20. [PMID: 36717860 PMCID: PMC9885587 DOI: 10.1186/s12934-023-02025-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 01/20/2023] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Advanced DNA synthesis, biosensor assembly, and genetic circuit development in synthetic biology and metabolic engineering have reinforced the application of filamentous bacteria, yeasts, and fungi as promising chassis cells for chemical production, but their industrial application remains a major challenge that needs to be solved. RESULTS As important chassis strains, filamentous microorganisms can synthesize important enzymes, chemicals, and niche pharmaceutical products through microbial fermentation. With the aid of metabolic engineering and synthetic biology, filamentous bacteria, yeasts, and fungi can be developed into efficient microbial cell factories through genome engineering, pathway engineering, tolerance engineering, and microbial engineering. Mutant screening and metabolic engineering can be used in filamentous bacteria, filamentous yeasts (Candida glabrata, Candida utilis), and filamentous fungi (Aspergillus sp., Rhizopus sp.) to greatly increase their capacity for chemical production. This review highlights the potential of using biotechnology to further develop filamentous bacteria, yeasts, and fungi as alternative chassis strains. CONCLUSIONS In this review, we recapitulate the recent progress in the application of filamentous bacteria, yeasts, and fungi as microbial cell factories. Furthermore, emphasis on metabolic engineering strategies involved in cellular tolerance, metabolic engineering, and screening are discussed. Finally, we offer an outlook on advanced techniques for the engineering of filamentous bacteria, yeasts, and fungi.
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Affiliation(s)
- Qiang Ding
- grid.252245.60000 0001 0085 4987School of Life Sciences, Anhui University, Hefei, 230601 China ,grid.252245.60000 0001 0085 4987Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei, 230601 Anhui China ,Anhui Key Laboratory of Modern Biomanufacturing, Hefei, 230601 Anhui China
| | - Chao Ye
- grid.260474.30000 0001 0089 5711School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023 China
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61
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Nikitin MP. Non-complementary strand commutation as a fundamental alternative for information processing by DNA and gene regulation. Nat Chem 2023; 15:70-82. [PMID: 36604607 DOI: 10.1038/s41557-022-01111-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 11/16/2022] [Indexed: 01/07/2023]
Abstract
The discovery of the DNA double helix has revolutionized our understanding of data processing in living systems, with the complementarity of the two DNA strands providing a reliable mechanism for the storage of hereditary information. Here I reveal the 'strand commutation' phenomenon-a fundamentally different mechanism of information storage and processing by DNA/RNA based on the reversible low-affinity interactions of essentially non-complementary nucleic acids. I demonstrate this mechanism by constructing a memory circuit, a 5-min square-root circuit for 4-bit inputs comprising only nine processing ssDNAs, simulating a 572-input AND gate (surpassing the bitness of current electronic computers), and elementary algebra systems with continuously changing variables. Most importantly, I show potential pathways of gene regulation with strands of maximum non-complementarity to the gene sequence that may be key to the reduction of off-target therapeutic effects. This Article uncovers the information-processing power of the low-affinity interactions that may underlie major processes in an organism-from short-term memory to cancer, ageing and evolution.
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Affiliation(s)
- Maxim P Nikitin
- Sirius University of Science and Technology, Sochi, Russia. .,Abisense LLC, Dolgoprudny, Moscow Region, Russia.
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62
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Kuzmin AA, Tomilin AN. Building Blocks of Artificial CRISPR-Based Systems beyond Nucleases. Int J Mol Sci 2022; 24:ijms24010397. [PMID: 36613839 PMCID: PMC9820447 DOI: 10.3390/ijms24010397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/19/2022] [Accepted: 12/19/2022] [Indexed: 12/28/2022] Open
Abstract
Tools developed in the fields of genome engineering, precise gene regulation, and synthetic gene networks have an increasing number of applications. When shared with the scientific community, these tools can be used to further unlock the potential of precision medicine and tissue engineering. A large number of different genetic elements, as well as modifications, have been used to create many different systems and to validate some technical concepts. New studies have tended to optimize or improve existing elements or approaches to create complex synthetic systems, especially those based on the relatively new CRISPR technology. In order to maximize the output of newly developed approaches and to move from proof-of-principle experiments to applications in regenerative medicine, it is important to navigate efficiently through the vast number of genetic elements to choose those most suitable for specific needs. In this review, we have collected information regarding the main genetic elements and their modifications, which can be useful in different synthetic systems with an emphasis of those based on CRISPR technology. We have indicated the most suitable elements and approaches to choose or combine in planning experiments, while providing their deeper understanding, and have also stated some pitfalls that should be avoided.
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63
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Cabrera A, Edelstein HI, Glykofrydis F, Love KS, Palacios S, Tycko J, Zhang M, Lensch S, Shields CE, Livingston M, Weiss R, Zhao H, Haynes KA, Morsut L, Chen YY, Khalil AS, Wong WW, Collins JJ, Rosser SJ, Polizzi K, Elowitz MB, Fussenegger M, Hilton IB, Leonard JN, Bintu L, Galloway KE, Deans TL. The sound of silence: Transgene silencing in mammalian cell engineering. Cell Syst 2022; 13:950-973. [PMID: 36549273 PMCID: PMC9880859 DOI: 10.1016/j.cels.2022.11.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 09/22/2022] [Accepted: 11/22/2022] [Indexed: 12/24/2022]
Abstract
To elucidate principles operating in native biological systems and to develop novel biotechnologies, synthetic biology aims to build and integrate synthetic gene circuits within native transcriptional networks. The utility of synthetic gene circuits for cell engineering relies on the ability to control the expression of all constituent transgene components. Transgene silencing, defined as the loss of expression over time, persists as an obstacle for engineering primary cells and stem cells with transgenic cargos. In this review, we highlight the challenge that transgene silencing poses to the robust engineering of mammalian cells, outline potential molecular mechanisms of silencing, and present approaches for preventing transgene silencing. We conclude with a perspective identifying future research directions for improving the performance of synthetic gene circuits.
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Affiliation(s)
- Alan Cabrera
- Department of Bioengineering, Rice University, Houston, TX 77005, USA; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Hailey I Edelstein
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA; The Eli and Edythe Broad CIRM Center, Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Fokion Glykofrydis
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA 90033-9080, USA
| | - Kasey S Love
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sebastian Palacios
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Josh Tycko
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Meng Zhang
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Champaign, Urbana, IL 61801, USA
| | - Sarah Lensch
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Cara E Shields
- Wallace H. Coulter Department of Biomedical Engineering, Emory University, Atlanta, GA 30322, USA
| | - Mark Livingston
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT 84112, USA
| | - Ron Weiss
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Champaign, Urbana, IL 61801, USA
| | - Karmella A Haynes
- Wallace H. Coulter Department of Biomedical Engineering, Emory University, Atlanta, GA 30322, USA
| | - Leonardo Morsut
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA 90033-9080, USA
| | - Yvonne Y Chen
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA; Parker Institute for Cancer Immunotherapy Center at UCLA, Los Angeles, CA 90095, USA
| | - Ahmad S Khalil
- Biological Design Center and Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Wilson W Wong
- Biological Design Center and Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - James J Collins
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA 90033-9080, USA; Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA; Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA; Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Susan J Rosser
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Karen Polizzi
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London, UK; Imperial College Centre for Synthetic Biology, South Kensington Campus, London, UK
| | - Michael B Elowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel 4058, Switzerland; Faculty of Science, University of Basel, Mattenstrasse 26, Basel 4058, Switzerland
| | - Isaac B Hilton
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
| | - Joshua N Leonard
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA; The Eli and Edythe Broad CIRM Center, Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Lacramioara Bintu
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Kate E Galloway
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Tara L Deans
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT 84112, USA.
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64
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Li HS, Israni DV, Gagnon KA, Gan KA, Raymond MH, Sander JD, Roybal KT, Joung JK, Wong WW, Khalil AS. Multidimensional control of therapeutic human cell function with synthetic gene circuits. Science 2022; 378:1227-1234. [PMID: 36520914 PMCID: PMC10054295 DOI: 10.1126/science.ade0156] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Synthetic gene circuits that precisely control human cell function could expand the capabilities of gene- and cell-based therapies. However, platforms for developing circuits in primary human cells that drive robust functional changes in vivo and have compositions suitable for clinical use are lacking. Here, we developed synthetic zinc finger transcription regulators (synZiFTRs), which are compact and based largely on human-derived proteins. As a proof of principle, we engineered gene switches and circuits that allow precise, user-defined control over therapeutically relevant genes in primary T cells using orthogonal, US Food and Drug Administration-approved small-molecule inducers. Our circuits can instruct T cells to sequentially activate multiple cellular programs such as proliferation and antitumor activity to drive synergistic therapeutic responses. This platform should accelerate the development and clinical translation of synthetic gene circuits in diverse human cell types and contexts.
