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de Rossi J, Arefeayne Y, Robinson A, Segatori L. Emerging technologies for genetic control systems in cellular therapies. Curr Opin Biotechnol 2022; 78:102833. [PMID: 36334445 PMCID: PMC10091305 DOI: 10.1016/j.copbio.2022.102833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/23/2022] [Accepted: 10/02/2022] [Indexed: 11/06/2022]
Abstract
Progress in synthetic biology has enabled the construction of designer cells that sense biological inputs, and, in response, activate user-defined biomolecular programs. Such engineered cells provide unique opportunities for treating a wide variety of diseases. Current strategies mostly rely on cell-surface receptor systems engineered to convert binding interactions into activation of a transcriptional program. Genetic control systems are emerging as an appealing alternative to receptor-based sensors as they overcome the need for receptor engineering and result in cellular behaviors that operate over therapeutically relevant timescales. Genetic control systems include synthetic gene networks, RNA-based sensors, and post-translational tools. These technologies present fundamental challenges, including the requirement for precise integration with innate pathways, the need for parts orthogonal to existing circuitries, and the metabolic burden induced by such complex cell engineering endeavors. This review discusses the challenges in the design of genetic control systems for cellular therapies and their translational applications.
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Affiliation(s)
- Jacopo de Rossi
- Systems, Synthetic, and Physical Biology, Rice University, Houston, United States
| | - Yafet Arefeayne
- Department of Bioengineering, Rice University, Houston, United States
| | - Ashley Robinson
- Systems, Synthetic, and Physical Biology, Rice University, Houston, United States
| | - Laura Segatori
- Systems, Synthetic, and Physical Biology, Rice University, Houston, United States; Department of Bioengineering, Rice University, Houston, United States; Department of Chemical and Biomolecular Engineering, Rice University, Houston, United States; Department of Biosciences, Rice University, Houston, United States.
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2
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Mahameed M, Fussenegger M. Engineering autonomous closed-loop designer cells for disease therapy. iScience 2022; 25:103834. [PMID: 35243222 PMCID: PMC8857602 DOI: 10.1016/j.isci.2022.103834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Mohamed Mahameed
- ETH Zurich, Department of Biosystems Science and Engineering, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Martin Fussenegger
- ETH Zurich, Department of Biosystems Science and Engineering, Mattenstrasse 26, CH-4058 Basel, Switzerland
- University of Basel, Faculty of Life Science, 4001 Basel, Switzerland
- Corresponding author
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3
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Da CM, Liao HY, Deng YS, Zhao GH, Ma L, Zhang HH. Transcription Factor SP2 Regulates Ski-mediated Astrocyte Proliferation In Vitro. Neuroscience 2021; 479:22-34. [PMID: 34687796 DOI: 10.1016/j.neuroscience.2021.10.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/24/2021] [Accepted: 10/11/2021] [Indexed: 10/20/2022]
Abstract
Transcription factors bind specific sequences upstream of the 5' end of their target genes to ensure proper spatiotemporal expression of the target gene. This study aims to demonstrate that the transcription factor SP2 regulates expression of the Ski gene, which has specific binding sites for SP2, and thus enables Ski to regulate astrocyte proliferation. The upstream regulation mechanism of astrocyte proliferation was explored to further regulate the formation of glial scar in specific time and space after spinal cord injury. JASPAR and UCSC databases were used to predict transcription factor binding and the threshold was gradually reduced to screen transcription factors upstream of Ski, leading to the identification of SP2. Next, we analyzed the correlation between the expression of SP2 and Ski in normal astrocytes and reactive astrocytes, as well as the changes in astrocyte proliferation. To confirm that SP2 regulates Ski during astrocyte proliferation, astrocytes were transfected siRNA targeting SP2 and then astrocyte proliferation were analyzed. Finally, a dual luciferase reporter assay and Chromatin immunoprecipitation (ChIP) assay confirmed that the promoter region of Ski contained a specific SP2 binding site. This is the first that SP2 has been identified and confirmed to play an important role in astrocyte proliferation by regulating Ski expression. These results may help identify novel targets for the treatment of spinal cord injury.
