1
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Ruolo I, Napolitano S, Postiglione L, Napolitano G, Ballabio A, di Bernardo D. Investigation of dynamic regulation of TFEB nuclear shuttling by microfluidics and quantitative modelling. Commun Biol 2025; 8:443. [PMID: 40089585 PMCID: PMC11910602 DOI: 10.1038/s42003-025-07870-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2024] [Accepted: 03/03/2025] [Indexed: 03/17/2025] Open
Abstract
Transcription Factor EB (TFEB) controls lysosomal biogenesis and autophagy in response to nutritional status and other stress factors. Although its regulation by nuclear translocation is known to involve a complex network of well-studied regulatory processes, the precise contribution of each of these mechanisms is unclear. Using microfluidics technology and real-time imaging coupled with mathematical modelling, we explored the dynamic regulation of TFEB under different conditions. We found that TFEB nuclear translocation upon nutrient deprivation happens in two phases: a fast one characterised by a transient boost in TFEB dephosphorylation dependent on transient calcium release mediated by mucolipin 1 (MCOLN1) followed by activation of the Calcineurin phosphatase, and a slower one driven by inhibition of mTORC1-dependent phosphorylation of TFEB. Upon refeeding, TFEB cytoplasmic relocalisation kinetics are determined by Exportin 1 (XPO1). Collectively, our results show how different mechanisms interact to regulate TFEB activation and the power of microfluidics and quantitative modelling to elucidate complex biological mechanisms.
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Affiliation(s)
- Iacopo Ruolo
- Department of Chemical, Materials and Industrial Production Engineering, University of Naples Federico II, Naples, Italy
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sara Napolitano
- Department of Chemical, Materials and Industrial Production Engineering, University of Naples Federico II, Naples, Italy
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
- Institut Pasteur, Inria, Université Paris Cité, Paris, France
| | - Lorena Postiglione
- Department of Chemical, Materials and Industrial Production Engineering, University of Naples Federico II, Naples, Italy
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Gennaro Napolitano
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
- Medical Genetics Unit, Department of Medical and Translational Science, Federico II University, Naples, Italy
- SSM School for Advanced Studies, Federico II University, Naples, Italy
| | - Andrea Ballabio
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
- Department of Translational Medicine, University of Naples "Federico II", Naples, Italy
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, US
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, US
| | - Diego di Bernardo
- Department of Chemical, Materials and Industrial Production Engineering, University of Naples Federico II, Naples, Italy.
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy.
- SSM School for Advanced Studies, Federico II University, Naples, Italy.
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2
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Liu Y, Wu Y, Wang L, Zhu L, Dong Y, Xu W. A ratiometric dual-fluorescent paper-based synthetic biosensor for visual detection of tetracycline on-site. JOURNAL OF HAZARDOUS MATERIALS 2024; 467:133647. [PMID: 38335608 DOI: 10.1016/j.jhazmat.2024.133647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/16/2024] [Accepted: 01/26/2024] [Indexed: 02/12/2024]
Abstract
The excessive use of tetracycline poses a threat to human health, making it essential to monitor and regulate its usage. While whole-cell biosensors offer a simple and cost-effective method, their utility is constrained by limitations in sensitivity, portability, and robustness, hindering real-time measurements within complex environmental contexts. In this study, a ratiometric i/cTetR synthetic biosensing test strip with an engineered modified dual-fluorescence reporting was developed for detecting Tet antibiotics in water and food. First, the standardized unidirectional promoter PtetR by tailoring and screening TetR transcription factor binding sites and verified by molecular docking, shortening the detection time. Secondly, decoupling the sensing and reporting modules enhances the biosensor's performance, eliminating genetic background leakage and tripling the output signal. Thirdly, a ratiometric dual fluorescence signal i/cTetR biosensing test strip was designed. Under the light box LED/UV light source, the dual signal output method significantly reduced false negative results and enhanced the anti-interference capability of the biosensor. The i/cTetR strips can detect Tet in tap water (5-1280 μg/mL) and milk (50-3200 μg/kg) within 45 min in high volume on-site without separation and purification. This study provides a standardized and universal sensing method for the field detection of antibiotic contaminants.
