151
|
Furukawa K, Hohmann S. A fungicide-responsive kinase as a tool for synthetic cell fate regulation. Nucleic Acids Res 2015; 43:7162-70. [PMID: 26138483 PMCID: PMC4538845 DOI: 10.1093/nar/gkv678] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Accepted: 06/19/2015] [Indexed: 01/22/2023] Open
Abstract
Engineered biological systems that precisely execute defined tasks have major potential for medicine and biotechnology. For instance, gene- or cell-based therapies targeting pathogenic cells may replace time- and resource-intensive drug development. Engineering signal transduction systems is a promising, yet presently underexplored approach. Here, we exploit a fungicide-responsive heterologous histidine kinase for pathway engineering and synthetic cell fate regulation in the budding yeast Saccharomyces cerevisiae. Rewiring the osmoregulatory Hog1 MAPK signalling system generates yeast cells programmed to execute three different tasks. First, a synthetic negative feedback loop implemented by employing the fungicide-responsive kinase and a fungicide-resistant derivative reshapes the Hog1 activation profile, demonstrating how signalling dynamics can be engineered. Second, combinatorial integration of different genetic parts including the histidine kinases, a pathway activator and chemically regulated promoters enables control of yeast growth and/or gene expression in a two-input Boolean logic manner. Finally, we implemented a genetic ‘suicide attack’ system, in which engineered cells eliminate target cells and themselves in a specific and controllable manner. Taken together, fungicide-responsive kinases can be applied in different constellations to engineer signalling behaviour. Sensitizing engineered cells to existing chemicals may be generally useful for future medical and biotechnological applications.
Collapse
Affiliation(s)
- Kentaro Furukawa
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Stefan Hohmann
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| |
Collapse
|
152
|
Zeng G, Zhang R, Xuan W, Wang W, Liang FS. Constructing de novo H2O2 signaling via induced protein proximity. ACS Chem Biol 2015; 10:1404-10. [PMID: 25775006 PMCID: PMC4849873 DOI: 10.1021/acschembio.5b00170] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A new chemical strategy has been developed to generate de novo signaling pathways that link a signaling molecule, H2O2, to different downstream cellular events in mammalian cells. This approach combines the reactivity-based H2O2 sensing with the chemically induced protein proximity technology. By chemically modifying abscisic acid with an H2O2-sensitive boronate ester probe, novel H2O2 signaling pathways can be engineered to induce transcription, protein translocation and membrane ruffle formation upon exogenous or endogenous H2O2 stimulation. This strategy has also been successfully applied to gibberellic acid, which provides the potential to build signaling networks based on orthogonal cell stimuli.
Collapse
Affiliation(s)
- Guihua Zeng
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Roushu Zhang
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Weimin Xuan
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Wei Wang
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Fu-Sen Liang
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| |
Collapse
|
153
|
Wong S, Slavcev R. Treating cancer with infection: a review on bacterial cancer therapy. Lett Appl Microbiol 2015; 61:107-12. [DOI: 10.1111/lam.12436] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 04/08/2015] [Accepted: 04/27/2015] [Indexed: 12/13/2022]
Affiliation(s)
- S. Wong
- School of Pharmacy; University of Waterloo; Waterloo ON Canada
| | - R.A. Slavcev
- School of Pharmacy; University of Waterloo; Waterloo ON Canada
| |
Collapse
|
154
|
Hörner M, Kaufmann B, Cotugno G, Wiedtke E, Büning H, Grimm D, Weber W. A chemical switch for controlling viral infectivity. Chem Commun (Camb) 2015; 50:10319-22. [PMID: 25058661 DOI: 10.1039/c4cc03292f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Chemically triggered molecular switches for controlling the fate and function of biological systems are fundamental to the emergence of synthetic biology and the development of biomedical applications. We here present the first chemically triggered switch for controlling the infectivity of adeno-associated viral (AAV) vectors.
Collapse
Affiliation(s)
- Maximilian Hörner
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany.
| | | | | | | | | | | | | |
Collapse
|
155
|
|
156
|
Kanakov O, Kotelnikov R, Alsaedi A, Tsimring L, Huerta R, Zaikin A, Ivanchenko M. Multi-input distributed classifiers for synthetic genetic circuits. PLoS One 2015; 10:e0125144. [PMID: 25946237 PMCID: PMC4450813 DOI: 10.1371/journal.pone.0125144] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Accepted: 03/09/2015] [Indexed: 11/18/2022] Open
Abstract
For practical construction of complex synthetic genetic networks able to perform elaborate functions it is important to have a pool of relatively simple modules with different functionality which can be compounded together. To complement engineering of very different existing synthetic genetic devices such as switches, oscillators or logical gates, we propose and develop here a design of synthetic multi-input classifier based on a recently introduced distributed classifier concept. A heterogeneous population of cells acts as a single classifier, whose output is obtained by summarizing the outputs of individual cells. The learning ability is achieved by pruning the population, instead of tuning parameters of an individual cell. The present paper is focused on evaluating two possible schemes of multi-input gene classifier circuits. We demonstrate their suitability for implementing a multi-input distributed classifier capable of separating data which are inseparable for single-input classifiers, and characterize performance of the classifiers by analytical and numerical results. The simpler scheme implements a linear classifier in a single cell and is targeted at separable classification problems with simple class borders. A hard learning strategy is used to train a distributed classifier by removing from the population any cell answering incorrectly to at least one training example. The other scheme implements a circuit with a bell-shaped response in a single cell to allow potentially arbitrary shape of the classification border in the input space of a distributed classifier. Inseparable classification problems are addressed using soft learning strategy, characterized by probabilistic decision to keep or discard a cell at each training iteration. We expect that our classifier design contributes to the development of robust and predictable synthetic biosensors, which have the potential to affect applications in a lot of fields, including that of medicine and industry.
