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Winter DL, Wairara AR, Bennett JL, Donald WA, Glover DJ. Protein Interaction Kinetics Delimit the Performance of Phosphorylation-Driven Protein Switches. ACS Synth Biol 2024; 13:1781-1797. [PMID: 38830815 DOI: 10.1021/acssynbio.4c00101] [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: 06/05/2024]
Abstract
Post-translational modifications (PTMs) such as phosphorylation and dephosphorylation can rapidly alter protein surface chemistry and structural conformation, which can switch protein-protein interactions (PPIs) within signaling networks. Recently, de novo-designed phosphorylation-responsive protein switches have been created that harness kinase- and phosphatase-mediated phosphorylation to modulate PPIs. PTM-driven protein switches are promising tools for investigating PTM dynamics in living cells, developing biocompatible nanodevices, and engineering signaling pathways to program cell behavior. However, little is known about the physical and kinetic constraints of PTM-driven protein switches, which limits their practical application. In this study, we present a framework to evaluate two-component PTM-driven protein switches based on four performance metrics: effective concentration, dynamic range, response time, and reversibility. Our computational models reveal an intricate relationship between the binding kinetics, phosphorylation kinetics, and switch concentration that governs the sensitivity and reversibility of PTM-driven protein switches. Building upon the insights of the interaction modeling, we built and evaluated novel phosphorylation-driven protein switches consisting of phosphorylation-sensitive coiled coils as sensor domains fused to fluorescent proteins as actuator domains. By modulating the phosphorylation state of the switches with a specific protein kinase and phosphatase, we demonstrate fast, reversible transitions between "on" and "off" states. The response of the switches linearly correlated to the kinase concentration, demonstrating its potential as a biosensor for kinase measurements in real time. As intended, the switches responded to specific kinase activity with an increase in the fluorescence signal and our model could be used to distinguish between two mechanisms of switch activation: dimerization or a structural rearrangement. The protein switch kinetics model developed here should enable PTM-driven switches to be designed with ideal performance for specific applications.
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Affiliation(s)
- Daniel L Winter
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
- Synthetic Biology Future Science Platform, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, ACT 2601, Australia
| | - Adelgisa R Wairara
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Jack L Bennett
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - William A Donald
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - Dominic J Glover
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
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2
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Xia S, Lu AC, Tobin V, Luo K, Moeller L, Shon DJ, Du R, Linton JM, Sui M, Horns F, Elowitz MB. Synthetic protein circuits for programmable control of mammalian cell death. Cell 2024; 187:2785-2800.e16. [PMID: 38657604 PMCID: PMC11127782 DOI: 10.1016/j.cell.2024.03.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 02/05/2024] [Accepted: 03/21/2024] [Indexed: 04/26/2024]
Abstract
Natural cell death pathways such as apoptosis and pyroptosis play dual roles: they eliminate harmful cells and modulate the immune system by dampening or stimulating inflammation. Synthetic protein circuits capable of triggering specific death programs in target cells could similarly remove harmful cells while appropriately modulating immune responses. However, cells actively influence their death modes in response to natural signals, making it challenging to control death modes. Here, we introduce naturally inspired "synpoptosis" circuits that proteolytically regulate engineered executioner proteins and mammalian cell death. These circuits direct cell death modes, respond to combinations of protease inputs, and selectively eliminate target cells. Furthermore, synpoptosis circuits can be transmitted intercellularly, offering a foundation for engineering synthetic killer cells that induce desired death programs in target cells without self-destruction. Together, these results lay the groundwork for programmable control of mammalian cell death.
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Affiliation(s)
- Shiyu Xia
- 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
| | - Andrew C Lu
- 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; UCLA-Caltech Medical Scientist Training Program, University of California, Los Angeles, CA 90095, USA
| | - Victoria Tobin
- 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; UC Davis-Caltech Veterinary Scientist Training Program, University of California, Davis, CA 95616, USA
| | - Kaiwen Luo
- 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
| | - Lukas Moeller
- 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
| | - D Judy Shon
- 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
| | - Rongrong Du
- 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
| | - James M Linton
- 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
| | - Margaret Sui
- 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
| | - Felix Horns
- 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
| | - 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.
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3
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Zhu B, Yin H, Zhang D, Zhang M, Chao X, Scimeca L, Wu MR. Synthetic biology approaches for improving the specificity and efficacy of cancer immunotherapy. Cell Mol Immunol 2024; 21:436-447. [PMID: 38605087 PMCID: PMC11061174 DOI: 10.1038/s41423-024-01153-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 03/03/2024] [Indexed: 04/13/2024] Open
Abstract
Immunotherapy has shown robust efficacy in treating a broad spectrum of hematological and solid cancers. Despite the transformative impact of immunotherapy on cancer treatment, several outstanding challenges remain. These challenges include on-target off-tumor toxicity, systemic toxicity, and the complexity of achieving potent and sustainable therapeutic efficacy. Synthetic biology has emerged as a promising approach to overcome these obstacles, offering innovative tools for engineering living cells with customized functions. This review provides an overview of the current landscape and future prospects of cancer immunotherapy, particularly emphasizing the role of synthetic biology in augmenting its specificity, controllability, and efficacy. We delineate and discuss two principal synthetic biology strategies: those targeting tumor surface antigens with engineered immune cells and those detecting intratumoral disease signatures with engineered gene circuits. This review concludes with a forward-looking perspective on the enduring challenges in cancer immunotherapy and the potential breakthroughs that synthetic biology may contribute to the field.
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Affiliation(s)
- Bo Zhu
- Department of Liver Surgery, Center of Hepato-Pancreato-Biliary Surgery, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China.
| | - Hang Yin
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Immunology, Harvard Medical School, Boston, MA, 02115, USA
| | - Di Zhang
- Drug Safety Research & Evaluation, Takeda Pharmaceuticals International Company, Cambridge, MA, 02139, USA
| | - Meiling Zhang
- Medical Research Institute, Guangdong Provincial People's Hospital, Southern Medical University, Guangzhou, 510080, China
| | - Xiaojuan Chao
- Department of Liver Surgery, Center of Hepato-Pancreato-Biliary Surgery, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Luca Scimeca
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Immunology, Harvard Medical School, Boston, MA, 02115, USA
| | - Ming-Ru Wu
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Department of Immunology, Harvard Medical School, Boston, MA, 02115, USA.