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Affiliation(s)
- Yanger Liu
- Key Laboratory of Veterinary Anatomy, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, People's Republic of China; Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Yifan Wu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Lei Wang
- Key Laboratory of Veterinary Anatomy, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Longjiao Zhu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Yulan Dong
- Key Laboratory of Veterinary Anatomy, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, People's Republic of China.
| | - Wentao Xu
- Key Laboratory of Veterinary Anatomy, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, People's Republic of China; Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, People's Republic of China.
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3
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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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4
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Hsiao YC, Dutta A. Nonlinear control designs and their application to cancer differentiation therapy. Math Biosci 2023; 366:109105. [PMID: 37944795 DOI: 10.1016/j.mbs.2023.109105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 10/29/2023] [Accepted: 10/31/2023] [Indexed: 11/12/2023]
Abstract
We designed three new controllers: a sigmoid-based controller, a polynomial dynamic inversion-based controller, and a proportional-integral-derivative (PID) impulsive controller for cancer differentiation therapy. We compared these three controllers to existing control strategies to show the improvement in performance and compare their robustness. The sigmoid-based controller adds a sigmoid term associated with the error of the controlled state and a selected observed state. The sigmoid term is multiplied by a control gain, thereby decreasing the control effort for state transition. The polynomial dynamic inversion-based controller adds a cubic error term in the error dynamic aiming to achieve a shorter convergence time to the desired value of the controlled state. The PID impulsive controller considers the accumulated controlled state error and the rate of change of the controlled state error, thereby forcing the controlled state to converge to the desired value and alleviating the damping effect in the steady state. For the considered cancer network, the 3 new cancer control strategies exhibit superior and robust performance. The PID impulsive controller has a significant improvement in robustness compared to the impulsive controller and has greater potential for cancer differentiation therapy.
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Affiliation(s)
- Yen-Che Hsiao
- Department of Electrical and Computer Engineering, University of Connecticut, Storrs, 06269, CT, USA.
| | - Abhishek Dutta
- Department of Electrical and Computer Engineering, University of Connecticut, Storrs, 06269, CT, USA
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5
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Merljak E, Malovrh B, Jerala R. Segmentation strategy of de novo designed four-helical bundles expands protein oligomerization modalities for cell regulation. Nat Commun 2023; 14:1995. [PMID: 37031229 PMCID: PMC10082849 DOI: 10.1038/s41467-023-37765-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 03/30/2023] [Indexed: 04/10/2023] Open
Abstract
Protein-protein interactions govern most biological processes. New protein assemblies can be introduced through the fusion of selected proteins with di/oligomerization domains, which interact specifically with their partners but not with other cellular proteins. While four-helical bundle proteins (4HB) have typically been assembled from two segments, each comprising two helices, here we show that they can be efficiently segmented in various ways, expanding the number of combinations generated from a single 4HB. We implement a segmentation strategy of 4HB to design two-, three-, or four-chain combinations for the recruitment of multiple protein components. Different segmentations provide new insight into the role of individual helices for 4HB assembly. We evaluate 4HB segmentations for potential use in mammalian cells for the reconstitution of a protein reporter, transcriptional activation, and inducible 4HB assembly. Furthermore, the implementation of trimerization is demonstrated as a modular chimeric antigen receptor for the recognition of multiple cancer antigens.
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Affiliation(s)
- Estera Merljak
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
- Interdisciplinary Doctoral Programme of Biomedicine, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Benjamin Malovrh
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia.