Collapse
Affiliation(s)
- Oleg Kanakov
- Oscillation Theory Department, Lobachevsky State University of Nizhniy Novgorod, Nizhniy Novgorod, Russia
- * E-mail:
| | - Roman Kotelnikov
- Department of Bioinformatics, Lobachevsky State University of Nizhniy Novgorod, Nizhniy Novgorod, Russia
| | - Ahmed Alsaedi
- Department of Mathematics, King AbdulAziz University, Jeddah, Saudi Arabia
| | - Lev Tsimring
- BioCircuits Institute, University of California San Diego, La Jolla CA, USA
| | - Ramón Huerta
- BioCircuits Institute, University of California San Diego, La Jolla CA, USA
| | - Alexey Zaikin
- Department of Bioinformatics, Lobachevsky State University of Nizhniy Novgorod, Nizhniy Novgorod, Russia
- Institute for Women’s Health and Department of Mathematics, University College London, London, United Kingdom
| | - Mikhail Ivanchenko
- Department of Bioinformatics, Lobachevsky State University of Nizhniy Novgorod, Nizhniy Novgorod, Russia
| |
Collapse
|
157
|
Wells DK, Chuang Y, Knapp LM, Brockmann D, Kath WL, Leonard JN. Spatial and functional heterogeneities shape collective behavior of tumor-immune networks. PLoS Comput Biol 2015; 11:e1004181. [PMID: 25905470 PMCID: PMC4408028 DOI: 10.1371/journal.pcbi.1004181] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 02/06/2015] [Indexed: 12/31/2022] Open
Abstract
Tumor growth involves a dynamic interplay between cancer cells and host cells, which collectively form a tumor microenvironmental network that either suppresses or promotes tumor growth under different conditions. The transition from tumor suppression to tumor promotion is mediated by a tumor-induced shift in the local immune state, and despite the clinical challenge this shift poses, little is known about how such dysfunctional immune states are initiated. Clinical and experimental observations have indicated that differences in both the composition and spatial distribution of different cell types and/or signaling molecules within the tumor microenvironment can strongly impact tumor pathogenesis and ultimately patient prognosis. How such “functional” and “spatial” heterogeneities confer such effects, however, is not known. To investigate these phenomena at a level currently inaccessible by direct observation, we developed a computational model of a nascent metastatic tumor capturing salient features of known tumor-immune interactions that faithfully recapitulates key features of existing experimental observations. Surprisingly, over a wide range of model formulations, we observed that heterogeneity in both spatial organization and cell phenotype drove the emergence of immunosuppressive network states. We determined that this observation is general and robust to parameter choice by developing a systems-level sensitivity analysis technique, and we extended this analysis to generate other parameter-independent, experimentally testable hypotheses. Lastly, we leveraged this model as an in silico test bed to evaluate potential strategies for engineering cell-based therapies to overcome tumor associated immune dysfunction and thereby identified modes of immune modulation predicted to be most effective. Collectively, this work establishes a new integrated framework for investigating and modulating tumor-immune networks and provides insights into how such interactions may shape early stages of tumor formation. Over the course of tumor growth, cancer cells interact with normal cells via processes that are difficult to understand by experiment alone. This challenge is particularly pronounced at early stages of tumor formation, when experimental observation is most limited. Elucidating such interactions could inform both understanding of cancer and clinical practice. To address this need we developed a computational model capturing the current understanding of how individual metastatic tumor cells and immune cells sense and contribute to the tumor environment, which in turn enabled us to investigate the complex, collective behavior of these systems. Surprisingly, we discovered that tumor escape from immune control was enhanced by the existence of small differences (or heterogeneities) in the responses of individual immune cells to their environment, as well as by heterogeneities in the way that cells and the molecules they secrete are arranged in space. These conclusions held true over a range of model formulations, suggesting that this is a general feature of these tumor-immune networks. Finally, we used this model as a test bed to evaluate potential strategies for enhancing immunological control of early tumors, ultimately predicting that specifically modulating tumor-associated immune dysfunction may be more effective than simply enhanced tumor killing.
Collapse
Affiliation(s)
- Daniel K. Wells
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, Illinois, United States of America
- Northwestern University Physical Sciences-Oncology Center, Evanston, Illinois, United States of America
| | - Yishan Chuang
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, United States of America
| | - Louis M. Knapp
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, United States of America
| | - Dirk Brockmann
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, Illinois, United States of America
- Northwestern University Physical Sciences-Oncology Center, Evanston, Illinois, United States of America
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, Illinois, United States of America
- Northwestern Institute on Complex Science, Northwestern University, Evanston, Illinois, United States of America
- Institute for Theoretical Biology, Humboldt University Berlin, Berlin, Germany
| | - William L. Kath
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, Illinois, United States of America
- Northwestern University Physical Sciences-Oncology Center, Evanston, Illinois, United States of America
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, Illinois, United States of America
- Northwestern Institute on Complex Science, Northwestern University, Evanston, Illinois, United States of America
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
| | - Joshua N. Leonard
- Northwestern University Physical Sciences-Oncology Center, Evanston, Illinois, United States of America
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, United States of America
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, Illinois, United States of America
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
- * E-mail:
| |
Collapse
|
158
|
Cao J, Arha M, Sudrik C, Mukherjee A, Wu X, Kane RS. A universal strategy for regulating mRNA translation in prokaryotic and eukaryotic cells. Nucleic Acids Res 2015; 43:4353-62. [PMID: 25845589 PMCID: PMC4417184 DOI: 10.1093/nar/gkv290] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 03/24/2015] [Indexed: 02/06/2023] Open
Abstract
We describe a simple strategy to control mRNA translation in both prokaryotic and eukaryotic cells which relies on a unique protein–RNA interaction. Specifically, we used the Pumilio/FBF (PUF) protein to repress translation by binding in between the ribosome binding site (RBS) and the start codon (in Escherichia coli), or by binding to the 5′ untranslated region of target mRNAs (in mammalian cells). The design principle is straightforward, the extent of translational repression can be tuned and the regulator is genetically encoded, enabling the construction of artificial signal cascades. We demonstrate that this approach can also be used to regulate polycistronic mRNAs; such regulation has rarely been achieved in previous reports. Since the regulator used in this study is a modular RNA-binding protein, which can be engineered to target different 8-nucleotide RNA sequences, our strategy could be used in the future to target endogenous mRNAs for regulating metabolic flows and signaling pathways in both prokaryotic and eukaryotic cells.
Collapse
Affiliation(s)
- Jicong Cao
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Manish Arha
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Chaitanya Sudrik
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Abhirup Mukherjee
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Xia Wu
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Ravi S Kane
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| |
Collapse
|
159
|
Abstract
A host's microbiota may increase, diminish, or have no effect at all on cancer susceptibility. Assigning causal roles in cancer to specific microbes and microbiotas, unraveling host-microbiota interactions with environmental factors in carcinogenesis, and exploiting such knowledge for cancer diagnosis and treatment are areas of intensive interest. This Review considers how microbes and the microbiota may amplify or mitigate carcinogenesis, responsiveness to cancer therapeutics, and cancer-associated complications.
Collapse
Affiliation(s)
- Wendy S Garrett
- Department of Immunology and Infectious Diseases and Department of Genetics and Complex Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA. Department of Medicine, Harvard Medical School, Boston, MA 02115, USA. Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| |
Collapse
|
160
|
Inducible suppression of global translation by overuse of rare codons. Appl Environ Microbiol 2015; 81:2544-53. [PMID: 25636849 DOI: 10.1128/aem.03708-14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Recently, artificial gene networks have been developed in synthetic biology to control gene expression and make organisms as controllable as robots. Here, I present an artificial posttranslational gene-silencing system based on the codon usage bias and low tRNA content corresponding to minor codons. I engineered the green fluorescent protein (GFP) gene to inhibit translation indirectly with the lowest-usage codons to monopolize various minor tRNAs (lgfp). The expression of lgfp interfered nonspecifically with the growth of Escherichia coli, Saccharomyces cerevisiae, human HeLa cervical cancer cells, MCF7 breast cancer cells, and HEK293 kidney cells, as well as phage and adenovirus expansion. Furthermore, insertion of lgfp downstream of a phage response promoter conferred phage resistance on E. coli. Such engineered gene silencers could act as components of biological networks capable of functioning with suitable promoters in E. coli, S. cerevisiae, and human cells to control gene expression. The results presented here show general suppressor artificial genes for live cells and viruses. This robust system provides a gene expression or cell growth control device for artificially synthesized gene networks.
