1
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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: 1] [Impact Index Per Article: 1.0] [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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2
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Shaw D, Miravet‐Verde S, Piñero‐Lambea C, Serrano L, Lluch‐Senar M. LoxTnSeq: random transposon insertions combined with cre/lox recombination and counterselection to generate large random genome reductions. Microb Biotechnol 2021; 14:2403-2419. [PMID: 33325626 PMCID: PMC8601177 DOI: 10.1111/1751-7915.13714] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 11/04/2020] [Accepted: 11/04/2020] [Indexed: 12/13/2022] Open
Abstract
The removal of unwanted genetic material is a key aspect in many synthetic biology efforts and often requires preliminary knowledge of which genomic regions are dispensable. Typically, these efforts are guided by transposon mutagenesis studies, coupled to deepsequencing (TnSeq) to identify insertion points and gene essentiality. However, epistatic interactions can cause unforeseen changes in essentiality after the deletion of a gene, leading to the redundancy of these essentiality maps. Here, we present LoxTnSeq, a new methodology to generate and catalogue libraries of genome reduction mutants. LoxTnSeq combines random integration of lox sites by transposon mutagenesis, and the generation of mutants via Cre recombinase, catalogued via deep sequencing. When LoxTnSeq was applied to the naturally genome reduced bacterium Mycoplasma pneumoniae, we obtained a mutant pool containing 285 unique deletions. These deletions spanned from > 50 bp to 28 Kb, which represents 21% of the total genome. LoxTnSeq also highlighted large regions of non-essential genes that could be removed simultaneously, and other non-essential regions that could not, providing a guide for future genome reductions.
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Affiliation(s)
- Daniel Shaw
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88Barcelona08003Spain
| | - Samuel Miravet‐Verde
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88Barcelona08003Spain
| | - Carlos Piñero‐Lambea
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88Barcelona08003Spain
- Present address:
Pulmobiotics ltdDr. Aiguader 88Barcelona08003Spain
| | - Luis Serrano
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88Barcelona08003Spain
- Universitat Pompeu Fabra (UPF)Barcelona08002Spain
- ICREAPg. Lluís Companys 23Barcelona08010Spain
| | - Maria Lluch‐Senar
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88Barcelona08003Spain
- Basic Sciences DepartmentFaculty of Medicine and Health SciencesUniversitat Internacional de CatalunyaSant Cugat del Vallès08195Spain
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3
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Facklam AL, Volpatti LR, Anderson DG. Biomaterials for Personalized Cell Therapy. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e1902005. [PMID: 31495970 DOI: 10.1002/adma.201902005] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 07/26/2019] [Indexed: 05/13/2023]
Abstract
Cell therapy has already had an important impact on healthcare and provided new treatments for previously intractable diseases. Notable examples include mesenchymal stem cells for tissue regeneration, islet transplantation for diabetes treatment, and T cell delivery for cancer immunotherapy. Biomaterials have the potential to extend the therapeutic impact of cell therapies by serving as carriers that provide 3D organization and support cell viability and function. With the growing emphasis on personalized medicine, cell therapies hold great potential for their ability to sense and respond to the biology of an individual patient. These therapies can be further personalized through the use of patient-specific cells or with precision biomaterials to guide cellular activity in response to the needs of each patient. Here, the role of biomaterials for applications in tissue regeneration, therapeutic protein delivery, and cancer immunotherapy is reviewed, with a focus on progress in engineering material properties and functionalities for personalized cell therapies.
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Affiliation(s)
- Amanda L Facklam
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Lisa R Volpatti
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Daniel G Anderson
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Anesthesiology, Boston Children's Hospital, Boston, MA, 02115, USA
- Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
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4
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Saeedi M, Eslamifar M, Khezri K, Dizaj SM. Applications of nanotechnology in drug delivery to the central nervous system. Biomed Pharmacother 2019; 111:666-675. [PMID: 30611991 DOI: 10.1016/j.biopha.2018.12.133] [Citation(s) in RCA: 158] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 12/21/2018] [Accepted: 12/30/2018] [Indexed: 12/31/2022] Open
Abstract
In recent years, the researchers and drug designers have given growing attention to new nanotechnology strategies to improve drug delivery to the central nervous system (CNS). Nanotechnology has a great potential to affect the treatment of neurological disorders, mainly Alzheimer's disease, Parkinson's disease, brain tumors, and stroke. With regard to neurodegeneration, several studies showed that nanomaterials have been successfully used for the treatments of CNS disorders. In this regard, nanocarriers have facilitated the targeted delivery of chemotherapeutics resulting in the efficient inhibition of disease progression in malignant brain tumors. Therefore, the most efficacious application of nanomaterials is the use of these substances in the treatment of CNS disease that enhances the overall effect of drug and highlights the importance of nano-therapeutics. This study was conducted to review the evidence on the applications of nanotechnology in designing drug delivery systems with the ability to cross through the blood-brain barrier (BBB) in order to transfer the therapeutic agents to the CNS.