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6
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Chatani T, Shiraishi S, Miyazako H, Onoe H, Hori Y. L-2L ladder digital-to-analogue converter for dynamics generation of chemical concentrations. ROYAL SOCIETY OPEN SCIENCE 2023; 10:230085. [PMID: 37090965 PMCID: PMC10113815 DOI: 10.1098/rsos.230085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 03/09/2023] [Indexed: 05/03/2023]
Abstract
Cellular response to dynamic chemical stimulation encodes rich information about the underlying reaction pathways and their kinetics. Microfluidic chemical stimulators play a key role in generating dynamic concentration waveforms by mixing several aqueous solutions. In this article, we propose a multi-layer microfluidic chemical stimulator capable of modulating chemical concentrations by a simple binary logic based on the electronic-hydraulic analogy of electronic R-2R ladder circuits. The proposed device, which we call L-2L ladder digital-to-analogue converter (DAC), allows us to systematically modulate 2 n levels of concentrations from single sources of solution and solvent by a single operation of 2n membrane valves, which contrasts with existing devices that require complex channel geometry with multiple input sources and valve operations. We fabricated the L-2L ladder DAC with n = 3 bit resolution and verified the concept by comparing the generated waveforms with computational simulations. The response time of the proposed DAC was within the order of seconds because of its simple operation logic of membrane valves. Furthermore, detailed analysis of the waveforms revealed that the transient concentration can be systematically predicted by a simple addition of the transient waveforms of 2n = 6 base patterns, enabling facile optimization of the channel geometry to fine-tune the output waveforms.
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Affiliation(s)
- Tomohito Chatani
- Department of Applied Physics and Physico-informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Suguru Shiraishi
- Department of Applied Physics and Physico-informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Hiroki Miyazako
- Graduate School of Information Science and Technology, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Hiroaki Onoe
- Department of Mechanical Engineering, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Yutaka Hori
- Department of Applied Physics and Physico-informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
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7
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The VersaLive platform enables microfluidic mammalian cell culture for versatile applications. Commun Biol 2022; 5:1034. [PMID: 36175545 PMCID: PMC9522807 DOI: 10.1038/s42003-022-03976-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 09/12/2022] [Indexed: 01/09/2023] Open
Abstract
Microfluidic-based cell culture allows for precise spatio-temporal regulation of microenvironment, live cell imaging and better recapitulation of physiological conditions, while minimizing reagents’ consumption. Despite their usefulness, most microfluidic systems are designed with one specific application in mind and usually require specialized equipment and expertise for their operation. All these requirements prevent microfluidic-based cell culture to be widely adopted. Here, we designed and implemented a versatile and easy-to-use perfusion cell culture microfluidic platform for multiple applications (VersaLive) requiring only standard pipettes. Here, we showcase the multiple uses of VersaLive (e.g., time-lapse live cell imaging, immunostaining, cell recovery, cell lysis, plasmid transfection) in mammalian cell lines and primary cells. VersaLive could replace standard cell culture formats in several applications, thus decreasing costs and increasing reproducibility across laboratories. The layout, documentation and protocols are open-source and available online at https://versalive.tigem.it/. VersaLive is a versatile microfluidic platform with flexible input modes and low-volume media reservoirs that can be used for time-lapse live cell imaging, immunostaining, cell recovery, cell lysis and plasmid transfection.
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8
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de Cesare I, Salzano D, di Bernardo M, Renson L, Marucci L. Control-Based Continuation: A New Approach to Prototype Synthetic Gene Networks. ACS Synth Biol 2022; 11:2300-2313. [PMID: 35729740 PMCID: PMC9295158 DOI: 10.1021/acssynbio.1c00632] [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] [Indexed: 11/23/2022]
Abstract
![]()
Control-Based Continuation
(CBC) is a general and systematic method
to carry out the bifurcation analysis of physical experiments. CBC
does not rely on a mathematical model and thus overcomes the uncertainty
introduced when identifying bifurcation curves indirectly through
modeling and parameter estimation. We demonstrate, in silico, CBC applicability to biochemical processes by tracking the equilibrium
curve of a toggle switch, which includes additive process noise and
exhibits bistability. We compare the results obtained when CBC uses
a model-free and model-based control strategy and show that both can
track stable and unstable solutions, revealing bistability. We then
demonstrate CBC in conditions more representative of an in
vivo experiment using an agent-based simulator describing
cell growth and division, cell-to-cell variability, spatial distribution,
and diffusion of chemicals. We further show how the identified curves
can be used for parameter estimation and discuss how CBC can significantly
accelerate the prototyping of synthetic gene regulatory networks.