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Affiliation(s)
- Chao-Ming Da
- The Second Clinical Medical College of Lanzhou University, 82 Cuiying Men, Lanzhou 730030, PR China; Gansu Provincial Maternal and Child Health Hospital, 143Qilihe North Street, Lanzhou 730050, PR China
| | - Hai-Yang Liao
- The Second Clinical Medical College of Lanzhou University, 82 Cuiying Men, Lanzhou 730030, PR China
| | - Yin-Shuan Deng
- Gansu Provincial Maternal and Child Health Hospital, 143Qilihe North Street, Lanzhou 730050, PR China
| | - Guang-Hai Zhao
- The Second Clinical Medical College of Lanzhou University, 82 Cuiying Men, Lanzhou 730030, PR China; Gansu Provincial Maternal and Child Health Hospital, 143Qilihe North Street, Lanzhou 730050, PR China
| | - Lin Ma
- The Second Clinical Medical College of Lanzhou University, 82 Cuiying Men, Lanzhou 730030, PR China; Gansu Provincial Maternal and Child Health Hospital, 143Qilihe North Street, Lanzhou 730050, PR China
| | - Hai-Hong Zhang
- The Second Clinical Medical College of Lanzhou University, 82 Cuiying Men, Lanzhou 730030, PR China.
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4
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Phage therapeutics: from promises to practices and prospectives. Appl Microbiol Biotechnol 2021; 105:9047-9067. [PMID: 34821965 PMCID: PMC8852341 DOI: 10.1007/s00253-021-11695-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 11/10/2021] [Accepted: 11/15/2021] [Indexed: 01/09/2023]
Abstract
The rise in multi-drug resistant bacteria and the inability to develop novel antibacterial agents limits our arsenal against infectious diseases. Antibiotic resistance is a global issue requiring an immediate solution, including the development of new antibiotic molecules and other alternative modes of therapy. This article highlights the mechanism of bacteriophage treatment that makes it a real solution for multidrug-resistant infectious diseases. Several case reports identified phage therapy as a potential solution to the emerging challenge of multi-drug resistance. Bacteriophages, unlike antibiotics, have special features, such as host specificity and do not impact other commensals. A new outlook has also arisen with recent advancements in the understanding of phage immunobiology, where phages are repurposed against both bacterial and viral infections. Thus, the potential possibility of phages in COVID-19 patients with secondary bacterial infections has been briefly elucidated. However, significant obstacles that need to be addressed are to design better clinical studies that may contribute to the widespread use of bacteriophage therapy against multi-drug resistant pathogens. In conclusion, antibacterial agents can be used with bacteriophages, i.e. bacteriophage-antibiotic combination therapy, or they can be administered alone in cases when antibiotics are ineffective. Key points • AMR, a consequence of antibiotic generated menace globally, has led to the resurgence of phage therapy as an effective and sustainable solution without any side effects and high specificity against refractory MDR bacterial infections. • Bacteriophages have fewer adverse reactions and can thus be used as monotherapy as well as in conjunction with antibiotics. • In the context of the COVID-19 pandemic, phage therapy may be a viable option.
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Huang X, Wang M, Liu Y, Gui Y. Synthesis of RNA-based gene regulatory devices for redirecting cellular signaling events mediated by p53. Am J Cancer Res 2021; 11:4688-4698. [PMID: 33754021 PMCID: PMC7978309 DOI: 10.7150/thno.55856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 02/12/2021] [Indexed: 11/05/2022] Open
Abstract
Rationale: The p53 gene is a well-known tumor suppressor, and its mutation often contributes to the occurrence and development of tumors. Due to the diversity and complexity of p53 mutations, there is still no effective p53 gene therapy. In this study, we designed and constructed an aptazyme switch that could effectively sense cellular wild-type p53 protein and regulate downstream gene function flexibly. The application of this artificial device in combination with Cre-LoxP and dCas9-VP64 tools achieved a precisely targeted killing effect on tumor cells. Methods: The affinity of the aptamer to p53 protein was verified by SPR. p53 aptazyme and gene circuits were chemically synthesized. The function of the gene circuit was detected by cell proliferation assay, apoptosis assay and Western blot. The nude mouse transplantation tumor experiment was used to evaluate the inhibitory effect of gene circuits on tumor cells in vivo. Results: The results of the SPR experiment showed that the p53 aptamer RNA sequence had a robust binding effect with p53 protein. The p53 aptazyme could efficiently sense wild-type p53 protein and initiate self-cleavage in cells. The Cre-p53 aptazyme gene circuit and dCas9-VP64/sgRNA mediated gene circuit designed based on p53 aptazyme significantly inhibited the growth and promoted the apoptosis of wild-type p53-deficient cancer cells in vitro. In addition, the gene circuits also had a significant inhibitory effect on tumors in vivo. Conclusion: The study developed a novel and efficient ribozyme switch for p53-specific recognition and provided a modular strategy for aptazyme binding to cellular proteins. In addition, the p53 aptazyme successfully inhibited tumor growth through a combined application with other synthetic biological tools, providing a new perspective for cancer therapy.