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Affiliation(s)
- Hui-Shan Li
- Biological Design Center, Boston University, Boston, MA, USA.,Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Divya V Israni
- Biological Design Center, Boston University, Boston, MA, USA.,Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Keith A Gagnon
- Biological Design Center, Boston University, Boston, MA, USA.,Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Kok Ann Gan
- Biological Design Center, Boston University, Boston, MA, USA.,Program in Molecular Biology, Cell Biology, and Biochemistry, Boston University, Boston, MA, USA
| | - Michael H Raymond
- Biological Design Center, Boston University, Boston, MA, USA.,Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Jeffry D Sander
- Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Pathology, Harvard Medical School, Boston, MA, USA.,Department of Genomics Technologies, Corteva Agriscience, Johnston, IA, USA
| | - Kole T Roybal
- Cell Design Institute and Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA.,Parker Institute for Cancer Immunotherapy, University of California, San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - J Keith Joung
- Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Wilson W Wong
- Biological Design Center, Boston University, Boston, MA, USA.,Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Ahmad S Khalil
- Biological Design Center, Boston University, Boston, MA, USA.,Department of Biomedical Engineering, Boston University, Boston, MA, USA.,Program in Molecular Biology, Cell Biology, and Biochemistry, Boston University, Boston, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
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65
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Kim SK, Kim H, Woo SG, Kim TH, Rha E, Kwon KK, Lee H, Lee SG, Lee DH. CRISPRi-based programmable logic inverter cascade for antibiotic-free selection and maintenance of multiple plasmids. Nucleic Acids Res 2022; 50:13155-13171. [PMID: 36511859 PMCID: PMC9825151 DOI: 10.1093/nar/gkac1104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 10/27/2022] [Accepted: 11/03/2022] [Indexed: 12/14/2022] Open
Abstract
Antibiotics have been widely used for plasmid-mediated cell engineering. However, continued use of antibiotics increases the metabolic burden, horizontal gene transfer risks, and biomanufacturing costs. There are limited approaches to maintaining multiple plasmids without antibiotics. Herein, we developed an inverter cascade using CRISPRi by building a plasmid containing a single guide RNA (sgRNA) landing pad (pSLiP); this inhibited host cell growth by repressing an essential cellular gene. Anti-sgRNAs on separate plasmids restored cell growth by blocking the expression of growth-inhibitory sgRNAs in pSLiP. We maintained three plasmids in Escherichia coli with a single antibiotic selective marker. To completely avoid antibiotic use and maintain the CRISPRi-based logic inverter cascade, we created a novel d-glutamate auxotrophic E. coli. This enabled the stable maintenance of the plasmid without antibiotics, enhanced the production of the terpenoid, (-)-α-bisabolol, and generation of an antibiotic-resistance gene-free plasmid. CRISPRi is therefore widely applicable in genetic circuits and may allow for antibiotic-free biomanufacturing.
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Affiliation(s)
| | | | - Seung Gyun Woo
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon 34143, Republic of Korea
| | - Tae Hyun Kim
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon 34143, Republic of Korea
| | - Eugene Rha
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Kil Koang Kwon
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Hyewon Lee
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Seung-Goo Lee
- To whom correspondence should be addressed. Tel: +82 42 860 4373; Fax: +82 42 860 4489;
| | - Dae-Hee Lee
- Correspondence may also be addressed to Dae-Hee Lee. Tel: +82 42 879 8225; Fax: +82 42 860 4489;
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66
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Engineering antiviral immune-like systems for autonomous virus detection and inhibition in mice. Nat Commun 2022; 13:7629. [PMID: 36494373 PMCID: PMC9734111 DOI: 10.1038/s41467-022-35425-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 12/02/2022] [Indexed: 12/13/2022] Open
Abstract
The ongoing COVID-19 pandemic has demonstrated that viral diseases represent an enormous public health and economic threat to mankind and that individuals with compromised immune systems are at greater risk of complications and death from viral diseases. The development of broad-spectrum antivirals is an important part of pandemic preparedness. Here, we have engineer a series of designer cells which we term autonomous, intelligent, virus-inducible immune-like (ALICE) cells as sense-and-destroy antiviral system. After developing a destabilized STING-based sensor to detect viruses from seven different genera, we have used a synthetic signal transduction system to link viral detection to the expression of multiple antiviral effector molecules, including antiviral cytokines, a CRISPR-Cas9 module for viral degradation and the secretion of a neutralizing antibody. We perform a proof-of-concept study using multiple iterations of our ALICE system in vitro, followed by in vivo functionality testing in mice. We show that dual output ALICESaCas9+Ab system delivered by an AAV-vector inhibited viral infection in herpetic simplex keratitis (HSK) mouse model. Our work demonstrates that viral detection and antiviral countermeasures can be paired for intelligent sense-and-destroy applications as a flexible and innovative method against virus infection.
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67
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Galvan S, Madderson O, Xue S, Teixeira AP, Fussenegger M. Regulation of Transgene Expression by the Natural Sweetener Xylose. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2203193. [PMID: 36316222 PMCID: PMC9731693 DOI: 10.1002/advs.202203193] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 09/15/2022] [Indexed: 06/16/2023]
Abstract
Next-generation gene and engineered-cell therapies benefit from incorporating synthetic gene networks that can precisely regulate the therapeutic output in response to externally administered signal inputs that are safe, readily bioavailable and pleasant to take. To enable such therapeutic control, a mammalian gene switch is designed to be responsive to the natural sweetener xylose and its functionality is assessed in mouse studies. The gene switch consists of the bacterial transcription regulator XylR fused to a mammalian transactivator, which binds to an optimized promoter in the presence of xylose, thereby allowing dose-dependent transgene expression. The sensitivity of SWEET (sweetener-inducible expression of transgene) is improved by coexpressing a xylose transporter. Mice implanted with encapsulated SWEET-engineered cells show increased blood levels of cargo protein when taking xylose-sweetened water or coffee, or highly concentrated apple extract, while they do not respond to intake of a usual amount of carrots, which contain xylose. In a proof-of-concept therapeutic application study, type-1 diabetic mice engineered with insulin-expressing SWEET show lowered glycemia and increased insulin levels when administered this fairly diabetic-compliant sweetener, compared to untreated mice. A SWEET-based therapy appears to have the potential to integrate seamlessly into patients' life-style and food habits in the move toward personalized medicine.
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Affiliation(s)
- Silvia Galvan
- Department of Biosystems Science and EngineeringETH ZurichMattenstrasse 26BaselCH‐4058Switzerland
| | - Oliver Madderson
- Department of Biosystems Science and EngineeringETH ZurichMattenstrasse 26BaselCH‐4058Switzerland
| | - Shuai Xue
- Department of Biosystems Science and EngineeringETH ZurichMattenstrasse 26BaselCH‐4058Switzerland
| | - Ana P. Teixeira
- Department of Biosystems Science and EngineeringETH ZurichMattenstrasse 26BaselCH‐4058Switzerland
| | - Martin Fussenegger
- Department of Biosystems Science and EngineeringETH ZurichMattenstrasse 26BaselCH‐4058Switzerland
- Faculty of Life ScienceUniversity of BaselMattenstrasse 26BaselCH‐4058Switzerland
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68
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Yu Y, Wu X, Wang M, Liu W, Zhang L, Zhang Y, Hu Z, Zhou X, Jiang W, Zou Q, Cai F, Ye H. Optogenetic-controlled immunotherapeutic designer cells for post-surgical cancer immunotherapy. Nat Commun 2022; 13:6357. [PMID: 36289204 PMCID: PMC9605972 DOI: 10.1038/s41467-022-33891-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 10/07/2022] [Indexed: 12/25/2022] Open
Abstract
Surgical resection is the main treatment option for most solid tumors, yet cancer recurrence after surgical resection remains a significant challenge in cancer therapy. Recent advances in cancer immunotherapy are enabling radical cures for many tumor patients, but these technologies remain challenging to apply because of side effects related to uncontrollable immune system activation. Here, we develop far-red light-controlled immunomodulatory engineered cells (FLICs) that we load into a hydrogel scaffold, enabling the precise optogenetic control of cytokines release (IFN-β, TNF-α, and IL-12) upon illumination. Experiments with a B16F10 melanoma resection mouse model show that FLICs-loaded hydrogel implants placed at the surgical wound site achieve sustainable release of immunomodulatory cytokines, leading to prevention of tumor recurrence and increased animal survival. Moreover, the FLICs-loaded hydrogel implants elicit long-term immunological memory that prevents against tumor recurrence. Our findings illustrate that this optogenetic perioperative immunotherapy with FLICs-loaded hydrogel implants offers a safe treatment option for solid tumors based on activating host innate and adaptive immune systems to inhibit tumor recurrence after surgery. Beyond extending the optogenetics toolbox for immunotherapy, we envision that our optogenetic-controlled living cell factory platform could be deployed for other biomedical contexts requiring precision induction of bio-therapeutic dosage.
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Affiliation(s)
- Yuanhuan Yu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai, 200241, China
| | - Xin Wu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai, 200241, China
| | - Meiyan Wang
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai, 200241, China
| | - Wenjing Liu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai, 200241, China
| | - Li Zhang
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai, 200241, China
| | - Ying Zhang
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai, 200241, China
| | - Zhilin Hu
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai, 200025, China
| | - Xuantong Zhou
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai, 200241, China
| | - Wenzheng Jiang
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai, 200241, China
| | - Qiang Zou
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai, 200025, China
| | - Fengfeng Cai
- Department of Breast Surgery, Yangpu Hospital, School of Medicine, Tongji University, Shanghai, 200090, China.
| | - Haifeng Ye
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai, 200241, China.