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Affiliation(s)
- Irene de Cesare
- Engineering Mathematics Department, University of Bristol, Bristol BS8 1TW, U.K.,Department of Electrical Engineering and Information Technologies, University of Naples Federico II, 80125 Naples, Italy
| | - Davide Salzano
- Engineering Mathematics Department, University of Bristol, Bristol BS8 1TW, U.K.,Department of Electrical Engineering and Information Technologies, University of Naples Federico II, 80125 Naples, Italy
| | - Mario di Bernardo
- Department of Electrical Engineering and Information Technologies, University of Naples Federico II, 80125 Naples, Italy
| | - Ludovic Renson
- Department of Mechanical Engineering, Imperial College London, London SW7 2BX, U.K
| | - Lucia Marucci
- Engineering Mathematics Department, University of Bristol, Bristol BS8 1TW, U.K.,BrisSynBio, University of Bristol, Bristol BS8 1TQ, U.K.,School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1UB, U.K
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9
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Civelekoglu O, Wang N, Arifuzzman A, Boya M, Sarioglu AF. Automated lightless cytometry on a microchip with adaptive immunomagnetic manipulation. Biosens Bioelectron 2022; 203:114014. [DOI: 10.1016/j.bios.2022.114014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 12/13/2021] [Accepted: 01/15/2022] [Indexed: 01/08/2023]
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10
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Abstract
Synthetic biology increasingly enables the construction of sophisticated functions in mammalian cells. A particularly promising frontier combines concepts drawn from industrial process control engineering-which is used to confer and balance properties such as stability and efficiency-with understanding as to how living systems have evolved to perform similar tasks with biological components. In this review, we first survey the state-of-the-art for both technologies and strategies available for genetic programming in mammalian cells. We then discuss recent progress in implementing programming objectives inspired by engineered and natural control mechanisms. Finally, we consider the transformative role of model-guided design in the present and future construction of customized mammalian cell functions for applications in biotechnology, medicine, and fundamental research.
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11
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Zannino L, Casali C, Siciliani S, Biggiogera M. The dynamics of the nuclear environment and their impact on gene function. J Biochem 2021; 169:259-264. [PMID: 32745171 DOI: 10.1093/jb/mvaa091] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 07/15/2020] [Indexed: 01/04/2023] Open
Abstract
In the last decades, it has become increasingly clear how the modulation of spatial organization of chromatin over time and through the cell cycle is closely connected to gene function regulation. Different physicochemical stimuli contribute to the realization of specific transcriptional programs and finally to a specific cellular phenotype. In this review, we aim to describe the current knowledge about the dynamics regulating the movements and the interactions of molecules within the nucleus and their impact on gene functions. In particular, taking into account that these forces exert their effect in a nuclear environment characterized by a high concentration of molecules, we will discuss the role of proteins and structures that regulate these movements and transduce physicochemical signals acting on the cell to the nucleus.
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Affiliation(s)
- Lorena Zannino
- Laboratory of Cell Biology and Neurobiology, Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | | | - Stella Siciliani
- Laboratory of Cell Biology and Neurobiology, Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
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12
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Pedone E, de Cesare I, Zamora-Chimal CG, Haener D, Postiglione L, La Regina A, Shannon B, Savery NJ, Grierson CS, di Bernardo M, Gorochowski TE, Marucci L. Cheetah: A Computational Toolkit for Cybergenetic Control. ACS Synth Biol 2021; 10:979-989. [PMID: 33904719 DOI: 10.1021/acssynbio.0c00463] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Advances in microscopy, microfluidics, and optogenetics enable single-cell monitoring and environmental regulation and offer the means to control cellular phenotypes. The development of such systems is challenging and often results in bespoke setups that hinder reproducibility. To address this, we introduce Cheetah, a flexible computational toolkit that simplifies the integration of real-time microscopy analysis with algorithms for cellular control. Central to the platform is an image segmentation system based on the versatile U-Net convolutional neural network. This is supplemented with functionality to robustly count, characterize, and control cells over time. We demonstrate Cheetah's core capabilities by analyzing long-term bacterial and mammalian cell growth and by dynamically controlling protein expression in mammalian cells. In all cases, Cheetah's segmentation accuracy exceeds that of a commonly used thresholding-based method, allowing for more accurate control signals to be generated. Availability of this easy-to-use platform will make control engineering techniques more accessible and offer new ways to probe and manipulate living cells.