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4
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Cui M, Lee S, Ban SH, Ryu JR, Shen M, Yang SH, Kim JY, Choi SK, Han J, Kim Y, Han K, Lee D, Sun W, Kwon HB, Lee D. A single-component, light-assisted uncaging switch for endoproteolytic release. Nat Chem Biol 2024; 20:353-364. [PMID: 37973890 DOI: 10.1038/s41589-023-01480-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 10/12/2023] [Indexed: 11/19/2023]
Abstract
Proteases function as pivotal molecular switches, initiating numerous biological events. Notably, potyviral protease, derived from plant viruses, has emerged as a trusted proteolytic switch in synthetic biological circuits. To harness their capabilities, we have developed a single-component photocleavable switch, termed LAUNCHER (Light-Assisted UNcaging switCH for Endoproteolytic Release), by employing a circularly permutated tobacco etch virus protease and a blue-light-gated substrate, which are connected by fine-tuned intermodular linkers. As a single-component system, LAUNCHER exhibits a superior signal-to-noise ratio compared with multi-component systems, enabling precise and user-controllable release of payloads. This characteristic renders LAUNCHER highly suitable for diverse cellular applications, including transgene expression, tailored subcellular translocation and optochemogenetics. Additionally, the plug-and-play integration of LAUNCHER into existing synthetic circuits facilitates the enhancement of circuit performance. The demonstrated efficacy of LAUNCHER in improving existing circuitry underscores its significant potential for expanding its utilization in various applications.
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Affiliation(s)
- Mingguang Cui
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Seunghwan Lee
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Sung Hwan Ban
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Jae Ryun Ryu
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Meiying Shen
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Soo Hyun Yang
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
| | - Jin Young Kim
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
| | - Seul Ki Choi
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
| | - Jaemin Han
- Korea University College of Medicine, Seoul, Republic of Korea
| | - Yoonhee Kim
- Department of Neuroscience, Korea University College of Medicine, Seoul, Republic of Korea
| | - Kihoon Han
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
- Department of Neuroscience, Korea University College of Medicine, Seoul, Republic of Korea
| | - Donghun Lee
- Department of Physics, Korea University, Seoul, Republic of Korea
| | - Woong Sun
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Hyung-Bae Kwon
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Dongmin Lee
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea.
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea.
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5
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Benman W, Huang Z, Iyengar P, Wilde D, Mumford TR, Bugaj LJ. A temperature-inducible protein module for control of mammalian cell fate. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.19.581019. [PMID: 38464222 PMCID: PMC10925237 DOI: 10.1101/2024.02.19.581019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Inducible protein switches are used throughout the biosciences to allow on-demand control of proteins in response to chemical or optical inputs. However, these inducers either cannot be controlled with precision in space and time or cannot be applied in optically dense settings, limiting their application in tissues and organisms. Here we introduce a protein module whose active state can be reversibly toggled with a small change in temperature, a stimulus that is both penetrant and dynamic. This protein, called Melt (Membrane localization through temperature), exists as a monomer in the cytoplasm at elevated temperatures but both oligomerizes and translocates to the plasma membrane when temperature is lowered. Using custom devices for rapid and high-throughput temperature control during live-cell microscopy, we find that the original Melt variant fully switches states between 28-32°C, and state changes can be observed within minutes of temperature changes. Melt was highly modular, permitting thermal control over diverse intracellular processes including signaling, proteolysis, and nuclear shuttling through straightforward end-to-end fusions with no further engineering. Melt was also highly tunable, giving rise to a library of Melt variants with switch point temperatures ranging from 30-40°C. The variants with higher switch points allowed control of molecular circuits between 37°C-41°C, a well-tolerated range for mammalian cells. Finally, Melt could thermally regulate important cell decisions over this range, including cytoskeletal rearrangement and apoptosis. Thus Melt represents a versatile thermogenetic module that provides straightforward, temperature-based, real-time control of mammalian cells with broad potential for biotechnology and biomedicine.
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Affiliation(s)
- William Benman
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Zikang Huang
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Pavan Iyengar
- Department of Biophysics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Delaney Wilde
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Thomas R. Mumford
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Lukasz J. Bugaj
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, 19104, USA
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6
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Teixeira AP, Fussenegger M. Synthetic Gene Circuits for Regulation of Next-Generation Cell-Based Therapeutics. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2309088. [PMID: 38126677 PMCID: PMC10885662 DOI: 10.1002/advs.202309088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Indexed: 12/23/2023]
Abstract
Arming human cells with synthetic gene circuits enables to expand their capacity to execute superior sensing and response actions, offering tremendous potential for innovative cellular therapeutics. This can be achieved by assembling components from an ever-expanding molecular toolkit, incorporating switches based on transcriptional, translational, or post-translational control mechanisms. This review provides examples from the three classes of switches, and discusses their advantages and limitations to regulate the activity of therapeutic cells in vivo. Genetic switches designed to recognize internal disease-associated signals often encode intricate actuation programs that orchestrate a reduction in the sensed signal, establishing a closed-loop architecture. Conversely, switches engineered to detect external molecular or physical cues operate in an open-loop fashion, switching on or off upon signal exposure. The integration of such synthetic gene circuits into the next generation of chimeric antigen receptor T-cells is already enabling precise calibration of immune responses in terms of magnitude and timing, thereby improving the potency and safety of therapeutic cells. Furthermore, pre-clinical engineered cells targeting other chronic diseases are gathering increasing attention, and this review discusses the path forward for achieving clinical success. With synthetic biology at the forefront, cellular therapeutics holds great promise for groundbreaking treatments.