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69
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Mansouri M, Ray PG, Franko N, Xue S, Fussenegger M. Design of programmable post-translational switch control platform for on-demand protein secretion in mammalian cells. Nucleic Acids Res 2022; 51:e1. [PMID: 36268868 PMCID: PMC9841418 DOI: 10.1093/nar/gkac916] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 09/11/2022] [Accepted: 10/20/2022] [Indexed: 01/29/2023] Open
Abstract
The development of novel strategies to program cellular behaviors is a central goal in synthetic biology, and post-translational control mediated by engineered protein circuits is a particularly attractive approach to achieve rapid protein secretion on demand. We have developed a programmable protease-mediated post-translational switch (POSH) control platform composed of a chimeric protein unit that consists of a protein of interest fused via a transmembrane domain to a cleavable ER-retention signal, together with two cytosolic inducer-sensitive split protease components. The protease components combine in the presence of the specific inducer to generate active protease, which cleaves the ER-retention signal, releasing the transmembrane-domain-linked protein for trafficking to the trans-Golgi region. A furin site placed downstream of the protein ensures cleavage and subsequent secretion of the desired protein. We show that stimuli ranging from plant-derived, clinically compatible chemicals to remotely controllable inducers such as light and electrostimulation can program protein secretion in various POSH-engineered designer mammalian cells. As proof-of-concept, an all-in-one POSH control plasmid encoding insulin and abscisic acid-activatable split protease units was hydrodynamically transfected into the liver of type-1 diabetic mice. Induction with abscisic acid attenuated glycemic excursions in glucose-tolerance tests. Increased blood levels of insulin were maintained for 12 days.
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Affiliation(s)
- Maysam Mansouri
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Preetam Guha Ray
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Nik Franko
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Shuai Xue
- Department of Biosystems Science and Engineering, ETH Zurich, 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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70
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Stefanov BA, Mansouri M, Charpin-El Hamri G, Fussenegger M. Sunlight-Controllable Biopharmaceutical Production for Remote Emergency Supply of Directly Injectable Therapeutic Proteins. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2202566. [PMID: 36084222 DOI: 10.1002/smll.202202566] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 08/12/2022] [Indexed: 06/15/2023]
Abstract
Biopharmaceutical manufacturing requires specialized facilities and a long-range cold supply chain for the delivery of the therapeutics to patients. In order to produce biopharmaceuticals in locations lacking such infrastructure, a production process is designed that utilizes the trigger-inducible release of large quantities of a stored therapeutic protein from engineered endocrine cells within minutes to generate a directly injectable saline solution of the protein. To illustrate the versatility of this approach, it is shown that not only insulin, but also glucagon-like peptide 1 (GLP-1), nanoluciferase (NLuc), and the model biopharmaceutical erythropoietin (EPO) can be trigger-inducibly released, even when using biologically inactive insulin as a carrier. The facilitating beta cells are engineered with a controllable TRPV1-mediated Ca2+ influx that induces the fusion of cytoplasmic storage vesicles with the membrane, leading to the release of the stored protein. When required, the growth medium is exchanged for saline solution, and the system is stimulated with the small molecule capsaicin, with a hand-warming pack, or simply by using sunlight. Injection of insulin saline solution obtained in this way into a type-1 diabetes mouse model results in the regulation of blood glucose levels. It is believed that this system will be readily adaptable to deliver various biopharmaceutical proteins at remote locations.
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Affiliation(s)
- Bozhidar-Adrian Stefanov
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, Basel, 4058, Switzerland
| | - Maysam Mansouri
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, Basel, 4058, Switzerland
| | - Ghislaine Charpin-El Hamri
- Département Génie Biologique, Institut Universitaire de Technologie, Villeurbanne, Cedex F-69622, France
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, Basel, 4058, Switzerland
- Faculty of Life Science, University of Basel, Basel, 4058, Switzerland
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71
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Xiao R, Wei W, Li J, Xiao C, Yao H, Liu H. Constructing combinational and sequential logic devices through an intelligent electrocatalytic interface with immobilized MoS2 quantum dots and enzymes. Talanta 2022; 248:123615. [DOI: 10.1016/j.talanta.2022.123615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 04/24/2022] [Accepted: 05/25/2022] [Indexed: 10/18/2022]
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72
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Stefanov BA, Fussenegger M. Biomarker-driven feedback control of synthetic biology systems for next-generation personalized medicine. Front Bioeng Biotechnol 2022; 10:986210. [PMID: 36225597 PMCID: PMC9548536 DOI: 10.3389/fbioe.2022.986210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 09/06/2022] [Indexed: 11/13/2022] Open
Abstract
Many current clinical therapies for chronic diseases involve administration of drugs using dosage and bioavailability parameters estimated for a generalized population. This standard approach carries the risk of under dosing, which may result in ineffective treatment, or overdosing, which may cause undesirable side effects. Consequently, maintaining a drug concentration in the therapeutic window often requires frequent monitoring, adversely affecting the patient’s quality of life. In contrast, endogenous biosystems have evolved finely tuned feedback control loops that govern the physiological functions of the body based on multiple input parameters. To provide personalized treatment for chronic diseases, therefore, we require synthetic systems that can similarly generate a calibrated therapeutic response. Such engineered autonomous closed-loop devices should incorporate a sensor that actively tracks and evaluates the disease severity based on one or more biomarkers, as well as components that utilize these molecular inputs to bio compute and deliver the appropriate level of therapeutic output. Here, we review recent advances in applications of the closed-loop design principle in biomedical implants for treating severe and chronic diseases, highlighting translational studies of cellular therapies. We describe the engineering principles and components of closed-loop therapeutic devices, and discuss their potential to become a key pillar of personalized medicine.
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Affiliation(s)
| | - Martin Fussenegger
- ETH Zürich, Department of Biosystems Science and Engineering, Basel, Switzerland
- Faculty of Life Science, University of Basel, Basel, Switzerland
- *Correspondence: Martin Fussenegger,
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73
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Ding M, Lin J, Qin C, Wei P, Tian J, Lin T, Xu T. Application of synthetic biology in bladder cancer. Chin Med J (Engl) 2022; 135:2178-2187. [PMID: 36209735 PMCID: PMC9771244 DOI: 10.1097/cm9.0000000000002344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Indexed: 12/24/2022] Open
Abstract
ABSTRACT Bladder cancer (BC) is the most common malignant tumor of the genitourinary system. The age of individuals diagnosed with BC tends to decrease in recent years. A variety of standard therapeutic options are available for the clinical management of BC, but limitations exist. It is difficult to surgically eliminate small lesions, while radiation and chemotherapy damage normal tissues, leading to severe side effects. Therefore, new approaches are required to improve the efficacy and specificity of BC treatment. Synthetic biology is a field emerging in the last decade that refers to biological elements, devices, and materials that are artificially synthesized according to users' needs. In this review, we discuss how to utilize genetic elements to regulate BC-related gene expression periodically and quantitatively to inhibit the initiation and progression of BC. In addition, the design and construction of gene circuits to distinguish cancer cells from normal cells to kill the former but spare the latter are elaborated. Then, we introduce the development of genetically modified T cells for targeted attacks on BC. Finally, synthetic nanomaterials specializing in detecting and killing BC cells are detailed. This review aims to describe the innovative details of the clinical diagnosis and treatment of BC from the perspective of synthetic biology.
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Affiliation(s)
- Mengting Ding
- Department of Urology, Peking University People's Hospital, Beijing 100044, China
| | - Jiaxing Lin
- Department of Urology, Peking University People's Hospital, Beijing 100044, China
| | - Caipeng Qin
- Department of Urology, Peking University People's Hospital, Beijing 100044, China
| | - Ping Wei
- Center for Cell and Gene Circuit Design, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China
| | - Jiahe Tian
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Tianxin Lin
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong 528403, China
| | - Tao Xu
- Department of Urology, Peking University People's Hospital, Beijing 100044, China
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74
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Zhang T, Liu C, Li W, Kuang J, Qiu XY, Min L, Zhu L. Targeted protein degradation in mammalian cells: A Promising Avenue toward Future. Comput Struct Biotechnol J 2022; 20:5477-5489. [PMID: 36249565 PMCID: PMC9535385 DOI: 10.1016/j.csbj.2022.09.038] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 09/24/2022] [Accepted: 09/26/2022] [Indexed: 12/04/2022] Open
Abstract
In the eukaryotic cellular milieu, proteins are continuously synthesized and degraded effectively via endogenous protein degradation machineries such as the ubiquitin–proteasome and lysosome pathways. By reengineering and repurposing these natural protein regulatory mechanisms, the targeted protein degradation (TPD) strategies are presenting biologists with powerful tools to manipulate the abundance of proteins of interest directly, precisely, and reversibly at the post-translational level. In recent years, TPD is gaining massive attention and is recognized as a paradigm shift both in basic research, application-oriented synthetic biology, and pioneering clinical work. In this review, we summarize the updated information, especially the engineering efforts and developmental route, of current state-of-the-art TPD technology such as Trim-Away, LYTACs, and AUTACs. Besides, the general design principle, benefits, problems, and opportunities to be addressed were further analyzed, with the aim of providing guidelines for exploration, discovery, and further application of novel TPD tools in the future.
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75
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Li Z, Fattah A, Timashev P, Zaikin A. An Account of Models of Molecular Circuits for Associative Learning with Reinforcement Effect and Forced Dissociation. SENSORS (BASEL, SWITZERLAND) 2022; 22:5907. [PMID: 35957464 PMCID: PMC9371404 DOI: 10.3390/s22155907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/23/2022] [Accepted: 07/28/2022] [Indexed: 06/15/2023]
Abstract
The development of synthetic biology has enabled massive progress in biotechnology and in approaching research questions from a brand-new perspective. In particular, the design and study of gene regulatory networks in vitro, in vivo, and in silico have played an increasingly indispensable role in understanding and controlling biological phenomena. Among them, it is of great interest to understand how associative learning is formed at the molecular circuit level. Mathematical models are increasingly used to predict the behaviours of molecular circuits. Fernando's model, which is one of the first works in this line of research using the Hill equation, attempted to design a synthetic circuit that mimics Hebbian learning in a neural network architecture. In this article, we carry out indepth computational analysis of the model and demonstrate that the reinforcement effect can be achieved by choosing the proper parameter values. We also construct a novel circuit that can demonstrate forced dissociation, which was not observed in Fernando's model. Our work can be readily used as reference for synthetic biologists who consider implementing circuits of this kind in biological systems.
