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Chew YH, Marucci L. Mechanistic Model-Driven Biodesign in Mammalian Synthetic Biology. Methods Mol Biol 2024; 2774:71-84. [PMID: 38441759 DOI: 10.1007/978-1-0716-3718-0_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
Mathematical modeling plays a vital role in mammalian synthetic biology by providing a framework to design and optimize design circuits and engineered bioprocesses, predict their behavior, and guide experimental design. Here, we review recent models used in the literature, considering mathematical frameworks at the molecular, cellular, and system levels. We report key challenges in the field and discuss opportunities for genome-scale models, machine learning, and cybergenetics to expand the capabilities of model-driven mammalian cell biodesign.
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Affiliation(s)
- Yin Hoon Chew
- School of Mathematics, University of Birmingham, Birmingham, UK
| | - Lucia Marucci
- Department of Engineering Mathematics, University of Bristol, Bristol, UK.
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK.
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2
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Hoces D, Miguens Blanco J, Hernández-López RA. A synthetic biology approach to engineering circuits in immune cells. Immunol Rev 2023; 320:120-137. [PMID: 37464881 DOI: 10.1111/imr.13244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 06/08/2023] [Indexed: 07/20/2023]
Abstract
A synthetic circuit in a biological system involves the designed assembly of genetic elements, biomolecules, or cells to create a defined function. These circuits are central in synthetic biology, enabling the reprogramming of cellular behavior and the engineering of cells with customized responses. In cancer therapeutics, engineering T cells with circuits have the potential to overcome the challenges of current approaches, for example, by allowing specific recognition and killing of cancer cells. Recent advances also facilitate engineering integrated circuits for the controlled release of therapeutic molecules at specified locations, for example, in a solid tumor. In this review, we discuss recent strategies and applications of synthetic receptor circuits aimed at enhancing immune cell functions for cancer immunotherapy. We begin by introducing the concept of circuits in networks at the molecular and cellular scales and provide an analysis of the development and implementation of several synthetic circuits in T cells that have the goal to overcome current challenges in cancer immunotherapy. These include specific targeting of cancer cells, increased T-cell proliferation, and persistence in the tumor microenvironment. By harnessing the power of synthetic biology, and the characteristics of certain circuit architectures, it is now possible to engineer a new generation of immune cells that recognize cancer cells, while minimizing off-target toxicities. We specifically discuss T-cell circuits for antigen density sensing. These circuits allow targeting of solid tumors that share antigens with normal tissues. Additionally, we explore designs for synthetic circuits that could control T-cell differentiation or T-cell fate as well as the concept of synthetic multicellular circuits that leverage cellular communication and division of labor to achieve improved therapeutic efficacy. As our understanding of cell biology expands and novel tools for genome, protein, and cell engineering are developed, we anticipate further innovative approaches to emerge in the design and engineering of circuits in immune cells.
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Affiliation(s)
- Daniel Hoces
- Department of Bioengineering, Stanford University, Stanford, California, USA
- Department of Genetics, Stanford University, Stanford, California, USA
| | - Jesús Miguens Blanco
- Department of Bioengineering, Stanford University, Stanford, California, USA
- Department of Genetics, Stanford University, Stanford, California, USA
| | - Rogelio A Hernández-López
- Department of Bioengineering, Stanford University, Stanford, California, USA
- Department of Genetics, Stanford University, Stanford, California, USA
- Stanford Cancer Institute, Stanford, California, USA
- Chan-Zuckerberg Biohub-San Francisco, San Francisco, California, USA
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3
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A synthetic gene circuit for imaging-free detection of signaling pulses. Cell Syst 2022; 13:131-142.e13. [PMID: 34739875 PMCID: PMC8857027 DOI: 10.1016/j.cels.2021.10.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 07/20/2021] [Accepted: 10/14/2021] [Indexed: 12/24/2022]
Abstract
Cells employ intracellular signaling pathways to sense and respond to changes in their external environment. In recent years, live-cell biosensors have revealed complex pulsatile dynamics in many pathways, but studies of these signaling dynamics are limited by the necessity of live-cell imaging at high spatiotemporal resolution. Here, we describe an approach to infer pulsatile signaling dynamics from a single measurement in fixed cells using a pulse-detecting gene circuit. We computationally screened for circuits with the capability to selectively detect signaling pulses, revealing an incoherent feedforward topology that robustly performs this computation. We implemented the motif experimentally for the Erk signaling pathway using a single engineered transcription factor and fluorescent protein reporter. Our "recorder of Erk activity dynamics" (READer) responds sensitively to spontaneous and stimulus-driven Erk pulses. READer circuits open the door to permanently labeling transient, dynamic cell populations to elucidate the mechanistic underpinnings and biological consequences of signaling dynamics.
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4
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Mathematical Modelling of p53 Signalling during DNA Damage Response: A Survey. Int J Mol Sci 2021; 22:ijms221910590. [PMID: 34638930 PMCID: PMC8508851 DOI: 10.3390/ijms221910590] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/14/2021] [Accepted: 09/26/2021] [Indexed: 02/05/2023] Open
Abstract
No gene has garnered more interest than p53 since its discovery over 40 years ago. In the last two decades, thanks to seminal work from Uri Alon and Ghalit Lahav, p53 has defined a truly synergistic topic in the field of mathematical biology, with a rich body of research connecting mathematic endeavour with experimental design and data. In this review we survey and distill the extensive literature of mathematical models of p53. Specifically, we focus on models which seek to reproduce the oscillatory dynamics of p53 in response to DNA damage. We review the standard modelling approaches used in the field categorising them into three types: time delay models, spatial models and coupled negative-positive feedback models, providing sample model equations and simulation results which show clear oscillatory dynamics. We discuss the interplay between mathematics and biology and show how one informs the other; the deep connections between the two disciplines has helped to develop our understanding of this complex gene and paint a picture of its dynamical response. Although yet more is to be elucidated, we offer the current state-of-the-art understanding of p53 response to DNA damage.