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Affiliation(s)
- Ana P. Teixeira
- Department of Biosystems Science and EngineeringETH ZurichKlingelbergstrasse 48BaselCH‐4056Switzerland
| | - Martin Fussenegger
- Department of Biosystems Science and EngineeringETH ZurichKlingelbergstrasse 48BaselCH‐4056Switzerland
- Faculty of ScienceUniversity of BaselKlingelbergstrasse 48BaselCH‐4056Switzerland
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7
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DeJulius CR, Walton BL, Colazo JM, d'Arcy R, Francini N, Brunger JM, Duvall CL. Engineering approaches for RNA-based and cell-based osteoarthritis therapies. Nat Rev Rheumatol 2024; 20:81-100. [PMID: 38253889 PMCID: PMC11129836 DOI: 10.1038/s41584-023-01067-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2023] [Indexed: 01/24/2024]
Abstract
Osteoarthritis (OA) is a chronic, debilitating disease that substantially impairs the quality of life of affected individuals. The underlying mechanisms of OA are diverse and are becoming increasingly understood at the systemic, tissue, cellular and gene levels. However, the pharmacological therapies available remain limited, owing to drug delivery barriers, and consist mainly of broadly immunosuppressive regimens, such as corticosteroids, that provide only short-term palliative benefits and do not alter disease progression. Engineered RNA-based and cell-based therapies developed with synthetic chemistry and biology tools provide promise for future OA treatments with durable, efficacious mechanisms of action that can specifically target the underlying drivers of pathology. This Review highlights emerging classes of RNA-based technologies that hold potential for OA therapies, including small interfering RNA for gene silencing, microRNA and anti-microRNA for multi-gene regulation, mRNA for gene supplementation, and RNA-guided gene-editing platforms such as CRISPR-Cas9. Various cell-engineering strategies are also examined that potentiate disease-dependent, spatiotemporally regulated production of therapeutic molecules, and a conceptual framework is presented for their application as OA treatments. In summary, this Review highlights modern genetic medicines that have been clinically approved for other diseases, in addition to emerging genome and cellular engineering approaches, with the goal of emphasizing their potential as transformative OA treatments.
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Affiliation(s)
- Carlisle R DeJulius
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Bonnie L Walton
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Juan M Colazo
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Richard d'Arcy
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Nora Francini
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Jonathan M Brunger
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA.
| | - Craig L Duvall
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA.
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8
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Teng F, Cui T, Zhou L, Gao Q, Zhou Q, Li W. Programmable synthetic receptors: the next-generation of cell and gene therapies. Signal Transduct Target Ther 2024; 9:7. [PMID: 38167329 PMCID: PMC10761793 DOI: 10.1038/s41392-023-01680-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 09/22/2023] [Accepted: 10/11/2023] [Indexed: 01/05/2024] Open
Abstract
Cell and gene therapies hold tremendous promise for treating a range of difficult-to-treat diseases. However, concerns over the safety and efficacy require to be further addressed in order to realize their full potential. Synthetic receptors, a synthetic biology tool that can precisely control the function of therapeutic cells and genetic modules, have been rapidly developed and applied as a powerful solution. Delicately designed and engineered, they can be applied to finetune the therapeutic activities, i.e., to regulate production of dosed, bioactive payloads by sensing and processing user-defined signals or biomarkers. This review provides an overview of diverse synthetic receptor systems being used to reprogram therapeutic cells and their wide applications in biomedical research. With a special focus on four synthetic receptor systems at the forefront, including chimeric antigen receptors (CARs) and synthetic Notch (synNotch) receptors, we address the generalized strategies to design, construct and improve synthetic receptors. Meanwhile, we also highlight the expanding landscape of therapeutic applications of the synthetic receptor systems as well as current challenges in their clinical translation.
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Affiliation(s)
- Fei Teng
- University of Chinese Academy of Sciences, Beijing, 101408, China.
| | - Tongtong Cui
- State Key Laboratory of Stem Cell and Regenerative Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
| | - Li Zhou
- University of Chinese Academy of Sciences, Beijing, 101408, China
- State Key Laboratory of Stem Cell and Regenerative Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qingqin Gao
- University of Chinese Academy of Sciences, Beijing, 101408, China
- State Key Laboratory of Stem Cell and Regenerative Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qi Zhou
- University of Chinese Academy of Sciences, Beijing, 101408, China.
- State Key Laboratory of Stem Cell and Regenerative Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
| | - Wei Li
- University of Chinese Academy of Sciences, Beijing, 101408, China.
- State Key Laboratory of Stem Cell and Regenerative Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
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9
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Malaguti M, Lebek T, Blin G, Lowell S. Enabling neighbour labelling: using synthetic biology to explore how cells influence their neighbours. Development 2024; 151:dev201955. [PMID: 38165174 PMCID: PMC10820747 DOI: 10.1242/dev.201955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 11/28/2023] [Indexed: 01/03/2024]
Abstract
Cell-cell interactions are central to development, but exploring how a change in any given cell relates to changes in the neighbour of that cell can be technically challenging. Here, we review recent developments in synthetic biology and image analysis that are helping overcome this problem. We highlight the opportunities presented by these advances and discuss opportunities and limitations in applying them to developmental model systems.
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Affiliation(s)
- Mattias Malaguti
- Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
| | - Tamina Lebek
- Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
| | - Guillaume Blin
- Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
| | - Sally Lowell
- Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
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10
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Yang X, Rocks JW, Jiang K, Walters AJ, Rai K, Liu J, Nguyen J, Olson SD, Mehta P, Collins JJ, Daringer NM, Bashor CJ. Engineering synthetic phosphorylation signaling networks in human cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.11.557100. [PMID: 37745327 PMCID: PMC10515791 DOI: 10.1101/2023.09.11.557100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Protein phosphorylation signaling networks play a central role in how cells sense and respond to their environment. Here, we describe the engineering of artificial phosphorylation networks in which "push-pull" motifs-reversible enzymatic phosphorylation cycles consisting of opposing kinase and phosphatase activities-are assembled from modular protein domain parts and then wired together to create synthetic phosphorylation circuits in human cells. We demonstrate that the composability of our design scheme enables model-guided tuning of circuit function and the ability to make diverse network connections; synthetic phosphorylation circuits can be coupled to upstream cell surface receptors to enable fast-timescale sensing of extracellular ligands, while downstream connections can regulate gene expression. We leverage these capabilities to engineer cell-based cytokine controllers that dynamically sense and suppress activated T cells. Our work introduces a generalizable approach for designing and building phosphorylation signaling circuits that enable user-defined sense-and-respond function for diverse biosensing and therapeutic applications.