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Affiliation(s)
- Majid Saeedi
- Department of Pharmaceutics, Faculty of Pharmacy, Mazandaran University of Medical Science, Sari, Iran
| | - Masoumeh Eslamifar
- Department of Environmental Health Engineering, Faculty of Health, Mazandaran University of Medical Science, Sari, Iran.
| | - Khadijeh Khezri
- Student Research Committee, Department of Pharmaceutics, Faculty of Pharmacy, Mazandaran University of Medical Science, Sari, Iran..
| | - Solmaz Maleki Dizaj
- Dental and Periodontal Research Center and Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
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5
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Dai Z, Huang S. Functional Dynamics Inside Nano- or Microscale Bio-Hybrid Systems. Front Chem 2018; 6:621. [PMID: 30619829 PMCID: PMC6305405 DOI: 10.3389/fchem.2018.00621] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 11/30/2018] [Indexed: 11/22/2022] Open
Abstract
Soft nano- or microgels made by natural or synthetic polymers have been investigated intensively because of their board applications. Due to their porosity and biocompatibility, nano- or microgels can be integrated with various biologics to form a bio-hybrid system. They can support living cells as a scaffold; entrap bioactive molecules as a drug carrier or encapsulate microorganisms as a semi-permeable membrane. Especially, researchers have created various modes of functional dynamics into these bio-hybrid systems. From one side, the encapsulating materials can respond to the external stimulus and release the cargo. From the other side, cells can respond to physical, or chemical properties of the matrix and differentiate into a specific cell type. With recent advancements of synthetic biology, cells can be further programed to respond to certain signals, and express therapeutics or other functional proteins for various purposes. Thus, the integration of nano- or microgels and programed cells becomes a potential candidate in applications spanning from biotechnology to new medicines. This brief review will first talk about several nano- or microgels systems fabricated by natural or synthetic polymers, and further discuss their applications when integrated with various types of biologics. In particular, we will concentrate on the dynamics embedded in these bio-hybrid systems, to dissect their designs and sophisticated functions.
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Affiliation(s)
- Zhuojun Dai
- Institute for Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
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6
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Sankaran S, Del Campo A. Optoregulated Protein Release from an Engineered Living Material. ACTA ACUST UNITED AC 2018; 3:e1800312. [PMID: 32627372 DOI: 10.1002/adbi.201800312] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 12/04/2018] [Indexed: 12/20/2022]
Abstract
Developing materials to encapsulate and deliver functional proteins inside the body is a challenging yet rewarding task for therapeutic purposes. High production costs, mostly associated with the purification process, short-term stability in vivo, and controlled and prolonged release are major hurdles for the clinical application of protein-based biopharmaceuticals. In an attempt to overcome these hurdles, herein, the possibility of incorporating bacteria as protein factories into a material and externally controlling protein release using optogenetics is demonstrated. By engineering bacteria to express and secrete a red fluorescent protein in response to low doses of blue light irradiation and embedding them in agarose hydrogels, living materials are fabricated capable of releasing proteins into the surrounding medium when exposed to light. These bacterial hydrogels allow spatially confined protein expression and dosed protein release over several weeks, regulated by the area and extent of light exposure. The possibility of incorporating such complex functions in a material using relatively simple material and genetic engineering strategies highlights the immense potential and versatility offered by living materials for protein-based biopharmaceutical delivery.
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Affiliation(s)
| | - Aránzazu Del Campo
- INM - Leibniz Institute for New Materials, Campus D2 2, 66123, Saarbrücken, Germany.,Chemistry Department, Saarland University, 66123, Saarbrücken, Germany
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7
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Singhvi G, Girdhar V, Patil S, Gupta G, Hansbro PM, Dua K. Microbiome as therapeutics in vesicular delivery. Biomed Pharmacother 2018; 104:738-741. [DOI: 10.1016/j.biopha.2018.05.099] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 05/20/2018] [Accepted: 05/21/2018] [Indexed: 01/20/2023] Open
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8
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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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9
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Sedlmayer F, Aubel D, Fussenegger M. Synthetic gene circuits for the detection, elimination and prevention of disease. Nat Biomed Eng 2018; 2:399-415. [PMID: 31011195 DOI: 10.1038/s41551-018-0215-0] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 03/05/2018] [Indexed: 12/13/2022]
Abstract
In living organisms, naturally evolved sensors that constantly monitor and process environmental cues trigger corrective actions that enable the organisms to cope with changing conditions. Such natural processes have inspired biologists to construct synthetic living sensors and signalling pathways, by repurposing naturally occurring proteins and by designing molecular building blocks de novo, for customized diagnostics and therapeutics. In particular, designer cells that employ user-defined synthetic gene circuits to survey disease biomarkers and to autonomously re-adjust unbalanced pathological states can coordinate the production of therapeutics, with controlled timing and dosage. Furthermore, tailored genetic networks operating in bacterial or human cells have led to cancer remission in experimental animal models, owing to the network's unprecedented specificity. Other applications of designer cells in infectious, metabolic and autoimmune diseases are also being explored. In this Review, we describe the biomedical applications of synthetic gene circuits in major disease areas, and discuss how the first genetically engineered devices developed on the basis of synthetic-biology principles made the leap from the laboratory to the clinic.
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Affiliation(s)
- Ferdinand Sedlmayer
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Dominique Aubel
- IUTA Département Génie Biologique, Université Claude Bernard Lyon 1, Lyon, France
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland. .,Faculty of Science, University of Basel, Basel, Switzerland.