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5
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Krzysztoń R, Wan Y, Petreczky J, Balázsi G. Gene-circuit therapy on the horizon: synthetic biology tools for engineered therapeutics. Acta Biochim Pol 2021; 68:377-383. [PMID: 34460209 PMCID: PMC8590856 DOI: 10.18388/abp.2020_5744] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 07/19/2021] [Indexed: 01/17/2023]
Abstract
Therapeutic genome modification requires precise control over the introduced therapeutic functions. Current approaches of gene and cell therapy fail to deliver such command and rely on semi-quantitative methods with limited influence on timing, contextuality and levels of transgene expression, and hence on therapeutic function. Synthetic biology offers new opportunities for quantitative functionality in designing therapeutic systems and their components. Here, we discuss synthetic biology tools in their therapeutic context, with examples of proof-of-principle and clinical applications of engineered synthetic biomolecules and higher-order functional systems, i.e. gene circuits. We also present the prospects of future development towards advanced gene-circuit therapy.
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Affiliation(s)
- Rafał Krzysztoń
- Biomedical Engineering Department, Stony Brook University, Stony Brook, NY 11974, USA
- The Louis & Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Yiming Wan
- Biomedical Engineering Department, Stony Brook University, Stony Brook, NY 11974, USA
- The Louis & Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Julia Petreczky
- Biomedical Engineering Department, Stony Brook University, Stony Brook, NY 11974, USA
- The Louis & Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Gábor Balázsi
- Biomedical Engineering Department, Stony Brook University, Stony Brook, NY 11974, USA
- The Louis & Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
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6
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Zhang Y, Liu H, Li Z, Miao Z, Zhou J. Oscillatory Dynamics of p53-Mdm2 Circuit in Response to DNA Damage Caused by Ionizing Radiation. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020; 17:1703-1713. [PMID: 30762566 DOI: 10.1109/tcbb.2019.2899574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Although the dynamical behavior of the p53-Mdm2 loop has been extensively studied, the understanding of the mechanism underlying the regulation of this pathway still remains limited. Herein, we developed an integrated model with five basic components and three ubiquitous time delays for the p53-Mdm2 interaction in response to DNA damage following ionizing radiation (IR). We showed that a sufficient amount of activated ATM level can initiate the p53 oscillations with nearly the same amplitude over a wide range of the ATM level; a proper range of p53 level is also required for generating the oscillations, for too high or too low levels it would fail to generate the oscillations; and increased Mdm2 level leads to decreased amplitude of the p53 oscillation and reduced expression of the p53 activity. Moreover, we found that the negative feedback loop formed between p53 and nuclear Mdm2 plays a dominant role in determining the p53 dynamics, whereas when interaction strength of the negative feedback loop becomes weaker, the positive feedback loop formed between p53 and cytoplasmatic Mdm2 can induce different types of dynamics. Furthermore, we demonstrated that the total time delay required for protein production and nuclear translocation of Mdm2 can induce p53 oscillations even when the p53 level is at a certain stable high steady state or at a certain stable low steady state. In addition, the two important features of the oscillatory dynamics-amplitude and period-can be controlled by such time delay. These results are in agreement with multiple experimental observations and may enrich our understanding of the dynamics of the p53 network.
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7
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Harton MD, Koh WS, Bunker AD, Singh A, Batchelor E. p53 pulse modulation differentially regulates target gene promoters to regulate cell fate decisions. Mol Syst Biol 2019; 15:e8685. [PMID: 31556489 PMCID: PMC6761572 DOI: 10.15252/msb.20188685] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 08/29/2019] [Accepted: 09/02/2019] [Indexed: 01/02/2023] Open
Abstract
The p53 tumor suppressor regulates distinct responses to cellular stresses. Although different stresses generate different p53 dynamics, the mechanisms by which cells decode p53 dynamics to differentially regulate target genes are not well understood. Here, we determined in individual cells how canonical p53 target gene promoters vary in responsiveness to features of p53 dynamics. Employing a chemical perturbation approach, we independently modulated p53 pulse amplitude, duration, or frequency, and we then monitored p53 levels and target promoter activation in individual cells. We identified distinct signal processing features-thresholding in response to amplitude modulation, a refractory period in response to duration modulation, and dynamic filtering in response to frequency modulation. We then showed that the signal processing features not only affect p53 target promoter activation, they also affect p53 regulation and downstream cellular functions. Our study shows how different promoters can differentially decode features of p53 dynamics to generate distinct responses, providing insight into how perturbing p53 dynamics can be used to generate distinct cell fates.
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Affiliation(s)
- Marie D Harton
- Laboratory of Cell BiologyCenter for Cancer ResearchNational Cancer InstituteNational Institutes of HealthBethesdaMDUSA
| | - Woo Seuk Koh
- Laboratory of Cell BiologyCenter for Cancer ResearchNational Cancer InstituteNational Institutes of HealthBethesdaMDUSA
| | - Amie D Bunker
- Laboratory of Cell BiologyCenter for Cancer ResearchNational Cancer InstituteNational Institutes of HealthBethesdaMDUSA
| | - Abhyudai Singh
- Department of Electrical and Computer EngineeringDepartment of Biomedical EngineeringDepartment of Mathematical Sciences, and Center for Bioinformatics and Computational BiologyUniversity of DelawareNewarkDEUSA
| | - Eric Batchelor
- Laboratory of Cell BiologyCenter for Cancer ResearchNational Cancer InstituteNational Institutes of HealthBethesdaMDUSA
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8
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Xie M, Fussenegger M. Designing cell function: assembly of synthetic gene circuits for cell biology applications. Nat Rev Mol Cell Biol 2019; 19:507-525. [PMID: 29858606 DOI: 10.1038/s41580-018-0024-z] [Citation(s) in RCA: 156] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Synthetic biology is the discipline of engineering application-driven biological functionalities that were not evolved by nature. Early breakthroughs of cell engineering, which were based on ectopic (over)expression of single sets of transgenes, have already had a revolutionary impact on the biotechnology industry, regenerative medicine and blood transfusion therapies. Now, we require larger-scale, rationally assembled genetic circuits engineered to programme and control various human cell functions with high spatiotemporal precision in order to solve more complex problems in applied life sciences, biomedicine and environmental sciences. This will open new possibilities for employing synthetic biology to advance personalized medicine by converting cells into living therapeutics to combat hitherto intractable diseases.
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Affiliation(s)
- Mingqi Xie
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland. .,University of Basel, Faculty of Science, Basel, Switzerland.