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Affiliation(s)
- Zonglun Li
- Department of Mathematics, University College London, London WC1E 6BT, UK
- Institute for Women’s Health, University College London, London WC1E 6BT, UK
| | - Alya Fattah
- Department of Mathematics, University College London, London WC1E 6BT, UK
| | - Peter Timashev
- World-Class Research Center “Digital Biodesign and Personalized Healthcare”, Sechenov University, Moscow 119991, Russia
| | - Alexey Zaikin
- Department of Mathematics, University College London, London WC1E 6BT, UK
- Institute for Women’s Health, University College London, London WC1E 6BT, UK
- World-Class Research Center “Digital Biodesign and Personalized Healthcare”, Sechenov University, Moscow 119991, Russia
- Department of Applied Mathematics and Laboratory of Systems Biology of Aging, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod 603022, Russia
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76
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Abstract
Bacterial proteases are a promising post-translational regulation strategy in synthetic circuits because they recognize specific amino acid degradation tags (degrons) that can be fine-tuned to modulate the degradation levels of tagged proteins. For this reason, recent efforts have been made in the search for new degrons. Here we review the up-to-date applications of degradation tags for circuit engineering in bacteria. In particular, we pay special attention to the effects of degradation bottlenecks in synthetic oscillators and introduce mathematical approaches to study queueing that enable the quantitative modelling of proteolytic queues.
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Affiliation(s)
- Prajakta Jadhav
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
| | - Yanyan Chen
- Program for Computational and Systems Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nicholas Butzin
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
| | - Javier Buceta
- Institute for Integrative Systems Biology (I2SysBio, CSIC-UV), Paterna, Valencia 46980, Spain
| | - Arantxa Urchueguía
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA.,Institute for Integrative Systems Biology (I2SysBio, CSIC-UV), Paterna, Valencia 46980, Spain
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77
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Mansouri M, Fussenegger M. Therapeutic cell engineering: designing programmable synthetic genetic circuits in mammalian cells. Protein Cell 2022; 13:476-489. [PMID: 34586617 PMCID: PMC9226217 DOI: 10.1007/s13238-021-00876-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 08/02/2021] [Indexed: 12/01/2022] Open
Abstract
Cell therapy approaches that employ engineered mammalian cells for on-demand production of therapeutic agents in the patient's body are moving beyond proof-of-concept in translational medicine. The therapeutic cells can be customized to sense user-defined signals, process them, and respond in a programmable and predictable way. In this paper, we introduce the available tools and strategies employed to design therapeutic cells. Then, various approaches to control cell behaviors, including open-loop and closed-loop systems, are discussed. We also highlight therapeutic applications of engineered cells for early diagnosis and treatment of various diseases in the clinic and in experimental disease models. Finally, we consider emerging technologies such as digital devices and their potential for incorporation into future cell-based therapies.
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Affiliation(s)
- Maysam Mansouri
- 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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78
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Guan Y, Chen X, Shao B, Ji X, Xiang Y, Jiang G, Xu L, Lin Z, Ouyang Q, Lou C. Mitigating Host Burden of Genetic Circuits by Engineering Autonegatively Regulated Parts and Improving Functional Prediction. ACS Synth Biol 2022; 11:2361-2371. [PMID: 35772024 DOI: 10.1021/acssynbio.2c00073] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Mitigating unintended interferences between circuits and host cells is key to realize applications of synthetic regulatory systems both for bacteria and mammalian cells. Here, we demonstrated that growth burden and circuit dysregulation occurred in a concentration-dependent manner for specific transcription factors (CymR*/CymR) in E.coli, and direct negative feedback modules were able to control the concentration of CymR*/CymR, mitigate growth burden, and restore circuit functions. A quantitative design scheme was developed for circuits embedded with autorepression modules. Four key parameters were theoretically identified to determine the performance of autoregulated switches and were experimentally modified by fine-tuning promoter architectures and cooperativity. Using this strategy, we synthesized a number of switches and demonstrated its improvement of product titers and host growth controlling the complex deoxyviolacein biosynthesis pathway. Furthermore, we restored functions of a dysregulated multilayer NOR gate by integrating autorepression modules. Our work provides a blueprint for engineering host-adaptable synthetic systems.
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Affiliation(s)
- Ying Guan
- Department of Chemical Engineering, Tsinghua University, Beijing 100871, China.,Center for Quantitative Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Physics, Peking University, Beijing 100871, China
| | - Xinmao Chen
- Center for Quantitative Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Physics, Peking University, Beijing 100871, China
| | - Bin Shao
- Center for Quantitative Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Physics, Peking University, Beijing 100871, China
| | - Xiangyu Ji
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Science, University of Chinese Academy of Science, Beijing 100149, China
| | - Yanhui Xiang
- Center for Cell and Gene Circuit Design, CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Guoqiang Jiang
- Department of Chemical Engineering, Tsinghua University, Beijing 100871, China
| | - Lina Xu
- National Protein Science Facility, Tsinghua University, Beijing 100871, China
| | - Zhanglin Lin
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Qi Ouyang
- Center for Quantitative Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Physics, Peking University, Beijing 100871, China
| | - Chunbo Lou
- Center for Cell and Gene Circuit Design, CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,College of Life Science, University of Chinese Academy of Science, Beijing 100149, China
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79
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Stevanovic M, Boukéké-Lesplulier T, Hupe L, Hasty J, Bittihn P, Schultz D. Nutrient Gradients Mediate Complex Colony-Level Antibiotic Responses in Structured Microbial Populations. Front Microbiol 2022; 13:740259. [PMID: 35572643 PMCID: PMC9093743 DOI: 10.3389/fmicb.2022.740259] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 03/07/2022] [Indexed: 11/13/2022] Open
Abstract
Antibiotic treatments often fail to eliminate bacterial populations due to heterogeneity in how individual cells respond to the drug. In structured bacterial populations such as biofilms, bacterial metabolism and environmental transport processes lead to an emergent phenotypic structure and self-generated nutrient gradients toward the interior of the colony, which can affect cell growth, gene expression and susceptibility to the drug. Even in single cells, survival depends on a dynamic interplay between the drug's action and the expression of resistance genes. How expression of resistance is coordinated across populations in the presence of such spatiotemporal environmental coupling remains elusive. Using a custom microfluidic device, we observe the response of spatially extended microcolonies of tetracycline-resistant E. coli to precisely defined dynamic drug regimens. We find an intricate interplay between drug-induced changes in cell growth and growth-dependent expression of resistance genes, resulting in the redistribution of metabolites and the reorganization of growth patterns. This dynamic environmental feedback affects the regulation of drug resistance differently across the colony, generating dynamic phenotypic structures that maintain colony growth during exposure to high drug concentrations and increase population-level resistance to subsequent exposures. A mathematical model linking metabolism and the regulation of gene expression is able to capture the main features of spatiotemporal colony dynamics. Uncovering the fundamental principles that govern collective mechanisms of antibiotic resistance in spatially extended populations will allow the design of optimal drug regimens to counteract them.
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Affiliation(s)
- Mirjana Stevanovic
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, United States
| | - Thomas Boukéké-Lesplulier
- Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany.,École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
| | - Lukas Hupe
- Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany.,Institute for the Dynamics of Complex Systems, University of Göttingen, Göttingen, Germany
| | - Jeff Hasty
- BioCircuits Institute, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, United States.,Department of Bioengineering, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, United States.,Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, United States
| | - Philip Bittihn
- Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany.,Institute for the Dynamics of Complex Systems, University of Göttingen, Göttingen, Germany.,BioCircuits Institute, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, United States
| | - Daniel Schultz
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, United States
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80
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Mansouri M, Fussenegger M. Electrogenetics: Bridging synthetic biology and electronics to remotely control the behavior of mammalian designer cells. Curr Opin Chem Biol 2022; 68:102151. [PMID: 35483127 DOI: 10.1016/j.cbpa.2022.102151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/21/2022] [Accepted: 03/24/2022] [Indexed: 11/03/2022]
Abstract
Electrogenetics, the combination of electronics and genetics, is an emerging field of mammalian synthetic biology in which electrostimulation is used to remotely program user-designed genetic elements within designer cells to generate desired outputs. Here, we describe recent advances in electro-induced therapeutic gene expression and therapeutic protein secretion in engineered mammalian cells. We also review available tools and strategies to engineer electro-sensitive therapeutic designer cells that are able to sense electrical pulses and produce appropriate clinically relevant outputs in response. We highlight current limitations facing mammalian electrogenetics and suggest potential future directions for research.
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Affiliation(s)
- Maysam Mansouri
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel, CH-4058, Switzerland
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel, CH-4058, Switzerland; Faculty of Science, University of Basel, Mattenstrasse 26, Basel, CH-4058, Switzerland.
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81
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Li L, Pan H, Pang G, Lang H, Shen Y, Sun T, Zhang Y, Liu J, Chang J, Kang J, Zheng H, Wang H. Precise Thermal Regulation of Engineered Bacteria Secretion for Breast Cancer Treatment In Vivo. ACS Synth Biol 2022; 11:1167-1177. [PMID: 35175748 DOI: 10.1021/acssynbio.1c00452] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
For the biomedical application of engineered bacteria, strictly regulating the function of engineered bacteria has always been the goal pursued. However, the existing regulation methods do not meet the needs of the in vivo application of engineered bacteria. Therefore, the exploration of the precise regulation of engineered bacteria is necessary. Herein, heat-sensitive engineered bacteria that can respond to thermal stimuli within 30 min were constructed, and the precise control of functions was verified in the intestines of various model organisms (including C. elegans, bees, and mice). Subsequently, heat-sensitive engineered bacteria were shown to colonize the mouse tumor microenvironment. Finally, thermal stimulation was proven to control engineered bacteria to produce the therapeutic protein tumor necrosis factor α (TNF-α) in the tumor. After three heat stimulation treatments, the growth of the tumor was significantly inhibited, suggesting that heat can be used as a strategy to precisely control engineered bacteria in vivo.