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Affiliation(s)
- Xiaoyu Yang
- Department of Bioengineering, Rice University; Houston, TX 77030, USA
- Graduate Program in Systems, Synthetic and Physical Biology, Rice University; Houston, TX 77030, USA
| | - Jason W. Rocks
- Department of Physics, Boston University; Boston, MA 02215, USA
| | - Kaiyi Jiang
- Department of Bioengineering, Rice University; Houston, TX 77030, USA
| | - Andrew J. Walters
- Department of Bioengineering, Rice University; Houston, TX 77030, USA
- Graduate Program in Bioengineering, Rice University; Houston, TX 77030, USA
- Department of Pediatric Surgery, McGovern Medical School, University of Texas Health Science Center at Houston; Houston, TX 77030, USA
| | - Kshitij Rai
- Graduate Program in Systems, Synthetic and Physical Biology, Rice University; Houston, TX 77030, USA
| | - Jing Liu
- Department of Bioengineering, Rice University; Houston, TX 77030, USA
| | - Jason Nguyen
- Department of Bioengineering, Rice University; Houston, TX 77030, USA
| | - Scott D. Olson
- Department of Pediatric Surgery, McGovern Medical School, University of Texas Health Science Center at Houston; Houston, TX 77030, USA
| | - Pankaj Mehta
- Department of Physics, Boston University; Boston, MA 02215, USA
- Biological Design Center, Boston University; Boston, MA 02215, USA
- Faculty of Computing and Data Science, Boston University; Boston, MA 02215, USA
| | - James J. Collins
- Institute for Medical Engineering and Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University; Boston, MA 02115, USA
| | - Nichole M Daringer
- Department of Biomedical Engineering, Rowan University; Glassboro, NJ 08028, USA
| | - Caleb J. Bashor
- Department of Bioengineering, Rice University; Houston, TX 77030, USA
- Department of Biosciences, Rice University; Houston, TX 77030, USA
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11
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Klumpe HE, Garcia-Ojalvo J, Elowitz MB, Antebi YE. The computational capabilities of many-to-many protein interaction networks. Cell Syst 2023; 14:430-446. [PMID: 37348461 PMCID: PMC10318606 DOI: 10.1016/j.cels.2023.05.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 04/14/2023] [Accepted: 05/11/2023] [Indexed: 06/24/2023]
Abstract
Many biological circuits comprise sets of protein variants that interact with one another in a many-to-many, or promiscuous, fashion. These architectures can provide powerful computational capabilities that are especially critical in multicellular organisms. Understanding the principles of biochemical computations in these circuits could allow more precise control of cellular behaviors. However, these systems are inherently difficult to analyze, due to their large number of interacting molecular components, partial redundancies, and cell context dependence. Here, we discuss recent experimental and theoretical advances that are beginning to reveal how promiscuous circuits compute, what roles those computations play in natural biological contexts, and how promiscuous architectures can be applied for the design of synthetic multicellular behaviors.
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Affiliation(s)
- Heidi E Klumpe
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA; Biological Design Center, Boston University, Boston, MA 02215, USA
| | - Jordi Garcia-Ojalvo
- Department of Medicine and Life Sciences, Pompeu Fabra University, 08003 Barcelona, Spain.
| | - Michael B Elowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
| | - Yaron E Antebi
- Department of Molecular Genetics, Weizmann Institute of Science 76100, Rehovot, Israel.
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12
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Wang Z, Liu J, Chen H, Qiu X, Xie L, Kaniskan HÜ, Chen X, Jin J, Wei W. Telomere Targeting Chimera Enables Targeted Destruction of Telomeric Repeat-Binding Factor Proteins. J Am Chem Soc 2023; 145:10872-10879. [PMID: 37141574 PMCID: PMC10976431 DOI: 10.1021/jacs.3c02783] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Telomeres are naturally shortened after each round of cell division in noncancerous normal cells, while the activation of telomerase activity to extend telomere in the cancer cell is essential for cell transformation. Therefore, telomeres are regarded as a potential anticancer target. In this study, we report the development of a nucleotide-based proteolysis-targeting chimera (PROTAC) designed to degrade TRF1/2 (telomeric repeat-binding factor 1/2), which are the key components of the shelterin complex (telosome) that regulates the telomere length by directly interacting with telomere DNA repeats. The prototype telomere-targeting chimeras (TeloTACs) efficiently degrade TRF1/2 in a VHL- and proteosome-dependent manner, resulting in the shortening of telomeres and suppressed cancer cell proliferation. Compared to the traditional receptor-based off-target therapy, TeloTACs have potential application in a broad spectrum of cancer cell lines due to their ability to selectively kill cancer cells that overexpress TRF1/2. In summary, TeloTACs provide a nucleotide-based degradation approach for shortening the telomere and inhibiting tumor cell growth, representing a promising avenue for cancer treatment.
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Affiliation(s)
- Zhen Wang
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Jing Liu
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - He Chen
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Xing Qiu
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Ling Xie
- Department of Biochemistry & Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - H Ümit Kaniskan
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Xian Chen
- Department of Biochemistry & Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, United States
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13
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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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14
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Chen Z. Protein circuit design using de novo proteins. Trends Biotechnol 2023; 41:593-594. [PMID: 36906493 DOI: 10.1016/j.tibtech.2023.02.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 02/28/2023] [Accepted: 02/28/2023] [Indexed: 03/12/2023]
Abstract
Protein-based biological circuits enable customized control of cellular functions, and de novo protein design enables circuit functionalities that are not possible by repurposing natural proteins. Here, I highlight recent progress in protein circuit design, including CHOMP, developed by Gao et al., and SPOC, developed by Fink et al.