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9
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Li Z, Liu S, Yang Q. Incoherent Inputs Enhance the Robustness of Biological Oscillators. Cell Syst 2019; 5:72-81.e4. [PMID: 28750200 DOI: 10.1016/j.cels.2017.06.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 03/30/2017] [Accepted: 06/22/2017] [Indexed: 11/25/2022]
Abstract
Robust biological oscillators retain the critical ability to function in the presence of environmental perturbations. Although central architectures that support robust oscillations have been extensively studied, networks containing the same core vary drastically in their potential to oscillate, and it remains elusive what peripheral modifications to the core contribute to this functional variation. Here, we have generated a complete atlas of two- and three-node oscillators computationally, then systematically analyzed the association between network structure and robustness. We found that, while certain core topologies are essential for producing a robust oscillator, local structures can substantially modulate the robustness of oscillations. Notably, local nodes receiving incoherent or coherent inputs respectively promote or attenuate the overall network robustness in an additive manner. We validated these relationships in larger-scale networks reflective of real biological oscillators. Our findings provide an explanation for why auxiliary structures not required for oscillation are evolutionarily conserved and suggest simple ways to evolve or design robust oscillators.
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Affiliation(s)
- Zhengda Li
- Department of Biophysics, University of Michigan, Ann Arbor, MI, USA; Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Shixuan Liu
- Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Qiong Yang
- Department of Biophysics, University of Michigan, Ann Arbor, MI, USA; Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
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10
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Andres J, Blomeier T, Zurbriggen MD. Synthetic Switches and Regulatory Circuits in Plants. PLANT PHYSIOLOGY 2019; 179:862-884. [PMID: 30692218 PMCID: PMC6393786 DOI: 10.1104/pp.18.01362] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 01/18/2019] [Indexed: 05/20/2023]
Abstract
Synthetic biology is an established but ever-growing interdisciplinary field of research currently revolutionizing biomedicine studies and the biotech industry. The engineering of synthetic circuitry in bacterial, yeast, and animal systems prompted considerable advances for the understanding and manipulation of genetic and metabolic networks; however, their implementation in the plant field lags behind. Here, we review theoretical-experimental approaches to the engineering of synthetic chemical- and light-regulated (optogenetic) switches for the targeted interrogation and control of cellular processes, including existing applications in the plant field. We highlight the strategies for the modular assembly of genetic parts into synthetic circuits of different complexity, ranging from Boolean logic gates and oscillatory devices up to semi- and fully synthetic open- and closed-loop molecular and cellular circuits. Finally, we explore potential applications of these approaches for the engineering of novel functionalities in plants, including understanding complex signaling networks, improving crop productivity, and the production of biopharmaceuticals.
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Affiliation(s)
- Jennifer Andres
- Institute of Synthetic Biology and CEPLAS, University of Düsseldorf, 40225 Duesseldorf, Germany
| | - Tim Blomeier
- Institute of Synthetic Biology and CEPLAS, University of Düsseldorf, 40225 Duesseldorf, Germany
| | - Matias D Zurbriggen
- Institute of Synthetic Biology and CEPLAS, University of Düsseldorf, 40225 Duesseldorf, Germany
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11
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Tomazou M, Barahona M, Polizzi KM, Stan GB. Computational Re-design of Synthetic Genetic Oscillators for Independent Amplitude and Frequency Modulation. Cell Syst 2018; 6:508-520.e5. [PMID: 29680377 DOI: 10.1016/j.cels.2018.03.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 12/14/2017] [Accepted: 03/19/2018] [Indexed: 01/27/2023]
Abstract
To perform well in biotechnology applications, synthetic genetic oscillators must be engineered to allow independent modulation of amplitude and period. This need is currently unmet. Here, we demonstrate computationally how two classic genetic oscillators, the dual-feedback oscillator and the repressilator, can be re-designed to provide independent control of amplitude and period and improve tunability-that is, a broad dynamic range of periods and amplitudes accessible through the input "dials." Our approach decouples frequency and amplitude modulation by incorporating an orthogonal "sink module" where the key molecular species are channeled for enzymatic degradation. This sink module maintains fast oscillation cycles while alleviating the translational coupling between the oscillator's transcription factors and output. We characterize the behavior of our re-designed oscillators over a broad range of physiologically reasonable parameters, explain why this facilitates broader function and control, and provide general design principles for building synthetic genetic oscillators that are more precisely controllable.
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Affiliation(s)
- Marios Tomazou
- Department of Bioengineering, Imperial College London, London SW7 2AZ, UK; Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
| | - Mauricio Barahona
- Department of Mathematics, Imperial College London, London SW7 2AZ, UK; Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
| | - Karen M Polizzi
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK; Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
| | - Guy-Bart Stan
- Department of Bioengineering, Imperial College London, London SW7 2AZ, UK; Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK.
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12
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Abstract
Background Self-sustained oscillations are a ubiquitous and vital phenomenon in living systems. From primitive single-cellular bacteria to the most sophisticated organisms, periodicities have been observed in a broad spectrum of biological processes such as neuron firing, heart beats, cell cycles, circadian rhythms, etc. Defects in these oscillators can cause diseases from insomnia to cancer. Elucidating their fundamental mechanisms is of great significance to diseases, and yet challenging, due to the complexity and diversity of these oscillators. Results Approaches in quantitative systems biology and synthetic biology have been most effective by simplifying the systems to contain only the most essential regulators. Here, we will review major progress that has been made in understanding biological oscillators using these approaches. The quantitative systems biology approach allows for identification of the essential components of an oscillator in an endogenous system. The synthetic biology approach makes use of the knowledge to design the simplest, de novo oscillators in both live cells and cell-free systems. These synthetic oscillators are tractable to further detailed analysis and manipulations. Conclusion With the recent development of biological and computational tools, both approaches have made significant achievements.