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10
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Alginate Utilization in Tissue Engineering and Cell Therapy. SPRINGER SERIES IN BIOMATERIALS SCIENCE AND ENGINEERING 2018. [DOI: 10.1007/978-981-10-6910-9_5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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11
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Sarker B, Zehnder T, Rath SN, Horch RE, Kneser U, Detsch R, Boccaccini AR. Oxidized Alginate-Gelatin Hydrogel: A Favorable Matrix for Growth and Osteogenic Differentiation of Adipose-Derived Stem Cells in 3D. ACS Biomater Sci Eng 2017; 3:1730-1737. [DOI: 10.1021/acsbiomaterials.7b00188] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Bapi Sarker
- Institute
of Biomaterials, Department of Materials Science and Engineering, University of Erlangen-Nuremberg, 91058 Erlangen, Germany
| | - Tobias Zehnder
- Institute
of Biomaterials, Department of Materials Science and Engineering, University of Erlangen-Nuremberg, 91058 Erlangen, Germany
| | - Subha N. Rath
- Department
of Plastic and Hand Surgery, University of Erlangen-Nuremberg, 91054 Erlangen, Germany
| | - Raymund E. Horch
- Department
of Plastic and Hand Surgery, University of Erlangen-Nuremberg, 91054 Erlangen, Germany
| | - Ulrich Kneser
- Department
of Hand, Plastic, and Reconstructive Surgery, Burn Center, BG Trauma
Center Ludwigshafen and Department of Plastic and Hand Surgery, University of Heidelberg, Heidelberg, Germany
| | - Rainer Detsch
- Institute
of Biomaterials, Department of Materials Science and Engineering, University of Erlangen-Nuremberg, 91058 Erlangen, Germany
| | - Aldo R. Boccaccini
- Institute
of Biomaterials, Department of Materials Science and Engineering, University of Erlangen-Nuremberg, 91058 Erlangen, Germany
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12
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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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13
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Ausländer S, Ausländer D, Fussenegger M. Synthetische Biologie - die Synthese der Biologie. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201609229] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Simon Ausländer
- Department of Biosystems Science and Engineering; ETH Zürich; Mattenstrasse 26 4058 Basel Schweiz
| | - David Ausländer
- Department of Biosystems Science and Engineering; ETH Zürich; Mattenstrasse 26 4058 Basel Schweiz
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering; ETH Zürich; Mattenstrasse 26 4058 Basel Schweiz
- Faculty of Science; Universität Basel; Mattenstrasse 26 4058 Basel Schweiz
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14
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Ausländer S, Ausländer D, Fussenegger M. Synthetic Biology-The Synthesis of Biology. Angew Chem Int Ed Engl 2017; 56:6396-6419. [PMID: 27943572 DOI: 10.1002/anie.201609229] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 11/17/2016] [Indexed: 01/01/2023]
Abstract
Synthetic biology concerns the engineering of man-made living biomachines from standardized components that can perform predefined functions in a (self-)controlled manner. Different research strategies and interdisciplinary efforts are pursued to implement engineering principles to biology. The "top-down" strategy exploits nature's incredible diversity of existing, natural parts to construct synthetic compositions of genetic, metabolic, or signaling networks with predictable and controllable properties. This mainly application-driven approach results in living factories that produce drugs, biofuels, biomaterials, and fine chemicals, and results in living pills that are based on engineered cells with the capacity to autonomously detect and treat disease states in vivo. In contrast, the "bottom-up" strategy seeks to be independent of existing living systems by designing biological systems from scratch and synthesizing artificial biological entities not found in nature. This more knowledge-driven approach investigates the reconstruction of minimal biological systems that are capable of performing basic biological phenomena, such as self-organization, self-replication, and self-sustainability. Moreover, the syntheses of artificial biological units, such as synthetic nucleotides or amino acids, and their implementation into polymers inside living cells currently set the boundaries between natural and artificial biological systems. In particular, the in vitro design, synthesis, and transfer of complete genomes into host cells point to the future of synthetic biology: the creation of designer cells with tailored desirable properties for biomedicine and biotechnology.
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Affiliation(s)
- Simon Ausländer
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - David Ausländer
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland.,Faculty of Science, University of Basel, Mattenstrasse 26, 4058, Basel, Switzerland
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15
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Müller M, Ausländer S, Spinnler A, Ausländer D, Sikorski J, Folcher M, Fussenegger M. Designed cell consortia as fragrance-programmable analog-to-digital converters. Nat Chem Biol 2017; 13:309-316. [DOI: 10.1038/nchembio.2281] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 11/22/2016] [Indexed: 01/09/2023]
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16
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Smole A, Lainšček D, Bezeljak U, Horvat S, Jerala R. A Synthetic Mammalian Therapeutic Gene Circuit for Sensing and Suppressing Inflammation. Mol Ther 2017; 25:102-119. [PMID: 28129106 DOI: 10.1016/j.ymthe.2016.10.005] [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: 05/27/2016] [Revised: 10/20/2016] [Accepted: 10/21/2016] [Indexed: 12/20/2022] Open
Abstract
Inflammation, which is a highly regulated host response against danger signals, may be harmful if it is excessive and deregulated. Ideally, anti-inflammatory therapy should autonomously commence as soon as possible after the onset of inflammation, should be controllable by a physician, and should not systemically block beneficial immune response in the long term. We describe a genetically encoded anti-inflammatory mammalian cell device based on a modular engineered genetic circuit comprising a sensor, an amplifier, a "thresholder" to restrict activation of a positive-feedback loop, a combination of advanced clinically used biopharmaceutical proteins, and orthogonal regulatory elements that linked modules into the functional device. This genetic circuit was autonomously activated by inflammatory signals, including endogenous cecal ligation and puncture (CLP)-induced inflammation in mice and serum from a systemic juvenile idiopathic arthritis (sIJA) patient, and could be reset externally by a chemical signal. The microencapsulated anti-inflammatory device significantly reduced the pathology in dextran sodium sulfate (DSS)-induced acute murine colitis, demonstrating a synthetic immunological approach for autonomous anti-inflammatory therapy.