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Affiliation(s)
- Zibo Chen
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China.
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15
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Kardynska M, Kogut D, Pacholczyk M, Smieja J. Mathematical modeling of regulatory networks of intracellular processes - Aims and selected methods. Comput Struct Biotechnol J 2023; 21:1523-1532. [PMID: 36851915 PMCID: PMC9958294 DOI: 10.1016/j.csbj.2023.02.006] [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: 11/30/2022] [Revised: 02/03/2023] [Accepted: 02/03/2023] [Indexed: 02/11/2023] Open
Abstract
Regulatory networks structure and signaling pathways dynamics are uncovered in time- and resource consuming experimental work. However, it is increasingly supported by modeling, analytical and computational techniques as well as discrete mathematics and artificial intelligence applied to to extract knowledge from existing databases. This review is focused on mathematical modeling used to analyze dynamics and robustness of these networks. This paper presents a review of selected modeling methods that facilitate advances in molecular biology.
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Affiliation(s)
- Malgorzata Kardynska
- Dept. of Biosensors and Processing of Biomedical Signals, Silesian University of Technology, Gliwice, Poland
| | - Daria Kogut
- Dept. of Biosensors and Processing of Biomedical Signals, Silesian University of Technology, Gliwice, Poland.,Dept. of Systems Biology and Engineering, Silesian University of Technology, Gliwice, Poland
| | - Marcin Pacholczyk
- Dept. of Biosensors and Processing of Biomedical Signals, Silesian University of Technology, Gliwice, Poland.,Dept. of Systems Biology and Engineering, Silesian University of Technology, Gliwice, Poland
| | - Jaroslaw Smieja
- Dept. of Biosensors and Processing of Biomedical Signals, Silesian University of Technology, Gliwice, Poland.,Dept. of Systems Biology and Engineering, Silesian University of Technology, Gliwice, Poland
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16
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Cleveland JD, Taslimi A, Liu Q, Van Keuren AM, Churchill MEA, Tucker CL. Reprogramming the Cleavage Specificity of Botulinum Neurotoxin Serotype B1. ACS Synth Biol 2022; 11:3318-3329. [PMID: 36153971 PMCID: PMC9907380 DOI: 10.1021/acssynbio.2c00235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Proteases with reprogrammed specificity for nonnative substrates are highly desired in synthetic biology and biomedicine. However, generating reprogrammed proteases that are orthogonal and highly specific for a new target has been a major challenge. In this work, we sought to expand the versatility of protease systems by engineering an orthogonal botulinum neurotoxin serotype B (BoNT/B) protease that recognizes an orthogonal substrate. We designed and validated an orthogonal BoNT/B protease system in mammalian cells, combining mutations in the protease with compensatory mutations in the protease substrate and incorporating a truncated target sequence and then demonstrated use of this orthogonal BoNT/B protease-substrate combination to regulate complex transcriptional circuitry in mammalian cells. Transposing this platform into yeast, we demonstrated utility of this approach for in vivo protease evolution. We tested this platform with the newly designed orthogonal protease and then used it in a high-throughput screen to identify novel orthogonal protease/protease substrate combinations. While carrying out this work, we also generated new cleavage reporters that could be used to report botulinum toxin protease activity in mammalian cells using simple fluorescent readouts. We envision that these approaches will expand the applications of botulinum protease in new directions and aid in the development of new reprogrammed proteases.
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Affiliation(s)
- Joseph D. Cleveland
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045 USA
| | - Amir Taslimi
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045 USA
| | - Qi Liu
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045 USA
| | - Anna M. Van Keuren
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045 USA
| | - Mair E. A. Churchill
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045 USA
| | - Chandra L. Tucker
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045 USA
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17
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North K, Benbarche S, Liu B, Pangallo J, Chen S, Stahl M, Bewersdorf JP, Stanley RF, Erickson C, Cho H, Pineda JMB, Thomas JD, Polaski JT, Belleville AE, Gabel AM, Udy DB, Humbert O, Kiem HP, Abdel-Wahab O, Bradley RK. Synthetic introns enable splicing factor mutation-dependent targeting of cancer cells. Nat Biotechnol 2022; 40:1103-1113. [PMID: 35241838 PMCID: PMC9288984 DOI: 10.1038/s41587-022-01224-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 01/17/2022] [Indexed: 11/16/2022]
Abstract
Many cancers carry recurrent, change-of-function mutations affecting RNA splicing factors. Here, we describe a method to harness this abnormal splicing activity to drive splicing factor mutation-dependent gene expression to selectively eliminate tumor cells. We engineered synthetic introns that were efficiently spliced in cancer cells bearing SF3B1 mutations, but unspliced in otherwise isogenic wild-type cells, to yield mutation-dependent protein production. A massively parallel screen of 8,878 introns delineated ideal intronic size and mapped elements underlying mutation-dependent splicing. Synthetic introns enabled mutation-dependent expression of herpes simplex virus-thymidine kinase (HSV-TK) and subsequent ganciclovir (GCV)-mediated killing of SF3B1-mutant leukemia, breast cancer, uveal melanoma and pancreatic cancer cells in vitro, while leaving wild-type cells unaffected. Delivery of synthetic intron-containing HSV-TK constructs to leukemia, breast cancer and uveal melanoma cells and GCV treatment in vivo significantly suppressed the growth of these otherwise lethal xenografts and improved mouse host survival. Synthetic introns provide a means to exploit tumor-specific changes in RNA splicing for cancer gene therapy.