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6
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Becskei A. Tuning up Transcription Factors for Therapy. Molecules 2020; 25:E1902. [PMID: 32326099 PMCID: PMC7221782 DOI: 10.3390/molecules25081902] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/16/2020] [Accepted: 04/17/2020] [Indexed: 12/19/2022] Open
Abstract
The recent developments in the delivery and design of transcription factors put their therapeutic applications within reach, exemplified by cell replacement, cancer differentiation and T-cell based cancer therapies. The success of such applications depends on the efficacy and precision in the action of transcription factors. The biophysical and genetic characterization of the paradigmatic prokaryotic repressors, LacI and TetR and the designer transcription factors, transcription activator-like effector (TALE) and CRISPR-dCas9 revealed common principles behind their efficacy, which can aid the optimization of transcriptional activators and repressors. Further studies will be required to analyze the linkage between dissociation constants and enzymatic activity, the role of phase separation and squelching in activation and repression and the long-range interaction of transcription factors with epigenetic regulators in the context of the chromosomes. Understanding these mechanisms will help to tailor natural and synthetic transcription factors to the needs of specific applications.
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Affiliation(s)
- Attila Becskei
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
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Krawczyk K, Scheller L, Kim H, Fussenegger M. Rewiring of endogenous signaling pathways to genomic targets for therapeutic cell reprogramming. Nat Commun 2020; 11:608. [PMID: 32001704 PMCID: PMC6992713 DOI: 10.1038/s41467-020-14397-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 12/12/2019] [Indexed: 12/22/2022] Open
Abstract
Rewiring cellular sensors to trigger non-natural responses is fundamental for therapeutic cell engineering. Current designs rely on engineered receptors that are limited to single inputs, and often suffer from high leakiness and low fold induction. Here, we present Generalized Engineered Activation Regulators (GEARs) that overcome these limitations by being pathway-specific rather than input-specific. GEARs consist of the MS2 bacteriophage coat protein fused to regulatory or transactivation domains, and work by rerouting activation of the NFAT, NFκB, MAPK or SMAD pathways to dCas9-directed gene expression from genomic loci. This system enables membrane depolarization-induced activation of insulin expression in β-mimetic cells and IL-12 expression in activated Jurkat cells, as well as IL-12 production in response to the immunomodulatory cytokines TGFβ and TNFα in HEK293T cells. Engineered cells with the ability to reinterpret the extracellular milieu have potential for applications in immunotherapy and in the treatment of metabolic diseases. Current cellular rewiring designs are typically tailored to detect single inputs. Here the authors present GEARs that function independently of engineered receptor/reporter systems and directly reroute endogenous signaling pathways to alternative genomic loci using dCas9-directed gene expression.
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Affiliation(s)
- Krzysztof Krawczyk
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058, Basel, Switzerland
| | - Leo Scheller
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058, Basel, Switzerland
| | - Hyojin Kim
- 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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9
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Healy CP, Deans TL. Genetic circuits to engineer tissues with alternative functions. J Biol Eng 2019; 13:39. [PMID: 31073328 PMCID: PMC6500048 DOI: 10.1186/s13036-019-0170-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 04/17/2019] [Indexed: 12/23/2022] Open
Abstract
Persistent and complex problems arising with respect to human physiology and pathology have led to intense investigation into therapies and tools that permit more targeted outcomes and biomimetic responses to pathological conditions. A primary goal in mammalian synthetic biology is to build genetic circuits that exert fine control over cell behavior for next-generation biomedical applications. In pursuit of this, synthetic biologists have engineered cells endowed with genetic circuits with sensor that are capable of reacting to a variety of stimuli and responding with targeted behavior. Here, we highlight how synthetic biology approaches are being used to program cells with novel functions for therapeutic applications, and how they can be used in stem cells to improve differentiation outcomes. These approaches open the possibilities for engineering synthetic tissues for employing personalized medicine and to develop next-generation biomedical therapies.