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Mönke G, Cristiano E, Finzel A, Friedrich D, Herzel H, Falcke M, Loewer A. Excitability in the p53 network mediates robust signaling with tunable activation thresholds in single cells. Sci Rep 2017; 7:46571. [PMID: 28417973 PMCID: PMC5394551 DOI: 10.1038/srep46571] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/17/2017] [Indexed: 01/07/2023] Open
Abstract
Cellular signaling systems precisely transmit information in the presence of molecular noise while retaining flexibility to accommodate the needs of individual cells. To understand design principles underlying such versatile signaling, we analyzed the response of the tumor suppressor p53 to varying levels of DNA damage in hundreds of individual cells and observed a switch between distinct signaling modes characterized by isolated pulses and sustained oscillations of p53 accumulation. Guided by dynamic systems theory we show that this requires an excitable network structure comprising positive feedback and provide experimental evidence for its molecular identity. The resulting data-driven model reproduced all features of measured signaling responses and is sufficient to explain their heterogeneity in individual cells. We present evidence that heterogeneity in the levels of the feedback regulator Wip1 sets cell-specific thresholds for p53 activation, providing means to modulate its response through interacting signaling pathways. Our results demonstrate how excitable signaling networks can provide high specificity, sensitivity and robustness while retaining unique possibilities to adjust their function to the physiology of individual cells.
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Affiliation(s)
- Gregor Mönke
- Mathematical Cell Physiology, Max Delbrueck Center in the Helmholtz Association, Berlin, Germany
| | - Elena Cristiano
- Berlin Institute for Medical Systems Biology, Max Delbrueck Center in the Helmholtz Association, Berlin, Germany
| | - Ana Finzel
- Berlin Institute for Medical Systems Biology, Max Delbrueck Center in the Helmholtz Association, Berlin, Germany
| | - Dhana Friedrich
- Berlin Institute for Medical Systems Biology, Max Delbrueck Center in the Helmholtz Association, Berlin, Germany
| | - Hanspeter Herzel
- Institute for Theoretical Biology, Charité and Humboldt University, Berlin, Germany
| | - Martin Falcke
- Mathematical Cell Physiology, Max Delbrueck Center in the Helmholtz Association, Berlin, Germany
| | - Alexander Loewer
- Berlin Institute for Medical Systems Biology, Max Delbrueck Center in the Helmholtz Association, Berlin, Germany
- Department of Biology, Technische Universitaet Darmstadt, Germany
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14
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Batchelor E, Loewer A. Recent progress and open challenges in modeling p53 dynamics in single cells. ACTA ACUST UNITED AC 2017; 3:54-59. [PMID: 29062976 DOI: 10.1016/j.coisb.2017.04.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
In mammalian cells, the tumor suppressor p53 is activated upon a variety of cellular stresses and ensures an appropriate response ranging from arrest and repair to the induction of senescence and apoptosis. Quantitative measurements in individual living cells showed stimulus-dependent dynamics of p53 accumulation upon stress induction. Due to the complexity of the underlying biochemical interactions, mathematical models were indispensable for understanding the topology of the network regulating p53 dynamics. Recent work provides furhter insights into the causes of heterogeneous responses in individual cells, the rewiring of the network in response to different inputs and the role of the downstream processes in determining the cellular fate upon stress.
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Affiliation(s)
- Eric Batchelor
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Drive, MSC 1500, Bethesda, MD 20892, USA
| | - Alexander Loewer
- Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 13, 64287 Darmstadt, Germany
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15
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Mathur M, Xiang JS, Smolke CD. Mammalian synthetic biology for studying the cell. J Cell Biol 2016; 216:73-82. [PMID: 27932576 PMCID: PMC5223614 DOI: 10.1083/jcb.201611002] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 11/16/2016] [Accepted: 11/18/2016] [Indexed: 12/25/2022] Open
Abstract
Synthetic biology is advancing the design of genetic devices that enable the study of cellular and molecular biology in mammalian cells. These genetic devices use diverse regulatory mechanisms to both examine cellular processes and achieve precise and dynamic control of cellular phenotype. Synthetic biology tools provide novel functionality to complement the examination of natural cell systems, including engineered molecules with specific activities and model systems that mimic complex regulatory processes. Continued development of quantitative standards and computational tools will expand capacities to probe cellular mechanisms with genetic devices to achieve a more comprehensive understanding of the cell. In this study, we review synthetic biology tools that are being applied to effectively investigate diverse cellular processes, regulatory networks, and multicellular interactions. We also discuss current challenges and future developments in the field that may transform the types of investigation possible in cell biology.
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Affiliation(s)
- Melina Mathur
- Department of Bioengineering, Stanford University, Stanford, CA 94305
| | - Joy S Xiang
- Department of Bioengineering, Stanford University, Stanford, CA 94305
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16
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Porter JR, Fisher BE, Batchelor E. p53 Pulses Diversify Target Gene Expression Dynamics in an mRNA Half-Life-Dependent Manner and Delineate Co-regulated Target Gene Subnetworks. Cell Syst 2016; 2:272-82. [PMID: 27135539 DOI: 10.1016/j.cels.2016.03.006] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 12/01/2015] [Accepted: 02/29/2016] [Indexed: 01/22/2023]
Abstract
The transcription factor p53 responds to DNA double-strand breaks by increasing in concentration in a series of pulses of fixed amplitude, duration, and period. How p53 pulses influence the dynamics of p53 target gene expression is not understood. Here, we show that, in bulk cell populations, patterns of p53 target gene expression cluster into groups with stereotyped temporal behaviors, including pulsing and rising dynamics. These behaviors correlate statistically with the mRNA decay rates of target genes: short mRNA half-lives produce pulses of gene expression. This relationship can be recapitulated by mathematical models of p53-dependent gene expression in single cells and cell populations. Single-cell transcriptional profiling demonstrates that expression of a subset of p53 target genes is coordinated across time within single cells; p53 pulsing attenuates this coordination. These results help delineate how p53 orchestrates the complex DNA damage response and give insight into the function of pulsatile signaling pathways.
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Affiliation(s)
- Joshua R Porter
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Drive, MSC 1500, Bethesda, MD 20892, USA
| | - Brian E Fisher
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Drive, MSC 1500, Bethesda, MD 20892, USA
| | - Eric Batchelor
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Drive, MSC 1500, Bethesda, MD 20892, USA.