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Affiliation(s)
- Khrystyna North
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Salima Benbarche
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bo Liu
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joseph Pangallo
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington, USA
| | - Sisi Chen
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maximilian Stahl
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jan Philipp Bewersdorf
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Robert F Stanley
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Caroline Erickson
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hana Cho
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jose Mario Bello Pineda
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - James D Thomas
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jacob T Polaski
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Andrea E Belleville
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Austin M Gabel
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Dylan B Udy
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington, USA
| | - Olivier Humbert
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Hans-Peter Kiem
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Robert K Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
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18
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Fink T, Jerala R. Designed protease-based signaling networks. Curr Opin Chem Biol 2022; 68:102146. [DOI: 10.1016/j.cbpa.2022.102146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/09/2022] [Accepted: 03/14/2022] [Indexed: 12/27/2022]
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19
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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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20
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Manhas J, Edelstein HI, Leonard JN, Morsut L. The evolution of synthetic receptor systems. Nat Chem Biol 2022; 18:244-255. [PMID: 35058646 PMCID: PMC9041813 DOI: 10.1038/s41589-021-00926-z] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 10/18/2021] [Indexed: 12/15/2022]
Abstract
Receptors enable cells to detect, process and respond to information about their environments. Over the past two decades, synthetic biologists have repurposed physical parts and concepts from natural receptors to engineer synthetic receptors. These technologies implement customized sense-and-respond programs that link a cell's interaction with extracellular and intracellular cues to user-defined responses. When combined with tools for information processing, these advances enable programming of sophisticated customized functions. In recent years, the library of synthetic receptors and their capabilities has substantially evolved-a term we employ here to mean systematic improvement and expansion. Here, we survey the existing mammalian synthetic biology toolkit of protein-based receptors and signal-processing components, highlighting efforts to evolve and integrate some of the foundational synthetic receptor systems. We then propose a generalized strategy for engineering and improving receptor systems to meet defined functional objectives called a 'metric-enabled approach for synthetic receptor engineering' (MEASRE).
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Affiliation(s)
- Janvie Manhas
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
- The Eli and Edythe Broad CIRM Center, Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Hailey I Edelstein
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
| | - Joshua N Leonard
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA.
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA.
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA.
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA.
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL, USA.
| | - Leonardo Morsut
- The Eli and Edythe Broad CIRM Center, Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
- Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA, USA.
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21
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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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22
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Chen Z, Elowitz MB. Programmable protein circuit design. Cell 2021; 184:2284-2301. [PMID: 33848464 PMCID: PMC8087657 DOI: 10.1016/j.cell.2021.03.007] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 02/22/2021] [Accepted: 03/02/2021] [Indexed: 12/11/2022]
Abstract
A fundamental challenge in synthetic biology is to create molecular circuits that can program complex cellular functions. Because proteins can bind, cleave, and chemically modify one another and interface directly and rapidly with endogenous pathways, they could extend the capabilities of synthetic circuits beyond what is possible with gene regulation alone. However, the very diversity that makes proteins so powerful also complicates efforts to harness them as well-controlled synthetic circuit components. Recent work has begun to address this challenge, focusing on principles such as orthogonality and composability that permit construction of diverse circuit-level functions from a limited set of engineered protein components. These approaches are now enabling the engineering of circuits that can sense, transmit, and process information; dynamically control cellular behaviors; and enable new therapeutic strategies, establishing a powerful paradigm for programming biology.
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Affiliation(s)
- Zibo Chen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - 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.
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23
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Hao Y, Li J, Li Q, Zhang L, Shi J, Zhang X, Aldalbahi A, Wang L, Fan C, Wang F. Programmable Live-Cell CRISPR Imaging with Toehold-Switch-Mediated Strand Displacement. Angew Chem Int Ed Engl 2020; 59:20612-20618. [PMID: 32744433 DOI: 10.1002/anie.202009062] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Indexed: 12/14/2022]
Abstract
The widespread application of CRISPR-Cas9 has transformed genome engineering. Nevertheless, the precision to control the targeting activity of Cas9 requires further improvement. We report a toehold-switch-based approach to engineer the conformation of single guide RNA (sgRNA) for programmable activation of Cas9. This activation circuit is responsive to multiple inputs and can regulate the conformation of the sgRNA through toehold-switch-mediated strand displacement. We demonstrate the orthogonal suppression and activation of Cas9 with orthogonal DNA inputs. Combination of toehold switches leads to a variety of intracellular Cas9 activation programs with simultaneous and orthogonal responses, through which multiple genome loci are displayed in different colors in a controllable manner. This approach provides a new route for programing CRISPR in living cells for genome imaging and engineering.
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Affiliation(s)
- Yaya Hao
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jiang Li
- Bioimaging Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Luhao Zhang
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Jiye Shi
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Xueli Zhang
- Joint Research Center for Precision Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital South Campus, Southern Medical University, Affiliated Fengxian Hospital, Shanghai, 201499, China
| | - Ali Aldalbahi
- Department of Chemistry, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Lihua Wang
- Bioimaging Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Fei Wang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
- Joint Research Center for Precision Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital South Campus, Southern Medical University, Affiliated Fengxian Hospital, Shanghai, 201499, China
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24
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Liu Y, Huang W, Cai Z. Synthesizing AND gate minigene circuits based on CRISPReader for identification of bladder cancer cells. Nat Commun 2020; 11:5486. [PMID: 33127914 PMCID: PMC7599332 DOI: 10.1038/s41467-020-19314-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/07/2020] [Indexed: 11/09/2022] Open
Abstract
The logical AND gate gene circuit based on the CRISPR-Cas9 system can distinguish bladder cancer cells from normal bladder epithelial cells. However, the layered artificial gene circuits have the problems of high complexity, difficulty in accurately predicting the behavior, and excessive redundancy, which cannot be applied to clinical translation. Here, we construct minigene circuits based on the CRISPReader, a technology used to control promoter-less gene expression in a robust manner. The minigene circuits significantly induce robust gene expression output in bladder cancer cells, but have nearly undetectable gene expression in normal bladder epithelial cells. The minigene circuits show a higher capability for cancer identification and intervention when compared with traditional gene circuits, and could be used for in vivo cancer gene therapy using the all-in-one AAV vector. This approach expands the design ideas and concepts of gene circuits in medical synthetic biology.