Collapse
|
161
|
Abstract
Synthetic biology employs rational engineering principles to build biological systems from the libraries of standard, well characterized biological parts. Biological systems designed and built by synthetic biologists fulfill a plethora of useful purposes, ranging from better healthcare and energy production to biomanufacturing. Recent advancements in the synthesis, assembly and "booting-up" of synthetic genomes and in low and high-throughput genome engineering have paved the way for engineering on the genome-wide scale. One of the key goals of genome engineering is the construction of minimal genomes consisting solely of essential genes (genes indispensable for survival of living organisms). Besides serving as a toolbox to understand the universal principles of life, the cell encoded by minimal genome could be used to build a stringently controlled "cell factory" with a desired phenotype. This review provides an update on recent advances in the genome-scale engineering with particular emphasis on the engineering of minimal genomes. Furthermore, it presents an ongoing discussion to the scientific community for better suitability of minimal or robust cells for industrial applications.
Collapse
Affiliation(s)
- Mario Juhas
- a Department of Pathology , University of Cambridge , Cambridge , UK
| |
Collapse
|
162
|
Abstract
Synthetic gene networks have evolved from simple proof-of-concept circuits to complex therapy-oriented networks over the past 15 years. This advancement has greatly facilitated the expansion of the emerging field of synthetic biology. In this review, we highlight the main applications ofsynthetic gene networks in understanding biological design principles, developing biosensors for diagnosis, producing industrial and biomedical compounds, and treating human diseases. Finally, we outline current challenges and future prospects of synthetic gene networks for advancing practical applications.
Collapse
Affiliation(s)
- Fuqing Wu
- Wuhan Institute of Virology, Chinese Academy of Sciences. Arizona State University, Tempe, AZ 85287, USA
| | - Xiao Wang
- Arizona State University. University of North Carolina at Chapel Hill in 2006
| |
Collapse
|
163
|
|
164
|
Jeong DE, Park SH, Pan JG, Kim EJ, Choi SK. Genome engineering using a synthetic gene circuit in Bacillus subtilis. Nucleic Acids Res 2014; 43:e42. [PMID: 25552415 PMCID: PMC4381049 DOI: 10.1093/nar/gku1380] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Accepted: 12/19/2014] [Indexed: 11/16/2022] Open
Abstract
Genome engineering without leaving foreign DNA behind requires an efficient counter-selectable marker system. Here, we developed a genome engineering method in Bacillus subtilis using a synthetic gene circuit as a counter-selectable marker system. The system contained two repressible promoters (B. subtilis xylA (Pxyl) and spac (Pspac)) and two repressor genes (lacI and xylR). Pxyl-lacI was integrated into the B. subtilis genome with a target gene containing a desired mutation. The xylR and Pspac–chloramphenicol resistant genes (cat) were located on a helper plasmid. In the presence of xylose, repression of XylR by xylose induced LacI expression, the LacIs repressed the Pspac promoter and the cells become chloramphenicol sensitive. Thus, to survive in the presence of chloramphenicol, the cell must delete Pxyl-lacI by recombination between the wild-type and mutated target genes. The recombination leads to mutation of the target gene. The remaining helper plasmid was removed easily under the chloramphenicol absent condition. In this study, we showed base insertion, deletion and point mutation of the B. subtilis genome without leaving any foreign DNA behind. Additionally, we successfully deleted a 2-kb gene (amyE) and a 38-kb operon (ppsABCDE). This method will be useful to construct designer Bacillus strains for various industrial applications.
Collapse
Affiliation(s)
- Da-Eun Jeong
- Super-Bacteria Research Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Seung-Hwan Park
- Super-Bacteria Research Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea Biosystems and Bioengineering Program, University of Science and Technology (UST), 217 Gajung-ro, Yuseong-gu, Daejeon 305-350, Republic of Korea
| | - Jae-Gu Pan
- Super-Bacteria Research Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Eui-Joong Kim
- Genofocus Inc., 533-1 Yongsan-dong, Yuseong-gu, Daejeon 305-500, Republic of Korea
| | - Soo-Keun Choi
- Super-Bacteria Research Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea Biosystems and Bioengineering Program, University of Science and Technology (UST), 217 Gajung-ro, Yuseong-gu, Daejeon 305-350, Republic of Korea
| |
Collapse
|
165
|
Ding Y, Wu F, Tan C. Synthetic Biology: A Bridge between Artificial and Natural Cells. Life (Basel) 2014; 4:1092-116. [PMID: 25532531 PMCID: PMC4284483 DOI: 10.3390/life4041092] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 12/02/2014] [Accepted: 12/11/2014] [Indexed: 12/24/2022] Open
Abstract
Artificial cells are simple cell-like entities that possess certain properties of natural cells. In general, artificial cells are constructed using three parts: (1) biological membranes that serve as protective barriers, while allowing communication between the cells and the environment; (2) transcription and translation machinery that synthesize proteins based on genetic sequences; and (3) genetic modules that control the dynamics of the whole cell. Artificial cells are minimal and well-defined systems that can be more easily engineered and controlled when compared to natural cells. Artificial cells can be used as biomimetic systems to study and understand natural dynamics of cells with minimal interference from cellular complexity. However, there remain significant gaps between artificial and natural cells. How much information can we encode into artificial cells? What is the minimal number of factors that are necessary to achieve robust functioning of artificial cells? Can artificial cells communicate with their environments efficiently? Can artificial cells replicate, divide or even evolve? Here, we review synthetic biological methods that could shrink the gaps between artificial and natural cells. The closure of these gaps will lead to advancement in synthetic biology, cellular biology and biomedical applications.
Collapse
Affiliation(s)
- Yunfeng Ding
- Department of Biomedical Engineering, University of California Davis, One Shields Ave., Davis, CA 95616-5270, USA.
| | - Fan Wu
- Department of Biomedical Engineering, University of California Davis, One Shields Ave., Davis, CA 95616-5270, USA.
| | - Cheemeng Tan
- Department of Biomedical Engineering, University of California Davis, One Shields Ave., Davis, CA 95616-5270, USA.
| |
Collapse
|
166
|
Stanton BC, Siciliano V, Ghodasara A, Wroblewska L, Clancy K, Trefzer AC, Chesnut JD, Weiss R, Voigt CA. Systematic transfer of prokaryotic sensors and circuits to mammalian cells. ACS Synth Biol 2014; 3:880-91. [PMID: 25360681 PMCID: PMC4277766 DOI: 10.1021/sb5002856] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Prokaryotic regulatory proteins respond to diverse signals and represent a rich resource for building synthetic sensors and circuits. The TetR family contains >10(5) members that use a simple mechanism to respond to stimuli and bind distinct DNA operators. We present a platform that enables the transfer of these regulators to mammalian cells, which is demonstrated using human embryonic kidney (HEK293) and Chinese hamster ovary (CHO) cells. The repressors are modified to include nuclear localization signals (NLS) and responsive promoters are built by incorporating multiple operators. Activators are also constructed by modifying the protein to include a VP16 domain. Together, this approach yields 15 new regulators that demonstrate 19- to 551-fold induction and retain both the low levels of crosstalk in DNA binding specificity observed between the parent regulators in Escherichia coli, as well as their dynamic range of activity. By taking advantage of the DAPG small molecule sensing mediated by the PhlF repressor, we introduce a new inducible system with 50-fold induction and a threshold of 0.9 μM DAPG, which is comparable to the classic Dox-induced TetR system. A set of NOT gates is constructed from the new repressors and their response function quantified. Finally, the Dox- and DAPG- inducible systems and two new activators are used to build a synthetic enhancer (fuzzy AND gate), requiring the coordination of 5 transcription factors organized into two layers. This work introduces a generic approach for the development of mammalian genetic sensors and circuits to populate a toolbox that can be applied to diverse applications from biomanufacturing to living therapeutics.