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Affiliation(s)
- C P Healy
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT 84112 USA
| | - T L Deans
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT 84112 USA
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10
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Ito A, Teranishi R, Kamei K, Yamaguchi M, Ono A, Masumoto S, Sonoda Y, Horie M, Kawabe Y, Kamihira M. Magnetically triggered transgene expression in mammalian cells by localized cellular heating of magnetic nanoparticles. J Biosci Bioeng 2019; 128:355-364. [PMID: 30962099 DOI: 10.1016/j.jbiosc.2019.03.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 03/07/2019] [Accepted: 03/11/2019] [Indexed: 10/27/2022]
Abstract
To develop a remote control system of transgene expression through localized cellular heating of magnetic nanoparticles, a heat-inducible transgene expression system was introduced into mammalian cells. Cells were labeled with magnetic nanoparticles and exposed to an alternating magnetic field. The magnetically labeled cells expressed the transgene in a monolayer and multilayered cell sheets in which cells were heated around the magnetic nanoparticles without an apparent temperature increase in the culture medium. Magnetic cells were also generated by genetically engineering with a ferritin gene, and transgene expression could be induced by exposure to an alternating magnetic field. This approach may be applicable to the development of novel gene therapies in cell-based medicine.
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Affiliation(s)
- Akira Ito
- Department of Chemical Engineering, Faculty of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Ryoji Teranishi
- Department of Chemical Engineering, Faculty of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Kazuki Kamei
- Department of Chemical Engineering, Faculty of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Masaki Yamaguchi
- Department of Chemical Engineering, Faculty of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Akihiko Ono
- Graduate School of Systems Life Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Shinya Masumoto
- Department of Chemical Engineering, Faculty of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Yuto Sonoda
- Department of Chemical Engineering, Faculty of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Masanobu Horie
- Division of Biochemical Engineering, Radioisotope Research Center, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yoshinori Kawabe
- Department of Chemical Engineering, Faculty of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Masamichi Kamihira
- Department of Chemical Engineering, Faculty of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan; Graduate School of Systems Life Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.
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11
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Zhan H, Xie H, Zhou Q, Liu Y, Huang W. Synthesizing a Genetic Sensor Based on CRISPR-Cas9 for Specifically Killing p53-Deficient Cancer Cells. ACS Synth Biol 2018; 7:1798-1807. [PMID: 29957992 DOI: 10.1021/acssynbio.8b00202] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Cancer is still one of the greatest medical challenges in the world. The p53 protein plays an important role in the process of cancer formation. In addition, p53 is found as the most common mutant gene in cancers. Because of the central role of p53 in oncology, it is necessary to construct effective sensors to detect this protein. However, there are few methods to detect wild type p53 protein (WTP53) or to distinguish the wild type and mutant p53 proteins. In our study, we designed and constructed a p53 genetic sensor that detected the expression of WTP53 in cells. Moreover, we combined the p53 sensor with diphtheria toxin using the CRISPR-Cas9 system to construct a p53 genetic sensor that specifically killed p53-deficient cells such as tumor cells. Our study therefore developed a new way to treat cancers by using an available genetic sensor based on p53 protein.
