1
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Galvan S, Teixeira AP, Fussenegger M. Enhancing cell-based therapies with synthetic gene circuits responsive to molecular stimuli. Biotechnol Bioeng 2024. [PMID: 38867466 DOI: 10.1002/bit.28770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 04/21/2024] [Accepted: 05/30/2024] [Indexed: 06/14/2024]
Abstract
Synthetic biology aims to contribute to the development of next-generation patient-specific cell-based therapies for chronic diseases especially through the construction of sophisticated synthetic gene switches to enhance the safety and spatiotemporal controllability of engineered cells. Indeed, switches that sense and process specific cues, which may be either externally administered triggers or endogenous disease-associated molecules, have emerged as powerful tools for programming and fine-tuning therapeutic outputs. Living engineered cells, often referred to as designer cells, incorporating such switches are delivered to patients either as encapsulated cell implants or by infusion, as in the case of the clinically approved CAR-T cell therapies. Here, we review recent developments in synthetic gene switches responsive to molecular stimuli, spanning regulatory mechanisms acting at the transcriptional, translational, and posttranslational levels. We also discuss current challenges facing clinical translation of cell-based therapies employing these devices.
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Affiliation(s)
- Silvia Galvan
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Ana P Teixeira
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- Faculty of Science, University of Basel, Basel, Switzerland
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2
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Kong D, Zhou Y, Wei Y, Wang X, Huang Q, Gao X, Wan H, Liu M, Kang L, Yu G, Yin J, Guan N, Ye H. Exploring plant-derived phytochrome chaperone proteins for light-switchable transcriptional regulation in mammals. Nat Commun 2024; 15:4894. [PMID: 38849338 PMCID: PMC11161646 DOI: 10.1038/s41467-024-49254-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 05/30/2024] [Indexed: 06/09/2024] Open
Abstract
Synthetic biology applications require finely tuned gene expression, often mediated by synthetic transcription factors (sTFs) compatible with the human genome and transcriptional regulation mechanisms. While various DNA-binding and activation domains have been developed for different applications, advanced artificially controllable sTFs with improved regulatory capabilities are required for increasingly sophisticated applications. Here, in mammalian cells and mice, we validate the transactivator function and homo-/heterodimerization activity of the plant-derived phytochrome chaperone proteins, FHY1 and FHL. Our results demonstrate that FHY1/FHL form a photosensing transcriptional regulation complex (PTRC) through interaction with the phytochrome, ΔPhyA, that can toggle between active and inactive states through exposure to red or far-red light, respectively. Exploiting this capability, we develop a light-switchable platform that allows for orthogonal, modular, and tunable control of gene transcription, and incorporate it into a PTRC-controlled CRISPRa system (PTRCdcas) to modulate endogenous gene expression. We then integrate the PTRC with small molecule- or blue light-inducible regulatory modules to construct a variety of highly tunable systems that allow rapid and reversible control of transcriptional regulation in vitro and in vivo. Validation and deployment of these plant-derived phytochrome chaperone proteins in a PTRC platform have produced a versatile, powerful tool for advanced research and biomedical engineering applications.
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Affiliation(s)
- Deqiang Kong
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai, 200241, China
| | - Yang Zhou
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai, 200241, China
- Wuhu Hospital, Health Science Center, East China Normal University, Middle Jiuhua Road 263, Wuhu City, China
| | - Yu Wei
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai, 200241, China
| | - Xinyi Wang
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai, 200241, China
| | - Qin Huang
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai, 200241, China
| | - Xianyun Gao
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai, 200241, China
| | - Hang Wan
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai, 200241, China
| | - Mengyao Liu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai, 200241, China
| | - Liping Kang
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai, 200241, China
| | - Guiling Yu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai, 200241, China
| | - Jianli Yin
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai, 200241, China
- Chongqing Key Laboratory of Precision Optics, Chongqing Institute of East China Normal University, Chongqing, 401120, China
| | - Ningzi Guan
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai, 200241, China.
| | - Haifeng Ye
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai, 200241, China.
- Wuhu Hospital, Health Science Center, East China Normal University, Middle Jiuhua Road 263, Wuhu City, China.
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Huang J, Xue S, Teixeira AP, Fussenegger M. A Gene-Switch Platform Interfacing with Reactive Oxygen Species Enables Transcription Fine-Tuning by Soluble and Volatile Pharmacologics and Food Additives. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306333. [PMID: 38526196 PMCID: PMC11132055 DOI: 10.1002/advs.202306333] [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: 09/03/2023] [Revised: 02/12/2024] [Indexed: 03/26/2024]
Abstract
Synthetic biology aims to engineer transgene switches for precise therapeutic protein control in cell-based gene therapies. However, off-the-shelf trigger-inducible gene circuits are usually switched on by single or structurally similar molecules. This study presents a mammalian gene-switch platform that controls therapeutic gene expression by a wide range of molecules generating low, non-toxic levels of reactive oxygen species (ROS). In this system, KEAP1 (Kelch-like ECH-associated protein 1) serves as ROS sensor, regulating the translocation of NRF2 (nuclear factor erythroid 2-related factor 2) to the nucleus, where NRF2 binds to antioxidant response elements (ARE) to activate the expression of a gene of interest. It is found that a promoter containing eight-tandem ARE repeats is highly sensitive to the low ROS levels generated by the soluble and volatile molecules, which include food preservatives, food additives, pharmaceuticals, and signal transduction inducers. In a proof-of-concept study, it is shown that many of these compounds can independently trigger microencapsulated engineered cells to produce sufficient insulin to restore normoglycemia in experimental type-1 diabetic mice. It is believed that this system greatly extends the variety of small-molecule inducers available to drive therapeutic gene switches.
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Affiliation(s)
- Jinbo Huang
- Department of Biosystems Science and EngineeringETH ZurichKlingelbergstrasse 48BaselCH‐4056Switzerland
| | - Shuai Xue
- Department of Biosystems Science and EngineeringETH ZurichKlingelbergstrasse 48BaselCH‐4056Switzerland
- Faculty of ScienceUniversity of BaselKlingelbergstrasse 48BaselCH‐4056Switzerland
| | - Ana Palma Teixeira
- Department of Biosystems Science and EngineeringETH ZurichKlingelbergstrasse 48BaselCH‐4056Switzerland
| | - Martin Fussenegger
- Department of Biosystems Science and EngineeringETH ZurichKlingelbergstrasse 48BaselCH‐4056Switzerland
- Present address:
Key Laboratory of Growth Regulation and Translational Research of Zhejiang ProvinceSchool of Life Sciences, Westlake UniversityHangzhou, ZhejiangChina
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4
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Mansouri M, Fussenegger M. Small-Molecule Regulators for Gene Switches to Program Mammalian Cell Behaviour. Chembiochem 2024; 25:e202300717. [PMID: 38081780 DOI: 10.1002/cbic.202300717] [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: 10/18/2023] [Revised: 12/11/2023] [Indexed: 01/13/2024]
Abstract
Synthetic or natural small molecules have been extensively employed as trigger signals or inducers to regulate engineered gene circuits introduced into living cells in order to obtain desired outputs in a controlled and predictable manner. Here, we provide an overview of small molecules used to drive synthetic-biology-based gene circuits in mammalian cells, together with examples of applications at different levels of control, including regulation of DNA manipulation, RNA synthesis and editing, and protein synthesis, maturation, and trafficking. We also discuss the therapeutic potential of these small-molecule-responsive gene circuits, focusing on the advantages and disadvantages of using small molecules as triggers, the mechanisms involved, and the requirements for selecting suitable molecules, including efficiency, specificity, orthogonality, and safety. Finally, we explore potential future directions for translation of these devices to clinical medicine.
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Affiliation(s)
- Maysam Mansouri
- ETH Zurich, Department of Biosystems Science and Engineering, Klingelbergstrasse 48, CH-4056, Basel, Switzerland
| | - Martin Fussenegger
- ETH Zurich, Department of Biosystems Science and Engineering, Klingelbergstrasse 48, CH-4056, Basel, Switzerland
- University of Basel, Faculty of Science, Klingelbergstrasse 48, CH-4056, Basel, Switzerland
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5
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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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6
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Ma Y, Chen R, Chen Z, Wang Z, Chen J, Zhang S. Probing covalent and non-covalent interactions between vanillic acid and starch and their effects on digestibility by solid-state NMR. Int J Biol Macromol 2023; 251:126304. [PMID: 37573923 DOI: 10.1016/j.ijbiomac.2023.126304] [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: 06/12/2023] [Revised: 08/01/2023] [Accepted: 08/10/2023] [Indexed: 08/15/2023]
Abstract
Intermolecular interactions play a significant role on the physicochemical properties and digestibility of starchy foods. This study investigated the covalent and non-covalent interactions between vanillic acid (VA) and porous starch (PS) as well as their effects on digestibility using solid-state NMR. VA-PS conjugates and mixtures were synthesized and characterized using 1H NMR, FT-IR, SEM and XRD. 13C NMR peaks at 163 ppm and FT-IR signals at 1737 cm-1 indicated the formation of ester bond in VA-PS conjugates. While differences between covalent and non-covalent interactions were also probed by solid-state NMR. The specific binding sites between VA and PS were subsequently identified by 1H13C HETCOR spectra before assessing the impact of covalent and non-covalent interactions on digestibility through an in vitro digestion test. The results revealed 13C chemical shifts of about 2.0 ppm, indicating stronger intermolecular interactions, and reduced mobility of the VA-PS conjugate due to its covalent bonding. Overall, the results showed that the VA-PS conjugate, characterized by stronger covalent interactions, exhibited superior effects in inhibiting starch digestibility compared with non-covalent interactions.
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Affiliation(s)
- Yunxiang Ma
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou 730070, Gansu, China; State Key Laboratory of Arid Land Crop Science, Gansu Agricultural University, Lanzhou 730070, Gansu, China.
| | - Ruixi Chen
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou 730070, Gansu, China
| | - Zidi Chen
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou 730070, Gansu, China
| | - Zhipeng Wang
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, Gansu, China
| | - Jinfeng Chen
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou 730070, Gansu, China
| | - Shenggui Zhang
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou 730070, Gansu, China; State Key Laboratory of Arid Land Crop Science, Gansu Agricultural University, Lanzhou 730070, Gansu, China.
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7
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Wang X, Zhou X, Kang L, Lai Y, Ye H. Engineering natural molecule-triggered genetic control systems for tunable gene- and cell-based therapies. Synth Syst Biotechnol 2023; 8:416-426. [PMID: 37384125 PMCID: PMC10293594 DOI: 10.1016/j.synbio.2023.06.002] [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: 04/11/2023] [Revised: 06/01/2023] [Accepted: 06/04/2023] [Indexed: 06/30/2023] Open
Abstract
The ability to precisely control activities of engineered designer cells provides a novel strategy for modern precision medicine. Dynamically adjustable gene- and cell-based precision therapies are recognized as next generation medicines. However, the translation of these controllable therapeutics into clinical practice is severely hampered by the lack of safe and highly specific genetic switches controlled by triggers that are nontoxic and side-effect free. Recently, natural products derived from plants have been extensively explored as trigger molecules to control genetic switches and synthetic gene networks for multiple applications. These controlled genetic switches could be further introduced into mammalian cells to obtain synthetic designer cells for adjustable and fine tunable cell-based precision therapy. In this review, we introduce various available natural molecules that were engineered to control genetic switches for controllable transgene expression, complex logic computation, and therapeutic drug delivery to achieve precision therapy. We also discuss current challenges and prospects in translating these natural molecule-controlled genetic switches developed for biomedical applications from the laboratory to the clinic.