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Affiliation(s)
- Elisa Pedone
- Department of Engineering Mathematics, University of Bristol, Ada Lovelace Building, University Walk, BS8 1TW Bristol, United Kingdom
- School of Cellular and Molecular Medicine, University of Bristol, Biomedical Sciences Building, University Walk, BS8 1TD Bristol, United Kingdom
| | - Irene de Cesare
- Department of Engineering Mathematics, University of Bristol, Ada Lovelace Building, University Walk, BS8 1TW Bristol, United Kingdom
| | - Criseida G. Zamora-Chimal
- Department of Engineering Mathematics, University of Bristol, Ada Lovelace Building, University Walk, BS8 1TW Bristol, United Kingdom
- BrisSynBio, Life Sciences Building, Tyndall Avenue, BS8 1TQ Bristol, United Kingdom
| | - David Haener
- Department of Engineering Mathematics, University of Bristol, Ada Lovelace Building, University Walk, BS8 1TW Bristol, United Kingdom
| | - Lorena Postiglione
- Department of Engineering Mathematics, University of Bristol, Ada Lovelace Building, University Walk, BS8 1TW Bristol, United Kingdom
| | - Antonella La Regina
- Department of Engineering Mathematics, University of Bristol, Ada Lovelace Building, University Walk, BS8 1TW Bristol, United Kingdom
- School of Cellular and Molecular Medicine, University of Bristol, Biomedical Sciences Building, University Walk, BS8 1TD Bristol, United Kingdom
| | - Barbara Shannon
- BrisSynBio, Life Sciences Building, Tyndall Avenue, BS8 1TQ Bristol, United Kingdom
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, BS8 1TD Bristol, United Kingdom
| | - Nigel J. Savery
- BrisSynBio, Life Sciences Building, Tyndall Avenue, BS8 1TQ Bristol, United Kingdom
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, BS8 1TD Bristol, United Kingdom
| | - Claire S. Grierson
- BrisSynBio, Life Sciences Building, Tyndall Avenue, BS8 1TQ Bristol, United Kingdom
- School of Biological Sciences, University of Bristol, Tyndall Avenue, BS8 1TQ Bristol, United Kingdom
| | - Mario di Bernardo
- Department of Engineering Mathematics, University of Bristol, Ada Lovelace Building, University Walk, BS8 1TW Bristol, United Kingdom
- BrisSynBio, Life Sciences Building, Tyndall Avenue, BS8 1TQ Bristol, United Kingdom
- Department of EE and ICT, University of Naples Federico II, Via Claudio 21, 80125 Naples, Italy
| | - Thomas E. Gorochowski
- BrisSynBio, Life Sciences Building, Tyndall Avenue, BS8 1TQ Bristol, United Kingdom
- School of Biological Sciences, University of Bristol, Tyndall Avenue, BS8 1TQ Bristol, United Kingdom
| | - Lucia Marucci
- Department of Engineering Mathematics, University of Bristol, Ada Lovelace Building, University Walk, BS8 1TW Bristol, United Kingdom
- School of Cellular and Molecular Medicine, University of Bristol, Biomedical Sciences Building, University Walk, BS8 1TD Bristol, United Kingdom
- BrisSynBio, Life Sciences Building, Tyndall Avenue, BS8 1TQ Bristol, United Kingdom
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13
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Perrino G, Napolitano S, Galdi F, La Regina A, Fiore D, Giuliano T, di Bernardo M, di Bernardo D. Automatic synchronisation of the cell cycle in budding yeast through closed-loop feedback control. Nat Commun 2021; 12:2452. [PMID: 33907191 PMCID: PMC8079375 DOI: 10.1038/s41467-021-22689-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 03/24/2021] [Indexed: 12/18/2022] Open
Abstract
The cell cycle is the process by which eukaryotic cells replicate. Yeast cells cycle asynchronously with each cell in the population budding at a different time. Although there are several experimental approaches to synchronise cells, these usually work only in the short-term. Here, we build a cyber-genetic system to achieve long-term synchronisation of the cell population, by interfacing genetically modified yeast cells with a computer by means of microfluidics to dynamically change medium, and a microscope to estimate cell cycle phases of individual cells. The computer implements a controller algorithm to decide when, and for how long, to change the growth medium to synchronise the cell-cycle across the population. Our work builds upon solid theoretical foundations provided by Control Engineering. In addition to providing an avenue for yeast cell cycle synchronisation, our work shows that control engineering can be used to automatically steer complex biological processes towards desired behaviours similarly to what is currently done with robots and autonomous vehicles.