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Affiliation(s)
- Lianyue Li
- School of Life Sciences, Tianjin University, Tianjin, 300072, China
- Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin, 300072, China
| | - Huizhuo Pan
- School of Life Sciences, Tianjin University, Tianjin, 300072, China
- Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin, 300072, China
| | - Gaoju Pang
- School of Life Sciences, Tianjin University, Tianjin, 300072, China
- Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin, 300072, China
| | - Haoyu Lang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Yue Shen
- School of Life Sciences, Tianjin University, Tianjin, 300072, China
- Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin, 300072, China
| | - Tao Sun
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin, 300072, China
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, China
| | - Yingying Zhang
- School of Life Sciences, Tianjin University, Tianjin, 300072, China
- Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin, 300072, China
| | - Jing Liu
- School of Life Sciences, Tianjin University, Tianjin, 300072, China
| | - Jin Chang
- School of Life Sciences, Tianjin University, Tianjin, 300072, China
- Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin, 300072, China
| | - Jun Kang
- School of Life Sciences, Tianjin University, Tianjin, 300072, China
- Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin, 300072, China
| | - Hao Zheng
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Hanjie Wang
- School of Life Sciences, Tianjin University, Tianjin, 300072, China
- Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin, 300072, China
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82
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Wang Y, Zhang G, Meng Q, Huang S, Guo P, Leng Q, Sun L, Liu G, Huang X, Liu J. Precise tumor immune rewiring via synthetic CRISPRa circuits gated by concurrent gain/loss of transcription factors. Nat Commun 2022; 13:1454. [PMID: 35304449 PMCID: PMC8933567 DOI: 10.1038/s41467-022-29120-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 03/01/2022] [Indexed: 12/14/2022] Open
Abstract
Reinvigoration of antitumor immunity has recently become the central theme for the development of cancer therapies. Nevertheless, the precise delivery of immunotherapeutic activities to the tumors remains challenging. Here, we explore a synthetic gene circuit-based strategy for specific tumor identification, and for subsequently engaging immune activation. By design, these circuits are assembled from two interactive modules, i.e., an oncogenic TF-driven CRISPRa effector, and a corresponding p53-inducible off-switch (NOT gate), which jointly execute an AND-NOT logic for accurate tumor targeting. In particular, two forms of the NOT gate are developed, via the use of an inhibitory sgRNA or an anti-CRISPR protein, with the second form showing a superior performance in gating CRISPRa by p53 loss. Functionally, the optimized AND-NOT logic circuit can empower a highly specific and effective tumor recognition/immune rewiring axis, leading to therapeutic effects in vivo. Taken together, our work presents an adaptable strategy for the development of precisely delivered immunotherapy. “Reinvigoration of antitumor immunity has recently become the central theme for the development of cancer therapies. Here the authors present an adaptable gene circuit to harness the CRISPRa for tumorlocalized immune activation.”
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Affiliation(s)
- Yafeng Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center at Medical School of Nanjing University, Nanjing, 210061, China.,Department of Rheumatology and Immunology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, 210008, China
| | - Guiquan Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center at Medical School of Nanjing University, Nanjing, 210061, China
| | - Qingzhou Meng
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, 78 Hengzhigang Road, Guangzhou, 510095, China
| | - Shisheng Huang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Panpan Guo
- Department of Rheumatology and Immunology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, 210008, China
| | - Qibin Leng
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, 78 Hengzhigang Road, Guangzhou, 510095, China
| | - Lingyun Sun
- Department of Rheumatology and Immunology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, 210008, China
| | - Geng Liu
- State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center at Medical School of Nanjing University, Nanjing, 210061, China. .,Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, 210093, China.
| | - Xingxu Huang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China. .,Zhejiang Laboratory, Hangzhou, 311100, China.
| | - Jianghuai Liu
- State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center at Medical School of Nanjing University, Nanjing, 210061, China. .,Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, 210093, China.
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83
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Aydin O, Passaro AP, Raman R, Spellicy SE, Weinberg RP, Kamm RD, Sample M, Truskey GA, Zartman J, Dar RD, Palacios S, Wang J, Tordoff J, Montserrat N, Bashir R, Saif MTA, Weiss R. Principles for the design of multicellular engineered living systems. APL Bioeng 2022; 6:010903. [PMID: 35274072 PMCID: PMC8893975 DOI: 10.1063/5.0076635] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 02/02/2022] [Indexed: 12/14/2022] Open
Abstract
Remarkable progress in bioengineering over the past two decades has enabled the formulation of fundamental design principles for a variety of medical and non-medical applications. These advancements have laid the foundation for building multicellular engineered living systems (M-CELS) from biological parts, forming functional modules integrated into living machines. These cognizant design principles for living systems encompass novel genetic circuit manipulation, self-assembly, cell-cell/matrix communication, and artificial tissues/organs enabled through systems biology, bioinformatics, computational biology, genetic engineering, and microfluidics. Here, we introduce design principles and a blueprint for forward production of robust and standardized M-CELS, which may undergo variable reiterations through the classic design-build-test-debug cycle. This Review provides practical and theoretical frameworks to forward-design, control, and optimize novel M-CELS. Potential applications include biopharmaceuticals, bioreactor factories, biofuels, environmental bioremediation, cellular computing, biohybrid digital technology, and experimental investigations into mechanisms of multicellular organisms normally hidden inside the "black box" of living cells.
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Affiliation(s)
| | - Austin P. Passaro
- Regenerative Bioscience Center, University of Georgia, Athens, Georgia 30602, USA
| | - Ritu Raman
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | | | - Robert P. Weinberg
- School of Pharmacy, Massachusetts College of Pharmacy and Health Sciences, Boston, Massachusetts 02115, USA
| | | | - Matthew Sample
- Center for Ethics and Law in the Life Sciences, Leibniz Universität Hannover, 30167 Hannover, Germany
| | - George A. Truskey
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA
| | - Jeremiah Zartman
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Roy D. Dar
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Sebastian Palacios
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, USA
| | - Jason Wang
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Jesse Tordoff
- Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Nuria Montserrat
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | | | - M. Taher A. Saif
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Ron Weiss
- Author to whom correspondence should be addressed:
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84
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Elliott KL, Fritzsch B, Yamoah EN, Zine A. Age-Related Hearing Loss: Sensory and Neural Etiology and Their Interdependence. Front Aging Neurosci 2022; 14:814528. [PMID: 35250542 PMCID: PMC8891613 DOI: 10.3389/fnagi.2022.814528] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 01/03/2022] [Indexed: 12/19/2022] Open
Abstract
Age-related hearing loss (ARHL) is a common, increasing problem for older adults, affecting about 1 billion people by 2050. We aim to correlate the different reductions of hearing from cochlear hair cells (HCs), spiral ganglion neurons (SGNs), cochlear nuclei (CN), and superior olivary complex (SOC) with the analysis of various reasons for each one on the sensory deficit profiles. Outer HCs show a progressive loss in a basal-to-apical gradient, and inner HCs show a loss in a apex-to-base progression that results in ARHL at high frequencies after 70 years of age. In early neonates, SGNs innervation of cochlear HCs is maintained. Loss of SGNs results in a considerable decrease (~50% or more) of cochlear nuclei in neonates, though the loss is milder in older mice and humans. The dorsal cochlear nuclei (fusiform neurons) project directly to the inferior colliculi while most anterior cochlear nuclei reach the SOC. Reducing the number of neurons in the medial nucleus of the trapezoid body (MNTB) affects the interactions with the lateral superior olive to fine-tune ipsi- and contralateral projections that may remain normal in mice, possibly humans. The inferior colliculi receive direct cochlear fibers and second-order fibers from the superior olivary complex. Loss of the second-order fibers leads to hearing loss in mice and humans. Although ARHL may arise from many complex causes, HC degeneration remains the more significant problem of hearing restoration that would replace the cochlear implant. The review presents recent findings of older humans and mice with hearing loss.
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Affiliation(s)
- Karen L. Elliott
- Department of Biology, University of Iowa, Iowa City, IA, United States
| | - Bernd Fritzsch
- Department of Biology, University of Iowa, Iowa City, IA, United States
- *Correspondence: Bernd Fritzsch
| | - Ebenezer N. Yamoah
- Department of Physiology and Cell Biology, School of Medicine, University of Nevada, Reno, NV, United States
| | - Azel Zine
- LBN, Laboratory of Bioengineering and Nanoscience, University of Montpellier, Montpellier, France
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85
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Li J, Dekanovsky L, Khezri B, Wu B, Zhou H, Sofer Z. Biohybrid Micro- and Nanorobots for Intelligent Drug Delivery. CYBORG AND BIONIC SYSTEMS 2022; 2022:9824057. [PMID: 36285309 PMCID: PMC9494704 DOI: 10.34133/2022/9824057] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 01/18/2022] [Indexed: 08/12/2023] Open
Abstract
Biohybrid micro- and nanorobots are integrated tiny machines from biological components and artificial components. They can possess the advantages of onboard actuation, sensing, control, and implementation of multiple medical tasks such as targeted drug delivery, single-cell manipulation, and cell microsurgery. This review paper is to give an overview of biohybrid micro- and nanorobots for smart drug delivery applications. First, a wide range of biohybrid micro- and nanorobots comprising different biological components are reviewed in detail. Subsequently, the applications of biohybrid micro- and nanorobots for active drug delivery are introduced to demonstrate how such biohybrid micro- and nanorobots are being exploited in the field of medicine and healthcare. Lastly, key challenges to be overcome are discussed to pave the way for the clinical translation and application of the biohybrid micro- and nanorobots.