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Affiliation(s)
- Hengji Zhan
- Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Carson International Cancer Center, Shenzhen University School of Medicine, Shenzhen 518039, China
| | - Haibiao Xie
- Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Carson International Cancer Center, Shenzhen University School of Medicine, Shenzhen 518039, China
| | - Qun Zhou
- Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Carson International Cancer Center, Shenzhen University School of Medicine, Shenzhen 518039, China
| | - Yuchen Liu
- Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Carson International Cancer Center, Shenzhen University School of Medicine, Shenzhen 518039, China
| | - Weiren Huang
- Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Carson International Cancer Center, Shenzhen University School of Medicine, Shenzhen 518039, China
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12
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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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13
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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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14
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Liu Y, Li J, Tschirhart T, Terrell JL, Kim E, Tsao C, Kelly DL, Bentley WE, Payne GF. Connecting Biology to Electronics: Molecular Communication via Redox Modality. Adv Healthc Mater 2017; 6. [PMID: 29045017 DOI: 10.1002/adhm.201700789] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 08/18/2017] [Indexed: 12/13/2022]
Abstract
Biology and electronics are both expert at for accessing, analyzing, and responding to information. Biology uses ions, small molecules, and macromolecules to receive, analyze, store, and transmit information, whereas electronic devices receive input in the form of electromagnetic radiation, process the information using electrons, and then transmit output as electromagnetic waves. Generating the capabilities to connect biology-electronic modalities offers exciting opportunities to shape the future of biosensors, point-of-care medicine, and wearable/implantable devices. Redox reactions offer unique opportunities for bio-device communication that spans the molecular modalities of biology and electrical modality of devices. Here, an approach to search for redox information through an interactive electrochemical probing that is analogous to sonar is adopted. The capabilities of this approach to access global chemical information as well as information of specific redox-active chemical entities are illustrated using recent examples. An example of the use of synthetic biology to recognize external molecular information, process this information through intracellular signal transduction pathways, and generate output responses that can be detected by electrical modalities is also provided. Finally, exciting results in the use of redox reactions to actuate biology are provided to illustrate that synthetic biology offers the potential to guide biological response through electrical cues.
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Affiliation(s)
- Yi Liu
- Institute for Bioscience and Biotechnology Research and Fischell Department of Bioengineering University of Maryland College Park MD 20742 USA
| | - Jinyang Li
- Institute for Bioscience and Biotechnology Research and Fischell Department of Bioengineering University of Maryland College Park MD 20742 USA
| | - Tanya Tschirhart
- Institute for Bioscience and Biotechnology Research and Fischell Department of Bioengineering University of Maryland College Park MD 20742 USA
| | - Jessica L. Terrell
- Institute for Bioscience and Biotechnology Research and Fischell Department of Bioengineering University of Maryland College Park MD 20742 USA
| | - Eunkyoung Kim
- Institute for Bioscience and Biotechnology Research and Fischell Department of Bioengineering University of Maryland College Park MD 20742 USA
| | - Chen‐Yu Tsao
- Institute for Bioscience and Biotechnology Research and Fischell Department of Bioengineering University of Maryland College Park MD 20742 USA
| | - Deanna L. Kelly
- Maryland Psychiatric Research Center University of Maryland School of Medicine Baltimore MD 21228 USA
| | - William E. Bentley
- Institute for Bioscience and Biotechnology Research and Fischell Department of Bioengineering University of Maryland College Park MD 20742 USA
| | - Gregory F. Payne
- Institute for Bioscience and Biotechnology Research and Fischell Department of Bioengineering University of Maryland College Park MD 20742 USA
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15
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Kojima R, Scheller L, Fussenegger M. Nonimmune cells equipped with T-cell-receptor-like signaling for cancer cell ablation. Nat Chem Biol 2017; 14:42-49. [PMID: 29131143 PMCID: PMC5730048 DOI: 10.1038/nchembio.2498] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 09/14/2017] [Indexed: 12/16/2022]
Abstract
The ability to engineer custom cell-contact-sensing output devices into
human non-immune cells would be useful for extending the applicability of
cell-based cancer therapies and avoiding risks associated with engineered immune
cells. Here, we have developed a new class of synthetic T-cell receptor-like
signal-transduction device that functions efficiently in human non-immune cells
and triggers release of output molecules specifically upon sensing contact with
a target cell. This device employs an interleukin signaling cascade, whose
OFF/ON switching is controlled by biophysical segregation of a transmembrane
signal-inhibitory protein from the sensor cell/target cell interface. We further
showed that designer non-immune cells equipped with this device driving
expression of a membrane-penetrator/prodrug-activating enzyme construct could
specifically kill target cells in the presence of the prodrug, indicating its
potential usefulness for target-cell-specific, cell-based enzyme-prodrug cancer
therapy. Our study also contributes to advancement of synthetic biology by
extending available design principles to transmit extracellular information to
cells.