Collapse
Affiliation(s)
- Brynne C. Stanton
- Synthetic
Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Velia Siciliano
- Synthetic
Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Amar Ghodasara
- Synthetic
Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Liliana Wroblewska
- Synthetic
Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Kevin Clancy
- Synthetic Biology R&D, Life Science Solutions Group, Thermo Fisher Scientific, Carlsbad, California 92008, United States
| | - Axel C. Trefzer
- Synthetic Biology R&D, Life Science Solutions Group, Thermo Fisher Scientific, Carlsbad, California 92008, United States
| | - Jonathan D. Chesnut
- Synthetic Biology R&D, Life Science Solutions Group, Thermo Fisher Scientific, Carlsbad, California 92008, United States
| | - Ron Weiss
- Synthetic
Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Christopher A. Voigt
- Synthetic
Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
167
|
Watanabe LH, Myers CJ. Hierarchical Stochastic Simulation Algorithm for SBML Models of Genetic Circuits. Front Bioeng Biotechnol 2014; 2:55. [PMID: 25506588 PMCID: PMC4246920 DOI: 10.3389/fbioe.2014.00055] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 10/29/2014] [Indexed: 11/21/2022] Open
Abstract
This paper describes a hierarchical stochastic simulation algorithm, which has been implemented within iBioSim, a tool used to model, analyze, and visualize genetic circuits. Many biological analysis tools flatten out hierarchy before simulation, but there are many disadvantages associated with this approach. First, the memory required to represent the model can quickly expand in the process. Second, the flattening process is computationally expensive. Finally, when modeling a dynamic cellular population within iBioSim, inlining the hierarchy of the model is inefficient since models must grow dynamically over time. This paper discusses a new approach to handle hierarchy on the fly to make the tool faster and more memory-efficient. This approach yields significant performance improvements as compared to the former flat analysis method.
Collapse
Affiliation(s)
- Leandro H Watanabe
- Department of Electrical and Computer Engineering, The University of Utah , Salt Lake City, UT , USA
| | - Chris J Myers
- Department of Electrical and Computer Engineering, The University of Utah , Salt Lake City, UT , USA
| |
Collapse
|
168
|
Kong W, Celik V, Liao C, Hua Q, Lu T. Programming the group behaviors of bacterial communities with synthetic cellular communication. BIORESOUR BIOPROCESS 2014. [DOI: 10.1186/s40643-014-0024-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Synthetic biology is a newly emerged research discipline that focuses on the engineering of novel cellular behaviors and functionalities through the creation of artificial gene circuits. One important class of synthetic circuits currently under active development concerns the programming of bacterial cellular communication and collective population-scale behaviors. Because of the ubiquity of cell-cell interactions within bacterial communities, having an ability of engineering these circuits is vital to programming robust cellular behaviors. Here, we highlight recent advances in communication-based synthetic gene circuits by first discussing natural communication systems and then surveying various functional engineered circuits, including those for population density control, temporal synchronization, spatial organization, and ecosystem formation. We conclude by summarizing recent advances, outlining existing challenges, and discussing potential applications and future opportunities.
Collapse
|
169
|
Duportet X, Wroblewska L, Guye P, Li Y, Eyquem J, Rieders J, Rimchala T, Batt G, Weiss R. A platform for rapid prototyping of synthetic gene networks in mammalian cells. Nucleic Acids Res 2014; 42:13440-51. [PMID: 25378321 PMCID: PMC4245948 DOI: 10.1093/nar/gku1082] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Mammalian synthetic biology may provide novel therapeutic strategies, help decipher new paths for drug discovery and facilitate synthesis of valuable molecules. Yet, our capacity to genetically program cells is currently hampered by the lack of efficient approaches to streamline the design, construction and screening of synthetic gene networks. To address this problem, here we present a framework for modular and combinatorial assembly of functional (multi)gene expression vectors and their efficient and specific targeted integration into a well-defined chromosomal context in mammalian cells. We demonstrate the potential of this framework by assembling and integrating different functional mammalian regulatory networks including the largest gene circuit built and chromosomally integrated to date (6 transcription units, 27kb) encoding an inducible memory device. Using a library of 18 different circuits as a proof of concept, we also demonstrate that our method enables one-pot/single-flask chromosomal integration and screening of circuit libraries. This rapid and powerful prototyping platform is well suited for comparative studies of genetic regulatory elements, genes and multi-gene circuits as well as facile development of libraries of isogenic engineered cell lines.
Collapse
Affiliation(s)
- Xavier Duportet
- INRIA Paris-Rocquencourt, Rocquencourt, France Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA Cellectis Therapeutics, Paris, France
| | - Liliana Wroblewska
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Patrick Guye
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yinqing Li
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Justin Eyquem
- Laboratoire Matière et Systèmes Complexes, Centre National de la Recherche Scientifique and Université Paris Diderot, Paris, France
| | - Julianne Rieders
- INRIA Paris-Rocquencourt, Rocquencourt, France Laboratoire Matière et Systèmes Complexes, Centre National de la Recherche Scientifique and Université Paris Diderot, Paris, France
| | - Tharathorn Rimchala
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Ron Weiss
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| |
Collapse
|
170
|
de Magalhães JP. The scientific quest for lasting youth: prospects for curing aging. Rejuvenation Res 2014; 17:458-67. [PMID: 25132068 PMCID: PMC4203147 DOI: 10.1089/rej.2014.1580] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2014] [Accepted: 08/17/2014] [Indexed: 12/22/2022] Open
Abstract
People have always sought eternal life and everlasting youth. Recent technological breakthroughs and our growing understanding of aging have given strength to the idea that a cure for human aging can eventually be developed. As such, it is crucial to debate the long-term goals and potential impact of the field. Here, I discuss the scientific prospect of eradicating human aging. I argue that curing aging is scientifically possible and not even the most challenging enterprise in the biosciences. Developing the means to abolish aging is also an ethical endeavor because the goal of biomedical research is to allow people to be as healthy as possible for as long as possible. There is no evidence, however, that we are near to developing the technologies permitting radical life extension. One major difficulty in aging research is the time and costs it takes to do experiments and test interventions. I argue that unraveling the functioning of the genome and developing predictive computer models of human biology and disease are essential to increase the accuracy of medical interventions, including in the context of life extension, and exponential growth in informatics and genomics capacity might lead to rapid progress. Nonetheless, developing the tools for significantly modifying human biology is crucial to intervening in a complex process like aging. Yet in spite of advances in areas like regenerative medicine and gene therapy, the development of clinical applications has been slow and this remains a key hurdle for achieving radical life extension in the foreseeable future.