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17
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Castillo-Hair SM, Villota ER, Coronado AM. Design principles for robust oscillatory behavior. SYSTEMS AND SYNTHETIC BIOLOGY 2015; 9:125-33. [PMID: 26279706 DOI: 10.1007/s11693-015-9178-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 07/29/2015] [Accepted: 07/31/2015] [Indexed: 11/29/2022]
Abstract
Oscillatory responses are ubiquitous in regulatory networks of living organisms, a fact that has led to extensive efforts to study and replicate the circuits involved. However, to date, design principles that underlie the robustness of natural oscillators are not completely known. Here we study a three-component enzymatic network model in order to determine the topological requirements for robust oscillation. First, by simulating every possible topological arrangement and varying their parameter values, we demonstrate that robust oscillators can be obtained by augmenting the number of both negative feedback loops and positive autoregulations while maintaining an appropriate balance of positive and negative interactions. We then identify network motifs, whose presence in more complex topologies is a necessary condition for obtaining oscillatory responses. Finally, we pinpoint a series of simple architectural patterns that progressively render more robust oscillators. Together, these findings can help in the design of more reliable synthetic biomolecular networks and may also have implications in the understanding of other oscillatory systems.
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Affiliation(s)
- Sebastian M Castillo-Hair
- Faculty of Mechanical Engineering, Universidad Nacional de Ingeniería, Av. Túpac Amaru s/n - Puerta 3, Pabellón A, 25 Lima, Peru
| | - Elizabeth R Villota
- Faculty of Mechanical Engineering, Universidad Nacional de Ingeniería, Av. Túpac Amaru s/n - Puerta 3, Pabellón A, 25 Lima, Peru
| | - Alberto M Coronado
- Faculty of Mechanical Engineering, Universidad Nacional de Ingeniería, Av. Túpac Amaru s/n - Puerta 3, Pabellón A, 25 Lima, Peru
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Porter JR, Batchelor E. Using computational modeling and experimental synthetic perturbations to probe biological circuits. Methods Mol Biol 2015; 1244:259-76. [PMID: 25487101 PMCID: PMC6311997 DOI: 10.1007/978-1-4939-1878-2_12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
This chapter describes approaches for using computational modeling of synthetic biology perturbations to analyze endogenous biological circuits, with a particular focus on signaling and metabolic pathways. We describe a bottom-up approach in which ordinary differential equations are constructed to model the core interactions of a pathway of interest. We then discuss methods for modeling synthetic perturbations that can be used to investigate properties of the natural circuit. Keeping in mind the importance of the interplay between modeling and experimentation, we next describe experimental methods for constructing synthetic perturbations to test the computational predictions. Finally, we present a case study of the p53 tumor-suppressor pathway, illustrating the process of modeling the core network, designing informative synthetic perturbations in silico, and testing the predictions in vivo.
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Affiliation(s)
- Joshua R. Porter
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Building 10, Room B1B42, 10 Center Dr., MSC 1500, Bethesda, MD, 20892, USA
| | - Eric Batchelor
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Building 10, Room B1B42, 10 Center Dr., MSC 1500, Bethesda, MD, 20892, USA
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19
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Zhang P, Brusic V. Mathematical modeling for novel cancer drug discovery and development. Expert Opin Drug Discov 2014; 9:1133-50. [PMID: 25062617 DOI: 10.1517/17460441.2014.941351] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
INTRODUCTION Mathematical modeling enables: the in silico classification of cancers, the prediction of disease outcomes, optimization of therapy, identification of promising drug targets and prediction of resistance to anticancer drugs. In silico pre-screened drug targets can be validated by a small number of carefully selected experiments. AREAS COVERED This review discusses the basics of mathematical modeling in cancer drug discovery and development. The topics include in silico discovery of novel molecular drug targets, optimization of immunotherapies, personalized medicine and guiding preclinical and clinical trials. Breast cancer has been used to demonstrate the applications of mathematical modeling in cancer diagnostics, the identification of high-risk population, cancer screening strategies, prediction of tumor growth and guiding cancer treatment. EXPERT OPINION Mathematical models are the key components of the toolkit used in the fight against cancer. The combinatorial complexity of new drugs discovery is enormous, making systematic drug discovery, by experimentation, alone difficult if not impossible. The biggest challenges include seamless integration of growing data, information and knowledge, and making them available for a multiplicity of analyses. Mathematical models are essential for bringing cancer drug discovery into the era of Omics, Big Data and personalized medicine.
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Affiliation(s)
- Ping Zhang
- CSIRO Computational Informatics , Marsfield, NSW , Australia
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20
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Margaliot M, Sontag ED, Tuller T. Entrainment to periodic initiation and transition rates in a computational model for gene translation. PLoS One 2014; 9:e96039. [PMID: 24800863 PMCID: PMC4011696 DOI: 10.1371/journal.pone.0096039] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 04/02/2014] [Indexed: 01/09/2023] Open
Abstract
Periodic oscillations play an important role in many biomedical systems. Proper functioning of biological systems that respond to periodic signals requires the ability to synchronize with the periodic excitation. For example, the sleep/wake cycle is a manifestation of an internal timing system that synchronizes to the solar day. In the terminology of systems theory, the biological system must entrain or phase-lock to the periodic excitation. Entrainment is also important in synthetic biology. For example, connecting several artificial biological systems that entrain to a common clock may lead to a well-functioning modular system. The cell-cycle is a periodic program that regulates DNA synthesis and cell division. Recent biological studies suggest that cell-cycle related genes entrain to this periodic program at the gene translation level, leading to periodically-varying protein levels of these genes. The ribosome flow model (RFM) is a deterministic model obtained via a mean-field approximation of a stochastic model from statistical physics that has been used to model numerous processes including ribosome flow along the mRNA. Here we analyze the RFM under the assumption that the initiation and/or transition rates vary periodically with a common period . We show that the ribosome distribution profile in the RFM entrains to this periodic excitation. In particular, the protein synthesis pattern converges to a unique periodic solution with period . To the best of our knowledge, this is the first proof of entrainment in a mathematical model for translation that encapsulates aspects such as initiation and termination rates, ribosomal movement and interactions, and non-homogeneous elongation speeds along the mRNA. Our results support the conjecture that periodic oscillations in tRNA levels and other factors related to the translation process can induce periodic oscillations in protein levels, and may suggest a new approach for re-engineering genetic systems to obtain a desired, periodic, protein synthesis rate.