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Affiliation(s)
- Ryosuke Kojima
- ETH Zurich, Department of Biosystems Science and Engineering, Basel, Switzerland
| | - Leo Scheller
- ETH Zurich, Department of Biosystems Science and Engineering, Basel, Switzerland
| | - Martin Fussenegger
- ETH Zurich, Department of Biosystems Science and Engineering, Basel, Switzerland.,Faculty of Life Science, University of Basel, Basel, Switzerland
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16
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Mircetic J, Dietrich A, Paszkowski-Rogacz M, Krause M, Buchholz F. Development of a genetic sensor that eliminates p53 deficient cells. Nat Commun 2017; 8:1463. [PMID: 29133879 PMCID: PMC5684360 DOI: 10.1038/s41467-017-01688-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 10/09/2017] [Indexed: 01/22/2023] Open
Abstract
The TP53 gene fulfills a central role in protecting cells from genetic insult. Given this crucial role it might be surprising that p53 itself is not essential for cell survival. Indeed, TP53 is the single most mutated gene across different cancer types. Thus, both a theoretical and a question of significant practical applicability arise: can cells be programmed to make TP53 an essential gene? Here we present a genetic p53 sensor, in which the loss of p53 is coupled to the rise of HSV-TK expression. We show that the sensor can distinguish both p53 knockout and cells expressing a common TP53 cancer mutation from otherwise isogenic TP53 wild-type cells. Importantly, the system is sensitive enough to specifically target TP53 loss-of-function cells with the HSV-TK pro-drug Ganciclovir both in vitro and in vivo. Our work opens new ways to programming cell intrinsic transformation protection systems that rely on endogenous components. TP53 is mutated in many cancers, a system to detect and selectively eliminate p53 mutant cells is an attractive therapeutic strategy. Here, the authors present a genetic sensor that can detect p53 activity and is coupled to the thymidine kinase gene, which can activate the drug Ganciclovir, resulting in cell death.
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Affiliation(s)
- Jovan Mircetic
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, TU Dresden, 01307, Dresden, Germany
| | - Antje Dietrich
- German Cancer Consortium (DKTK), OncoRay-National Center for Radiation Research in Oncology, Medical Faculty and University Hospital Carl Gustav Carus, TU Dresden, Dresden and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Maciej Paszkowski-Rogacz
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, TU Dresden, 01307, Dresden, Germany
| | - Mechthild Krause
- German Cancer Consortium (DKTK), OncoRay-National Center for Radiation Research in Oncology, Medical Faculty and University Hospital Carl Gustav Carus, TU Dresden, Dresden and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Department of Radiation Oncology, Medical Faculty and University Hospital Carl Gustav Carus, TU Dresden, 01307, Dresden, Germany.,Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiooncology, 01328, Dresden, Germany.,German Cancer Research Center (DKFZ), Heidelberg and German Cancer Consortium (DKTK) Partner Site Dresden, 01307, Dresden, Germany.,National Center for Tumor Diseases (NCT), University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
| | - Frank Buchholz
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, TU Dresden, 01307, Dresden, Germany. .,German Cancer Research Center (DKFZ), Heidelberg and German Cancer Consortium (DKTK) Partner Site Dresden, 01307, Dresden, Germany. .,National Center for Tumor Diseases (NCT), University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany. .,Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany.
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18
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Rampley CPN, Davison PA, Qian P, Preston GM, Hunter CN, Thompson IP, Wu LJ, Huang WE. Development of SimCells as a novel chassis for functional biosensors. Sci Rep 2017; 7:7261. [PMID: 28775370 PMCID: PMC5543166 DOI: 10.1038/s41598-017-07391-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 06/28/2017] [Indexed: 01/31/2023] Open
Abstract
This work serves as a proof-of-concept for bacterially derived SimCells (Simple Cells), which contain the cell machinery from bacteria and designed DNA (or potentially a simplified genome) to instruct the cell to carry out novel, specific tasks. SimCells represent a reprogrammable chassis without a native chromosome, which can host designed DNA to perform defined functions. In this paper, the use of Escherichia coli MC1000 ∆minD minicells as a non-reproducing chassis for SimCells was explored, as demonstrated by their ability to act as sensitive biosensors for small molecules. Highly purified minicells derived from E. coli strains containing gene circuits for biosensing were able to transduce the input signals from several small molecules (glucarate, acrylate and arabinose) into the production of green fluorescent protein (GFP). A mathematical model was developed to fit the experimental data for induction of gene expression in SimCells. The intracellular ATP level was shown to be important for SimCell function. A purification and storage protocol was developed to prepare SimCells which could retain their functions for an extended period of time. This study demonstrates that SimCells are able to perform as ‘smart bioparticles’ controlled by designed gene circuits.