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Affiliation(s)
- Anže Smole
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Duško Lainšček
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Urban Bezeljak
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia; Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Simon Horvat
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia; EN-FIST Centre of Excellence, 1000 Ljubljana, Slovenia; Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia; EN-FIST Centre of Excellence, 1000 Ljubljana, Slovenia.
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17
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Abstract
Mammalian cells have been microencapsulated within both natural and synthetic polymers for over half a century. Specifically, in the last 36 years microencapsulated cells have been used therapeutically to deliver a wide range of drugs, cytokines, growth factors, and hormones while enjoying the immunoisolation provided by the encapsulating material. In addition to preventing immune attack, microencapsulation prevents migration of entrapped cells. Cells can be microencapsulated in a variety of geometries, the most common being solid microspheres and hollow microcapsules. The micrometer scale permits delivery by injection and is within diffusion limits that allow the cells to provide the necessary factors that are missing at a target site, while also permitting the exchange of nutrients and waste products. The majority of cell microencapsulation is performed with alginate/poly-L-lysine microspheres. Since alginate itself can be immunogenic, for cell-based therapy applications various groups are investigating synthetic polymers to microencapsulate cells. We describe a protocol for the formation of microspheres and microcapsules using the synthetic polymer poly(ethylene glycol) diacrylate (PEGDA).
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Affiliation(s)
- A Aijaz
- Department of Biomedical Engineering, Rutgers University, 599 Taylor Road, Piscataway, NJ, 08854, USA
| | - D Perera
- Department of Biomedical Engineering, Rutgers University, 599 Taylor Road, Piscataway, NJ, 08854, USA
| | - Ronke M Olabisi
- Department of Biomedical Engineering, Rutgers University, 599 Taylor Road, Piscataway, NJ, 08854, USA.
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18
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Fliervoet LAL, Mastrobattista E. Drug delivery with living cells. Adv Drug Deliv Rev 2016; 106:63-72. [PMID: 27129442 DOI: 10.1016/j.addr.2016.04.021] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2016] [Revised: 04/18/2016] [Accepted: 04/19/2016] [Indexed: 12/25/2022]
Abstract
The field of drug delivery has grown tremendously in the past few decades by developing a wide range of advanced drug delivery systems. An interesting category is cell-based drug delivery, which includes encapsulation of drugs inside cells or attached to the surface and subsequent transportation through the body. Another approach involves genetic engineering of cells to secrete therapeutic molecules in a controlled way. The next-generation systems integrate expertise from synthetic biology to generate therapeutic gene networks for highly advanced sensory and output devices. These developments are very exciting for the drug delivery field and could radically change the way we administer biological medicines to chronically ill patients. This review is covering the use of living cells, either as transport system or production-unit, to deliver therapeutic molecules and bioactive proteins inside the body. It describes a wide range of approaches in cell-based drug delivery and highlights exceptional examples.
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Affiliation(s)
- Lies A L Fliervoet
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences (UIPS), Faculty of Science, Utrecht University, P.O. Box 80082, 3508 TB Utrecht, The Netherlands
| | - Enrico Mastrobattista
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences (UIPS), Faculty of Science, Utrecht University, P.O. Box 80082, 3508 TB Utrecht, The Netherlands.
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Krishnamurthy M, Moore RT, Rajamani S, Panchal RG. Bacterial genome engineering and synthetic biology: combating pathogens. BMC Microbiol 2016; 16:258. [PMID: 27814687 PMCID: PMC5097395 DOI: 10.1186/s12866-016-0876-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 10/28/2016] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The emergence and prevalence of multidrug resistant (MDR) pathogenic bacteria poses a serious threat to human and animal health globally. Nosocomial infections and common ailments such as pneumonia, wound, urinary tract, and bloodstream infections are becoming more challenging to treat due to the rapid spread of MDR pathogenic bacteria. According to recent reports by the World Health Organization (WHO) and Centers for Disease Control and Prevention (CDC), there is an unprecedented increase in the occurrence of MDR infections worldwide. The rise in these infections has generated an economic strain worldwide, prompting the WHO to endorse a global action plan to improve awareness and understanding of antimicrobial resistance. This health crisis necessitates an immediate action to target the underlying mechanisms of drug resistance in bacteria. RESEARCH The advent of new bacterial genome engineering and synthetic biology (SB) tools is providing promising diagnostic and treatment plans to monitor and treat widespread recalcitrant bacterial infections. Key advances in genetic engineering approaches can successfully aid in targeting and editing pathogenic bacterial genomes for understanding and mitigating drug resistance mechanisms. In this review, we discuss the application of specific genome engineering and SB methods such as recombineering, clustered regularly interspaced short palindromic repeats (CRISPR), and bacterial cell-cell signaling mechanisms for pathogen targeting. The utility of these tools in developing antibacterial strategies such as novel antibiotic production, phage therapy, diagnostics and vaccine production to name a few, are also highlighted. CONCLUSIONS The prevalent use of antibiotics and the spread of MDR bacteria raise the prospect of a post-antibiotic era, which underscores the need for developing novel therapeutics to target MDR pathogens. The development of enabling SB technologies offers promising solutions to deliver safe and effective antibacterial therapies.