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8
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Dahabiyeh LA, Nimer RM, Sumaily KM, Alabdaljabar MS, Jacob M, Sabi EM, Hussein MH, Abdel Rahman A. Metabolomics profiling distinctively identified end-stage renal disease patients from chronic kidney disease patients. Sci Rep 2023; 13:6161. [PMID: 37061630 PMCID: PMC10105740 DOI: 10.1038/s41598-023-33377-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 04/12/2023] [Indexed: 04/17/2023] Open
Abstract
Chronic kidney disease (CKD) is a serious public health problem characterized by progressive kidney function loss leading to end-stage renal disease (ESRD) that demands dialysis or kidney transplantation. Early detection can prevent or delay progression to ESRD. The study aimed to gain new insights into the perturbed biochemical reactions and to identify novel distinct biomarkers between ESRD and CKD. Serum samples of 32 patients with ESRD (n = 13) and CKD (n = 19) were analyzed using chemical isotope labeling liquid chromatography-mass spectrometry metabolomics approach. A total of 193 metabolites were significantly altered in ESRD compared to CKD and were mainly involved in aminoacyl-tRNA biosynthesis, branched-chain amino acid (BCAA) biosynthesis, taurine metabolism, and tryptophan metabolism. Three kynurenine derivatives, namely, 2-aminobenzoic acid, xanthurenic acid, and hydroxypicolinic acid were upregulated in ESRD compared to CKD due to the significant decrease in glomerular filtration rate with the progression of CKD to ESRD. N-Hydroxy-isoleucine, 2-aminobenzoic acid, and picolinic acid yielded AUC > 0.99 when analyzed using Receiver Operating Characteristic (ROC) analysis. Our findings suggest that inhibiting the kynurenine pathway might be a promising target to delay CKD progression and that metabolites with high discriminative ability might serve as potential prognostic biomarkers to monitor the progression of CKD to ESRD or used in combination with current markers to indicate the status of kidney damage better.
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Affiliation(s)
- Lina A Dahabiyeh
- Division of Pharmaceutical Sciences, School of Pharmacy, The University of Jordan, Amman, 11942, Jordan
| | - Refat M Nimer
- Department of Medical Laboratory Sciences, Jordan University of Science and Technology, Irbid, 22110, Jordan
| | - Khalid M Sumaily
- Clinical Biochemistry Unit, Pathology Department, College of Medicine, King Saud University, Riyadh, 11461, Saudi Arabia
- Clinical Biochemistry Unit, Laboratory Medicine, King Saud University Medical City, King Saud University, Riyadh, 11461, Saudi Arabia
| | - Mohamad S Alabdaljabar
- Metabolomics Section, Department of Clinical Genomics, Center for Genomics Medicine, King Faisal Specialist Hospital and Research Centre (KFSHRC), Riyadh, 11211, Saudi Arabia
- Department of Internal Medicine, Mayo Clinic, Rochester, MN, 55902, USA
| | - Minnie Jacob
- Metabolomics Section, Department of Clinical Genomics, Center for Genomics Medicine, King Faisal Specialist Hospital and Research Centre (KFSHRC), Riyadh, 11211, Saudi Arabia
| | - Essa M Sabi
- Clinical Biochemistry Unit, Pathology Department, College of Medicine, King Saud University, Riyadh, 11461, Saudi Arabia
| | - Maged H Hussein
- Department of Medicine, King Faisal Specialist Hospital and Research Centre (KFSHRC), Riyadh, 11211, Saudi Arabia
| | - Anas Abdel Rahman
- Metabolomics Section, Department of Clinical Genomics, Center for Genomics Medicine, King Faisal Specialist Hospital and Research Centre (KFSHRC), Riyadh, 11211, Saudi Arabia.
- Department of Biochemistry and Molecular Medicine, College of Medicine, Alfaisal University, Riyadh, 11533, Saudi Arabia.
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9
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Bertschi A, Stefanov BA, Xue S, Charpin-El Hamri G, Teixeira AP, Fussenegger M. Controlling therapeutic protein expression via inhalation of a butter flavor molecule. Nucleic Acids Res 2023; 51:e28. [PMID: 36625292 PMCID: PMC10018347 DOI: 10.1093/nar/gkac1256] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 11/29/2022] [Accepted: 12/20/2022] [Indexed: 01/11/2023] Open
Abstract
Precise control of the delivery of therapeutic proteins is critical for gene- and cell-based therapies, and expression should only be switched on in the presence of a specific trigger signal of appropriate magnitude. Focusing on the advantages of delivering the trigger by inhalation, we have developed a mammalian synthetic gene switch that enables regulation of transgene expression by exposure to the semi-volatile small molecule acetoin, a widely used, FDA-approved food flavor additive. The gene switch capitalizes on the bacterial regulatory protein AcoR fused to a mammalian transactivation domain, which binds to promoter regions with specific DNA sequences in the presence of acetoin and dose-dependently activates expression of downstream transgenes. Wild-type mice implanted with alginate-encapsulated cells transgenic for the acetoin gene switch showed a dose-dependent increase in blood levels of reporter protein in response to either administration of acetoin solution via oral gavage or longer exposure to acetoin aerosol generated by a commercial portable inhaler. Intake of typical acetoin-containing foods, such as butter, lychees and cheese, did not activate transgene expression. As a proof of concept, we show that blood glucose levels were normalized by acetoin aerosol inhalation in type-I diabetic mice implanted with acetoin-responsive insulin-producing cells. Delivery of trigger molecules using portable inhalers may facilitate regular administration of therapeutic proteins via next-generation cell-based therapies to treat chronic diseases for which frequent dosing is required.
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Affiliation(s)
- Adrian Bertschi
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Bozhidar-Adrian Stefanov
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Shuai Xue
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Ghislaine Charpin-El Hamri
- Département Génie Biologique, Institut Universitaire de Technologie, Université Claude Bernard, Lyon 1 Villeurbanne Cedex F-69622, France
| | - Ana Palma Teixeira
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Martin Fussenegger
- To whom correspondence should be addressed. Tel: +41 61 387 31 60; Fax: +41 61 387 39 88;
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10
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Bertschi A, Wang P, Galvan S, Teixeira AP, Fussenegger M. Combinatorial protein dimerization enables precise multi-input synthetic computations. Nat Chem Biol 2023; 19:767-777. [PMID: 36894721 DOI: 10.1038/s41589-023-01281-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 02/01/2023] [Indexed: 03/11/2023]
Abstract
Bacterial transcription factors (TFs) with helix-turn-helix (HTH) DNA-binding domains have been widely explored to build orthogonal transcriptional regulation systems in mammalian cells. Here we capitalize on the modular structure of these proteins to build a framework for multi-input logic gates relying on serial combinations of inducible protein-protein interactions. We found that for some TFs, their HTH domain alone is sufficient for DNA binding. By fusing the HTH domain to TFs, we established dimerization dependent rather than DNA-binding-dependent activation. This enabled us to convert gene switches from OFF-type into more widely applicable ON-type systems and to create mammalian gene switches responsive to new inducers. By combining both OFF and ON modes of action, we built a compact, high-performance bandpass filter. Furthermore, we were able to show cytosolic and extracellular dimerization. Cascading up to five pairwise fusion proteins yielded robust multi-input AND logic gates. Combinations of different pairwise fusion proteins afforded a variety of 4-input 1-output AND and OR logic gate configurations.
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Affiliation(s)
- Adrian Bertschi
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Pengli Wang
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Silvia Galvan
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Ana Palma Teixeira
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland. .,University of Basel, Faculty of Science, Basel, Switzerland.
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11
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Li S, Tang H, Li C, Ma J, Ali M, Dong Q, Wu J, Hui Y, Sun C. Synthetic Biology Technologies And Genetically Engineering Strategies For Enhanced Cell Therapeutics. Stem Cell Rev Rep 2023; 19:309-321. [PMID: 36166137 PMCID: PMC9514184 DOI: 10.1007/s12015-022-10454-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/13/2022] [Indexed: 02/07/2023]
Abstract
Stem cell therapy mainly uses natural stem cells for transplantation, and the use of genetic engineering to optimize stem cell products is a very important process. This article reviews successful gene modification methods in the field of immune cell therapy and summarizes some attempts at stem cell gene editing in current research. Cell bridging is an innovative cutting-edge strategy that includes the specific recognition and signal transduction of artificial receptors. The "off-the-shelf" cell strategies mainly introduce the advantages of allogeneic cell therapy and how to overcome issues such as immunogenicity. Gene regulatory systems allow us to manipulate cells with small molecules to control cellular phenotypes. In addition, we also summarize some important genes that can provide a reference for cell genetic engineering. In conclusion, we summarize a variety of technical strategies for gene editing cells to provide useful ideas and experiences for future stem cell therapy research.
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Affiliation(s)
- Siyu Li
- Department of Biochemistry and Molecular Biology, Harbin Medical University, 157 BaoJian Road Nangang Dist, Harbin, 150086, People's Republic of China
| | - Hao Tang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, People's Republic of China
| | - Cheng Li
- Department of Biochemistry and Molecular Biology, Harbin Medical University, 157 BaoJian Road Nangang Dist, Harbin, 150086, People's Republic of China
| | - Jiajia Ma
- Department of Biochemistry and Molecular Biology, Harbin Medical University, 157 BaoJian Road Nangang Dist, Harbin, 150086, People's Republic of China
| | - Maqsood Ali
- Department of Biochemistry and Molecular Biology, Harbin Medical University, 157 BaoJian Road Nangang Dist, Harbin, 150086, People's Republic of China
| | - Qi Dong
- Department of Biochemistry and Molecular Biology, Harbin Medical University, 157 BaoJian Road Nangang Dist, Harbin, 150086, People's Republic of China
| | - Jiajia Wu
- Department of Biochemistry and Molecular Biology, Harbin Medical University, 157 BaoJian Road Nangang Dist, Harbin, 150086, People's Republic of China
| | - Yang Hui
- Department of Biochemistry and Molecular Biology, Harbin Medical University, 157 BaoJian Road Nangang Dist, Harbin, 150086, People's Republic of China.
- Basic Medical Institute of Heilongjiang Medical Science Academy, Harbin, China.
| | - Chongran Sun
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, 866 Yuhangtang Road, Hangzhou City, Xihu District, 310058, People's Republic of China.
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Galvan S, Madderson O, Xue S, Teixeira AP, Fussenegger M. Regulation of Transgene Expression by the Natural Sweetener Xylose. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2203193. [PMID: 36316222 PMCID: PMC9731693 DOI: 10.1002/advs.202203193] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 09/15/2022] [Indexed: 06/16/2023]
Abstract
Next-generation gene and engineered-cell therapies benefit from incorporating synthetic gene networks that can precisely regulate the therapeutic output in response to externally administered signal inputs that are safe, readily bioavailable and pleasant to take. To enable such therapeutic control, a mammalian gene switch is designed to be responsive to the natural sweetener xylose and its functionality is assessed in mouse studies. The gene switch consists of the bacterial transcription regulator XylR fused to a mammalian transactivator, which binds to an optimized promoter in the presence of xylose, thereby allowing dose-dependent transgene expression. The sensitivity of SWEET (sweetener-inducible expression of transgene) is improved by coexpressing a xylose transporter. Mice implanted with encapsulated SWEET-engineered cells show increased blood levels of cargo protein when taking xylose-sweetened water or coffee, or highly concentrated apple extract, while they do not respond to intake of a usual amount of carrots, which contain xylose. In a proof-of-concept therapeutic application study, type-1 diabetic mice engineered with insulin-expressing SWEET show lowered glycemia and increased insulin levels when administered this fairly diabetic-compliant sweetener, compared to untreated mice. A SWEET-based therapy appears to have the potential to integrate seamlessly into patients' life-style and food habits in the move toward personalized medicine.