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Affiliation(s)
- Cordelia P N Rampley
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, United Kingdom
| | - Paul A Davison
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Pu Qian
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Gail M Preston
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, Oxford, United Kingdom
| | - C Neil Hunter
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Ian P Thompson
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, United Kingdom
| | - Ling Juan Wu
- The Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, United Kingdom
| | - Wei E Huang
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, United Kingdom.
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19
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Brown R, Lengeling A, Wang B. Phage engineering: how advances in molecular biology and synthetic biology are being utilized to enhance the therapeutic potential of bacteriophages. QUANTITATIVE BIOLOGY 2017. [DOI: 10.1007/s40484-017-0094-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Liu Y, Tsao C, Kim E, Tschirhart T, Terrell JL, Bentley WE, Payne GF. Using a Redox Modality to Connect Synthetic Biology to Electronics: Hydrogel-Based Chemo-Electro Signal Transduction for Molecular Communication. Adv Healthc Mater 2017; 6. [PMID: 27863177 DOI: 10.1002/adhm.201600908] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 10/15/2016] [Indexed: 01/08/2023]
Abstract
A hydrogel-based dual film coating is electrofabricated for transducing bio-relevant chemical information into electronical output. The outer film has a synthetic biology construct that recognizes an external molecular signal and transduces this input into the expression of an enzyme that converts redox-inactive substrate into a redox-active intermediate, which is detected through an amplification mechanism of the inner redox-capacitor film.
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Affiliation(s)
- Yi Liu
- Institute for Bioscience and Biotechnology Research University of Maryland College Park MD 20742 USA
| | - Chen‐Yu Tsao
- Fischell Department of Bioengineering University of Maryland College Park MD 20742 USA
| | - Eunkyoung Kim
- Institute for Bioscience and Biotechnology Research University of Maryland College Park MD 20742 USA
| | - Tanya Tschirhart
- Fischell Department of Bioengineering University of Maryland College Park MD 20742 USA
| | - Jessica L. Terrell
- Fischell Department of Bioengineering University of Maryland College Park MD 20742 USA
| | - William E. Bentley
- Institute for Bioscience and Biotechnology Research University of Maryland College Park MD 20742 USA
- Fischell Department of Bioengineering University of Maryland College Park MD 20742 USA
| | - Gregory F. Payne
- Institute for Bioscience and Biotechnology Research University of Maryland College Park MD 20742 USA
- Fischell Department of Bioengineering University of Maryland College Park MD 20742 USA
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21
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Giessen TW, Silver PA. Converting a Natural Protein Compartment into a Nanofactory for the Size-Constrained Synthesis of Antimicrobial Silver Nanoparticles. ACS Synth Biol 2016; 5:1497-1504. [PMID: 27276075 DOI: 10.1021/acssynbio.6b00117] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Engineered biological systems are used extensively for the production of high value and commodity organics. On the other hand, most inorganic nanomaterials are still synthesized via chemical routes. By engineering cellular compartments, functional nanoarchitectures can be produced under environmentally sustainable conditions. Encapsulins are a new class of microbial nanocompartments with promising applications in nanobiotechnology. Here, we engineer the Thermotoga maritima encapsulin EncTm to yield a designed compartment for the size-constrained synthesis of silver nanoparticles (Ag NPs). These Ag NPs exhibit uniform shape and size distributions as well as long-term stability. Ambient aqueous conditions can be used for Ag NP synthesis, while no reducing agents or solvents need to be added. The antimicrobial activity of the synthesized protein-coated or shell-free Ag NPs is superior to that of silver nitrate and citrate-capped Ag NPs. This study establishes encapsulins as an engineerable platform for the synthesis of biogenic functional nanomaterials.