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Affiliation(s)
- Michael Margaliot
- School of Electrical Engineering and the Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv, Israel
| | - Eduardo D. Sontag
- Dept. of Mathematics and Cancer Institute of New Jersey, Rutgers University, Piscataway, New Jersey, United States of America
| | - Tamir Tuller
- Dept. of Biomedical Engineering and the Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv, Israel
- * E-mail:
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21
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Kim JK, Jackson TL. Mechanisms that enhance sustainability of p53 pulses. PLoS One 2013; 8:e65242. [PMID: 23755198 PMCID: PMC3670918 DOI: 10.1371/journal.pone.0065242] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 04/26/2013] [Indexed: 02/07/2023] Open
Abstract
The tumor suppressor p53 protein shows various dynamic responses depending on the types and extent of cellular stresses. In particular, in response to DNA damage induced by γ-irradiation, cells generate a series of p53 pulses. Recent research has shown the importance of sustaining repeated p53 pulses for recovery from DNA damage. However, far too little attention has been paid to understanding how cells can sustain p53 pulses given the complexities of genetic heterogeneity and intrinsic noise. Here, we explore potential molecular mechanisms that enhance the sustainability of p53 pulses by developing a new mathematical model of the p53 regulatory system. This model can reproduce many experimental results that describe the dynamics of p53 pulses. By simulating the model both deterministically and stochastically, we found three potential mechanisms that improve the sustainability of p53 pulses: 1) the recently identified positive feedback loop between p53 and Rorα allows cells to sustain p53 pulses with high amplitude over a wide range of conditions, 2) intrinsic noise can often prevent the dampening of p53 pulses even after mutations, and 3) coupling of p53 pulses in neighboring cells via cytochrome-c significantly reduces the chance of failure in sustaining p53 pulses in the presence of heterogeneity among cells. Finally, in light of these results, we propose testable experiments that can reveal important mechanisms underlying p53 dynamics.
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Affiliation(s)
- Jae Kyoung Kim
- Department of Mathematics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Trachette L. Jackson
- Department of Mathematics, University of Michigan, Ann Arbor, Michigan, United States of America
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22
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Chen S, Harrigan P, Heineike B, Stewart-Ornstein J, El-Samad H. Building robust functionality in synthetic circuits using engineered feedback regulation. Curr Opin Biotechnol 2013; 24:790-6. [PMID: 23566378 DOI: 10.1016/j.copbio.2013.02.025] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2013] [Revised: 02/11/2013] [Accepted: 02/25/2013] [Indexed: 01/02/2023]
Abstract
The ability to engineer novel functionality within cells, to quantitatively control cellular circuits, and to manipulate the behaviors of populations, has many important applications in biotechnology and biomedicine. These applications are only beginning to be explored. In this review, we advocate the use of feedback control as an essential strategy for the engineering of robust homeostatic control of biological circuits and cellular populations. We also describe recent works where feedback control, implemented in silico or with biological components, was successfully employed for this purpose.
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Affiliation(s)
- Susan Chen
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
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23
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Qi H, Blanchard A, Lu T. Engineered genetic information processing circuits. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2013; 5:273-87. [DOI: 10.1002/wsbm.1216] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Abstract
The korAB operon in RK2 plasmids is a beautiful natural example of a negatively and cooperatively self-regulating operon. It has been particularly well characterized both experimentally and with mathematical models. We have carried out a detailed investigation of the role of the regulatory mechanism using a biologically grounded mechanistic multi-scale stochastic model that includes plasmid gene regulation and replication in the context of host growth and cell division. We use the model to compare four hypotheses for the action of the regulatory mechanism: increased robustness to extrinsic factors, decreased protein fluctuations, faster response-time of the operon and reduced host burden through improved efficiency of protein production. We find that the strongest impact of all elements of the regulatory architecture is on improving the efficiency of protein synthesis by reduction in the number of mRNA molecules needed to be produced, leading to a greater than ten-fold reduction in host energy required to express these plasmid proteins. A smaller but still significant role is seen for speeding response times, but this is not materially improved by the cooperativity. The self-regulating mechanisms have the least impact on protein fluctuations and robustness. While reduction of host burden is evident in a plasmid context, negative self-regulation is a widely seen motif for chromosomal genes. We propose that an important evolutionary driver for negatively self-regulated genes is to improve the efficiency of protein synthesis.
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Affiliation(s)
- Dorota Herman
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
- School of Biosciences, University of Nottingham, Sutton Bonington, Leicestershire, United Kingdom
- Department of Plant Systems Biology, VIB – Ghent University, Ghent, Belgium
| | | | - Dov J. Stekel
- School of Biosciences, University of Nottingham, Sutton Bonington, Leicestershire, United Kingdom
- * E-mail:
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25
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Analyzing and engineering cell signaling modules with synthetic biology. Curr Opin Biotechnol 2012; 23:785-90. [DOI: 10.1016/j.copbio.2012.01.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2011] [Revised: 01/11/2012] [Accepted: 01/12/2012] [Indexed: 12/20/2022]
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26
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Synthetic signaling networks for therapeutic applications. Curr Opin Biotechnol 2012; 23:773-9. [DOI: 10.1016/j.copbio.2012.01.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Revised: 01/03/2012] [Accepted: 01/08/2012] [Indexed: 01/02/2023]
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Goldbeter A, Gérard C, Gonze D, Leloup JC, Dupont G. Systems biology of cellular rhythms. FEBS Lett 2012; 586:2955-65. [PMID: 22841722 DOI: 10.1016/j.febslet.2012.07.041] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 07/17/2012] [Accepted: 07/17/2012] [Indexed: 12/22/2022]
Abstract
Rhythms abound in biological systems, particularly at the cellular level where they originate from the feedback loops present in regulatory networks. Cellular rhythms can be investigated both by experimental and modeling approaches, and thus represent a prototypic field of research for systems biology. They have also become a major topic in synthetic biology. We review advances in the study of cellular rhythms of biochemical rather than electrical origin by considering a variety of oscillatory processes such as Ca++ oscillations, circadian rhythms, the segmentation clock, oscillations in p53 and NF-κB, synthetic oscillators, and the oscillatory dynamics of cyclin-dependent kinases driving the cell cycle. Finally we discuss the coupling between cellular rhythms and their robustness with respect to molecular noise.