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Affiliation(s)
- Malathy Krishnamurthy
- Department of Target Discovery and Experimental Microbiology, Division of Molecular and Translational Sciences, U. S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD 21702 USA
| | - Richard T. Moore
- Department of Target Discovery and Experimental Microbiology, Division of Molecular and Translational Sciences, U. S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD 21702 USA
| | - Sathish Rajamani
- Department of Target Discovery and Experimental Microbiology, Division of Molecular and Translational Sciences, U. S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD 21702 USA
| | - Rekha G. Panchal
- Department of Target Discovery and Experimental Microbiology, Division of Molecular and Translational Sciences, U. S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD 21702 USA
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Ausländer S, Fussenegger M. Engineering Gene Circuits for Mammalian Cell-Based Applications. Cold Spring Harb Perspect Biol 2016; 8:cshperspect.a023895. [PMID: 27194045 DOI: 10.1101/cshperspect.a023895] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Synthetic gene switches are basic building blocks for the construction of complex gene circuits that transform mammalian cells into useful cell-based machines for next-generation biotechnological and biomedical applications. Ligand-responsive gene switches are cellular sensors that are able to process specific signals to generate gene product responses. Their involvement in complex gene circuits results in sophisticated circuit topologies that are reminiscent of electronics and that are capable of providing engineered cells with the ability to memorize events, oscillate protein production, and perform complex information-processing tasks. Microencapsulated mammalian cells that are engineered with closed-loop gene networks can be implanted into mice to sense disease-related input signals and to process this information to produce a custom, fine-tuned therapeutic response that rebalances animal metabolism. Progress in gene circuit design, in combination with recent breakthroughs in genome engineering, may result in tailored engineered mammalian cells with great potential for future cell-based therapies.
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Affiliation(s)
- Simon Ausländer
- Department of Biosystems Science and Engineering, ETH Zurich, CH-4058 Basel, Switzerland
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, CH-4058 Basel, Switzerland Faculty of Science, University of Basel, CH-4058 Basel, Switzerland
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21
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Schukur L, Fussenegger M. Engineering of synthetic gene circuits for (re-)balancing physiological processes in chronic diseases. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2016; 8:402-22. [DOI: 10.1002/wsbm.1345] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 04/12/2016] [Accepted: 04/26/2016] [Indexed: 12/17/2022]
Affiliation(s)
- Lina Schukur
- 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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22
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Wang H, Ye H, Xie M, Daoud El-Baba M, Fussenegger M. Cosmetics-triggered percutaneous remote control of transgene expression in mice. Nucleic Acids Res 2015; 43:e91. [PMID: 25943548 PMCID: PMC4538802 DOI: 10.1093/nar/gkv326] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 03/31/2015] [Indexed: 12/24/2022] Open
Abstract
Synthetic biology has significantly advanced the rational design of trigger-inducible gene switches that program cellular behavior in a reliable and predictable manner. Capitalizing on genetic componentry, including the repressor PmeR and its cognate operator OPmeR, that has evolved in Pseudomonas syringae pathovar tomato DC3000 to sense and resist plant-defence metabolites of the paraben class, we have designed a set of inducible and repressible mammalian transcription-control devices that could dose-dependently fine-tune transgene expression in mammalian cells and mice in response to paraben derivatives. With an over 60-years track record as licensed preservatives in the cosmetics industry, paraben derivatives have become a commonplace ingredient of most skin-care products including shower gels, cleansing toners and hand creams. As parabens can rapidly reach the bloodstream of mice following topical application, we used this feature to percutaneously program transgene expression of subcutaneous designer cell implants using off-the-shelf commercial paraben-containing skin-care cosmetics. The combination of non-invasive, transdermal and orthogonal trigger-inducible remote control of transgene expression may provide novel opportunities for dynamic interventions in future gene and cell-based therapies.
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Affiliation(s)
- Hui Wang
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Haifeng Ye
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, 200241 Shanghai, China
| | - Mingqi Xie
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Marie Daoud El-Baba
- Département Génie Biologique, Institut Universitaire de Technologie, F-69622 Villeurbanne Cedex, France
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland Faculty of Science, University of Basel, CH-4058 Basel, Switzerland
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23
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Geering B, Fussenegger M. Synthetic immunology: modulating the human immune system. Trends Biotechnol 2015; 33:65-79. [DOI: 10.1016/j.tibtech.2014.10.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 10/13/2014] [Accepted: 10/20/2014] [Indexed: 12/30/2022]
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24
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Xie M, Ye H, Hamri GCE, Fussenegger M. Antagonistic control of a dual-input mammalian gene switch by food additives. Nucleic Acids Res 2014; 42:e116. [PMID: 25030908 PMCID: PMC4132709 DOI: 10.1093/nar/gku545] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Synthetic biology has significantly advanced the design of mammalian trigger-inducible transgene-control devices that are able to programme complex cellular behaviour. Fruit-based benzoate derivatives licensed as food additives, such as flavours (e.g. vanillate) and preservatives (e.g. benzoate), are a particularly attractive class of trigger compounds for orthogonal mammalian transgene control devices because of their innocuousness, physiological compatibility and simple oral administration. Capitalizing on the genetic componentry of the soil bacterium Comamonas testosteroni, which has evolved to catabolize a variety of aromatic compounds, we have designed different mammalian gene expression systems that could be induced and repressed by the food additives benzoate and vanillate. When implanting designer cells engineered for gene switch-driven expression of the human placental secreted alkaline phosphatase (SEAP) into mice, blood SEAP levels of treated animals directly correlated with a benzoate-enriched drinking programme. Additionally, the benzoate-/vanillate-responsive device was compatible with other transgene control systems and could be assembled into higher-order control networks providing expression dynamics reminiscent of a lap-timing stopwatch. Designer gene switches using licensed food additives as trigger compounds to achieve antagonistic dual-input expression profiles and provide novel control topologies and regulation dynamics may advance future gene- and cell-based therapies.