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Affiliation(s)
- Silvia Galvan
- Department of Biosystems Science and EngineeringETH ZurichMattenstrasse 26BaselCH‐4058Switzerland
| | - Oliver Madderson
- Department of Biosystems Science and EngineeringETH ZurichMattenstrasse 26BaselCH‐4058Switzerland
| | - Shuai Xue
- Department of Biosystems Science and EngineeringETH ZurichMattenstrasse 26BaselCH‐4058Switzerland
| | - Ana P. Teixeira
- Department of Biosystems Science and EngineeringETH ZurichMattenstrasse 26BaselCH‐4058Switzerland
| | - Martin Fussenegger
- Department of Biosystems Science and EngineeringETH ZurichMattenstrasse 26BaselCH‐4058Switzerland
- Faculty of Life ScienceUniversity of BaselMattenstrasse 26BaselCH‐4058Switzerland
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13
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Alhadid A, Bustanji Y, Harb A, Al-Hiari Y, Abdalla S. Vanillic Acid Inhibited the Induced Glycation Using In Vitro and In Vivo Models. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2022; 2022:7119256. [PMID: 36437826 PMCID: PMC9699731 DOI: 10.1155/2022/7119256] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 09/21/2022] [Accepted: 10/28/2022] [Indexed: 09/19/2023]
Abstract
BACKGROUND Glycation is implicated in the pathophysiology of many diseases, including diabetes, cancer, neurodegenerative diseases, and aging. Several natural and synthetic compounds were investigated for their antiglycation activity. We evaluated the antiglycation effect of vanillic acid (VA) using in vitro and in vivo experimental models. METHODS In vitro, bovine serum albumin (BSA) (50 mg/ml) was incubated with glucose (50 mM) with or without VA at 1.0-100 mM for 1 week at 37°C, and then, excitation/emission fluorescence was measured at 370/440 nm to determine glycation inhibition. The cytoprotective effect of VA was evaluated using RAW 264.7 cells incubated with or without VA at 7.8-500 μM along with 100-400 μM of methylglyoxal for 48 hours, and cell viability was determined using the MTT assay. Aminoguanidine (AMG) was used as a positive control in both in vitro and cell culture experiments. In vivo, 52 streptozotocin-induced diabetic rats were randomly assigned to 4 groups and treated with 0, 1.5, 4.5, or 15 mg/kg VA for four weeks. Serum fructosamine and blood glycosylated hemoglobin (HbA1c) were then measured, and advanced glycation end-products (AGEs) were detected in the kidneys and the skin of deboned tails using an immunohistochemistry assay. RESULTS VA caused a concentration-dependent effect against BSA glycation (IC50 of 45.53 mM vs. 5.09 mM for AMG). VA enhanced cell viability at all concentrations of VA and methylglyoxal. VA did not affect serum fructosamine or blood HbA1c levels, although it markedly decreased AGEs in the kidney in a dose-dependent manner and decreased AGEs in the skin of deboned tail tissues. CONCLUSION VA had significant antiglycation activity at cellular and long-term glycation.
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Affiliation(s)
- Amani Alhadid
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, Amman, Jordan
| | - Yasser Bustanji
- Department of Biopharmaceuticals and Clinical Pharmacy, School of Pharmacy, The University of Jordan, Amman 11942, Jordan
- Department of Basic Medical Sciences, College of Medicine, University of Sharjeh, Sharjeh 27272, UAE
| | - Amani Harb
- Department of Basic Sciences, Faculty of Arts and Sciences, Al-Ahliyya Amman University, Amman, Jordan
| | - Yusuf Al-Hiari
- Department of Pharmaceutical Sciences, School of Pharmacy, The University of Jordan, Amman 11942, Jordan
| | - Shtaywy Abdalla
- Department of Biological Sciences, School of Science, The University of Jordan, Amman 11942, Jordan
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Ackee (Blighia sapida K.D. Koenig) Leaves and Arils Methanolic Extracts Ameliorate CdCl2-Induced Oxidative Stress Biomarkers in Drosophila melanogaster. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:3235031. [DOI: 10.1155/2022/3235031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 09/19/2022] [Accepted: 10/15/2022] [Indexed: 11/15/2022]
Abstract
Different ethnomedical benefits have been documented on different parts of Ackee (Blighia sapida); however, their roles in ameliorating oxidative damages are not well established. CdCl2 inhibitory effects on some oxidative-stress biomarkers and ameliorative potentials of Ackee leaves (AL) and arils (AS) methanolic extracts were studied using Drosophila melanogaster as a model. One to 3-day-old D. melanogaster flies were orally exposed to different concentrations of CdCl2 in their diet for 7 days. The fly’s survival profile and negative geotaxis assays were subsequently analysed. Methanolic extracts of AL and AS treatments showed negative geotaxis behaviour, and extracts were able to ameliorate the effect of Cd2+ on catalase and GST activities and increase total thiol and GSH levels, while it reduced the H2O2 generation (
) when compared to the control. Furthermore, Cd2+ exhibited noncompetitive and uncompetitive enzyme inhibition on catalase and GST activities, respectively, which may have resulted in the formation of Enzyme-substrate-Cd2+ transition complexes, thus inhibiting the conversion of substrate to product. This study, thus, suggests that the Cd2+ mechanism of toxicity was associated with oxidative damage, as evidenced by the alteration in the oxidative stress-antioxidant imbalance, and that the AL and AS extracts possess essential phytochemicals that could alleviate possibly deleterious oxidative damage effects of environmental pollutants such as CdCl2. Thus, Ackee plant parts possess essential phytonutrients which could serve as valuable resources in heavy metal toxicity management.
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15
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Mansouri M, Ray PG, Franko N, Xue S, Fussenegger M. Design of programmable post-translational switch control platform for on-demand protein secretion in mammalian cells. Nucleic Acids Res 2022; 51:e1. [PMID: 36268868 PMCID: PMC9841418 DOI: 10.1093/nar/gkac916] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 09/11/2022] [Accepted: 10/20/2022] [Indexed: 01/29/2023] Open
Abstract
The development of novel strategies to program cellular behaviors is a central goal in synthetic biology, and post-translational control mediated by engineered protein circuits is a particularly attractive approach to achieve rapid protein secretion on demand. We have developed a programmable protease-mediated post-translational switch (POSH) control platform composed of a chimeric protein unit that consists of a protein of interest fused via a transmembrane domain to a cleavable ER-retention signal, together with two cytosolic inducer-sensitive split protease components. The protease components combine in the presence of the specific inducer to generate active protease, which cleaves the ER-retention signal, releasing the transmembrane-domain-linked protein for trafficking to the trans-Golgi region. A furin site placed downstream of the protein ensures cleavage and subsequent secretion of the desired protein. We show that stimuli ranging from plant-derived, clinically compatible chemicals to remotely controllable inducers such as light and electrostimulation can program protein secretion in various POSH-engineered designer mammalian cells. As proof-of-concept, an all-in-one POSH control plasmid encoding insulin and abscisic acid-activatable split protease units was hydrodynamically transfected into the liver of type-1 diabetic mice. Induction with abscisic acid attenuated glycemic excursions in glucose-tolerance tests. Increased blood levels of insulin were maintained for 12 days.
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Affiliation(s)
- Maysam Mansouri
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Preetam Guha Ray
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Nik Franko
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Shuai Xue
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Martin Fussenegger
- To whom correspondence should be addressed. Tel: +41 61 387 31 60; Fax: +41 61 387 39 88;
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Mechanisms and Therapeutic Effects of Benzoquinone Ring Analogs in Primary CoQ Deficiencies. Antioxidants (Basel) 2022; 11:antiox11040665. [PMID: 35453349 PMCID: PMC9029335 DOI: 10.3390/antiox11040665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 03/26/2022] [Accepted: 03/28/2022] [Indexed: 11/16/2022] Open
Abstract
Coenzyme Q (CoQ) is a conserved polyprenylated lipid composed of a redox-active benzoquinone ring and a long polyisoprenyl tail that serves as a membrane anchor. CoQ biosynthesis involves multiple steps, including multiple modifications of the precursor ring 4-hydroxybenzoic acid. Mutations in the enzymes involved in CoQ biosynthesis pathway result in primary coenzyme Q deficiencies, mitochondrial disorders whose clinical heterogenicity reflects the multiple biological function of CoQ. Patients with these disorders do not always respond to CoQ supplementation, and CoQ analogs have not been successful as alternative approaches. Progress made in understanding the CoQ biosynthesis pathway and studies of supplementation with 4-hydroxybenzoic acid ring analogs have opened a new area in the field of primary CoQ deficiencies treatment. Here, we will review these studies, focusing on efficacy of the different 4-hydroxybenzoic acid ring analogs, models in which they have been tested, and their mechanisms of action. Understanding how these compounds ameliorate biochemical, molecular, and/or clinical phenotypes of CoQ deficiencies is important to develop the most rational treatment for CoQ deficient patients, depending on their molecular defects.
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17
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Doshi A, Bandey I, Nevozhay D, Varadarajan N, Cirino PC. Design and characterization of a salicylic acid-inducible gene expression system for Jurkat cells. J Biotechnol 2022; 346:11-14. [PMID: 35051448 PMCID: PMC9618363 DOI: 10.1016/j.jbiotec.2022.01.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 12/11/2021] [Accepted: 01/13/2022] [Indexed: 11/29/2022]
Abstract
With continued progress in cell and gene therapies, there is an immediate need for exogenously tunable gene expression systems with safe and predictable behavior in specific human cell types. Here, we demonstrate the ability of the salicylic acid (SA)-inducible MarR repressor protein from Escherichia coli to regulate target gene expression in a human T lymphocyte cell line. Two lentiviral vectors, one encoding an enhanced green fluorescent protein (EGFP) reporter cassette and the other a repressor cassette, were sequentially transduced into Jurkat cells, using fluorescence-activated cell sorting (FACS) to isolate stable Jurkat progeny. As a result, EGFP expression was repressed by MarR and was inducible upon the addition of SA (~1.3 fold). This represents the first example of functional expression of bacterial MarR in mammalian cells, and opens the possibility for further development of regulated, SA-tunable gene expression system for T-cells.