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Affiliation(s)
- Jinhua Li
- School of Medical Technology, Beijing Institute of Technology, Beijing 100081, China
- Department of Inorganic Chemistry, University of Chemistry and Technology Prague, Technicka 5, 166 28 Prague 6, Czech Republic
| | - Lukas Dekanovsky
- Department of Inorganic Chemistry, University of Chemistry and Technology Prague, Technicka 5, 166 28 Prague 6, Czech Republic
| | - Bahareh Khezri
- Department of Inorganic Chemistry, University of Chemistry and Technology Prague, Technicka 5, 166 28 Prague 6, Czech Republic
| | - Bing Wu
- Department of Inorganic Chemistry, University of Chemistry and Technology Prague, Technicka 5, 166 28 Prague 6, Czech Republic
| | - Huaijuan Zhou
- Department of Inorganic Chemistry, University of Chemistry and Technology Prague, Technicka 5, 166 28 Prague 6, Czech Republic
| | - Zdenek Sofer
- Department of Inorganic Chemistry, University of Chemistry and Technology Prague, Technicka 5, 166 28 Prague 6, Czech Republic
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86
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Nakajima K, Nakabayashi H, Kawahara M. Cell fate‐inducing CARs orthogonally control multiple signaling pathways. Biotechnol J 2022; 17:e2100463. [DOI: 10.1002/biot.202100463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 01/05/2022] [Accepted: 01/07/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Kyoko Nakajima
- Laboratory of Cell Vaccine Center for Vaccine and Adjuvant Research (CVAR) National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN) 7‐6‐8 Saito‐Asagi Ibaraki‐shi Osaka 567‐0085 Japan
| | - Hideto Nakabayashi
- Department of Chemistry and Biotechnology Graduate School of Engineering The University of Tokyo 7‐3‐1 Hongo Bunkyo‐ku Tokyo 113–8656 Japan
| | - Masahiro Kawahara
- Laboratory of Cell Vaccine Center for Vaccine and Adjuvant Research (CVAR) National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN) 7‐6‐8 Saito‐Asagi Ibaraki‐shi Osaka 567‐0085 Japan
- Department of Chemistry and Biotechnology Graduate School of Engineering The University of Tokyo 7‐3‐1 Hongo Bunkyo‐ku Tokyo 113–8656 Japan
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87
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Zhang Y, Marchisio MA. Interaction of Bare dSpCas9, Scaffold gRNA, and Type II Anti-CRISPR Proteins Highly Favors the Control of Gene Expression in the Yeast S. cerevisiae. ACS Synth Biol 2022; 11:176-190. [PMID: 34994540 DOI: 10.1021/acssynbio.1c00352] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Type II CRISPR-(d)SpCas9 and anti-CRISPR proteins (AcrIIs) show evidence of coevolution and competition for survival between bacteria and phages. In biotechnology, CRISPR-(d)SpCas9 is utilized for gene editing and transcriptional regulation. Moreover, its activity is controlled by AcrIIs. However, studies of dSpCas9/AcrII-based transcription regulation in Saccharomyces cerevisiae are rare. In this work, we used dSpCas9 as a template to engineer new transcription activators. We found that the most performant activation system requires the use of bare dSpCas9 in conjunction with scaffold gRNA (scRNA). This means that activation domains shall not be fused to dSpCas9 but rather interact with scRNA. We showed that a low amount of sgRNA is not a limiting factor in dSpCas9-driven transcription regulation. Moreover, a high quantity of sgRNA does not improve, generally, activation (and repression) efficiency. Importantly, we analyzed the performance of AcrIIA2, AcrIIA4, and AcrIIA5 in S. cerevisiae in depth. AcrIIA4 is the strongest of the three AcrIIs and also the only one able to induce high inhibition at low concentrations. However, the activation domains fused to dSpCas9 hindered interactions with the AcrIIs as well and limited their control of gene transcription regulation, confirming that bare dSpCas9 is the best solution for building synthetic genetic networks in yeast.
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Affiliation(s)
- Yadan Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, 300072 Tianjin, China
| | - Mario Andrea Marchisio
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, 300072 Tianjin, China
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88
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Andres J, Zurbriggen MD. Genetically Encoded Biosensors for the Quantitative Analysis of Auxin Dynamics in Plant Cells. Methods Mol Biol 2022; 2379:183-195. [PMID: 35188663 DOI: 10.1007/978-1-0716-1791-5_11] [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: 06/14/2023]
Abstract
Plants, as sessile organisms, possess complex and intertwined signaling networks to react and adapt their behavior toward different internal and external stimuli. Due to this high level of complexity, the implementation of quantitative molecular tools in planta remains challenging. Synthetic biology as an ever-growing interdisciplinary field applies basic engineering principles in life sciences. A plethora of synthetic switches, circuits, and even higher order networks has been implemented in different organisms, such as bacteria and mammalian cells, and facilitates the study of signaling and metabolic pathways. However, the application of such tools in plants lags behind, and thus only a few genetically encoded biosensors and switches have been engineered toward the quantitative investigation of plant signaling. Here, we present a protocol for the quantitative analysis of auxin signaling in Arabidopsis thaliana protoplasts. We implemented genetically encoded, ratiometric, degradation-based luminescent biosensors and applied them for studying auxin perception dynamics. For this, we utilized three different Aux/IAAs as sensor modules and analyzed their degradation behavior in response to auxin. Our experimental approach requires simple hardware and experimental reagents and can thus be implemented in every plant-related or cell culture laboratory. The system allows for the analysis of auxin perception and signaling aspects on various levels and can be easily expanded to other hormones, as for example strigolactones. In addition, the modular sensor design enables the implementation of sensor modules in a straightforward and time-saving approach.
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Affiliation(s)
- Jennifer Andres
- Institute of Synthetic Biology and CEPLAS, University of Düsseldorf, Düsseldorf, Germany
| | - Matias D Zurbriggen
- Institute of Synthetic Biology and CEPLAS, University of Düsseldorf, Düsseldorf, Germany.
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89
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Dong Z, Chang L. Recent electroporation-based systems for intracellular molecule delivery. NANOTECHNOLOGY AND PRECISION ENGINEERING 2021. [DOI: 10.1063/10.0005649] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Zaizai Dong
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Lingqian Chang
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
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90
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Dey A, Barik D. Emergent Bistable Switches from the Incoherent Feed-Forward Signaling of a Positive Feedback Loop. ACS Synth Biol 2021; 10:3117-3128. [PMID: 34694110 DOI: 10.1021/acssynbio.1c00373] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bistability is intrinsically connected to various decision making processes in living systems. The operating principles of a bistable switch, generated from a positive feedback loop, are well understood both in natural and synthetic settings. However, the fate of dynamic modularity of a positive feedback loop is unknown when it is connected to another dynamically modular signaling motif. In order to address this, here we investigate feed-forward signaling of a positive feedback loop to determine the fate of a bistable switch under such signaling. Using the potential energy based high-throughput bifurcation analysis method, we uncover that in addition to the conventional bistability the hybrid motifs generate various emergent bistable switches, namely mushroom and isola switches, which are not produced by the individual motifs. Using random parameter sampling, network perturbation, and phase plane analysis, we establish the design principles of such emergent behaviors. Incoherent feed-forward signaling of a positive feedback loop with distinct regulatory thresholds of the two arms of the feed-forward loop are the key requirements for such emergent behaviors. Our calculations show that the specific types of atypical bistable responses depend on the logic gate configuration of the signals. However, the emergent bistable behaviors of the hybrid networks do not depend on the nature of the positive feedback loop.
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Affiliation(s)
- Anupam Dey
- School of Chemistry, University of Hyderabad, Central University P.O., Hyderabad, 500046, Telangana, India
| | - Debashis Barik
- School of Chemistry, University of Hyderabad, Central University P.O., Hyderabad, 500046, Telangana, India
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91
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Savanur MA, Weinstein-Marom H, Gross G. Implementing Logic Gates for Safer Immunotherapy of Cancer. Front Immunol 2021; 12:780399. [PMID: 34804073 PMCID: PMC8600566 DOI: 10.3389/fimmu.2021.780399] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 10/21/2021] [Indexed: 12/14/2022] Open
Abstract
Targeting solid tumors with absolute precision is a long-standing challenge in cancer immunotherapy. The identification of antigens, which are expressed by a large fraction of tumors of a given type and, preferably, across various types, but not by normal cells, holds the key to developing safe, off-the-shelf immunotherapies. Although the quest for widely shared, strictly tumor-specific antigens has been the focus of tremendous effort, only few such candidates have been implicated. Almost all antigens that are currently explored as targets for chimeric antigen receptor (CAR) or T cell receptor (TCR)-T cell therapy are also expressed by healthy cells and the risk of on-target off-tumor toxicity has remained a major concern. Recent studies suggest that this risk could be obviated by targeting instead combinations of two or more antigens, which are co-expressed by tumor but not normal cells and, as such, are tumor-specific. Moreover, the expression of a shared tumor antigen along with the lack of a second antigen that is expressed by normal tissues can also be exploited for precise recognition. Additional cues, antigenic or non-antigenic ones, which characterize the tumor microenvironment, could be harnessed to further increase precision. This review focuses on attempts to define the targetable signatures of tumors and assesses different strategies employing advanced synthetic biology for translating such information into safer modes of immunotherapy, implementing the principles of Boolean logic gates.