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Affiliation(s)
- Yuchen Liu
- National and Local Joint Engineering Laboratory of Medical Synthetic Biology, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University Health Science Center, 518035, Shenzhen, China. .,Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University Health Science Center, 518035, Shenzhen, China. .,Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University Health Science Center, 518035, Shenzhen, China.
| | - Weiren Huang
- National and Local Joint Engineering Laboratory of Medical Synthetic Biology, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University Health Science Center, 518035, Shenzhen, China.,Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University Health Science Center, 518035, Shenzhen, China.,Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University Health Science Center, 518035, Shenzhen, China
| | - Zhiming Cai
- National and Local Joint Engineering Laboratory of Medical Synthetic Biology, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University Health Science Center, 518035, Shenzhen, China.,Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University Health Science Center, 518035, Shenzhen, China.,Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University Health Science Center, 518035, Shenzhen, China
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25
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Edelstein HI, Donahue PS, Muldoon JJ, Kang AK, Dolberg TB, Battaglia LM, Allchin ER, Hong M, Leonard JN. Elucidation and refinement of synthetic receptor mechanisms. Synth Biol (Oxf) 2020; 5:ysaa017. [PMID: 33392392 PMCID: PMC7759213 DOI: 10.1093/synbio/ysaa017] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 08/13/2020] [Accepted: 09/02/2020] [Indexed: 12/22/2022] Open
Abstract
Synthetic receptors are powerful tools for engineering mammalian cell-based devices. These biosensors enable cell-based therapies to perform complex tasks such as regulating therapeutic gene expression in response to sensing physiological cues. Although multiple synthetic receptor systems now exist, many aspects of receptor performance are poorly understood. In general, it would be useful to understand how receptor design choices influence performance characteristics. In this study, we examined the modular extracellular sensor architecture (MESA) and systematically evaluated previously unexamined design choices, yielding substantially improved receptors. A key finding that might extend to other receptor systems is that the choice of transmembrane domain (TMD) is important for generating high-performing receptors. To provide mechanistic insights, we adopted and employed a Förster resonance energy transfer-based assay to elucidate how TMDs affect receptor complex formation and connected these observations to functional performance. To build further insight into these phenomena, we developed a library of new MESA receptors that sense an expanded set of ligands. Based upon these explorations, we conclude that TMDs affect signaling primarily by modulating intracellular domain geometry. Finally, to guide the design of future receptors, we propose general principles for linking design choices to biophysical mechanisms and performance characteristics.
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Affiliation(s)
- Hailey I Edelstein
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Patrick S Donahue
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL 60208, USA
- Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Joseph J Muldoon
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL 60208, USA
| | - Anthony K Kang
- Honors Program in Medical Education, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Program in Biological Sciences, Northwestern University, Evanston, IL, 60208, USA
| | - Taylor B Dolberg
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Lauren M Battaglia
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Everett R Allchin
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Mihe Hong
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Joshua N Leonard
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL 60208, USA
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26
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Hao Y, Li J, Li Q, Zhang L, Shi J, Zhang X, Aldalbahi A, Wang L, Fan C, Wang F. Programmable Live‐Cell CRISPR Imaging with Toehold‐Switch‐Mediated Strand Displacement. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202009062] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Yaya Hao
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules Institute of Molecular Medicine, Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200240 China
| | - Jiang Li
- Bioimaging Center Shanghai Synchrotron Radiation Facility Zhangjiang Laboratory Shanghai Advanced Research Institute Chinese Academy of Sciences Shanghai 201210 China
- Division of Physical Biology CAS Key Laboratory of Interfacial Physics and Technology Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai 201800 China
| | - Qian Li
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules Institute of Molecular Medicine, Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200240 China
| | - Luhao Zhang
- Division of Physical Biology CAS Key Laboratory of Interfacial Physics and Technology Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai 201800 China
| | - Jiye Shi
- Division of Physical Biology CAS Key Laboratory of Interfacial Physics and Technology Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai 201800 China
| | - Xueli Zhang
- Joint Research Center for Precision Medicine Shanghai Jiao Tong University Affiliated Sixth People's Hospital South Campus Southern Medical University Affiliated Fengxian Hospital Shanghai 201499 China
| | - Ali Aldalbahi
- Department of Chemistry College of Science King Saud University Riyadh 11451 Saudi Arabia
| | - Lihua Wang
- Bioimaging Center Shanghai Synchrotron Radiation Facility Zhangjiang Laboratory Shanghai Advanced Research Institute Chinese Academy of Sciences Shanghai 201210 China
- Division of Physical Biology CAS Key Laboratory of Interfacial Physics and Technology Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai 201800 China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules Institute of Molecular Medicine, Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200240 China
| | - Fei Wang
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules Institute of Molecular Medicine, Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200240 China
- Joint Research Center for Precision Medicine Shanghai Jiao Tong University Affiliated Sixth People's Hospital South Campus Southern Medical University Affiliated Fengxian Hospital Shanghai 201499 China
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27
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On the cutting edge: protease-based methods for sensing and controlling cell biology. Nat Methods 2020; 17:885-896. [PMID: 32661424 DOI: 10.1038/s41592-020-0891-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 06/09/2020] [Indexed: 02/06/2023]
Abstract
Sequence-specific proteases have proven to be versatile building blocks for tools that report or control cellular function. Reporting methods link protease activity to biochemical signals, whereas control methods rely on engineering proteases to respond to exogenous inputs such as light or chemicals. In turn, proteases have inherent control abilities, as their native functions are to release, activate or destroy proteins by cleavage, with the irreversibility of proteolysis allowing sustained downstream effects. As a result, protease-based synthetic circuits have been created for diverse uses such as reporting cellular signaling, tuning protein expression, controlling viral replication and detecting cancer states. Here, we comprehensively review the development and application of protease-based methods for reporting and controlling cellular function in eukaryotes.