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Affiliation(s)
- Mingqi Xie
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Haifeng Ye
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | | | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland Faculty of Science, University of Basel, CH-4058 Basel, Switzerland
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25
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Rössger K, Charpin-El-Hamri G, Fussenegger M. A closed-loop synthetic gene circuit for the treatment of diet-induced obesity in mice. Nat Commun 2014; 4:2825. [PMID: 24281397 PMCID: PMC3868331 DOI: 10.1038/ncomms3825] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 10/28/2013] [Indexed: 01/05/2023] Open
Abstract
Diet-induced obesity is a lifestyle-associated medical condition that increases the risk of developing cardiovascular disease, type 2 diabetes and certain types of cancer. Here we report the design of a closed-loop genetic circuit that constantly monitors blood fatty acid levels in the setting of diet-associated hyperlipidemia and coordinates reversible and adjustable expression of the clinically licensed appetite-suppressing peptide hormone pramlintide. Grafting of the peroxisome proliferator-activated receptor-α onto the phloretin-responsive repressor TtgR produces a synthetic intracellular lipid-sensing receptor (LSR) that reversibly induces chimeric TtgR-specific promoters in a fatty acid-adjustable manner. Mice with diet-induced obesity in which microencapsulated cells engineered for LSR-driven expression of pramlintide are implanted show significant reduction in food consumption, blood lipid levels and body weight when put on a high-fat diet. Therapeutic designer circuits that monitor levels of pathologic metabolites and link these with the tailored expression of protein pharmaceuticals may provide new opportunities for the treatment of metabolic disorders.
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Affiliation(s)
- Katrin Rössger
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
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26
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Ye H, Fussenegger M. Synthetic therapeutic gene circuits in mammalian cells. FEBS Lett 2014; 588:2537-44. [PMID: 24844435 DOI: 10.1016/j.febslet.2014.05.003] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 05/05/2014] [Indexed: 12/19/2022]
Abstract
In the emerging field of synthetic biology, scientists are focusing on designing and creating functional devices, systems, and organisms with novel functions by engineering and assembling standardised biological building blocks. The progress of synthetic biology has significantly advanced the design of functional gene networks that can reprogram metabolic activities in mammalian cells and provide new therapeutic opportunities for future gene- and cell-based therapies. In this review, we describe the most recent advances in synthetic mammalian gene networks designed for biomedical applications, including how these synthetic therapeutic gene circuits can be assembled to control signalling networks and applied to treat metabolic disorders, cancer, and immune diseases. We conclude by discussing the various challenges and future prospects of using synthetic mammalian gene networks for disease therapy.
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Affiliation(s)
- 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; 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 Life Science, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland.
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Biomedically relevant circuit-design strategies in mammalian synthetic biology. Mol Syst Biol 2014; 9:691. [PMID: 24061539 PMCID: PMC3792348 DOI: 10.1038/msb.2013.48] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2013] [Accepted: 08/07/2013] [Indexed: 12/24/2022] Open
Abstract
The development and progress in synthetic biology has been remarkable. Although still in its infancy, synthetic biology has achieved much during the past decade. Improvements in genetic circuit design have increased the potential for clinical applicability of synthetic biology research. What began as simple transcriptional gene switches has rapidly developed into a variety of complex regulatory circuits based on the transcriptional, translational and post-translational regulation. Instead of compounds with potential pharmacologic side effects, the inducer molecules now used are metabolites of the human body and even members of native cell signaling pathways. In this review, we address recent progress in mammalian synthetic biology circuit design and focus on how novel designs push synthetic biology toward clinical implementation. Groundbreaking research on the implementation of optogenetics and intercellular communications is addressed, as particularly optogenetics provides unprecedented opportunities for clinical application. Along with an increase in synthetic network complexity, multicellular systems are now being used to provide a platform for next-generation circuit design.
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Abstract
Biological systems perform computations at multiple scales and they do so in a robust way. Engineering metaphors have often been used in order to provide a rationale for modeling cellular and molecular computing networks and as the basis for their synthetic design. However, a major constraint in this mapping between electronic and wet computational circuits is the wiring problem. Although wires are identical within electronic devices, they must be different when using synthetic biology designs. Moreover, in most cases the designed molecular systems cannot be reused for other functions. A new approximation allows us to simplify the problem by using synthetic cellular consortia where the output of the computation is distributed over multiple engineered cells. By evolving circuits in silico, we can obtain the minimal sets of Boolean units required to solve the given problem at the lowest cost using cellular consortia. Our analysis reveals that the basic set of logic units is typically non-standard. Among the most common units, the so called inverted IMPLIES (N-Implies) appears to be one of the most important elements along with the NOT and AND functions. Although NOR and NAND gates are widely used in electronics, evolved circuits based on combinations of these gates are rare, thus suggesting that the strategy of combining the same basic logic gates might be inappropriate in order to easily implement synthetic computational constructs. The implications for future synthetic designs, the general view of synthetic biology as a standard engineering domain, as well as potencial drawbacks are outlined.