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Affiliation(s)
- A Goldbeter
- Unité de Chronobiologie théorique, Faculté des Sciences, Université Libre de Bruxelles (ULB), Campus Plaine, CP 231, B-1050 Brussels, Belgium.
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28
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Ganesan A, Zhang J. How cells process information: quantification of spatiotemporal signaling dynamics. Protein Sci 2012; 21:918-28. [PMID: 22573643 DOI: 10.1002/pro.2089] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Accepted: 04/23/2012] [Indexed: 02/03/2023]
Abstract
Arguably, one of the foremost distinctions between life and non-living matter is the ability to sense environmental changes and respond appropriately--an ability that is invested in every living cell. Within a single cell, this function is largely carried out by networks of signaling molecules. However, the details of how signaling networks help cells make complicated decisions are still not clear. For instance, how do cells read graded, analog stress signals but convert them into digital live-or-die responses? The answer to such questions may originate from the fact that signaling molecules are not static but dynamic entities, changing in numbers and activity over time and space. In the past two decades, researchers have been able to experimentally monitor signaling dynamics and use mathematical techniques to quantify and abstract general principles of how cells process information. In this review, the authors first introduce and discuss various experimental and computational methodologies that have been used to study signaling dynamics. The authors then discuss the different types of temporal dynamics such as oscillations and bistability that can be exhibited by signaling systems and highlight studies that have investigated such dynamics in physiological settings. Finally, the authors illustrate the role of spatial compartmentalization in regulating cellular responses with examples of second-messenger signaling in cardiac myocytes.
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Affiliation(s)
- Ambhighainath Ganesan
- Department of Biomedical Engineering, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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29
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Modeling of hysteresis in gene regulatory networks. Bull Math Biol 2012; 74:1727-53. [PMID: 22588784 DOI: 10.1007/s11538-012-9733-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Accepted: 04/30/2012] [Indexed: 12/26/2022]
Abstract
Hysteresis, observed in many gene regulatory networks, has a pivotal impact on biological systems, which enhances the robustness of cell functions. In this paper, a general model is proposed to describe the hysteretic gene regulatory network by combining the hysteresis component and the transient dynamics. The Bouc-Wen hysteresis model is modified to describe the hysteresis component in the mammalian gene regulatory networks. Rigorous mathematical analysis on the dynamical properties of the model is presented to ensure the bounded-input-bounded-output (BIBO) stability and demonstrates that the original Bouc-Wen model can only generate a clockwise hysteresis loop while the modified model can describe both clockwise and counter clockwise hysteresis loops. Simulation studies have shown that the hysteresis loops from our model are consistent with the experimental observations in three mammalian gene regulatory networks and two E.coli gene regulatory networks, which demonstrate the ability and accuracy of the mathematical model to emulate natural gene expression behavior with hysteresis. A comparison study has also been conducted to show that this model fits the experiment data significantly better than previous ones in the literature. The successful modeling of the hysteresis in all the five hysteretic gene regulatory networks suggests that the new model has the potential to be a unified framework for modeling hysteresis in gene regulatory networks and provide better understanding of the general mechanism that drives the hysteretic function.
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Ausländer S, Wieland M, Fussenegger M. Smart medication through combination of synthetic biology and cell microencapsulation. Metab Eng 2012; 14:252-60. [DOI: 10.1016/j.ymben.2011.06.003] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Revised: 05/11/2011] [Accepted: 06/09/2011] [Indexed: 01/05/2023]
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31
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Karlsson M, Weber W. Therapeutic synthetic gene networks. Curr Opin Biotechnol 2012; 23:703-11. [PMID: 22305476 DOI: 10.1016/j.copbio.2012.01.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Revised: 01/09/2012] [Accepted: 01/09/2012] [Indexed: 10/14/2022]
Abstract
The field of synthetic biology is rapidly expanding and has over the past years evolved from the development of simple gene networks to complex treatment-oriented circuits. The reprogramming of cell fate with open-loop or closed-loop synthetic control circuits along with biologically implemented logical functions have fostered applications spanning over a wide range of disciplines, including artificial insemination, personalized medicine and the treatment of cancer and metabolic disorders. In this review we describe several applications of interactive gene networks, a synthetic biology-based approach for future gene therapy, as well as the utilization of synthetic gene circuits as blueprints for the design of stimuli-responsive biohybrid materials. The recent progress in synthetic biology, including the rewiring of biosensing devices with the body's endogenous network as well as novel therapeutic approaches originating from interdisciplinary work, generates numerous opportunities for future biomedical applications.
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Affiliation(s)
- Maria Karlsson
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
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32
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Botezatu L, Sievers S, Gama-Norton L, Schucht R, Hauser H, Wirth D. Genetic aspects of cell line development from a synthetic biology perspective. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2012; 127:251-284. [PMID: 22068842 DOI: 10.1007/10_2011_117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Animal cells can be regarded as factories for the production of relevant proteins. The advances described in this chapter towards the development of cell lines with higher productivity capacities, certain metabolic and proliferation properties, reduced apoptosis and other features must be regarded in an integrative perspective. The systematic application of systems biology approaches in combination with a synthetic arsenal for targeted modification of endogenous networks are proposed to lead towards the achievement of a predictable and technologically advanced cell system with high biotechnological impact.
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Affiliation(s)
- L Botezatu
- Helmholtz Centre for Infection Research, Braunschweig, Germany
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33
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Ganesan A, Levchenko A. Principles of model building: an experimentation-aided approach to development of models for signaling networks. Methods Cell Biol 2012; 110:1-17. [PMID: 22482943 DOI: 10.1016/b978-0-12-388403-9.00001-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Living cells continuously probe their environment and respond to a multitude of external cues. The information about the environment is carried by signaling cascades that act as "internal transducing and computing modules," coupled into complex and interconnected networks. A comprehensive understanding of how cells make decisions therefore necessitates a sound theoretical framework, which can be achieved through mathematical modeling of the signaling networks. In this chapter, we conceptually describe the typical workflow involved in building mathematical models that are motivated by and are developed in a tight integration with experimental analysis. In particular, we delineate the steps involved in a generic, iterative experimentation-driven model-building process, both through informal discussion and using a recently published study as an example. Experiments guide the initial development of mathematical models, including choice of appropriate template model and parameter revision. The model can then be used to generate and test hypotheses quickly and inexpensively, aiding in judicious design of future experiments. These experiments, in turn, are used to update the model. The model developed at the end of this exercise not only predicts functional behavior of the system under study but also provides insight into the biophysical underpinnings of signaling networks.