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Affiliation(s)
| | - Sara Napolitano
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
- Department of Chemical, Materials and Industrial Production Engineering, University of Naples Federico II, Naples, Italy
| | - Francesca Galdi
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | | | - Davide Fiore
- Department of Mathematics and Applications "R. Caccioppoli", University of Naples Federico II, Naples, Italy
| | - Teresa Giuliano
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Mario di Bernardo
- Department of Electrical Engineering and Information Technology, University of Naples Federico II, Naples, Italy
- SSM - School for Advanced Studies, Naples, Italy
| | - Diego di Bernardo
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy.
- Department of Chemical, Materials and Industrial Production Engineering, University of Naples Federico II, Naples, Italy.
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14
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de Cesare I, Zamora-Chimal CG, Postiglione L, Khazim M, Pedone E, Shannon B, Fiore G, Perrino G, Napolitano S, di Bernardo D, Savery NJ, Grierson C, di Bernardo M, Marucci L. ChipSeg: An Automatic Tool to Segment Bacterial and Mammalian Cells Cultured in Microfluidic Devices. ACS OMEGA 2021; 6:2473-2476. [PMID: 33553865 PMCID: PMC7859942 DOI: 10.1021/acsomega.0c03906] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 11/20/2020] [Indexed: 05/14/2023]
Abstract
Extracting quantitative measurements from time-lapse images is necessary in external feedback control applications, where segmentation results are used to inform control algorithms. We describe ChipSeg, a computational tool that segments bacterial and mammalian cells cultured in microfluidic devices and imaged by time-lapse microscopy, which can be used also in the context of external feedback control. The method is based on thresholding and uses the same core functions for both cell types. It allows us to segment individual cells in high cell density microfluidic devices, to quantify fluorescent protein expression over a time-lapse experiment, and to track individual mammalian cells. ChipSeg enables robust segmentation in external feedback control experiments and can be easily customized for other experimental settings and research aims.
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Affiliation(s)
- Irene de Cesare
- Department
of Engineering Mathematics, University of
Bristol, Woodland Road, Bristol BS8 1UB, U.K.
| | - Criseida G. Zamora-Chimal
- Department
of Engineering Mathematics, University of
Bristol, Woodland Road, Bristol BS8 1UB, U.K.
- BrisSynBio,
Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, U.K.
| | - Lorena Postiglione
- Department
of Engineering Mathematics, University of
Bristol, Woodland Road, Bristol BS8 1UB, U.K.
| | - Mahmoud Khazim
- Department
of Engineering Mathematics, University of
Bristol, Woodland Road, Bristol BS8 1UB, U.K.
- School
of Cellular and Molecular Medicine, University
of Bristol, University Walk, Bristol BS8 1TD, U.K.
| | - Elisa Pedone
- Department
of Engineering Mathematics, University of
Bristol, Woodland Road, Bristol BS8 1UB, U.K.