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Affiliation(s)
- Javier Macia
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra, Barcelona, Spain
- Institut de Biologia Evolutiva, UPF-CSIC, Barcelona, Spain
- * E-mail: (JM); (RS)
| | - Ricard Sole
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra, Barcelona, Spain
- Institut de Biologia Evolutiva, UPF-CSIC, Barcelona, Spain
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
- * E-mail: (JM); (RS)
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29
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Sarker B, Papageorgiou DG, Silva R, Zehnder T, Gul-E-Noor F, Bertmer M, Kaschta J, Chrissafis K, Detsch R, Boccaccini AR. Fabrication of alginate–gelatin crosslinked hydrogel microcapsules and evaluation of the microstructure and physico-chemical properties. J Mater Chem B 2014; 2:1470-1482. [DOI: 10.1039/c3tb21509a] [Citation(s) in RCA: 261] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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30
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Reward-based hypertension control by a synthetic brain-dopamine interface. Proc Natl Acad Sci U S A 2013; 110:18150-5. [PMID: 24127594 DOI: 10.1073/pnas.1312414110] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Synthetic biology has significantly advanced the design of synthetic trigger-controlled devices that can reprogram mammalian cells to interface with complex metabolic activities. In the brain, the neurotransmitter dopamine coordinates communication with target neurons via a set of dopamine receptors that control behavior associated with reward-driven learning. This dopamine transmission has recently been suggested to increase central sympathetic outflow, resulting in plasma dopamine levels that correlate with corresponding brain activities. By functionally rewiring the human dopamine receptor D1 (DRD1) via the second messenger cyclic adenosine monophosphate (cAMP) to synthetic promoters containing cAMP response element-binding protein 1(CREB1)-specific cAMP-responsive operator modules, we have designed a synthetic dopamine-sensitive transcription controller that reversibly fine-tunes specific target gene expression at physiologically relevant brain-derived plasma dopamine levels. Following implantation of circuit-transgenic human cell lines insulated by semipermeable immunoprotective microcontainers into mice, the designer device interfaced with dopamine-specific brain activities and produced a systemic expression response when the animal's reward system was stimulated by food, sexual arousal, or addictive drugs. Reward-triggered brain activities were able to remotely program peripheral therapeutic implants to produce sufficient amounts of the atrial natriuretic peptide, which reduced the blood pressure of hypertensive mice to the normal physiologic range. Seamless control of therapeutic transgenes by subconscious behavior may provide opportunities for treatment strategies of the future.
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31
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Heng BC, Aubel D, Fussenegger M. G protein-coupled receptors revisited: therapeutic applications inspired by synthetic biology. Annu Rev Pharmacol Toxicol 2013; 54:227-49. [PMID: 24160705 DOI: 10.1146/annurev-pharmtox-011613-135921] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
G protein-coupled receptors (GPCRs) mediate the majority of cellular responses to hormones and neurotransmitters within the human body. They have much potential in the emerging field of synthetic biology, which is the rational, systematic design of biological systems with desired functionality. The responsiveness of GPCRs to a plethora of endogenous and exogenous ligands and stimuli make them ideal sensory receptor modules of synthetic gene networks. Such networks can activate target gene expression in response to a specific stimulus. Additionally, because GPCRs are important pharmacological targets of various human diseases, genes encoding their protein/peptide ligands can also be incorporated as target genes of the response output elements of synthetic gene networks. This review aims to critically examine the potential role of GPCRs in constructing therapeutic synthetic gene networks and to discuss various challenges in utilizing GPCRs for synthetic biology applications.
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Affiliation(s)
- Boon Chin Heng
- Department of Biosystems Science and Engineering, ETH Zürich, CH-4058 Basel, Switzerland;
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32
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Ausländer S, Fussenegger M. From gene switches to mammalian designer cells: present and future prospects. Trends Biotechnol 2013; 31:155-68. [DOI: 10.1016/j.tibtech.2012.11.006] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Revised: 11/14/2012] [Accepted: 11/14/2012] [Indexed: 10/27/2022]
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Abstract
Synthetic biology, application of synthetic chemistry to biology, is a broad term that covers the engineering of biological systems with structures and functions not found in nature to process information, manipulate chemicals, produce energy, maintain cell environment and enhance human health. Synthetic biology devices contribute not only to improve our understanding of disease mechanisms, but also provide novel diagnostic tools. Methods based on synthetic biology enable the design of novel strategies for the treatment of cancer, immune diseases metabolic disorders and infectious diseases as well as the production of cheap drugs. The potential of synthetic genome, using an expanded genetic code that is designed for specific drug synthesis as well as delivery and activation of the drug in vivo by a pathological signal, was already pointed out during a lecture delivered at Kuwait University in 2005. Of two approaches to synthetic biology, top-down and bottom-up, the latter is more relevant to the development of personalized medicines as it provides more flexibility in constructing a partially synthetic cell from basic building blocks for a desired task.