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Affiliation(s)
- Aarti Doshi
- Dept. of Biology and Biochemistry, University of Houston, Houston, TX, USA.
| | - Irfan Bandey
- Dept. of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA.
| | - Dmitry Nevozhay
- Dept. of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; School of Biomedicine, Far Eastern Federal University, Vladivostok, Russia.
| | - Navin Varadarajan
- Dept. of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA.
| | - Patrick C. Cirino
- Dept. of Biology and Biochemistry, University of Houston, Houston, TX,Dept. of Chemical and Biomolecular Engineering, University of Houston, Houston, TX
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18
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Yu G, Zhang M, Gao L, Zhou Y, Qiao L, Yin J, Wang Y, Zhou J, Ye H. Far-red light-activated human islet-like designer cells enable sustained fine-tuned secretion of insulin for glucose control. Mol Ther 2022; 30:341-354. [PMID: 34530162 PMCID: PMC8753431 DOI: 10.1016/j.ymthe.2021.09.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 08/02/2021] [Accepted: 09/07/2021] [Indexed: 01/07/2023] Open
Abstract
Diabetes affects almost half a billion people, and all individuals with type 1 diabetes (T1D) and a large portion of individuals with type 2 diabetes rely on self-administration of the peptide hormone insulin to achieve glucose control. However, this treatment modality has cumbersome storage and equipment requirements and is susceptible to fatal user error. Here, reasoning that a cell-based therapy could be coupled to an external induction circuit for blood glucose control, as a proof of concept we developed far-red light (FRL)-activated human islet-like designer (FAID) cells and demonstrated how FAID cell implants achieved safe and sustained glucose control in diabetic model mice. Specifically, by introducing a FRL-triggered optogenetic device into human mesenchymal stem cells (hMSCs), which we encapsulated in poly-(l-lysine)-alginate and implanted subcutaneously under the dorsum of T1D model mice, we achieved FRL illumination-inducible secretion of insulin that yielded improvements in glucose tolerance and sustained blood glucose control over traditional insulin glargine treatment. Moreover, the FAID cell implants attenuated both oxidative stress and development of multiple diabetes-related complications in kidneys. This optogenetics-controlled "living cell factory" platform could be harnessed to develop multiple synthetic designer therapeutic cells to achieve long-term yet precisely controllable drug delivery.
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Affiliation(s)
- Guiling Yu
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Mingliang Zhang
- Department of Endocrinology and Metabolism, Shanghai Clinical Center for Diabetes, Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Ling Gao
- Department of Endocrinology, Renmin Hospital of Wuhan University, Wuhan 430061, China
| | - Yang Zhou
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Longliang Qiao
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Jianli Yin
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Yiwen Wang
- Electron Microscopy Center, School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Jian Zhou
- Department of Endocrinology and Metabolism, Shanghai Clinical Center for Diabetes, Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China.
| | - Haifeng Ye
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China.
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19
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Kemsawasd V, Chaikham P. Alteration of Bioactive Compounds and Antioxidative Properties in Thermal, Ultra-High Pressure and Ultrasound Treated Maoberry (Antidesma Bunius L.) Juice during Refrigerated Storage. CURRENT RESEARCH IN NUTRITION AND FOOD SCIENCE JOURNAL 2021. [DOI: 10.12944/crnfsj.9.3.17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Maoberry (Antidesma bunius L.) is a tropical fruit locally referred to as “Mao-Luang” in Thailand. The fruit contains high amounts of ascorbic acid and phenolic compounds with antioxidative potential, which has demonstrated medicinal value in terms of anti-cancer and anti-diabetic effects. In this term, this research purposed to determine the changes of predominant bioactive phytochemicals, antioxidant capacity and microbiological quality of pasteurized (85ºC/1 min), pressurized (500 and 600 MPa/30ºC/30 min), and ultra-sonicated (20 kHz/60% and 80% amplitude/30 min) maoberry juices during storage at 4°C for 30 days. The results displayed that ascorbic acid, phenolic acids (gallic and vanillic acids), anthocyanins (cyanidin 3-o-glucoside and cyanidin 3-rutinoside), flavonoids [(+)-catechin and (˗)-epicatechin), 2,2-diphenyl-1-picryl hydrazyl hydrate (DPPH) radical inhibition and ferric reducing antioxidant power (FRAP) value in pressurized and ultra-sonicated juices displayed higher reduction rate during storage than those in pasteurized juice. Nevertheless, at the final stage of storage, both juices still contained higher levels of antioxidant compounds and properties than in thermally treated juice. All the treated samples were shown to reduce initial microbial load of fresh maoberry juice to a non-detectable amount, while maintaining their quality during prolonged refrigerated storage.
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Affiliation(s)
- Varongsiri Kemsawasd
- 1Institute of Nutrition, Mahidol University, Nakorn Pathom Campus, Nakorn Pathom, Thailand
| | - Pittaya Chaikham
- 2Faculty of Science and Technology, Phranakhon Si Ayutthaya Rajabhat University, Phranakhon Si Ayutthay, Thailand
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20
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Gamez S, Vesga LC, Mendez-Sanchez SC, Akbari OS. Spatial control of gene expression in flies using bacterially derived binary transactivation systems. INSECT MOLECULAR BIOLOGY 2021; 30:461-471. [PMID: 33963794 PMCID: PMC8459377 DOI: 10.1111/imb.12717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 04/20/2021] [Accepted: 04/30/2021] [Indexed: 06/12/2023]
Abstract
Controlling gene expression is an instrumental tool for biotechnology, as it enables the dissection of gene function, affording precise spatial-temporal resolution. To generate this control, binary transactivational systems have been used employing a modular activator consisting of a DNA binding domain(s) fused to activation domain(s). For fly genetics, many binary transactivational systems have been exploited in vivo; however, as the study of complex problems often requires multiple systems that can be used in parallel, there is a need to identify additional bipartite genetic systems. To expand this molecular genetic toolbox, we tested multiple bacterially derived binary transactivational systems in Drosophila melanogaster including the p-CymR operon from Pseudomonas putida, PipR operon from Streptomyces coelicolor, TtgR operon from Pseudomonas putida and the VanR operon from Caulobacter crescentus. Our work provides the first characterization of these systems in an animal model in vivo. For each system, we demonstrate robust tissue-specific spatial transactivation of reporter gene expression, enabling future studies to exploit these transactivational systems for molecular genetic studies.
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Affiliation(s)
- Stephanie Gamez
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, California, USA
| | - Luis C. Vesga
- Group for Research in Biochemistry and Microbiology (Grupo de Investigación en Bioquímica Y Microbiología-GIBIM), School of Chemistry, Universidad Industrial de Santander, Bucaramanga, Colombia
| | - Stelia C. Mendez-Sanchez
- Group for Research in Biochemistry and Microbiology (Grupo de Investigación en Bioquímica Y Microbiología-GIBIM), School of Chemistry, Universidad Industrial de Santander, Bucaramanga, Colombia
| | - Omar S. Akbari
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, California, USA
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21
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Melguizo-Rodríguez L, de Luna-Bertos E, Ramos-Torrecillas J, Illescas-Montesa R, Costela-Ruiz VJ, García-Martínez O. Potential Effects of Phenolic Compounds That Can Be Found in Olive Oil on Wound Healing. Foods 2021; 10:1642. [PMID: 34359512 PMCID: PMC8307686 DOI: 10.3390/foods10071642] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/08/2021] [Accepted: 07/13/2021] [Indexed: 01/03/2023] Open
Abstract
The treatment of tissue damage produced by physical, chemical, or mechanical agents involves considerable direct and indirect costs to health care systems. Wound healing involves a series of molecular and cellular events aimed at repairing the defect in tissue integrity. These events can be favored by various natural agents, including the polyphenols in extra virgin olive oil (EVOO). The objective of this study was to review data on the potential effects of different phenolic compounds that can also be found in EVOO on wound healing and closure. Results of in vitro and animal studies demonstrate that polyphenols from different plant species, also present in EVOO, participate in different aspects of wound healing, accelerating this process through their anti-inflammatory, antioxidant, and antimicrobial properties and their stimulation of angiogenic activities required for granulation tissue formation and wound re-epithelialization. These results indicate the potential usefulness of EVOO phenolic compounds for wound treatment, either alone or in combination with other therapies. Human studies are warranted to verify this proposition.
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Affiliation(s)
- Lucia Melguizo-Rodríguez
- Biomedical Group (BIO277), Department of Nursing, Faculty of Health Sciences, University of Granada, Avda. Ilustración 60, 18016 Granada, Spain; (L.M.-R.); (E.d.L.-B.); (J.R.-T.); (R.I.-M.); (O.G.-M.)
- Institute of Biosanitary Research, ibs.Granada, C/Doctor Azpitarte 4, 4 planta, 18012 Granada, Spain
| | - Elvira de Luna-Bertos
- Biomedical Group (BIO277), Department of Nursing, Faculty of Health Sciences, University of Granada, Avda. Ilustración 60, 18016 Granada, Spain; (L.M.-R.); (E.d.L.-B.); (J.R.-T.); (R.I.-M.); (O.G.-M.)
- Institute of Biosanitary Research, ibs.Granada, C/Doctor Azpitarte 4, 4 planta, 18012 Granada, Spain
| | - Javier Ramos-Torrecillas
- Biomedical Group (BIO277), Department of Nursing, Faculty of Health Sciences, University of Granada, Avda. Ilustración 60, 18016 Granada, Spain; (L.M.-R.); (E.d.L.-B.); (J.R.-T.); (R.I.-M.); (O.G.-M.)
- Institute of Biosanitary Research, ibs.Granada, C/Doctor Azpitarte 4, 4 planta, 18012 Granada, Spain
| | - Rebeca Illescas-Montesa
- Biomedical Group (BIO277), Department of Nursing, Faculty of Health Sciences, University of Granada, Avda. Ilustración 60, 18016 Granada, Spain; (L.M.-R.); (E.d.L.-B.); (J.R.-T.); (R.I.-M.); (O.G.-M.)
- Institute of Biosanitary Research, ibs.Granada, C/Doctor Azpitarte 4, 4 planta, 18012 Granada, Spain
| | - Victor Javier Costela-Ruiz
- Biomedical Group (BIO277), Department of Nursing, Faculty of Health Sciences, University of Granada, Avda. Ilustración 60, 18016 Granada, Spain; (L.M.-R.); (E.d.L.-B.); (J.R.-T.); (R.I.-M.); (O.G.-M.)
- Institute of Biosanitary Research, ibs.Granada, C/Doctor Azpitarte 4, 4 planta, 18012 Granada, Spain
| | - Olga García-Martínez
- Biomedical Group (BIO277), Department of Nursing, Faculty of Health Sciences, University of Granada, Avda. Ilustración 60, 18016 Granada, Spain; (L.M.-R.); (E.d.L.-B.); (J.R.-T.); (R.I.-M.); (O.G.-M.)
- Institute of Biosanitary Research, ibs.Granada, C/Doctor Azpitarte 4, 4 planta, 18012 Granada, Spain
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22
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Haellman V, Saxena P, Jiang Y, Fussenegger M. Rational design and optimization of synthetic gene switches for controlling cell-fate decisions in pluripotent stem cells. Metab Eng 2021; 65:99-110. [PMID: 33744461 DOI: 10.1016/j.ymben.2021.03.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 02/25/2021] [Accepted: 03/09/2021] [Indexed: 11/26/2022]
Abstract
Advances in synthetic biology have enabled robust control of cell behavior by using tunable genetic circuits to regulate gene expression in a ligand-dependent manner. Such circuits can be used to direct the differentiation of pluripotent stem cells (PSCs) towards desired cell types, but rational design of synthetic gene circuits in PSCs is challenging due to the variable intracellular environment. Here, we provide a framework for implementing synthetic gene switches in PSCs based on combinations of tunable transcriptional, structural, and posttranslational elements that can be engineered as required, using the vanillic acid-controlled transcriptional activator (VanA) as a model system. We further show that the VanA system can be multiplexed with the well-established reverse tetracycline-controlled transcriptional activator (rtTA) system to enable independent control of the expression of different transcription factors in human induced PSCs in order to enhance lineage specification towards early pancreatic progenitors. This work represents a first step towards standardizing the design and construction of synthetic gene switches for building robust gene-regulatory networks to guide stem cell differentiation towards a desired cell fate.
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Affiliation(s)
- Viktor Haellman
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH, 4058, Basel, Switzerland
| | - Pratik Saxena
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH, 4058, Basel, Switzerland
| | - Yanrui Jiang
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH, 4058, Basel, Switzerland
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH, 4058, Basel, Switzerland; Faculty of Science, University of Basel, Mattenstrasse 26, CH, 4058, Basel, Switzerland.