- School
of Cellular and Molecular Medicine, University
of Bristol, University Walk, Bristol BS8 1TD, U.K.
| | - Barbara Shannon
- BrisSynBio,
Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, U.K.
- School
of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, U.K.
| | - Gianfranco Fiore
- Department
of Engineering Mathematics, University of
Bristol, Woodland Road, Bristol BS8 1UB, U.K.
- BrisSynBio,
Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, U.K.
| | - Giansimone Perrino
- Telethon
Institute of Genetic and Medicine Via Campi Flegrei 34, 80078 Pozzuoli, Italy
| | - Sara Napolitano
- Telethon
Institute of Genetic and Medicine Via Campi Flegrei 34, 80078 Pozzuoli, Italy
| | - Diego di Bernardo
- Telethon
Institute of Genetic and Medicine Via Campi Flegrei 34, 80078 Pozzuoli, Italy
- Department
of Chemical, Materials and Industrial Production Engineering, University of Naples Federico II, 80125 Naples, Italy
| | - Nigel J. Savery
- BrisSynBio,
Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, U.K.
- School
of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, U.K.
| | - Claire Grierson
- BrisSynBio,
Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, U.K.
- School
of Biological Sciences, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, U.K.
| | - Mario di Bernardo
- Department
of Engineering Mathematics, University of
Bristol, Woodland Road, Bristol BS8 1UB, U.K.
- BrisSynBio,
Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, U.K.
- Department
of EE and ICT, University of Naples Federico
II, Via Claudio 21, 80125 Naples, Italy
| | - Lucia Marucci
- Department
of Engineering Mathematics, University of
Bristol, Woodland Road, Bristol BS8 1UB, U.K.
- BrisSynBio,
Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, U.K.
- School
of Cellular and Molecular Medicine, University
of Bristol, University Walk, Bristol BS8 1TD, U.K.
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15
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Khazim M, Pedone E, Postiglione L, di Bernardo D, Marucci L. A Microfluidic/Microscopy-Based Platform for on-Chip Controlled Gene Expression in Mammalian Cells. Methods Mol Biol 2021; 2229:205-219. [PMID: 33405224 DOI: 10.1007/978-1-0716-1032-9_10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Applications of control engineering to mammalian cell biology have been recently implemented for precise regulation of gene expression. In this chapter, we report the main experimental and computational methodologies to implement automatic feedback control of gene expression in mammalian cells using a microfluidics/microscopy platform.
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Affiliation(s)
- Mahmoud Khazim
- Department of Engineering Mathematics, University of Bristol, Bristol, UK
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
- BrisSynBio, Bristol, UK
| | - Elisa Pedone
- Department of Engineering Mathematics, University of Bristol, Bristol, UK
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
- BrisSynBio, Bristol, UK
| | - Lorena Postiglione
- Department of Engineering Mathematics, University of Bristol, Bristol, UK
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
- BrisSynBio, Bristol, UK
| | | | - Lucia Marucci
- Department of Engineering Mathematics, University of Bristol, Bristol, UK.
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK.
- BrisSynBio, Bristol, UK.