Collapse
Affiliation(s)
- João Pedro de Magalhães
- Integrative Genomics of Ageing Group, Institute of Integrative Biology, University of Liverpool , Liverpool, United Kingdom
| |
Collapse
|
171
|
Huang H, Densmore D. Integration of microfluidics into the synthetic biology design flow. LAB ON A CHIP 2014; 14:3459-74. [PMID: 25012162 DOI: 10.1039/c4lc00509k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
One goal of synthetic biology is to design and build genetic circuits in living cells for a range of applications. Major challenges in these efforts include increasing the scalability and robustness of engineered biological systems and streamlining and automating the synthetic biology workflow of specification-design-assembly-verification. We present here a summary of the advances in microfluidic technology, particularly microfluidic large scale integration, that can be used to address the challenges facing each step of the synthetic biology workflow. Microfluidic technologies allow precise control over the flow of biological content within microscale devices, and thus may provide more reliable and scalable construction of synthetic biological systems. The integration of microfluidics and synthetic biology has the capability to produce rapid prototyping platforms for characterization of genetic devices, testing of biotherapeutics, and development of biosensors.
Collapse
Affiliation(s)
- Haiyao Huang
- Department of Electrical and Computer Engineering, Boston University, Boston, MA 02215, USA.
| | | |
Collapse
|
172
|
Torella JP, Lienert F, Boehm CR, Chen JH, Way JC, Silver PA. Unique nucleotide sequence-guided assembly of repetitive DNA parts for synthetic biology applications. Nat Protoc 2014; 9:2075-89. [PMID: 25101822 DOI: 10.1038/nprot.2014.145] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Recombination-based DNA construction methods, such as Gibson assembly, have made it possible to easily and simultaneously assemble multiple DNA parts, and they hold promise for the development and optimization of metabolic pathways and functional genetic circuits. Over time, however, these pathways and circuits have become more complex, and the increasing need for standardization and insulation of genetic parts has resulted in sequence redundancies--for example, repeated terminator and insulator sequences--that complicate recombination-based assembly. We and others have recently developed DNA assembly methods, which we refer to collectively as unique nucleotide sequence (UNS)-guided assembly, in which individual DNA parts are flanked with UNSs to facilitate the ordered, recombination-based assembly of repetitive sequences. Here we present a detailed protocol for UNS-guided assembly that enables researchers to convert multiple DNA parts into sequenced, correctly assembled constructs, or into high-quality combinatorial libraries in only 2-3 d. If the DNA parts must be generated from scratch, an additional 2-5 d are necessary. This protocol requires no specialized equipment and can easily be implemented by a student with experience in basic cloning techniques.
Collapse
Affiliation(s)
- Joseph P Torella
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Florian Lienert
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Christian R Boehm
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Jan-Hung Chen
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Jeffrey C Way
- 1] Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA. [2] Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - Pamela A Silver
- 1] Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA. [2] Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| |
Collapse
|
173
|
A designer cell-based histamine-specific human allergy profiler. Nat Commun 2014; 5:4408. [PMID: 25093291 PMCID: PMC4143915 DOI: 10.1038/ncomms5408] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 06/13/2014] [Indexed: 11/09/2022] Open
Abstract
Allergic disorders are markedly increasing in industrialized countries. The identification of compounds that trigger the immunoglobulin E-dependent allergic reaction remains the key to limit patients’ exposure to critical allergens and improve their quality of life. Here we use synthetic biology principles to design a mammalian cell-based allergy profiler that scores the allergen-triggered release of histamine from whole-blood-derived human basophils. A synthetic signalling cascade engineered within the allergy profiler rewires histamine input to the production of reporter protein, thereby integrating histamine levels in whole-blood samples with remarkable sensitivity and a wide dynamic range, allowing for rapid results or long-term storage of output, respectively. This approach provides non-intrusive allergy profiles for the personalized medicine era. The advancement of sensitive, accurate and non-invasive methods to identify the allergen that drives allergic disease in an individual remains a challenge. Here, the authors develop a synthetic biology approach using human designer cells to profile allergic reactions against an array of allergens measuring histamine release from whole blood.
Collapse
|
174
|
Kong W, Lu T. Cloning and optimization of a nisin biosynthesis pathway for bacteriocin harvest. ACS Synth Biol 2014; 3:439-45. [PMID: 24847677 DOI: 10.1021/sb500225r] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Nisin is an important antimicrobial peptide that has enormous applications in biotechnology. Despite many encouraging efforts, its overproduction has been a long-standing challenge due to the complexity of the underlying pathway and the difficulty in genetic modification of lactic acid bacteria. Here, we cloned an entire nisin biosynthesis pathway from a nisin-producing strain (Lactococcus lactis K29) into a plasmid and transplanted the plasmid into a nisin deficient strain Lactococcus lactis MG1363, resulting in successful heterologous expression of bioactive recombinant nisin. To increase nisin harvest, we also overexpressed nisA, a gene responsible for nisin precursor production, with a set of constitutive promoters. To further optimize nisin yield, we minimized the metabolic cost of the engineered strains by integrating nisA overexpression cassettes and the recombinant pathway into a single circuit. With our rational construction and optimization, our engineered optimized strain is able to produce bioactive nisin with a yield of 1098 IU/mL, which is more than six times higher than that of the original strain.
Collapse
Affiliation(s)
- Wentao Kong
- Department
of Bioengineering and Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Ting Lu
- Department
of Bioengineering and Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Department
of Physics, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| |
Collapse
|
175
|
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.
Collapse
Affiliation(s)
- Katrin Rössger
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | | | | |
Collapse
|
176
|
Song H, Ding MZ, Jia XQ, Ma Q, Yuan YJ. Synthetic microbial consortia: from systematic analysis to construction and applications. Chem Soc Rev 2014; 43:6954-81. [PMID: 25017039 DOI: 10.1039/c4cs00114a] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Synthetic biology is an emerging research field that focuses on using rational engineering strategies to program biological systems, conferring on them new functions and behaviours. By developing genetic parts and devices based on transcriptional, translational, post-translational modules, many genetic circuits and metabolic pathways had been programmed in single cells. Extending engineering capabilities from single-cell behaviours to multicellular microbial consortia represents a new frontier of synthetic biology. Herein, we first reviewed binary interaction modes of microorganisms in microbial consortia and their underlying molecular mechanisms, which lay the foundation of programming cell-cell interactions in synthetic microbial consortia. Systems biology studies on cellular systems enable systematic understanding of diverse physiological processes of cells and their interactions, which in turn offer insights into the optimal design of synthetic consortia. Based on such fundamental understanding, a comprehensive array of synthetic microbial consortia constructed in the last decade were reviewed, including isogenic microbial communities programmed by quorum sensing-based cell-cell communications, sender-receiver microbial communities with one-way communications, and microbial ecosystems wired by two-way (bi-directional) communications. Furthermore, many applications including using synthetic microbial consortia for distributed bio-computations, chemicals and bioenergy production, medicine and human health, and environments were reviewed. Synergistic development of systems and synthetic biology will provide both a thorough understanding of naturally occurring microbial consortia and rational engineering of these complicated consortia for novel applications.
Collapse
Affiliation(s)
- Hao Song
- Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, and Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, P. R. China.
| | | | | | | | | |
Collapse
|
177
|
Kiani S, Beal J, Ebrahimkhani MR, Huh J, Hall RN, Xie Z, Li Y, Weiss R. CRISPR transcriptional repression devices and layered circuits in mammalian cells. Nat Methods 2014; 11:723-6. [PMID: 24797424 PMCID: PMC4228775 DOI: 10.1038/nmeth.2969] [Citation(s) in RCA: 167] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 04/29/2014] [Indexed: 12/21/2022]
Abstract
A key obstacle to creating sophisticated genetic circuits has been the lack of scalable device libraries. Here we present a modular transcriptional repression architecture based on clustered regularly interspaced palindromic repeats (CRISPR) system and examine approaches for regulated expression of guide RNAs in human cells. Subsequently we demonstrate that CRISPR regulatory devices can be layered to create functional cascaded circuits, which provide a valuable toolbox for engineering purposes.