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23
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Margesin R, Volgger G, Wagner AO, Zhang D, Poyntner C. Biodegradation of lignin monomers and bioconversion of ferulic acid to vanillic acid by Paraburkholderia aromaticivorans AR20-38 isolated from Alpine forest soil. Appl Microbiol Biotechnol 2021; 105:2967-2977. [PMID: 33687503 PMCID: PMC8007519 DOI: 10.1007/s00253-021-11215-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/10/2021] [Accepted: 02/28/2021] [Indexed: 11/24/2022]
Abstract
Abstract Lignin bio-valorization is an emerging field of applied biotechnology and has not yet been studied at low temperatures. Paraburkholderia aromaticivorans AR20-38 was examined for its potential to degrade six selected lignin monomers (syringic acid, p-coumaric acid, 4-hydroxybenzoic acid, ferulic acid, vanillic acid, benzoic acid) from different upper funneling aromatic pathways. The strain degraded four of these compounds at 10°C, 20°C, and 30°C; syringic acid and vanillic acid were not utilized as sole carbon source. The degradation of 5 mM and 10 mM ferulic acid was accompanied by the stable accumulation of high amounts of the value-added product vanillic acid (85–89% molar yield; 760 and 1540 mg l−1, respectively) over the whole temperature range tested. The presence of essential genes required for reactions in the upper funneling pathways was confirmed in the genome. This is the first report on biodegradation of lignin monomers and the stable vanillic acid production at low and moderate temperatures by P. aromaticivorans. Key points • Paraburkholderia aromaticivorans AR20-38 successfully degrades four lignin monomers. • Successful degradation study at low (10°C) and moderate temperatures (20–30°C). • Biotechnological value: high yield of vanillic acid produced from ferulic acid.
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Affiliation(s)
- Rosa Margesin
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria.
| | - Georg Volgger
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - Andreas O Wagner
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - Dechao Zhang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Caroline Poyntner
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
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Wang G, Møller-Hansen I, Babaei M, D'Ambrosio V, Christensen HB, Darbani B, Jensen MK, Borodina I. Transportome-wide engineering of Saccharomyces cerevisiae. Metab Eng 2021; 64:52-63. [PMID: 33465478 PMCID: PMC7970624 DOI: 10.1016/j.ymben.2021.01.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/16/2020] [Accepted: 01/10/2021] [Indexed: 12/17/2022]
Abstract
Synthetic biology enables the production of small molecules by recombinant microbes for pharma, food, and materials applications. The secretion of products reduces the cost of separation and purification, but it is challenging to engineer due to the limited understanding of the transporter proteins' functions. Here we describe a method for genome-wide transporter disruption that, in combination with a metabolite biosensor, enables the identification of transporters impacting the production of a given target metabolite in yeast Saccharomyces cerevisiae. We applied the method to study the transport of xenobiotic compounds, cis,cis-muconic acid (CCM), protocatechuic acid (PCA), and betaxanthins. We found 22 transporters that influenced the production of CCM or PCA. The transporter of the 12-spanner drug:H(+) antiporter (DHA1) family Tpo2p was further confirmed to import CCM and PCA in Xenopus expression assays. We also identified three transporter proteins (Qdr1p, Qdr2p, and Apl1p) involved in betaxanthins transport. In summary, the described method enables high-throughput transporter identification for small molecules in cell factories.
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Affiliation(s)
- Guokun Wang
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Iben Møller-Hansen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Mahsa Babaei
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Vasil D'Ambrosio
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Hanne Bjerre Christensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Behrooz Darbani
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Michael Krogh Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark.
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Page A, Fusil F, Cosset FL. Toward Tightly Tuned Gene Expression Following Lentiviral Vector Transduction. Viruses 2020; 12:v12121427. [PMID: 33322556 PMCID: PMC7764518 DOI: 10.3390/v12121427] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/05/2020] [Accepted: 12/08/2020] [Indexed: 12/12/2022] Open
Abstract
Lentiviral vectors are versatile tools for gene delivery purposes. While in the earlier versions of retroviral vectors, transgene expression was controlled by the long terminal repeats (LTRs), the latter generations of vectors, including those derived from lentiviruses, incorporate internal constitutive or regulated promoters in order to regulate transgene expression. This allows to temporally and/or quantitatively control transgene expression, which is required for many applications such as for clinical applications, when transgene expression is required in specific tissues and at a specific timing. Here we review the main systems that have been developed for transgene regulated expression following lentiviral gene transfer. First, the induction of gene expression can be triggered either by external or by internal cues. Indeed, these regulated vector systems may harbor promoters inducible by exogenous stimuli, such as small molecules (e.g., antibiotics) or temperature variations, offering the possibility to tune rapidly transgene expression in case of adverse events. Second, expression can be indirectly adjusted by playing on inserted sequence copies, for instance by gene excision. Finally, synthetic networks can be developed to sense specific endogenous signals and trigger defined responses after information processing. Regulatable lentiviral vectors (LV)-mediated transgene expression systems have been widely used in basic research to uncover gene functions or to temporally reprogram cells. Clinical applications are also under development to induce therapeutic molecule secretion or to implement safety switches. Such regulatable approaches are currently focusing much attention and will benefit from the development of other technologies in order to launch autonomously controlled systems.
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26
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Khalil A, Tazeddinova D. The upshot of Polyphenolic compounds on immunity amid COVID-19 pandemic and other emerging communicable diseases: An appraisal. NATURAL PRODUCTS AND BIOPROSPECTING 2020; 10:411-429. [PMID: 33057955 PMCID: PMC7558243 DOI: 10.1007/s13659-020-00271-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 10/06/2020] [Indexed: 05/15/2023]
Abstract
Polyphenols are a large family of more than 10,000 naturally occurring compounds, which exert countless pharmacological, biological and physiological benefits for human health including several chronic diseases such as cancer, diabetes, cardiovascular, and neurological diseases. Their role in traditional medicine, such as the use of a wide range of remedial herbs (thyme, oregano, rosemary, sage, mint, basil), has been well and long known for treating common respiratory problems and cold infections. This review reports on the most highlighted polyphenolic compounds present in up to date literature and their specific antiviral perceptive properties that might enhance the body immunity facing COVID-19, and other viral infectious diseases. In fact, several studies and clinical trials increasingly proved the role of polyphenols in controlling numerous human pathogens including SARS and MERS, which are quite similar to COVID-19 through the enhancement of host immune response against viral infections by different biological mechanisms. Thus, polyphenols ought to be considered as a potential and valuable source for designing new drugs that could be used effectively in the combat against COVID-19 and other rigorous diseases.
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Affiliation(s)
- Ayman Khalil
- Department of Food Technology, South Ural State University, Chelyabinsk, Russian Federation
| | - Diana Tazeddinova
- Department of Food Technology, South Ural State University, Chelyabinsk, Russian Federation
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Suzuki S, Ohta KI, Nakajima Y, Shigeto H, Abe H, Kawai A, Miura R, Kazuki Y, Oshimura M, Miki T. Meganuclease-Based Artificial Transcription Factors. ACS Synth Biol 2020; 9:2679-2691. [PMID: 32907319 DOI: 10.1021/acssynbio.0c00083] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Embedding middle-scale artificial gene networks in live mammalian cells is one of the most important future goals for cell engineering. However, the applications of the highly orthogonal and conventional artificial transcription factors currently available are limited. In this study, we present a scalable pipeline to produce artificial transcription factors based on homing endonucleases, also known as meganucleases. The introduction of mutations at critical sites for nuclease activity renders these homing endonucleases a simple but highly specific DNA binding domain for their specific DNA target. The introduction of inactivated meganucleases linked to transcriptional activator domains strongly induced reporter gene expression, while their fusion to transcriptional repressor domains suppressed them. In addition, we show that inactivated meganuclease-based transcription factors could be embedded in the synthetic membrane receptor synNotch and used to construct synthetic circuits. These results suggest that inactivated meganucleases are useful DNA-binding domains for the construction of synthetic transcription factors in mammalian cells.
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Affiliation(s)
- Shingo Suzuki
- Department of Anatomy and Neurobiology, Faculty of Medicine, Kagawa University, Miki-cho, Kagawa 761-0793, Japan
| | - Ken-ichi Ohta
- Department of Anatomy and Neurobiology, Faculty of Medicine, Kagawa University, Miki-cho, Kagawa 761-0793, Japan
| | - Yoshihiro Nakajima
- Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Takamatsu, Kagawa 761-0395, Japan
| | - Hajime Shigeto
- Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Takamatsu, Kagawa 761-0395, Japan
| | - Hiroko Abe
- Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Takamatsu, Kagawa 761-0395, Japan
| | - Anna Kawai
- Department of Anatomy and Neurobiology, Faculty of Medicine, Kagawa University, Miki-cho, Kagawa 761-0793, Japan
| | - Ryuichiro Miura
- Department of Anatomy and Neurobiology, Faculty of Medicine, Kagawa University, Miki-cho, Kagawa 761-0793, Japan
| | - Yasuhiro Kazuki
- Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science, Chromosome Engineering Research Center, Tottori University, Yonago, 683-8503, Japan
| | - Mitsuo Oshimura
- Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science, Chromosome Engineering Research Center, Tottori University, Yonago, 683-8503, Japan
| | - Takanori Miki
- Department of Anatomy and Neurobiology, Faculty of Medicine, Kagawa University, Miki-cho, Kagawa 761-0793, Japan
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28
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Zúñiga A, Guiziou S, Mayonove P, Meriem ZB, Camacho M, Moreau V, Ciandrini L, Hersen P, Bonnet J. Rational programming of history-dependent logic in cellular populations. Nat Commun 2020; 11:4758. [PMID: 32958811 PMCID: PMC7506022 DOI: 10.1038/s41467-020-18455-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 07/24/2020] [Indexed: 12/16/2022] Open
Abstract
Genetic programs operating in a history-dependent fashion are ubiquitous in nature and govern sophisticated processes such as development and differentiation. The ability to systematically and predictably encode such programs would advance the engineering of synthetic organisms and ecosystems with rich signal processing abilities. Here we implement robust, scalable history-dependent programs by distributing the computational labor across a cellular population. Our design is based on standardized recombinase-driven DNA scaffolds expressing different genes according to the order of occurrence of inputs. These multicellular computing systems are highly modular, do not require cell-cell communication channels, and any program can be built by differential composition of strains containing well-characterized logic scaffolds. We developed automated workflows that researchers can use to streamline program design and optimization. We anticipate that the history-dependent programs presented here will support many applications using cellular populations for material engineering, biomanufacturing and healthcare.