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Affiliation(s)
- Mohammed Azharuddin Savanur
- Laboratory of Immunology, MIGAL - Galilee Research Institute, Kiryat Shmona, Israel
- Department of Biotechnology, Tel-Hai College, Upper Galilee, Israel
| | - Hadas Weinstein-Marom
- Laboratory of Immunology, MIGAL - Galilee Research Institute, Kiryat Shmona, Israel
- Department of Biotechnology, Tel-Hai College, Upper Galilee, Israel
| | - Gideon Gross
- Laboratory of Immunology, MIGAL - Galilee Research Institute, Kiryat Shmona, Israel
- Department of Biotechnology, Tel-Hai College, Upper Galilee, Israel
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92
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McNerney MP, Doiron KE, Ng TL, Chang TZ, Silver PA. Theranostic cells: emerging clinical applications of synthetic biology. Nat Rev Genet 2021; 22:730-746. [PMID: 34234299 PMCID: PMC8261392 DOI: 10.1038/s41576-021-00383-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/28/2021] [Indexed: 02/06/2023]
Abstract
Synthetic biology seeks to redesign biological systems to perform novel functions in a predictable manner. Recent advances in bacterial and mammalian cell engineering include the development of cells that function in biological samples or within the body as minimally invasive diagnostics or theranostics for the real-time regulation of complex diseased states. Ex vivo and in vivo cell-based biosensors and therapeutics have been developed to target a wide range of diseases including cancer, microbiome dysbiosis and autoimmune and metabolic diseases. While probiotic therapies have advanced to clinical trials, chimeric antigen receptor (CAR) T cell therapies have received regulatory approval, exemplifying the clinical potential of cellular therapies. This Review discusses preclinical and clinical applications of bacterial and mammalian sensing and drug delivery platforms as well as the underlying biological designs that could enable new classes of cell diagnostics and therapeutics. Additionally, we describe challenges that must be overcome for more rapid and safer clinical use of engineered systems.
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Affiliation(s)
- Monica P McNerney
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Kailyn E Doiron
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Tai L Ng
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Timothy Z Chang
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Pamela A Silver
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
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93
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Abstract
The steadfast advance of the synthetic biology field has enabled scientists to use genetically engineered cells, instead of small molecules or biologics, as the basis for the development of novel therapeutics. Cells endowed with synthetic gene circuits can control the localization, timing and dosage of therapeutic activities in response to specific disease biomarkers and thus represent a powerful new weapon in the fight against disease. Here, we conceptualize how synthetic biology approaches can be applied to programme living cells with therapeutic functions and discuss the advantages that they offer over conventional therapies in terms of flexibility, specificity and predictability, as well as challenges for their development. We present notable advances in the creation of engineered cells that harbour synthetic gene circuits capable of biological sensing and computation of signals derived from intracellular or extracellular biomarkers. We categorize and describe these developments based on the cell scaffold (human or microbial) and the site at which the engineered cell exerts its therapeutic function within its human host. The design of cell-based therapeutics with synthetic biology is a rapidly growing strategy in medicine that holds great promise for the development of effective treatments for a wide variety of human diseases.
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94
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Shui S, Gainza P, Scheller L, Yang C, Kurumida Y, Rosset S, Georgeon S, Di Roberto RB, Castellanos-Rueda R, Reddy ST, Correia BE. A rational blueprint for the design of chemically-controlled protein switches. Nat Commun 2021; 12:5754. [PMID: 34599176 PMCID: PMC8486872 DOI: 10.1038/s41467-021-25735-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 08/24/2021] [Indexed: 12/20/2022] Open
Abstract
Small-molecule responsive protein switches are crucial components to control synthetic cellular activities. However, the repertoire of small-molecule protein switches is insufficient for many applications, including those in the translational spaces, where properties such as safety, immunogenicity, drug half-life, and drug side-effects are critical. Here, we present a computational protein design strategy to repurpose drug-inhibited protein-protein interactions as OFF- and ON-switches. The designed binders and drug-receptors form chemically-disruptable heterodimers (CDH) which dissociate in the presence of small molecules. To design ON-switches, we converted the CDHs into a multi-domain architecture which we refer to as activation by inhibitor release switches (AIR) that incorporate a rationally designed drug-insensitive receptor protein. CDHs and AIRs showed excellent performance as drug responsive switches to control combinations of synthetic circuits in mammalian cells. This approach effectively expands the chemical space and logic responses in living cells and provides a blueprint to develop new ON- and OFF-switches. Small-molecule responsive protein switches are crucial components to control synthetic cellular activities. Here, we present a computational protein design strategy to repurpose drug-inhibited protein-protein interactions into OFF- and ON-switches active in cells.
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Affiliation(s)
- Sailan Shui
- Laboratory of Protein Design and Immunoengineering (LPDI) - STI - EPFL, Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, CH-1015, Switzerland
| | - Pablo Gainza
- Laboratory of Protein Design and Immunoengineering (LPDI) - STI - EPFL, Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, CH-1015, Switzerland
| | - Leo Scheller
- Laboratory of Protein Design and Immunoengineering (LPDI) - STI - EPFL, Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, CH-1015, Switzerland
| | - Che Yang
- Laboratory of Protein Design and Immunoengineering (LPDI) - STI - EPFL, Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, CH-1015, Switzerland
| | - Yoichi Kurumida
- Department of Life Science, School and Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan
| | - Stéphane Rosset
- Laboratory of Protein Design and Immunoengineering (LPDI) - STI - EPFL, Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, CH-1015, Switzerland
| | - Sandrine Georgeon
- Laboratory of Protein Design and Immunoengineering (LPDI) - STI - EPFL, Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, CH-1015, Switzerland
| | - Raphaël B Di Roberto
- Department of Biosystems Science and Engineering, ETH Zürich, 4058, Basel, Switzerland
| | | | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zürich, 4058, Basel, Switzerland
| | - Bruno E Correia
- Laboratory of Protein Design and Immunoengineering (LPDI) - STI - EPFL, Lausanne, Switzerland. .,Swiss Institute of Bioinformatics (SIB), Lausanne, CH-1015, Switzerland.
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95
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Abstract
Synthetic biology increasingly enables the construction of sophisticated functions in mammalian cells. A particularly promising frontier combines concepts drawn from industrial process control engineering-which is used to confer and balance properties such as stability and efficiency-with understanding as to how living systems have evolved to perform similar tasks with biological components. In this review, we first survey the state-of-the-art for both technologies and strategies available for genetic programming in mammalian cells. We then discuss recent progress in implementing programming objectives inspired by engineered and natural control mechanisms. Finally, we consider the transformative role of model-guided design in the present and future construction of customized mammalian cell functions for applications in biotechnology, medicine, and fundamental research.
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96
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Mansouri M, Xue S, Hussherr MD, Strittmatter T, Camenisch G, Fussenegger M. Smartphone-Flashlight-Mediated Remote Control of Rapid Insulin Secretion Restores Glucose Homeostasis in Experimental Type-1 Diabetes. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2101939. [PMID: 34227232 DOI: 10.1002/smll.202101939] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/26/2021] [Indexed: 06/13/2023]
Abstract
Emerging digital assessment of biomarkers by linking health-related data obtained from wearable electronic devices and embedded health and fitness sensors in smartphones is opening up the possibility of creating a continuous remote-monitoring platform for disease management. It is considered that the built-in flashlight of smartphones may be utilized to remotely program genetically engineered designer cells for on-demand delivery of protein-based therapeutics. Here, the authors present smartphone-induced insulin release in β-cell line (iβ-cell) technology for traceless light-triggered rapid insulin secretion, employing the light-activatable receptor melanopsin to induce calcium influx and membrane depolarization upon illumination. This iβ-cell-based system enables repeated, reversible secretion of insulin within 15 min in response to light stimulation, with a high induction fold both in vitro and in vivo. It is shown that programmable percutaneous remote control of implanted microencapsulated iβ-cells with a smartphone's flashlight rapidly reverses hyperglycemia in a mouse model of type-1 diabetes.
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Affiliation(s)
- Maysam Mansouri
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel, CH-4058, Switzerland
| | - Shuai Xue
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel, CH-4058, Switzerland
| | - Marie-Didiée Hussherr
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel, CH-4058, Switzerland
| | - Tobias Strittmatter
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel, CH-4058, Switzerland
| | - Gieri Camenisch
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel, CH-4058, Switzerland
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel, CH-4058, Switzerland
- Faculty of Science, University of Basel, Mattenstrasse 26, Basel, CH-4058, Switzerland
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97
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Li Z, Wang Y, Liu J, Rawding P, Bu J, Hong S, Hu Q. Chemically and Biologically Engineered Bacteria-Based Delivery Systems for Emerging Diagnosis and Advanced Therapy. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2102580. [PMID: 34347325 DOI: 10.1002/adma.202102580] [Citation(s) in RCA: 91] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 05/10/2021] [Indexed: 06/13/2023]
Abstract
Bacteria are one of the main groups of organisms, which dynamically and closely participate in human health and disease development. With the integration of chemical biotechnology, bacteria have been utilized as an emerging delivery system for various biomedical applications. Given the unique features of bacteria such as their intrinsic biocompatibility and motility, bacteria-based delivery systems have drawn wide interest in the diagnosis and treatment of various diseases, including cancer, infectious diseases, kidney failure, and hyperammonemia. Notably, at the interface of chemical biotechnology and bacteria, many research opportunities have been initiated, opening a promising frontier in biomedical application. Herein, the current synergy of chemical biotechnology and bacteria, the design principles for bacteria-based delivery systems, the microbial modulation, and the clinical translation are reviewed, with a special focus on the emerging advances in diagnosis and therapy.