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Affiliation(s)
- Ambhighainath Ganesan
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA
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Abstract
Synthetic biology aims to create functional devices, systems and organisms with novel and useful functions on the basis of catalogued and standardized biological building blocks. Although they were initially constructed to elucidate the dynamics of simple processes, designed devices now contribute to the understanding of disease mechanisms, provide novel diagnostic tools, enable economic production of therapeutics and allow the design of novel strategies for the treatment of cancer, immune diseases and metabolic disorders, such as diabetes and gout, as well as a range of infectious diseases. In this Review, we cover the impact and potential of synthetic biology for biomedical applications.
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Affiliation(s)
- Wilfried Weber
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, Freiburg, D-79104 Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Hebelstrasse 25, Freiburg, D-79104 Germany
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel, CH-4058 Switzerland
- Faculty of Science, University of Basel, Mattenstrasse 26, Basel, CH-4058 Switzerland
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Miró-Bueno JM, Rodríguez-Patón A. A simple negative interaction in the positive transcriptional feedback of a single gene is sufficient to produce reliable oscillations. PLoS One 2011; 6:e27414. [PMID: 22205920 PMCID: PMC3244268 DOI: 10.1371/journal.pone.0027414] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Accepted: 10/17/2011] [Indexed: 11/19/2022] Open
Abstract
Negative and positive transcriptional feedback loops are present in natural and synthetic genetic oscillators. A single gene with negative transcriptional feedback needs a time delay and sufficiently strong nonlinearity in the transmission of the feedback signal in order to produce biochemical rhythms. A single gene with only positive transcriptional feedback does not produce oscillations. Here, we demonstrate that this single-gene network in conjunction with a simple negative interaction can also easily produce rhythms. We examine a model comprised of two well-differentiated parts. The first is a positive feedback created by a protein that binds to the promoter of its own gene and activates the transcription. The second is a negative interaction in which a repressor molecule prevents this protein from binding to its promoter. A stochastic study shows that the system is robust to noise. A deterministic study identifies that the dynamics of the oscillator are mainly driven by two types of biomolecules: the protein, and the complex formed by the repressor and this protein. The main conclusion of this paper is that a simple and usual negative interaction, such as degradation, sequestration or inhibition, acting on the positive transcriptional feedback of a single gene is a sufficient condition to produce reliable oscillations. One gene is enough and the positive transcriptional feedback signal does not need to activate a second repressor gene. This means that at the genetic level an explicit negative feedback loop is not necessary. The model needs neither cooperative binding reactions nor the formation of protein multimers. Therefore, our findings could help to clarify the design principles of cellular clocks and constitute a new efficient tool for engineering synthetic genetic oscillators.
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Affiliation(s)
- Jesús M. Miró-Bueno
- Departamento de Inteligencia Artificial, Facultad de Informática, Universidad Politécnica de Madrid, Madrid, Spain
- * E-mail: (JMMB); (ARP)
| | - Alfonso Rodríguez-Patón
- Departamento de Inteligencia Artificial, Facultad de Informática, Universidad Politécnica de Madrid, Madrid, Spain
- * E-mail: (JMMB); (ARP)
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Abstract
A major goal of synthetic biology is to develop a deeper understanding of biological design principles from the bottom up, by building circuits and studying their behavior in cells. Investigators initially sought to design circuits "from scratch" that functioned as independently as possible from the underlying cellular system. More recently, researchers have begun to develop a new generation of synthetic circuits that integrate more closely with endogenous cellular processes. These approaches are providing fundamental insights into the regulatory architecture, dynamics, and evolution of genetic circuits and enabling new levels of control across diverse biological systems.
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Affiliation(s)
- Nagarajan Nandagopal
- Department of Bioengineering, California Institute of Technology, Pasadena, CA 91125, USA
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37
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Weber W, Fussenegger M. Molecular diversity—the toolbox for synthetic gene switches and networks. Curr Opin Chem Biol 2011; 15:414-20. [PMID: 21470897 DOI: 10.1016/j.cbpa.2011.03.003] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Accepted: 03/15/2011] [Indexed: 01/16/2023]
Affiliation(s)
- Wilfried Weber
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
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38
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Abstract
Organisms have the ability to counteract environmental perturbations and keep certain components within a cell homeostatically regulated. Closely related to homeostasis is the behavior of perfect adaptation where an organism responds to a step-wise perturbation by regulating some of its components, after a transient period, to their original pre-perturbation values. A particular interesting type of model relates to the so-called robust behavior where the homeostatic or perfect adaptation property is independent of the magnitude of the applied step-wise perturbation. It has been shown that this type of behavior is related to the control-theoretic concept of integral feedback (or integral control). Using downloadable MATLAB examples, we demonstrate how robust perfect adaptation sites can be identified in reaction kinetic networks by linearizing the system, applying the Laplace transform and inspecting the transfer function. We also show how the homeostatic set point in perfect adaptation is related to the presence of zero-order fluxes.
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39
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Aubel D, Fussenegger M. Watch the clock-engineering biological systems to be on time. Curr Opin Genet Dev 2010; 20:634-43. [PMID: 20934319 DOI: 10.1016/j.gde.2010.09.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2010] [Revised: 08/02/2010] [Accepted: 09/15/2010] [Indexed: 11/20/2022]
Abstract
Inspired by natural time-keeping devices controlling the circadian clock, managing information processing in the brain and coordinating physiological activities on a daily (feeding and sleeping) or seasonal timescale (reproductive activity or hibernation), synthetic biologists have successfully assembled functional synthetic clocks from cataloged genetic components with standardized activities and arranging them in transcription circuits containing positive and negative feedback loops with integrated time-delay dynamics. While the positive feedback loop drives the clock like the (balance) spring in a mechanical watch the negative time-delay circuit represents the pulse generator defining a minimal time unit and precision of the clock like the pendulum fallback or the movement of the balance wheel in a classical mechanic watch. This basic design principle enabled the construction of a variety of synthetic oscillators whose design details are concisely covered in this review.
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Affiliation(s)
- Dominique Aubel
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
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