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Affiliation(s)
- Ana Zúñiga
- Centre de Biochimie Structurale (CBS), INSERM U154, CNRS UMR5048, University of Montpellier, Montpellier, France
| | - Sarah Guiziou
- Centre de Biochimie Structurale (CBS), INSERM U154, CNRS UMR5048, University of Montpellier, Montpellier, France
- Department of Biology, University of Washington, Seattle, WA, 98195, USA
| | - Pauline Mayonove
- Centre de Biochimie Structurale (CBS), INSERM U154, CNRS UMR5048, University of Montpellier, Montpellier, France
| | - Zachary Ben Meriem
- Laboratoire Matière et Systèmes Complexes, UMR 7057 CNRS & Université Paris Diderot, 10 rue Alice Domon et Léonie Duquet, 75013, Paris, France
| | - Miguel Camacho
- Centre de Biochimie Structurale (CBS), INSERM U154, CNRS UMR5048, University of Montpellier, Montpellier, France
| | - Violaine Moreau
- Centre de Biochimie Structurale (CBS), INSERM U154, CNRS UMR5048, University of Montpellier, Montpellier, France
| | - Luca Ciandrini
- Centre de Biochimie Structurale (CBS), INSERM U154, CNRS UMR5048, University of Montpellier, Montpellier, France
- Laboratoire Charles Coulomb (L2C), University of Montpellier & CNRS, Montpellier, France
| | - Pascal Hersen
- Laboratoire Matière et Systèmes Complexes, UMR 7057 CNRS & Université Paris Diderot, 10 rue Alice Domon et Léonie Duquet, 75013, Paris, France
- Laboratoire Physico Chimie Curie, UMR168, Institut Curie, Paris, France
| | - Jerome Bonnet
- Centre de Biochimie Structurale (CBS), INSERM U154, CNRS UMR5048, University of Montpellier, Montpellier, France.
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Yin J, Yang L, Mou L, Dong K, Jiang J, Xue S, Xu Y, Wang X, Lu Y, Ye H. A green tea-triggered genetic control system for treating diabetes in mice and monkeys. Sci Transl Med 2020; 11:11/515/eaav8826. [PMID: 31645456 DOI: 10.1126/scitranslmed.aav8826] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 05/20/2019] [Accepted: 08/27/2019] [Indexed: 12/11/2022]
Abstract
Cell-based therapies are recognized as the next frontier in medicine, but the translation of many promising technologies into the clinic is currently limited by a lack of remote-control inducers that are safe and can be tightly regulated. Here, we developed therapeutically active engineered cells regulated by a control system that is responsive to protocatechuic acid (PCA), a metabolite found in green tea. We constructed multiple genetic control technologies that could toggle a PCA-responsive ON/OFF switch based on a transcriptional repressor from Streptomyces coelicolor We demonstrated that PCA-controlled switches can be used for guide RNA expression-mediated control of the CRISPR-Cas9 systems for gene editing and epigenetic remodeling. We showed how these technologies could be used as implantable biocomputers in live mice to perform complex logic computations that integrated signals from multiple food metabolites. Last, we used our system to treat type 1 and type 2 diabetes in mice and cynomolgus monkeys. This biocompatible and versatile food phenolic acid-controlled transgenic device opens opportunities for dynamic interventions in gene- and cell-based precision medicine.
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Affiliation(s)
- Jianli Yin
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Linfeng Yang
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Lisha Mou
- Shenzhen Xenotransplantation Medical Engineering Research and Development Center, Institute of Translational Medicine, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong 518035, China
| | - Kaili Dong
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Jian Jiang
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Shuai Xue
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Ying Xu
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Xinyi Wang
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Ying Lu
- Shenzhen Xenotransplantation Medical Engineering Research and Development Center, Institute of Translational Medicine, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong 518035, China
| | - Haifeng Ye
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China.
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30
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Regulatory control circuits for stabilizing long-term anabolic product formation in yeast. Metab Eng 2020; 61:369-380. [DOI: 10.1016/j.ymben.2020.07.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 07/02/2020] [Accepted: 07/14/2020] [Indexed: 12/12/2022]
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Doshi A, Sadeghi F, Varadarajan N, Cirino PC. Small-molecule inducible transcriptional control in mammalian cells. Crit Rev Biotechnol 2020; 40:1131-1150. [PMID: 32862714 DOI: 10.1080/07388551.2020.1808583] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Tools for tuning transcription in mammalian cells have broad applications, from basic biological discovery to human gene therapy. While precise control over target gene transcription via dosing with small molecules (drugs) is highly sought, the design of such inducible systems that meets required performance metrics poses a great challenge in mammalian cell synthetic biology. Important characteristics include tight and tunable gene expression with a low background, minimal drug toxicity, and orthogonality. Here, we review small-molecule-inducible transcriptional control devices that have demonstrated success in mammalian cells and mouse models. Most of these systems employ natural or designed ligand-binding protein domains to directly or indirectly communicate with transcription machinery at a target sequence, via carefully constructed fusions. Example fusions include those to transcription activator-like effectors (TALEs), DNA-targeting proteins (e.g. dCas systems) fused to transactivating domains, and recombinases. Similar to the architecture of Type I nuclear receptors, many of the systems are designed such that the transcriptional controller is excluded from the nucleus in the absence of an inducer. Techniques that use ligand-induced proteolysis and antibody-based chemically induced dimerizers are also described. Collectively, these transcriptional control devices take advantage of a variety of recently developed molecular biology tools and cell biology insights and represent both proof of concept (e.g. targeting reporter gene expression) and disease-targeting studies.
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Affiliation(s)
- Aarti Doshi
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Fatemeh Sadeghi
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Navin Varadarajan
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Patrick C Cirino
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA.,Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
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MIRZA AC, PANCHAL SS. Safety Assessment of Vanillic Acid: Subacute Oral Toxicity Studies in Wistar Rats. Turk J Pharm Sci 2020; 17:432-439. [PMID: 32939140 PMCID: PMC7489355 DOI: 10.4274/tjps.galenos.2019.92678] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 05/30/2019] [Indexed: 01/07/2023]
Abstract
OBJECTIVES Vanillic acid (VA) is a flavoring agent, a phenolic acid, and an intermediary by-product formed during transformation of ferulic acid to vanillin. It has been investigated for diverse pharmacological actions and used in Chinese medicine for decades. However, there is no information in the literature about its mechanism of toxicity or safety with long-term use. The present study will not only supply information on its pharmacological profile but also encourage evidence-based pharmacotherapeutic use. Hence, we performed a subacute toxicity study. MATERIALS AND METHODS According to the Organisation for Economic Co-operation and Development Test Guideline 407 (2008), 3 groups of rats were formed consisting of 12 rats (6 male and 6 female) in each group. For the subacute toxicity, the dose was chosen after a limit test was conducted. VA (1000 mg/kg/day) was orally administered for 2 weeks to the treatment group, whereas the control group received an equivalent volume of the vehicle. To assess reversibility, VA (1000 mg/kg/day, p.o.) was administered to the satellite group for 2 weeks and animals were observed for an additional 2 weeks after treatment. The adverse signs, variation in body weight, and mortality were evaluated throughout the study period. On days 15 and 29, blood was collected to evaluate essential biochemical and hematological parameters. The animals were subsequently weighed and sacrificed. The weights of internal organs were recorded; gross necroscopy and histopathological studies were performed. RESULTS The hematological parameters of the satellite group increased and the serum sodium level decreased after the treatment. Satellite groups showed no other major change in biochemical parameters when compared to the control group. In addition, relative organ weights, gross necropsy examinations and histopathological structure of the internal organs showed no major alterations. CONCLUSION VA showed no adverse effect on the process of leukopoiesis, erythropoiesis or on internal organs, as verified by hematological and biochemical evaluations, gross necropsy, and histopathological studies. The decrease in serum sodium is not considered as a major toxic effect.
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Affiliation(s)
- Anwarbaig Chandbaig MIRZA
- Anjuman-i-Islams’s Kalsekar Technical Campus, School of Pharmacy, Department of Pharmacology, Navi Mumbai, India
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Wang Y, Liao S, Guan N, Liu Y, Dong K, Weber W, Ye H. A versatile genetic control system in mammalian cells and mice responsive to clinically licensed sodium ferulate. SCIENCE ADVANCES 2020; 6:eabb9484. [PMID: 32821842 PMCID: PMC7413729 DOI: 10.1126/sciadv.abb9484] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/26/2020] [Indexed: 05/11/2023]
Abstract
Dynamically adjustable gene- and cell-based therapies are recognized as next-generation medicine. However, the translation of precision therapies into clinics is limited by lack of specific switches controlled by inducers that are safe and ready for clinical use. Ferulic acid (FA) is a phytochemical with a wide range of therapeutic effects, and its salt sodium ferulate (SF) is used as an antithrombotic drug in clinics. Here, we describe an FA/SF-adjustable transcriptional switch controlled by the clinically licensed drug SF. We demonstrated that SF-responsive switches can be engineered to control CRISPR-Cas9 systems for on-command genome/epigenome engineering. In addition, we integrated FA-controlled switches into programmable biocomputers to process logic operations. We further demonstrated the dose-dependent SF-inducible transgene expression in mice by oral administration of SF tablets. Engineered switches responsive to small-molecule clinically licensed drugs to achieve adjustable transgene expression profiles provide new opportunities for dynamic interventions in gene- and cell-based precision medicine.
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Affiliation(s)
- Yidan Wang
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Shuyong Liao
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Ningzi Guan
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Yuanxiao Liu
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Kaili Dong
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Wilfried Weber
- Faculty of Biology, and Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg im Breisgau, Germany
| | - Haifeng Ye
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
- Corresponding author.
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Krawczyk K, Xue S, Buchmann P, Charpin-El-Hamri G, Saxena P, Hussherr MD, Shao J, Ye H, Xie M, Fussenegger M. Electrogenetic cellular insulin release for real-time glycemic control in type 1 diabetic mice. Science 2020; 368:993-1001. [DOI: 10.1126/science.aau7187] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 02/11/2020] [Accepted: 04/03/2020] [Indexed: 12/11/2022]
Abstract
Sophisticated devices for remote-controlled medical interventions require an electrogenetic interface that uses digital electronic input to directly program cellular behavior. We present a cofactor-free bioelectronic interface that directly links wireless-powered electrical stimulation of human cells to either synthetic promoter–driven transgene expression or rapid secretion of constitutively expressed protein therapeutics from vesicular stores. Electrogenetic control was achieved by coupling ectopic expression of the L-type voltage-gated channel CaV1.2 and the inwardly rectifying potassium channel Kir2.1 to the desired output through endogenous calcium signaling. Focusing on type 1 diabetes, we engineered electrosensitive human β cells (Electroβ cells). Wireless electrical stimulation of Electroβ cells inside a custom-built bioelectronic device provided real-time control of vesicular insulin release; insulin levels peaked within 10 minutes. When subcutaneously implanted, this electrotriggered vesicular release system restored normoglycemia in type 1 diabetic mice.