Collapse
Affiliation(s)
- Samira Kiani
- 1] Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. [2] Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jacob Beal
- Raytheon BBN Technologies, Cambridge, Massachusetts, USA
| | - Mohammad R Ebrahimkhani
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jin Huh
- 1] Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. [2] Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. [3] Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Richard N Hall
- 1] Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. [2] Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Zhen Xie
- 1] Bioinformatics Division, Center for Synthetic & Systems Biology, Tsinghua National Laboratory for Information Science and Technology, Beijing, China. [2] Department of Automation, Tsinghua University, Beijing, China
| | - Yinqing Li
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Ron Weiss
- 1] Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. [2] Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. [3] Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| |
Collapse
|
178
|
Brophy JAN, Voigt CA. Principles of genetic circuit design. Nat Methods 2014; 11:508-20. [PMID: 24781324 DOI: 10.1038/nmeth.2926] [Citation(s) in RCA: 576] [Impact Index Per Article: 57.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 03/18/2014] [Indexed: 12/17/2022]
Abstract
Cells navigate environments, communicate and build complex patterns by initiating gene expression in response to specific signals. Engineers seek to harness this capability to program cells to perform tasks or create chemicals and materials that match the complexity seen in nature. This Review describes new tools that aid the construction of genetic circuits. Circuit dynamics can be influenced by the choice of regulators and changed with expression 'tuning knobs'. We collate the failure modes encountered when assembling circuits, quantify their impact on performance and review mitigation efforts. Finally, we discuss the constraints that arise from circuits having to operate within a living cell. Collectively, better tools, well-characterized parts and a comprehensive understanding of how to compose circuits are leading to a breakthrough in the ability to program living cells for advanced applications, from living therapeutics to the atomic manufacturing of functional materials.
Collapse
Affiliation(s)
- Jennifer A N Brophy
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Christopher A Voigt
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| |
Collapse
|
179
|
Citorik RJ, Mimee M, Lu TK. Bacteriophage-based synthetic biology for the study of infectious diseases. Curr Opin Microbiol 2014; 19:59-69. [PMID: 24997401 PMCID: PMC4125527 DOI: 10.1016/j.mib.2014.05.022] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 05/14/2014] [Accepted: 05/28/2014] [Indexed: 01/01/2023]
Abstract
Since their discovery, bacteriophages have contributed enormously to our understanding of molecular biology as model systems. Furthermore, bacteriophages have provided many tools that have advanced the fields of genetic engineering and synthetic biology. Here, we discuss bacteriophage-based technologies and their application to the study of infectious diseases. New strategies for engineering genomes have the potential to accelerate the design of novel phages as therapies, diagnostics, and tools. Though almost a century has elapsed since their discovery, bacteriophages continue to have a major impact on modern biological sciences, especially with the growth of multidrug-resistant bacteria and interest in the microbiome.
Collapse
Affiliation(s)
- Robert J. Citorik
- MIT Microbiology Program, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- MIT Synthetic Biology Center, 500 Technology Square, Cambridge, MA 02139, USA
| | - Mark Mimee
- MIT Microbiology Program, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- MIT Synthetic Biology Center, 500 Technology Square, Cambridge, MA 02139, USA
| | - Timothy K. Lu
- MIT Microbiology Program, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- MIT Synthetic Biology Center, 500 Technology Square, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| |
Collapse
|
180
|
Chuang CH, Lin CL. Synthesizing genetic sequential logic circuit with clock pulse generator. BMC SYSTEMS BIOLOGY 2014; 8:63. [PMID: 24884665 PMCID: PMC4049394 DOI: 10.1186/1752-0509-8-63] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 05/15/2014] [Indexed: 02/06/2023]
Abstract
Background Rhythmic clock widely occurs in biological systems which controls several aspects of cell physiology. For the different cell types, it is supplied with various rhythmic frequencies. How to synthesize a specific clock signal is a preliminary but a necessary step to further development of a biological computer in the future. Results This paper presents a genetic sequential logic circuit with a clock pulse generator based on a synthesized genetic oscillator, which generates a consecutive clock signal whose frequency is an inverse integer multiple to that of the genetic oscillator. An analogous electronic waveform-shaping circuit is constructed by a series of genetic buffers to shape logic high/low levels of an oscillation input in a basic sinusoidal cycle and generate a pulse-width-modulated (PWM) output with various duty cycles. By controlling the threshold level of the genetic buffer, a genetic clock pulse signal with its frequency consistent to the genetic oscillator is synthesized. A synchronous genetic counter circuit based on the topology of the digital sequential logic circuit is triggered by the clock pulse to synthesize the clock signal with an inverse multiple frequency to the genetic oscillator. The function acts like a frequency divider in electronic circuits which plays a key role in the sequential logic circuit with specific operational frequency. Conclusions A cascaded genetic logic circuit generating clock pulse signals is proposed. Based on analogous implement of digital sequential logic circuits, genetic sequential logic circuits can be constructed by the proposed approach to generate various clock signals from an oscillation signal.
Collapse
Affiliation(s)
| | - Chun-Liang Lin
- Department of Electrical Engineering, National Chung Hsing University, Taichung 402, Taiwan, ROC.
| |
Collapse
|
181
|
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.
Collapse
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.
| |
Collapse
|
182
|
Abstract
Cellular memory - conversion of a transient signal into a sustained response - is a common feature of biological systems. Synthetic biologists aim to understand and re-engineer such systems in a reliable and predictable manner. Synthetic memory circuits have been designed and built in vitro and in vivo based on diverse mechanisms, such as oligonucleotide hybridization, recombination, transcription, phosphorylation, and RNA editing. Thus far, building these circuits has helped us explore the basic principles required for stable memory and ask novel biological questions. Here we discuss strategies for building synthetic memory circuits, their use as research tools, and future applications of these devices in medicine and industry.
Collapse
Affiliation(s)
- Mara C Inniss
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | | |
Collapse
|
183
|
A versatile framework for microbial engineering using synthetic non-coding RNAs. Nat Rev Microbiol 2014; 12:341-54. [DOI: 10.1038/nrmicro3244] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
|
184
|
A versatile cis-acting inverter module for synthetic translational switches. Nat Commun 2014; 4:2393. [PMID: 23999119 PMCID: PMC3778853 DOI: 10.1038/ncomms3393] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 08/02/2013] [Indexed: 11/09/2022] Open
Abstract
Artificial genetic switches have been designed and tuned individually in living cells. A method to directly invert an existing OFF switch to an ON switch should be highly convenient to construct complex circuits from well-characterized modules, but developing such a technique has remained a challenge. Here we present a cis-acting RNA module to invert the function of a synthetic translational OFF switch to an ON switch in mammalian cells. This inversion maintains the property of the parental switch in response to a particular input signal. In addition, we demonstrate simultaneous and specific expression control of both the OFF and ON switches. The module fits the criteria of universality and expands the versatility of mRNA-based information processing systems developed for artificially controlling mammalian cellular behaviour. Artificial genetic circuits have been designed to enable precise control of cellular behaviour and phenotypes. Saito and colleagues present a new RNA module that can invert the function of a translational OFF to an ON switch and demonstrate its utility in mammalian cells.