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28
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Bojar D, Fussenegger M. The Role of Protein Engineering in Biomedical Applications of Mammalian Synthetic Biology. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e1903093. [PMID: 31588687 DOI: 10.1002/smll.201903093] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 09/05/2019] [Indexed: 06/10/2023]
Abstract
Engineered proteins with enhanced or altered functionality, generated for example by mutation or domain fusion, are at the core of nearly all synthetic biology endeavors in the context of precision medicine, also known as personalized medicine. From designer receptors sensing elevated blood markers to effectors rerouting signaling pathways to synthetic transcription factors and the customized therapeutics they regulate, engineered proteins play a crucial role at every step of novel therapeutic approaches using synthetic biology. Here, recent developments in protein engineering aided by advances in directed evolution, de novo design, and machine learning are discussed. Building on clinical successes already achieved with chimeric antigen receptor (CAR-) T cells and other cell-based therapies, these developments are expected to further enhance the capabilities of mammalian synthetic biology in biomedical and other applications.
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Affiliation(s)
- Daniel Bojar
- ETH Zurich, Department of Biosystems Science and Engineering, Faculty of Life Science, University of Basel, Mattenstrasse 26, CH-4058, Basel, Switzerland
| | - Martin Fussenegger
- ETH Zurich, Department of Biosystems Science and Engineering, Faculty of Life Science, University of Basel, Mattenstrasse 26, CH-4058, Basel, Switzerland
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29
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Phosphoregulated orthogonal signal transduction in mammalian cells. Nat Commun 2020; 11:3085. [PMID: 32555187 PMCID: PMC7303213 DOI: 10.1038/s41467-020-16895-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 05/28/2020] [Indexed: 12/17/2022] Open
Abstract
Orthogonal tools for controlling protein function by post-translational modifications open up new possibilities for protein circuit engineering in synthetic biology. Phosphoregulation is a key mechanism of signal processing in all kingdoms of life, but tools to control the involved processes are very limited. Here, we repurpose components of bacterial two-component systems (TCSs) for chemically induced phosphotransfer in mammalian cells. TCSs are the most abundant multi-component signal-processing units in bacteria, but are not found in the animal kingdom. The presented phosphoregulated orthogonal signal transduction (POST) system uses induced nanobody dimerization to regulate the trans-autophosphorylation activity of engineered histidine kinases. Engineered response regulators use the phosphohistidine residue as a substrate to autophosphorylate an aspartate residue, inducing their own homodimerization. We verify this approach by demonstrating control of gene expression with engineered, dimerization-dependent transcription factors and propose a phosphoregulated relay system of protein dimerization as a basic building block for next-generation protein circuits. Phosphoregulation is a key mechanism of signal processing. Here the authors build a phosphoregulated relay system in mammalian cells for orthogonal signal transduction.
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30
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Leydon AR, Gala HP, Guiziou S, Nemhauser JL. Engineering Synthetic Signaling in Plants. ANNUAL REVIEW OF PLANT BIOLOGY 2020; 71:767-788. [PMID: 32092279 DOI: 10.1146/annurev-arplant-081519-035852] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Synthetic signaling is a branch of synthetic biology that aims to understand native genetic regulatory mechanisms and to use these insights to engineer interventions and devices that achieve specified design parameters. Applying synthetic signaling approaches to plants offers the promise of mitigating the worst effects of climate change and providing a means to engineer crops for entirely novel environments, such as those in space travel. The ability to engineer new traits using synthetic signaling methods will require standardized libraries of biological parts and methods to assemble them; the decoupling of complex processes into simpler subsystems; and mathematical models that can accelerate the design-build-test-learn cycle. The field of plant synthetic signaling is relatively new, but it is poised for rapid advancement. Translation from the laboratory to the field is likely to be slowed, however, by the lack of constructive dialogue between researchers and other stakeholders.
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Affiliation(s)
- Alexander R Leydon
- Department of Biology, University of Washington, Seattle, Washington 98195, USA; , , ,
| | - Hardik P Gala
- Department of Biology, University of Washington, Seattle, Washington 98195, USA; , , ,
| | - Sarah Guiziou
- Department of Biology, University of Washington, Seattle, Washington 98195, USA; , , ,
| | - Jennifer L Nemhauser
- Department of Biology, University of Washington, Seattle, Washington 98195, USA; , , ,
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31
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Multiple Input Sensing and Signal Integration Using a Split Cas12a System. Mol Cell 2020; 78:184-191.e3. [DOI: 10.1016/j.molcel.2020.01.016] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 12/19/2019] [Accepted: 01/13/2020] [Indexed: 01/18/2023]
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32
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Herholt A, Galinski S, Geyer PE, Rossner MJ, Wehr MC. Multiparametric Assays for Accelerating Early Drug Discovery. Trends Pharmacol Sci 2020; 41:318-335. [PMID: 32223968 DOI: 10.1016/j.tips.2020.02.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 02/21/2020] [Accepted: 02/27/2020] [Indexed: 02/07/2023]
Abstract
Drug discovery campaigns are hampered by substantial attrition rates largely due to a lack of efficacy and safety reasons associated with candidate drugs. This is true in particular for genetically complex diseases, where insufficient knowledge of the modulatory actions of candidate drugs on targets and entire target pathways further adds to the problem of attrition. To better profile compound actions on targets, potential off-targets, and disease-linked pathways, new innovative technologies need to be developed that can elucidate the complex cellular signaling networks in health and disease. Here, we discuss progress in genetically encoded multiparametric assays and mass spectrometry (MS)-based proteomics, which both represent promising toolkits to profile multifactorial actions of drug candidates in disease-relevant cellular systems to promote drug discovery and personalized medicine.
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Affiliation(s)
- Alexander Herholt
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany; Systasy Bioscience GmbH, Balanstr. 6, 81669, Munich, Germany
| | - Sabrina Galinski
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany; Systasy Bioscience GmbH, Balanstr. 6, 81669, Munich, Germany
| | - Philipp E Geyer
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Planegg, Germany; NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark; OmicEra Diagnostics GmbH, Am Klopferspitz 19, 82152, Planegg, Germany
| | - Moritz J Rossner
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany
| | - Michael C Wehr
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany; Systasy Bioscience GmbH, Balanstr. 6, 81669, Munich, Germany.
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