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Affiliation(s)
- Krzysztof Krawczyk
- Department of Biosystems Science and Engineering, ETH Zurich, CH-4058 Basel, Switzerland
| | - Shuai Xue
- Department of Biosystems Science and Engineering, ETH Zurich, CH-4058 Basel, Switzerland
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, People’s Republic of China
| | - Peter Buchmann
- Department of Biosystems Science and Engineering, ETH Zurich, CH-4058 Basel, Switzerland
| | - Ghislaine Charpin-El-Hamri
- Département Génie Biologique, Institut Universitaire de Technologie Lyon 1, F-69622 Villeurbanne Cedex, France
| | - Pratik Saxena
- Department of Biosystems Science and Engineering, ETH Zurich, CH-4058 Basel, Switzerland
| | - Marie-Didiée Hussherr
- Department of Biosystems Science and Engineering, ETH Zurich, CH-4058 Basel, Switzerland
| | - Jiawei Shao
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, People’s Republic of China
- Key Laboratory of Growth Regulation and Transformation Research of Zheijang Province, School of Life Sciences, Westlake University, Hangzhou, People’s Republic of China
| | - Haifeng Ye
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, People’s Republic of China
| | - Mingqi Xie
- Department of Biosystems Science and Engineering, ETH Zurich, CH-4058 Basel, Switzerland
- Key Laboratory of Growth Regulation and Transformation Research of Zheijang Province, School of Life Sciences, Westlake University, Hangzhou, People’s Republic of China
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, CH-4058 Basel, Switzerland
- Faculty of Science, University of Basel, CH-4058 Basel, Switzerland
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35
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Vanillic Acid Alleviates Acute Myocardial Hypoxia/Reoxygenation Injury by Inhibiting Oxidative Stress. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2020; 2020:8348035. [PMID: 32377308 PMCID: PMC7191373 DOI: 10.1155/2020/8348035] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 03/23/2020] [Indexed: 02/07/2023]
Abstract
Oxidative stress is an important factor of myocardial hypoxia/reoxygenation (H/R) injury. Our research focuses on how to reduce the cardiac toxicity caused by oxidative stress through natural plant extracts. Vanillic acid (VA) is a phenolic compound found in edible plants and rich in the roots of Angelica sinensis. Experimental studies have provided evidence for this compound's effectiveness in cardiovascular diseases; however, its mechanism is still unclear. In this study, molecular mechanisms related to the protective effects of VA were investigated in H9c2 cells in the context of H/R injury. The results showed that pretreatment with VA significantly increased cell viability and decreased the percentage of apoptotic cells, as well as lactate dehydrogenase and creatine phosphokinase activity, in the supernatant, accompanied by reduced levels of reactive oxygen species and reduced caspase-3 activity. VA pretreatment also restored mitochondrial membrane potentials. Moreover, preincubation with VA significantly attenuated mitochondrial permeability transition pore activity. VA administration upregulated adenosine monophosphate-activated protein kinase α2 (AMPKα2) protein expression, and interestingly, pretreatment with AMPKα2-siRNA lentivirus effectively attenuated the cardioprotective effects of VA in response to H/R injury.
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36
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Ambri F, D’Ambrosio V, Di Blasi R, Maury J, Jacobsen SAB, McCloskey D, Jensen MK, Keasling JD. High-Resolution Scanning of Optimal Biosensor Reporter Promoters in Yeast. ACS Synth Biol 2020; 9:218-226. [PMID: 31935067 DOI: 10.1021/acssynbio.9b00333] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Small-molecule binding allosteric transcription factors (aTFs) derived from bacteria enable real-time monitoring of metabolite abundances, high-throughput screening of genetic designs, and dynamic control of metabolism. Yet, engineering of reporter promoter designs of prokaryotic aTF biosensors in eukaryotic cells is complex. Here we investigate the impact of aTF binding site positions at single-nucleotide resolution in >300 reporter promoter designs in Saccharomyces cerevisiae. From this we identify biosensor output landscapes with transient and distinct aTF binding site position effects for aTF repressors and activators, respectively. Next, we present positions for tunable reporter promoter outputs enabling metabolite-responsive designs for a total of four repressor-type and three activator-type aTF biosensors with dynamic output ranges up to 8- and 26-fold, respectively. This study highlights aTF binding site positions in reporter promoters as key for successful biosensor engineering and that repressor-type aTF biosensors allows for more flexibility in terms of choice of binding site positioning compared to activator-type aTF biosensors.
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Affiliation(s)
- Francesca Ambri
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - Vasil D’Ambrosio
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - Roberto Di Blasi
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - Jerome Maury
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | | | - Douglas McCloskey
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - Michael K. Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - Jay. D Keasling
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Chemical and Biomolecular Engineering & Department of Bioengineering, University of California, Berkeley, California 94720, United States
- Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes of Advanced Technologies, Shenzhen 518055, China
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37
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Bayrak S, Öztürk C, Demir Y, Alım Z, Küfrevioglu Öİ. Purification of Polyphenol Oxidase from Potato and Investigation of the Inhibitory Effects of Phenolic Acids on Enzyme Activity. Protein Pept Lett 2020; 27:187-192. [DOI: 10.2174/0929866526666191002142301] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 08/27/2019] [Accepted: 08/28/2019] [Indexed: 11/22/2022]
Abstract
Background:
Polyphenol Oxidase (PPO) belongs to the oxidoreductase enzyme family.
Methods:
Here, PPO was purified from potato using Sepharose 4B-L-tyrosine-p-aminobenzoic acid
affinity chromatography. It determined the interactions between some phenolic acids and the
enzyme.
Results:
The enzyme was obtained with a specific activity of 15333.33 EU/mg protein and 7.87-
fold purification. It was found that phenolic acids exhibited inhibitory properties for PPO. The IC50
values of the phenolic acids were found in the range of 0.36-2.12 mM, and their Ki values were
found in the range of 0.28± 0.07-1.72±0.32 mM. It was determined that all studied compounds
displayed a competitive inhibition effect. Among these compounds, 3-hydroxybenzoic acid was
found to be the most effective PPO inhibitor (Ki: 0.28±0.07 mM).
Conclusion:
Investigating the inhibition kinetics of the enzyme will simplify the testing of PPO
inhibitor candidates.
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Affiliation(s)
- Songül Bayrak
- Department of Chemistry, Faculty of Sciences, Ataturk University, Erzurum, 25240, Turkey
| | - Cansu Öztürk
- Department of Chemistry, Faculty of Sciences, Ataturk University, Erzurum, 25240, Turkey
| | - Yeliz Demir
- Department of Pharmacy Services, Nihat Delibalta Göle Vocational High School, Ardahan University, Ardahan, 75700, Turkey
| | - Zuhal Alım
- Department of Chemistry, Faculty of Science and Arts, Ahievran University, Kırsehir, 40100, Turkey
| | - Ömer İrfan Küfrevioglu
- Department of Chemistry, Faculty of Sciences, Ataturk University, Erzurum, 25240, Turkey
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38
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D'Ambrosio V, Pramanik S, Goroncy K, Jakočiūnas T, Schönauer D, Davari MD, Schwaneberg U, Keasling JD, Jensen MK. Directed evolution of VanR biosensor specificity in yeast. ACTA ACUST UNITED AC 2020. [DOI: 10.1016/j.biotno.2020.01.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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39
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Vanillic Acid Restores Coenzyme Q Biosynthesis and ATP Production in Human Cells Lacking COQ6. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:3904905. [PMID: 31379988 PMCID: PMC6652073 DOI: 10.1155/2019/3904905] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 04/30/2019] [Accepted: 05/26/2019] [Indexed: 11/18/2022]
Abstract
Coenzyme Q (CoQ), a redox-active lipid, is comprised of a quinone group and a polyisoprenoid tail. It is an electron carrier in the mitochondrial respiratory chain, a cofactor of other mitochondrial dehydrogenases, and an essential antioxidant. CoQ requires a large set of enzymes for its biosynthesis; mutations in genes encoding these proteins cause primary CoQ deficiency, a clinically and genetically heterogeneous group of diseases. Patients with CoQ deficiency often respond to oral CoQ10 supplementation. Treatment is however problematic because of the low bioavailability of CoQ10 and the poor tissue delivery. In recent years, bypass therapy using analogues of the precursor of the aromatic ring of CoQ has been proposed as a promising alternative. We have previously shown using a yeast model that vanillic acid (VA) can bypass mutations of COQ6, a monooxygenase required for the hydroxylation of the C5 carbon of the ring. In this work, we have generated a human cell line lacking functional COQ6 using CRISPR/Cas9 technology. We show that these cells cannot synthesize CoQ and display severe ATP deficiency. Treatment with VA can recover CoQ biosynthesis and ATP production. Moreover, these cells display increased ROS production, which is only partially corrected by exogenous CoQ, while VA restores ROS to normal levels. Furthermore, we show that these cells accumulate 3-decaprenyl-1,4-benzoquinone, suggesting that in mammals, the decarboxylation and C1 hydroxylation reactions occur before or independently of the C5 hydroxylation. Finally, we show that COQ6 isoform c (transcript NM_182480) does not encode an active enzyme. VA can be produced in the liver by the oxidation of vanillin, a nontoxic compound commonly used as a food additive, and crosses the blood-brain barrier. These characteristics make it a promising compound for the treatment of patients with CoQ deficiency due to COQ6 mutations.
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40
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Vieira J, Mantovani R, Raposo M, Coimbra M, Vicente A, Cunha R. Effect of extraction temperature on rheological behavior and antioxidant capacity of flaxseed gum. Carbohydr Polym 2019; 213:217-227. [DOI: 10.1016/j.carbpol.2019.02.078] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 02/21/2019] [Accepted: 02/21/2019] [Indexed: 01/20/2023]
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41
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Bojar D, Fussenegger M. Programming mammalian gene expression with the antibiotic simocyclinone D8 and the flavonoid luteolin. AIChE J 2018. [DOI: 10.1002/aic.16365] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Daniel Bojar
- Dept. of Biosystems Science and Engineering; ETH Zurich; Basel Switzerland
| | - Martin Fussenegger
- Dept. of Biosystems Science and Engineering; ETH Zurich; Basel Switzerland
- Faculty of Science; University of Basel; Basel Switzerland
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42
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Weisenberger MS, Deans TL. Bottom-up approaches in synthetic biology and biomaterials for tissue engineering applications. J Ind Microbiol Biotechnol 2018; 45:599-614. [PMID: 29552703 PMCID: PMC6041164 DOI: 10.1007/s10295-018-2027-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Accepted: 03/11/2018] [Indexed: 12/30/2022]
Abstract
Synthetic biologists use engineering principles to design and construct genetic circuits for programming cells with novel functions. A bottom-up approach is commonly used to design and construct genetic circuits by piecing together functional modules that are capable of reprogramming cells with novel behavior. While genetic circuits control cell operations through the tight regulation of gene expression, a diverse array of environmental factors within the extracellular space also has a significant impact on cell behavior. This extracellular space offers an addition route for synthetic biologists to apply their engineering principles to program cell-responsive modules within the extracellular space using biomaterials. In this review, we discuss how taking a bottom-up approach to build genetic circuits using DNA modules can be applied to biomaterials for controlling cell behavior from the extracellular milieu. We suggest that, by collectively controlling intrinsic and extrinsic signals in synthetic biology and biomaterials, tissue engineering outcomes can be improved.
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Affiliation(s)
| | - Tara L Deans
- Department of Bioengineering, University of Utah, Salt Lake City, UT, 84112, USA.
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43
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Programmable full-adder computations in communicating three-dimensional cell cultures. Nat Methods 2017; 15:57-60. [DOI: 10.1038/nmeth.4505] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 10/04/2017] [Indexed: 02/07/2023]
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44
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Alim Z, Kilinç N, Şengül B, Beydemir Ş. Inhibition behaviours of some phenolic acids on rat kidney aldose reductase enzyme: an in vitro study. J Enzyme Inhib Med Chem 2017; 32:277-284. [PMID: 28111996 PMCID: PMC6009866 DOI: 10.1080/14756366.2016.1250752] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 10/07/2016] [Accepted: 10/11/2016] [Indexed: 12/17/2022] Open
Abstract
Aldose reductase (AR) inhibitors have vital importance in the treatment and prevention of diabetic complications. In this study, rat kidney AR was purified 19.34-fold with a yield of 3.49% and a specific activity of 0.88 U/mg using DE-52 Cellulose anion exchange chromatography, gel filtration chromatography and 2'5' ADP Sepharose-4B affinity chromatography, respectively. After purification, the in vitro inhibition effects of some phenolic acids (tannic acid, chlorogenic acid, sinapic acid, protocatechuic acid, 4-hydroxybenzoic acid, p-coumaric acid, ferulic acid, vanillic acid, syringic acid, α-resorcylic acid, 3-hydroxybenzoic acid and gallic acid) were investigated on purified enzyme. We determined IC50, Ki values and inhibition types of these phenolic acids. As a result, tannic and chlorogenic acid had a strong inhibition effect. On the other hand, gallic acid had a weak inhibition effect. In this study, all phenolic acids except for chlorogenic acid and p-coumaric acid showed non-competitive inhibition effects on rat kidney AR.