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Affiliation(s)
- K K Jain
- PharmaBiotech, Basel, Switzerland.
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34
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Singh AV, Khare M, Gade WN, Zamboni P. Theranostic implications of nanotechnology in multiple sclerosis: a future perspective. Autoimmune Dis 2012; 2012:160830. [PMID: 23346386 PMCID: PMC3546454 DOI: 10.1155/2012/160830] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Accepted: 11/09/2012] [Indexed: 11/17/2022] Open
Abstract
Multiple Sclerosis is a multifactorial disease with several pathogenic mechanisms and pathways. Successful MS management and medical care requires early accurate diagnosis along with specific treatment protocols based upon multifunctional nanotechnology approach. This paper highlights advances in nanotechnology that have enabled the clinician to target the brain and CNS in patient with multiple sclerosis with nanoparticles having therapeutic and imaging components. The multipartite theranostic (thera(py) + (diag)nostics) approach puts forth strong implications for medical care and cure in MS. The current nanotheranostics utilize tamed drug vehicles and contain cargo, targeting ligands, and imaging labels for delivery to specific tissues, cells, or subcellular components. A brief overview of nonsurgical nanorepair advances as future perspective is also described. Considering the potential inflammatory triggers in MS pathogenesis, a multifunctional nanotechnology approach will be needed for the prognosis.
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Affiliation(s)
- Ajay Vikram Singh
- Department of Biotechnology, University of Pune, Ganeshkhind Road, Pune 411 007, India
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Room 2145, 110 8th Street, Troy, NY 12180, USA
| | - Manish Khare
- Department of Applied Sciences, Maharashtra Academy of Engineering, Alandi (D), Pune 412 105, India
| | - W. N. Gade
- Department of Biotechnology, University of Pune, Ganeshkhind Road, Pune 411 007, India
| | - Paolo Zamboni
- Centre for Vascular Disease, University of Ferrara, 41100 Ferrara, Italy
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Bugaj LJ, Schaffer DV. Bringing next-generation therapeutics to the clinic through synthetic biology. Curr Opin Chem Biol 2012; 16:355-61. [DOI: 10.1016/j.cbpa.2012.04.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Accepted: 04/15/2012] [Indexed: 01/21/2023]
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36
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Affiliation(s)
- David Ausländer
- Department of Biosystems Science and Engineering, Basel, Switzerland
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37
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Wieland M, Fussenegger M. Engineering Molecular Circuits Using Synthetic Biology in Mammalian Cells. Annu Rev Chem Biomol Eng 2012; 3:209-34. [DOI: 10.1146/annurev-chembioeng-061010-114145] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Markus Wieland
- Department of Biosystems Science and Bioengineering, ETH Zurich, CH-4058 Basel, Switzerland; ,
| | - Martin Fussenegger
- Department of Biosystems Science and Bioengineering, ETH Zurich, CH-4058 Basel, Switzerland; ,
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38
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Smolke CD, Tyo KE. Synthetic biology: Emerging methodologies to catalyze the metabolic engineering design cycle. Metab Eng 2012; 14:187-8. [DOI: 10.1016/j.ymben.2012.03.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Perán M, García MA, López-Ruiz E, Bustamante M, Jiménez G, Madeddu R, Marchal JA. Functionalized nanostructures with application in regenerative medicine. Int J Mol Sci 2012; 13:3847-3886. [PMID: 22489186 PMCID: PMC3317746 DOI: 10.3390/ijms13033847] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2012] [Revised: 03/03/2012] [Accepted: 03/06/2012] [Indexed: 12/16/2022] Open
Abstract
In the last decade, both regenerative medicine and nanotechnology have been broadly developed leading important advances in biomedical research as well as in clinical practice. The manipulation on the molecular level and the use of several functionalized nanoscaled materials has application in various fields of regenerative medicine including tissue engineering, cell therapy, diagnosis and drug and gene delivery. The themes covered in this review include nanoparticle systems for tracking transplanted stem cells, self-assembling peptides, nanoparticles for gene delivery into stem cells and biomimetic scaffolds useful for 2D and 3D tissue cell cultures, transplantation and clinical application.
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Affiliation(s)
- Macarena Perán
- Department of Health Sciences, University of Jaén, Jaén E-23071, Spain; E-Mails: (M.P.); (E.L.-R.)
| | - María A. García
- Research Unit, Hospital Universitario Virgen de las Nieves, Granada E-18014, Spain; E-Mail:
| | - Elena López-Ruiz
- Department of Health Sciences, University of Jaén, Jaén E-23071, Spain; E-Mails: (M.P.); (E.L.-R.)
| | - Milán Bustamante
- Biosciences Institute, University College Cork, Cork, Ireland; E-Mail:
| | - Gema Jiménez
- Biopathology and Regenerative Medicine Institute (IBIMER), Biomedical Research Centre, University of Granada, Granada E-18100, Spain; E-Mail:
| | - Roberto Madeddu
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; E-Mail:
| | - Juan A. Marchal
- Biopathology and Regenerative Medicine Institute (IBIMER), Biomedical Research Centre, University of Granada, Granada E-18100, Spain; E-Mail:
- Department of Human Anatomy and Embryology, Faculty of Medicine, University of Granada, Granada E-18012, Spain
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +34-958-249-321; Fax: +34-958-246-296
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