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Affiliation(s)
- Zhaoting Li
- Pharmaceutical Sciences Division, School of Pharmacy, Wisconsin Center for NanoBioSystems, Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin, Madison (UW-Madison), Madison, Wisconsin, 53705, USA
| | - Yixin Wang
- Pharmaceutical Sciences Division, School of Pharmacy, Wisconsin Center for NanoBioSystems, Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin, Madison (UW-Madison), Madison, Wisconsin, 53705, USA
| | - Jun Liu
- Pharmaceutical Sciences Division, School of Pharmacy, Wisconsin Center for NanoBioSystems, Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin, Madison (UW-Madison), Madison, Wisconsin, 53705, USA
| | - Piper Rawding
- Pharmaceutical Sciences Division, School of Pharmacy, Wisconsin Center for NanoBioSystems, Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin, Madison (UW-Madison), Madison, Wisconsin, 53705, USA
| | - Jiyoon Bu
- Pharmaceutical Sciences Division, School of Pharmacy, Wisconsin Center for NanoBioSystems, Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin, Madison (UW-Madison), Madison, Wisconsin, 53705, USA
| | - Seungpyo Hong
- Pharmaceutical Sciences Division, School of Pharmacy, Wisconsin Center for NanoBioSystems, Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin, Madison (UW-Madison), Madison, Wisconsin, 53705, USA
| | - Quanyin Hu
- Pharmaceutical Sciences Division, School of Pharmacy, Wisconsin Center for NanoBioSystems, Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin, Madison (UW-Madison), Madison, Wisconsin, 53705, USA
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98
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Yang L, Yin J, Wu J, Qiao L, Zhao EM, Cai F, Ye H. Engineering genetic devices for in vivo control of therapeutic T cell activity triggered by the dietary molecule resveratrol. Proc Natl Acad Sci U S A 2021; 118:e2106612118. [PMID: 34404729 PMCID: PMC8403971 DOI: 10.1073/pnas.2106612118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chimeric antigen receptor (CAR)-engineered T cell therapies have been recognized as powerful strategies in cancer immunotherapy; however, the clinical application of CAR-T is currently constrained by severe adverse effects in patients, caused by excessive cytotoxic activity and poor T cell control. Herein, we harnessed a dietary molecule resveratrol (RES)-responsive transactivator and a transrepressor to develop a repressible transgene expression (RESrep) device and an inducible transgene expression (RESind) device, respectively. After optimization, these tools enabled the control of CAR expression and CAR-mediated antitumor function in engineered human cells. We demonstrated that a resveratrol-repressible CAR expression (RESrep-CAR) device can effectively inhibit T cell activation upon resveratrol administration in primary T cells and a xenograft tumor mouse model. Additionally, we exhibit how a resveratrol-inducible CAR expression (RESind-CAR) device can achieve fine-tuned and reversible control over T cell activation via a resveratrol-titratable mechanism. Furthermore, our results revealed that the presence of RES can activate RESind-CAR T cells with strong anticancer cytotoxicity against cells in vitro and in vivo. Our study demonstrates the utility of RESrep and RESind devices as effective tools for transgene expression and illustrates the potential of RESrep-CAR and RESind-CAR devices to enhance patient safety in precision cancer immunotherapies.
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MESH Headings
- Animals
- Apoptosis
- Cell Proliferation
- Cytotoxicity, Immunologic/immunology
- Disease Models, Animal
- Female
- Humans
- Immunotherapy, Adoptive/methods
- Leukemia, Erythroblastic, Acute/genetics
- Leukemia, Erythroblastic, Acute/immunology
- Leukemia, Erythroblastic, Acute/metabolism
- Leukemia, Erythroblastic, Acute/therapy
- Lymphocyte Activation/immunology
- Mice
- Mice, Inbred NOD
- Mice, SCID
- Receptors, Antigen, T-Cell/immunology
- Receptors, Chimeric Antigen/immunology
- T-Lymphocytes/immunology
- Tumor Cells, Cultured
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Linfeng Yang
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jianli Yin
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jiali Wu
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Longliang Qiao
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Evan M Zhao
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02215
| | - Fengfeng Cai
- Department of Breast Surgery, Yangpu Hospital, School of Medicine, Tongji University, Shanghai 200090, China
| | - Haifeng Ye
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China;
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99
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Dvorak V, Wiedmer T, Ingles-Prieto A, Altermatt P, Batoulis H, Bärenz F, Bender E, Digles D, Dürrenberger F, Heitman LH, IJzerman AP, Kell DB, Kickinger S, Körzö D, Leippe P, Licher T, Manolova V, Rizzetto R, Sassone F, Scarabottolo L, Schlessinger A, Schneider V, Sijben HJ, Steck AL, Sundström H, Tremolada S, Wilhelm M, Wright Muelas M, Zindel D, Steppan CM, Superti-Furga G. An Overview of Cell-Based Assay Platforms for the Solute Carrier Family of Transporters. Front Pharmacol 2021; 12:722889. [PMID: 34447313 PMCID: PMC8383457 DOI: 10.3389/fphar.2021.722889] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 07/19/2021] [Indexed: 12/12/2022] Open
Abstract
The solute carrier (SLC) superfamily represents the biggest family of transporters with important roles in health and disease. Despite being attractive and druggable targets, the majority of SLCs remains understudied. One major hurdle in research on SLCs is the lack of tools, such as cell-based assays to investigate their biological role and for drug discovery. Another challenge is the disperse and anecdotal information on assay strategies that are suitable for SLCs. This review provides a comprehensive overview of state-of-the-art cellular assay technologies for SLC research and discusses relevant SLC characteristics enabling the choice of an optimal assay technology. The Innovative Medicines Initiative consortium RESOLUTE intends to accelerate research on SLCs by providing the scientific community with high-quality reagents, assay technologies and data sets, and to ultimately unlock SLCs for drug discovery.
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Affiliation(s)
- Vojtech Dvorak
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Tabea Wiedmer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Alvaro Ingles-Prieto
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | | | - Helena Batoulis
- Drug Discovery Sciences–Lead Discovery, Bayer Pharmaceuticals, Wuppertal, Germany
| | - Felix Bärenz
- Sanofi-Aventis Deutschland GmbH, Frankfurt am Main, Germany
| | - Eckhard Bender
- Drug Discovery Sciences–Lead Discovery, Bayer Pharmaceuticals, Wuppertal, Germany
| | - Daniela Digles
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | | | - Laura H. Heitman
- Division of Drug Discovery and Safety, LACDR, Leiden University, Leiden, Netherlands
| | - Adriaan P. IJzerman
- Division of Drug Discovery and Safety, LACDR, Leiden University, Leiden, Netherlands
| | - Douglas B. Kell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Stefanie Kickinger
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Daniel Körzö
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Philipp Leippe
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Thomas Licher
- Sanofi-Aventis Deutschland GmbH, Frankfurt am Main, Germany
| | | | | | | | | | - Avner Schlessinger
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Vanessa Schneider
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Hubert J. Sijben
- Division of Drug Discovery and Safety, LACDR, Leiden University, Leiden, Netherlands
| | | | | | | | | | - Marina Wright Muelas
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Diana Zindel
- Drug Discovery Sciences–Lead Discovery, Bayer Pharmaceuticals, Wuppertal, Germany
| | - Claire M. Steppan
- Pfizer Worldwide Research, Development and Medical, Groton, MA, United States
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
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100
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Robinson D, Place M, Hose J, Jochem A, Gasch AP. Natural variation in the consequences of gene overexpression and its implications for evolutionary trajectories. eLife 2021; 10:e70564. [PMID: 34338637 PMCID: PMC8352584 DOI: 10.7554/elife.70564] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 07/30/2021] [Indexed: 12/13/2022] Open
Abstract
Copy number variation through gene or chromosome amplification provides a route for rapid phenotypic variation and supports the long-term evolution of gene functions. Although the evolutionary importance of copy-number variation is known, little is understood about how genetic background influences its tolerance. Here, we measured fitness costs of over 4000 overexpressed genes in 15 Saccharomyces cerevisiae strains representing different lineages, to explore natural variation in tolerating gene overexpression (OE). Strain-specific effects dominated the fitness costs of gene OE. We report global differences in the consequences of gene OE, independent of the amplified gene, as well as gene-specific effects that were dependent on the genetic background. Natural variation in the response to gene OE could be explained by several models, including strain-specific physiological differences, resource limitations, and regulatory sensitivities. This work provides new insight on how genetic background influences tolerance to gene amplification and the evolutionary trajectories accessible to different backgrounds.
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Affiliation(s)
- DeElegant Robinson
- Microbiology Doctoral Training Program, University of Wisconsin-MadisonMadisonUnited States
| | - Michael Place
- Great Lakes Bioenergy Research Center, University of Wisconsin-MadisonMadisonUnited States
| | - James Hose
- Center for Genomic Science Innovation, University of Wisconsin-MadisonMadisonUnited States
| | - Adam Jochem
- Center for Genomic Science Innovation, University of Wisconsin-MadisonMadisonUnited States
| | - Audrey P Gasch
- Great Lakes Bioenergy Research Center, University of Wisconsin-MadisonMadisonUnited States
- Center for Genomic Science Innovation, University of Wisconsin-MadisonMadisonUnited States
- Department of Medical Genetics, University of Wisconsin-MadisonMadisonUnited States
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