Collapse
|
185
|
|
186
|
Sarpeshkar R. Analog synthetic biology. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2014; 372:20130110. [PMID: 24567476 PMCID: PMC3928905 DOI: 10.1098/rsta.2013.0110] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
We analyse the pros and cons of analog versus digital computation in living cells. Our analysis is based on fundamental laws of noise in gene and protein expression, which set limits on the energy, time, space, molecular count and part-count resources needed to compute at a given level of precision. We conclude that analog computation is significantly more efficient in its use of resources than deterministic digital computation even at relatively high levels of precision in the cell. Based on this analysis, we conclude that synthetic biology must use analog, collective analog, probabilistic and hybrid analog-digital computational approaches; otherwise, even relatively simple synthetic computations in cells such as addition will exceed energy and molecular-count budgets. We present schematics for efficiently representing analog DNA-protein computation in cells. Analog electronic flow in subthreshold transistors and analog molecular flux in chemical reactions obey Boltzmann exponential laws of thermodynamics and are described by astoundingly similar logarithmic electrochemical potentials. Therefore, cytomorphic circuits can help to map circuit designs between electronic and biochemical domains. We review recent work that uses positive-feedback linearization circuits to architect wide-dynamic-range logarithmic analog computation in Escherichia coli using three transcription factors, nearly two orders of magnitude more efficient in parts than prior digital implementations.
Collapse
|
187
|
Church GM, Elowitz MB, Smolke CD, Voigt CA, Weiss R. Realizing the potential of synthetic biology. Nat Rev Mol Cell Biol 2014; 15:289-94. [PMID: 24622617 DOI: 10.1038/nrm3767] [Citation(s) in RCA: 125] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Synthetic biology, despite still being in its infancy, is increasingly providing valuable information for applications in the clinic, the biotechnology industry and in basic molecular research. Both its unique potential and the challenges it presents have brought together the expertise of an eclectic group of scientists, from cell biologists to engineers. In this Viewpoint article, five experts discuss their views on the future of synthetic biology, on its main achievements in basic and applied science, and on the bioethical issues that are associated with the design of new biological systems.
Collapse
Affiliation(s)
- George M Church
- Department of Genetics, Harvard Medical School, Harvard University, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
| | - Michael B Elowitz
- Division of Biology and Biological Engineering and Department of Applied Physics, Howard Hughes Medical Institute, California Institute of Technology (Caltech), M/C 114-96, Pasadena, California 91125, USA
| | - Christina D Smolke
- Stanford University School of Medicine, 473 Via Ortega, University of Stanford, Stanford, California 94305, USA
| | - Christopher A Voigt
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology (MIT), 500 Technology Square, Cambridge, Massachusetts 02139, USA
| | - Ron Weiss
- Synthetic Biology Center, Department of Biological Engineering, Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology (MIT), NE47-223, 500 Technology Square, Cambridge, Massachusetts 02139, USA
| |
Collapse
|
188
|
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.
Collapse
|
189
|
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.
Collapse
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)
| |
Collapse
|
190
|
Rice MK, Ruder WC. Creating biological nanomaterials using synthetic biology. SCIENCE AND TECHNOLOGY OF ADVANCED MATERIALS 2014; 15:014401. [PMID: 27877637 PMCID: PMC5090598 DOI: 10.1088/1468-6996/15/1/014401] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 12/03/2013] [Accepted: 09/10/2013] [Indexed: 05/08/2023]
Abstract
Synthetic biology is a new discipline that combines science and engineering approaches to precisely control biological networks. These signaling networks are especially important in fields such as biomedicine and biochemical engineering. Additionally, biological networks can also be critical to the production of naturally occurring biological nanomaterials, and as a result, synthetic biology holds tremendous potential in creating new materials. This review introduces the field of synthetic biology, discusses how biological systems naturally produce materials, and then presents examples and strategies for incorporating synthetic biology approaches in the development of new materials. In particular, strategies for using synthetic biology to produce both organic and inorganic nanomaterials are discussed. Ultimately, synthetic biology holds the potential to dramatically impact biological materials science with significant potential applications in medical systems.
Collapse
|
191
|
Gajbhiye V, Escalante L, Chen G, Laperle A, Zheng Q, Steyer B, Gong S, Saha K. Drug-loaded nanoparticles induce gene expression in human pluripotent stem cell derivatives. NANOSCALE 2014; 6:521-31. [PMID: 24232694 PMCID: PMC3974914 DOI: 10.1039/c3nr04794f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Tissue engineering and advanced manufacturing of human stem cells requires a suite of tools to control gene expression spatiotemporally in culture. Inducible gene expression systems offer cell-extrinsic control, typically through addition of small molecules, but small molecule inducers typically contain few functional groups for further chemical modification. Doxycycline (DXC), a potent small molecule inducer of tetracycline (Tet) transgene systems, was conjugated to a hyperbranched dendritic polymer (Boltorn H40) and subsequently reacted with polyethylene glycol (PEG). The resulting PEG-H40-DXC nanoparticle exhibited pH-sensitive drug release behavior and successfully controlled gene expression in stem-cell-derived fibroblasts with a Tet-On system. While free DXC inhibited fibroblast proliferation and matrix metalloproteinase (MMP) activity, PEG-H40-DXC nanoparticles maintained higher fibroblast proliferation levels and MMP activity. The results demonstrate that the PEG-H40-DXC nanoparticle system provides an effective tool to controlling gene expression in human stem cell derivatives.
Collapse
Affiliation(s)
- Virendra Gajbhiye
- Department of Biomedical Engineering and Wisconsin Institute for Discovery and, University of Wisconsin-Madison, Madison, WI 53715 USA
| | - Leah Escalante
- Department of Biomedical Engineering and Wisconsin Institute for Discovery and, University of Wisconsin-Madison, Madison, WI 53715 USA
| | - Guojun Chen
- Material Science Program and Wisconsin Institute for Discovery and, University of Wisconsin-Madison, Madison, WI 53715 USA
| | - Alex Laperle
- Department of Biomedical Engineering and Wisconsin Institute for Discovery and, University of Wisconsin-Madison, Madison, WI 53715 USA
| | - Qifeng Zheng
- Material Science Program and Wisconsin Institute for Discovery and, University of Wisconsin-Madison, Madison, WI 53715 USA
| | - Benjamin Steyer
- Department of Biomedical Engineering and Wisconsin Institute for Discovery and, University of Wisconsin-Madison, Madison, WI 53715 USA
| | - Shaoqin Gong
- Department of Biomedical Engineering and Wisconsin Institute for Discovery and, University of Wisconsin-Madison, Madison, WI 53715 USA
- Material Science Program and Wisconsin Institute for Discovery and, University of Wisconsin-Madison, Madison, WI 53715 USA
| | - Krishanu Saha
- Department of Biomedical Engineering and Wisconsin Institute for Discovery and, University of Wisconsin-Madison, Madison, WI 53715 USA
| |
Collapse
|
192
|
Abstract
Engineering of translation provides an alternative regulatory layer for controlling transgene expression in addition to transcriptional regulation. Synthetic mRNA switches that modulate translation of a target gene of interest in response to an intracellular protein could be a key regulator to construct a genetic circuit. Insertion of a protein binding RNA sequence in the 5' UTR of mRNA would allow for the generation of a protein-responsive RNA switch. Here we describe the design principle of the switch and methods for tuning and analyzing its translational activity in mammalian cells.