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Affiliation(s)
- Tobias W. Giessen
- Department
of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
| | - Pamela A. Silver
- Department
of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
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22
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Li J, Zhuang C, Liu Y, Chen M, Zhou Q, Chen Z, He A, Zhao G, Guo Y, Wu H, Cai Z, Huang W. shRNA targeting long non-coding RNA CCAT2 controlled by tetracycline-inducible system inhibits progression of bladder cancer cells. Oncotarget 2016; 7:28989-97. [PMID: 27015551 PMCID: PMC5045372 DOI: 10.18632/oncotarget.8259] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 03/04/2016] [Indexed: 02/05/2023] Open
Abstract
Recent reports show that long non-coding RNAs (lncRNAs) are emerging as significant functional regulators in the development of tumors, including bladder cancer. Here, we found that CCAT2 was upregulated in bladder cancer tissues and cell lines. Through the statistical analyses, we also found that the high expression level of CCAT2 was positively correlated with histological grade and TNM stage of bladder cancer. Further experimental results revealed that knockdown of CCAT2 could decrease cell proliferation and migration as well as induce apoptosis in bladder cancer cells. Besides, using the post-transcriptional device of synthetic biology, we create the tetracycline-inducible double small hairpin RNAs (shRNAs) vector to control the expression level of CCAT2 which was induced by doxycycline in a dosage-dependent manner. In summary, our data indicated that CCAT2 may be an oncogene and a therapeutic target in bladder cancer. The expression of CCAT2 can be quantitatively controlled by the synthetic "tetracycline-on" switch system in bladder cancer in response to different concentrations of doxycycline to inhibit the development of bladder cancer cells.
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Affiliation(s)
- Jianfa Li
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, China
- Shantou University Medical College, Shantou, China
| | - Chengle Zhuang
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, China
- Shantou University Medical College, Shantou, China
| | - Yuchen Liu
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Mingwei Chen
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, China
- Anhui Medical University, Hefei, China
| | - Qing Zhou
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Zhicong Chen
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, China
- Shantou University Medical College, Shantou, China
| | - Anbang He
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, China
- Anhui Medical University, Hefei, China
| | - Guoping Zhao
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Yinglu Guo
- Department of Urology, Peking University First Hospital, Institute of Urology, Peking University, National Urological Cancer Center, Beijing, China
| | - Hanwei Wu
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Zhiming Cai
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, China
- Shantou University Medical College, Shantou, China
- Anhui Medical University, Hefei, China
- Department of Urology, Peking University First Hospital, Institute of Urology, Peking University, National Urological Cancer Center, Beijing, China
| | - Weiren Huang
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, China
- Shantou University Medical College, Shantou, China
- Anhui Medical University, Hefei, China
- Department of Urology, Peking University First Hospital, Institute of Urology, Peking University, National Urological Cancer Center, Beijing, China
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Lu TK, Chandrasegaran S, Hodak H. The Era of Synthetic Biology and Genome Engineering: Where No Man Has Gone Before. J Mol Biol 2016; 428:835-6. [PMID: 26827726 DOI: 10.1016/j.jmb.2016.01.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Timothy K Lu
- MIT Microbiology Program, Massachusetts Institute of Technology, Cambridge, MA, United States; MIT Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, United States; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, United States; Harvard Biophysics Program, Harvard University, Boston, MA, United States; Broad Institute of MIT and Harvard, Cambridge, MA, United States.
| | - Srinivasan Chandrasegaran
- Department of Environmental Health Sciences, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States.
| | - Hélène Hodak
- Journal of Molecular Biology, Cambridge, MA, United States.
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24
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Zhang C, Tsoi R, You L. Addressing biological uncertainties in engineering gene circuits. Integr Biol (Camb) 2015; 8:456-64. [PMID: 26674800 DOI: 10.1039/c5ib00275c] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Synthetic biology has grown tremendously over the past fifteen years. It represents a new strategy to develop biological understanding and holds great promise for diverse practical applications. Engineering of a gene circuit typically involves computational design of the circuit, selection of circuit components, and test and optimization of circuit functions. A fundamental challenge in this process is the predictable control of circuit function due to multiple layers of biological uncertainties. These uncertainties can arise from different sources. We categorize these uncertainties into incomplete quantification of parts, interactions between heterologous components and the host, or stochastic dynamics of chemical reactions and outline potential design strategies to minimize or exploit them.
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Affiliation(s)
- Carolyn Zhang
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA
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