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Affiliation(s)
- Zuhal Alim
- Department of Chemistry, Faculty of Science and Arts, Ahi Evran University, Kirşehir, Turkey
| | - Namik Kilinç
- Department of Medical Services and Techniques, Vocational School of Health Service, Iğdir University, Iğdir, Turkey
| | - Bülent Şengül
- Deparment of Health Care Service, Vocational School of Health Service, Bayburt University, Bayburt, Turkey
| | - Şükrü Beydemir
- Department of Chemistry, Faculty of Sciences, Atatürk University, Erzurum, Turkey
- Department of Biochemistry, Faculty of Pharmacy, Anadolu University, Eskişehir, Turkey
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45
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Wang Y, Wang M, Dong K, Ye H. Engineering Mammalian Designer Cells for the Treatment of Metabolic Diseases. Biotechnol J 2017; 13:e1700160. [PMID: 29144600 DOI: 10.1002/biot.201700160] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 11/03/2017] [Indexed: 12/22/2022]
Abstract
Synthetic biology applies engineering principles to biological systems and has significantly advanced the design of synthetic gene circuits that can reprogram cell activities to perform new functions. The ability to engineer mammalian designer cells with robust therapeutic behaviors has brought new opportunities for treating metabolic diseases. In this review, the authors highlight the most recent advances in the development of synthetic designer cells uploaded with open- or closed-loop gene circuits for the treatment of metabolic disorders including diabetes, hypertension, hyperuricemia, and obesity, and discuss the current technologies and future perspectives in applying these designer cells for clinical applications. In the future, more and more rationally designed cells will be constructed and revolutionized to treat a number of metabolic disorders in an intelligent manner.
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Affiliation(s)
- Yidan Wang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Meiyan Wang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Kaili Dong
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Haifeng Ye
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
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46
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Fitzgerald M, Gibbs C, Shimpi AA, Deans TL. Adoption of the Q Transcriptional System for Regulating Gene Expression in Stem Cells. ACS Synth Biol 2017; 6:2014-2020. [PMID: 28776984 DOI: 10.1021/acssynbio.7b00149] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The field of mammalian synthetic biology seeks to engineer enabling technologies to create novel approaches for programming cells to probe, perturb, and regulate gene expression with unprecedented precision. To accomplish this, new genetic parts continue to be identified that can be used to build novel genetic circuits to re-engineer cells to perform specific functions. Here, we establish a new transcription-based genetic circuit that combines genes from the quinic acid sensing metabolism of Neorospora crassa and the bacterial Lac repressor system to create a new orthogonal genetic tool to be used in mammalian cells. This work establishes a novel genetic tool, called LacQ, that functions to regulate gene expression in Chinese hamster ovarian (CHO) cells, human embryonic kidney 293 (HEK293) cells, and in mouse embryonic stem (ES) cells.
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Affiliation(s)
- Michael Fitzgerald
- Department of Bioengineering, University of Utah , Salt Lake City, Utah 84112, United States
| | - Chelsea Gibbs
- Department of Bioengineering, University of Utah , Salt Lake City, Utah 84112, United States
| | - Adrian A Shimpi
- Department of Bioengineering, University of Utah , Salt Lake City, Utah 84112, United States
| | - Tara L Deans
- Department of Bioengineering, University of Utah , Salt Lake City, Utah 84112, United States
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47
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Brown AJ, Gibson SJ, Hatton D, James DC. In silico design of context-responsive mammalian promoters with user-defined functionality. Nucleic Acids Res 2017; 45:10906-10919. [PMID: 28977454 PMCID: PMC5737543 DOI: 10.1093/nar/gkx768] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 08/22/2017] [Indexed: 12/19/2022] Open
Abstract
Comprehensive de novo-design of complex mammalian promoters is restricted by unpredictable combinatorial interactions between constituent transcription factor regulatory elements (TFREs). In this study, we show that modular binding sites that do not function cooperatively can be identified by analyzing host cell transcription factor expression profiles, and subsequently testing cognate TFRE activities in varying homotypic and heterotypic promoter architectures. TFREs that displayed position-insensitive, additive function within a specific expression context could be rationally combined together in silico to create promoters with highly predictable activities. As TFRE order and spacing did not affect the performance of these TFRE-combinations, compositions could be specifically arranged to preclude the formation of undesirable sequence features. This facilitated simple in silico-design of promoters with context-required, user-defined functionalities. To demonstrate this, we de novo-created promoters for biopharmaceutical production in CHO cells that exhibited precisely designed activity dynamics and long-term expression-stability, without causing observable retroactive effects on cellular performance. The design process described can be utilized for applications requiring context-responsive, customizable promoter function, particularly where co-expression of synthetic TFs is not suitable. Although the synthetic promoter structure utilized does not closely resemble native mammalian architectures, our findings also provide additional support for a flexible billboard model of promoter regulation.
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Affiliation(s)
- Adam J Brown
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin St., Sheffield S1 3JD, UK
| | - Suzanne J Gibson
- Biopharmaceutical Development, MedImmune, Cambridge CB21 6GH, UK
| | - Diane Hatton
- Biopharmaceutical Development, MedImmune, Cambridge CB21 6GH, UK
| | - David C James
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin St., Sheffield S1 3JD, UK
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48
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Vishnu KV, Chatterjee NS, Ajeeshkumar KK, Lekshmi RGK, Tejpal CS, Mathew S, Ravishankar CN. Microencapsulation of sardine oil: Application of vanillic acid grafted chitosan as a bio-functional wall material. Carbohydr Polym 2017; 174:540-548. [PMID: 28821102 DOI: 10.1016/j.carbpol.2017.06.076] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 06/15/2017] [Accepted: 06/20/2017] [Indexed: 10/19/2022]
Abstract
Vanillic acid grafted chitosan (Va-g-Ch) was evaluated as a new antioxidant wall material for microencapsulation of polyunsaturated fatty acid rich sardine oil. A high grafting ratio of 305mg vanillic acid equivalent/g of polymer was achieved using a free radical mediated grafting reaction. Oil in water emulsion was prepared with an optimised combination of Va-g-Ch and Tween 20 (3.2:1). Sardine oil loaded microparticles (SO-M) were produced (∼75% yield) by spray drying. The average diameter and polydispersity Index (PDI) of the particles were found to be 2.3μ and 0.345. XRD spectra of SO-M showed reduction in crystallinity due to microencapsulation. After four weeks of storage, a moderate (∼12%) decrease in the EPA and DHA content and a low PV of 5.5±0.51meq/kg oil in SO-M demonstrated good oxidative stability. Satisfactory encapsulation efficiency (84±0.84%) and loading efficiency (67±0.51%) values, also demonstrated the suitability of Va-g-Ch for microencapsulation of sardine oil.
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Affiliation(s)
- K V Vishnu
- ICAR-Central Institute of Fisheries Technology (CIFT), Matsyapuri P.O, Kerala-682029, India
| | - Niladri S Chatterjee
- ICAR-Central Institute of Fisheries Technology (CIFT), Matsyapuri P.O, Kerala-682029, India.
| | - K K Ajeeshkumar
- ICAR-Central Institute of Fisheries Technology (CIFT), Matsyapuri P.O, Kerala-682029, India
| | - R G K Lekshmi
- ICAR-Central Institute of Fisheries Technology (CIFT), Matsyapuri P.O, Kerala-682029, India
| | - C S Tejpal
- ICAR-Central Institute of Fisheries Technology (CIFT), Matsyapuri P.O, Kerala-682029, India
| | - Suseela Mathew
- ICAR-Central Institute of Fisheries Technology (CIFT), Matsyapuri P.O, Kerala-682029, India
| | - C N Ravishankar
- ICAR-Central Institute of Fisheries Technology (CIFT), Matsyapuri P.O, Kerala-682029, India
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49
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Pierrel F. Impact of Chemical Analogs of 4-Hydroxybenzoic Acid on Coenzyme Q Biosynthesis: From Inhibition to Bypass of Coenzyme Q Deficiency. Front Physiol 2017; 8:436. [PMID: 28690551 PMCID: PMC5479927 DOI: 10.3389/fphys.2017.00436] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 06/08/2017] [Indexed: 12/21/2022] Open
Abstract
Coenzyme Q is a lipid that participates to important physiological functions. Coenzyme Q is synthesized in multiple steps from the precursor 4-hydroxybenzoic acid. Mutations in enzymes that participate to coenzyme Q biosynthesis result in primary coenzyme Q deficiency, a type of mitochondrial disease. Coenzyme Q10 supplementation of patients is the classical treatment but it shows limited efficacy in some cases. The molecular understanding of the coenzyme Q biosynthetic pathway allowed the design of experiments to bypass deficient biosynthetic steps with analogs of 4-hydroxybenzoic acid. These molecules provide the defective chemical group and can reactivate endogenous coenzyme Q biosynthesis as demonstrated recently in yeast, mammalian cell cultures, and mouse models of primary coenzyme Q deficiency. This mini review presents how the chemical properties of various analogs of 4-hydroxybenzoic acid dictate the effect of the molecules on CoQ biosynthesis and how the reactivation of endogenous coenzyme Q biosynthesis may achieve better results than exogenous CoQ10 supplementation.
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Affiliation(s)
- Fabien Pierrel
- Centre National de la Recherche Scientifique, Grenoble INP, TIMC-IMAG, University Grenoble AlpesGrenoble, France
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50
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Xue S, Yin J, Shao J, Yu Y, Yang L, Wang Y, Xie M, Fussenegger M, Ye H. A Synthetic-Biology-Inspired Therapeutic Strategy for Targeting and Treating Hepatogenous Diabetes. Mol Ther 2017; 25:443-455. [PMID: 28153094 DOI: 10.1016/j.ymthe.2016.11.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 11/11/2016] [Accepted: 11/15/2016] [Indexed: 12/31/2022] Open
Abstract
Hepatogenous diabetes is a complex disease that is typified by the simultaneous presence of type 2 diabetes and many forms of liver disease. The chief pathogenic determinant in this pathophysiological network is insulin resistance (IR), an asymptomatic disease state in which impaired insulin signaling in target tissues initiates a variety of organ dysfunctions. However, pharmacotherapies targeting IR remain limited and are generally inapplicable for liver disease patients. Oleanolic acid (OA) is a plant-derived triterpenoid that is frequently used in Chinese medicine as a safe but slow-acting treatment in many liver disorders. Here, we utilized the congruent pharmacological activities of OA and glucagon-like-peptide 1 (GLP-1) in relieving IR and improving liver and pancreas functions and used a synthetic-biology-inspired design principle to engineer a therapeutic gene circuit that enables a concerted action of both drugs. In particular, OA-triggered short human GLP-1 (shGLP-1) expression in hepatogenous diabetic mice rapidly and simultaneously attenuated many disease-specific metabolic failures, whereas OA or shGLP-1 monotherapy failed to achieve corresponding therapeutic effects. Collectively, this work shows that rationally engineered synthetic gene circuits are capable of treating multifactorial diseases in a synergistic manner by multiplexing the targeting efficacies of single therapeutics.
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Affiliation(s)
- Shuai Xue
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Jianli Yin
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Jiawei Shao
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Yuanhuan Yu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Linfeng Yang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Yidan Wang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Mingqi Xie
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China; Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Haifeng Ye
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China.
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