Collapse
|
193
|
Innate immunity in disease: insights from mathematical modeling and analysis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 844:227-43. [PMID: 25480644 DOI: 10.1007/978-1-4939-2095-2_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The acute inflammatory response is a complex defense mechanism that has evolved to respond rapidly to injury, infection, and other disruptions in homeostasis. This robust responsiveness to biological stress likely endows the host with increased fitness, but over-robust or inadequate inflammation predisposes the host to various diseases. Importantly, well-compartmentalized inflammation is generally beneficial, but spillover of inflammation into the blood is a hallmark-and likely also a driver-of self-maintaining inflammation. The blood is also a key entry point and immunological interface for vectors of parasitic diseases, diseases that themselves incite systemic inflammation. The complex role of inflammation in health and disease has made this biological system difficult to understand comprehensively and modulate rationally for therapeutic purposes. Consequently, systems approaches have been applied in order to characterize dynamical properties and identify key control points in inflammation. This process begins with the collection of high-dimensional, experimental, and clinical data, followed by data reduction and data-driven modeling that finally informs mechanistic computational models for analysis, prediction, and rational modulation. These studies have suggested that the overall architecture of the inflammatory response includes a multiscale positive feedback from inflammation → tissue damage → inflammation, which is often inadequately controlled by negative feedback from anti-inflammatory mediators. Given the importance of the blood interface for the inflammatory response, and the accessibility of this compartment both as an immunological sampling reservoir for vectors as well as for diagnosis and therapy, we suggest that any rational efforts at modulating inflammation via the blood compartment must involve computational modeling.
Collapse
|
194
|
Dudek RM, Chuang Y, Leonard JN. Engineered cell-based therapies: a vanguard of design-driven medicine. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 844:369-91. [PMID: 25480651 DOI: 10.1007/978-1-4939-2095-2_18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Engineered cell-based therapies are uniquely capable of performing sophisticated therapeutic functions in vivo, and this strategy is yielding promising clinical benefits for treating cancer. In this review, we discuss key opportunities and challenges for engineering customized cellular functions using cell-based therapy for cancer as a representative case study. We examine the historical development of chimeric antigen receptor (CAR) therapies as an illustration of the engineering design cycle. We also consider the potential roles that the complementary disciplines of systems biology and synthetic biology may play in realizing safe and effective treatments for a broad range of patients and diseases. In particular, we discuss how systems biology may facilitate both fundamental research and clinical translation, and we describe how the emerging field of synthetic biology is providing novel modalities for building customized cellular functions to overcome existing clinical barriers. Together, these approaches provide a powerful set of conceptual and experimental tools for transforming information into understanding, and for translating understanding into novel therapeutics to establish a new framework for design-driven medicine.
Collapse
Affiliation(s)
- Rachel M Dudek
- Northwestern University, 2145 Sheridan Road, Technological Institute, Rm. E136, Evanston, IL, 60208-3120, USA,
| | | | | |
Collapse
|
195
|
Lee EJ, Tabor JJ, Mikos AG. Leveraging synthetic biology for tissue engineering applications. Inflamm Regen 2014. [DOI: 10.2492/inflammregen.34.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
|
196
|
|
197
|
Advances in genetic circuit design: novel biochemistries, deep part mining, and precision gene expression. Curr Opin Chem Biol 2013; 17:878-92. [DOI: 10.1016/j.cbpa.2013.10.003] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 10/03/2013] [Indexed: 01/14/2023]
|
198
|
Vazquez-Anderson J, Contreras LM. Regulatory RNAs: charming gene management styles for synthetic biology applications. RNA Biol 2013; 10:1778-97. [PMID: 24356572 DOI: 10.4161/rna.27102] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
RNAs have many important functional properties, including that they are independently controllable and highly tunable. As a result of these advantageous properties, their use in a myriad of sophisticated devices has been widely explored. Yet, the exploitation of RNAs for synthetic applications is highly dependent on the ability to characterize the many new molecules that continue to be discovered by large-scale sequencing and high-throughput screening techniques. In this review, we present an exhaustive survey of the most recent synthetic bacterial riboswitches and small RNAs while emphasizing their virtues in gene expression management. We also explore the use of these RNA components as building blocks in the RNA synthetic biology toolbox and discuss examples of synthetic RNA components used to rewire bacterial regulatory circuitry. We anticipate that this field will expand its catalog of smart devices by mimicking and manipulating natural RNA mechanisms and functions.
Collapse
Affiliation(s)
- Jorge Vazquez-Anderson
- McKetta Department of Chemical Engineering; University of Texas at Austin; Austin, TX USA
| | - Lydia M Contreras
- McKetta Department of Chemical Engineering; University of Texas at Austin; Austin, TX USA
| |
Collapse
|
199
|
Synthetic regulatory RNAs as tools for engineering biological systems: Design and applications. Chem Eng Sci 2013. [DOI: 10.1016/j.ces.2013.01.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
200
|
Iyer S, Karig DK, Norred SE, Simpson ML, Doktycz MJ. Multi-input regulation and logic with T7 promoters in cells and cell-free systems. PLoS One 2013; 8:e78442. [PMID: 24194933 PMCID: PMC3806817 DOI: 10.1371/journal.pone.0078442] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 09/10/2013] [Indexed: 11/21/2022] Open
Abstract
Engineered gene circuits offer an opportunity to harness biological systems for biotechnological and biomedical applications. However, reliance on native host promoters for the construction of circuit elements, such as logic gates, can make the implementation of predictable, independently functioning circuits difficult. In contrast, T7 promoters offer a simple orthogonal expression system for use in a variety of cellular backgrounds and even in cell-free systems. Here we develop a T7 promoter system that can be regulated by two different transcriptional repressors for the construction of a logic gate that functions in cells and in cell-free systems. We first present LacI repressible T7lacO promoters that are regulated from a distal lac operator site for repression. We next explore the positioning of a tet operator site within the T7lacO framework to create T7 promoters that respond to tet and lac repressors and realize an IMPLIES gate. Finally, we demonstrate that these dual input sensitive promoters function in an E. coli cell-free protein expression system. Our results expand the utility of T7 promoters in cell based as well as cell-free synthetic biology applications.
Collapse
Affiliation(s)
- Sukanya Iyer
- Graduate Program in Genome Science and Technology, University of Tennessee, Knoxville, Knoxville, Tennessee, United States of America
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - David K. Karig
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - S. Elizabeth Norred
- Department of Materials Science and Engineering, University of Tennessee, Knoxville, Knoxville, Tennessee, United States of America
| | - Michael L. Simpson
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Department of Materials Science and Engineering, University of Tennessee, Knoxville, Knoxville, Tennessee, United States of America
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Knoxville, Tennessee, United States of America
| | - Mitchel J. Doktycz
- Graduate Program in Genome Science and Technology, University of Tennessee, Knoxville, Knoxville, Tennessee, United States of America
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- * E-mail:
| |
Collapse
|