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16
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17
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Carrasco-López C, García-Echauri SA, Kichuk T, Avalos JL. Optogenetics and biosensors set the stage for metabolic cybergenetics. Curr Opin Biotechnol 2020; 65:296-309. [DOI: 10.1016/j.copbio.2020.07.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/23/2020] [Accepted: 07/25/2020] [Indexed: 12/17/2022]
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18
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Perrino G, Wilson C, Santorelli M, di Bernardo D. Quantitative Characterization of α-Synuclein Aggregation in Living Cells through Automated Microfluidics Feedback Control. Cell Rep 2020; 27:916-927.e5. [PMID: 30995486 PMCID: PMC6484782 DOI: 10.1016/j.celrep.2019.03.081] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 02/20/2019] [Accepted: 03/22/2019] [Indexed: 12/21/2022] Open
Abstract
Aggregation of α-synuclein and formation of inclusions are hallmarks of Parkinson’s disease (PD). Aggregate formation is affected by cellular environment, but it has been studied almost exclusively in cell-free systems. We quantitatively analyzed α-synuclein inclusion formation and clearance in a yeast cell model of PD expressing either wild-type (WT) α-synuclein or the disease-associated A53T mutant from the galactose (Gal)-inducible promoter. A computer-controlled microfluidics device regulated α-synuclein in cells by means of closed-loop feedback control. We demonstrated that inclusion formation is strictly concentration dependent and that the aggregation threshold of the A53T mutant is about half of the WT α-synuclein (56%). We chemically modulated the proteasomal and autophagic pathways and demonstrated that autophagy is the main determinant of A53T α-synuclein inclusions’ clearance. In addition to proposing a technology to overcome current limitations in dynamically regulating protein expression levels, our results contribute to the biology of PD and have relevance for therapeutic applications. In silico feedback control enables regulation of α-synuclein expression in yeast α-Synuclein inclusion formation is strictly concentration, but not time, dependent The aggregation threshold of the α-synuclein A53T mutant is 56% of the wild-type Autophagy induction speeds up inclusion clearance in the A53T α-synuclein strain
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Affiliation(s)
- Giansimone Perrino
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy
| | - Cathal Wilson
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy
| | - Marco Santorelli
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy
| | - Diego di Bernardo
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy; Department of Chemical, Materials and Industrial Production Engineering, University of Naples Federico II, Piazzale Tecchio 80, 80125 Naples, Italy.
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19
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Täuber S, von Lieres E, Grünberger A. Dynamic Environmental Control in Microfluidic Single-Cell Cultivations: From Concepts to Applications. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e1906670. [PMID: 32157796 DOI: 10.1002/smll.201906670] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 01/16/2020] [Indexed: 06/10/2023]
Abstract
Microfluidic single-cell cultivation (MSCC) is an emerging field within fundamental as well as applied biology. During the last years, most MSCCs were performed at constant environmental conditions. Recently, MSCC at oscillating and dynamic environmental conditions has started to gain significant interest in the research community for the investigation of cellular behavior. Herein, an overview of this topic is given and microfluidic concepts that enable oscillating and dynamic control of environmental conditions with a focus on medium conditions are discussed, and their application in single-cell research for the cultivation of both mammalian and microbial cell systems is demonstrated. Furthermore, perspectives for performing MSCC at complex dynamic environmental profiles of single parameters and multiparameters (e.g., pH and O2 ) in amplitude and time are discussed. The technical progress in this field provides completely new experimental approaches and lays the foundation for systematic analysis of cellular metabolism at fluctuating environments.
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Affiliation(s)
- Sarah Täuber
- Multiscale Bioengineering, Faculty of Technology, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Eric von Lieres
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Alexander Grünberger
- Multiscale Bioengineering, Faculty of Technology, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
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20
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Scott HL, Buckner N, Fernandez-Albert F, Pedone E, Postiglione L, Shi G, Allen N, Wong LF, Magini L, Marucci L, O'Sullivan GA, Cole S, Powell J, Maycox P, Uney JB. A dual druggable genome-wide siRNA and compound library screening approach identifies modulators of parkin recruitment to mitochondria. J Biol Chem 2020; 295:3285-3300. [PMID: 31911436 PMCID: PMC7062187 DOI: 10.1074/jbc.ra119.009699] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 12/20/2019] [Indexed: 01/07/2023] Open
Abstract
Genetic and biochemical evidence points to an association between mitochondrial dysfunction and Parkinson's disease (PD). PD-associated mutations in several genes have been identified and include those encoding PTEN-induced putative kinase 1 (PINK1) and parkin. To identify genes, pathways, and pharmacological targets that modulate the clearance of damaged or old mitochondria (mitophagy), here we developed a high-content imaging-based assay of parkin recruitment to mitochondria and screened both a druggable genome-wide siRNA library and a small neuroactive compound library. We used a multiparameter principal component analysis and an unbiased parameter-agnostic machine-learning approach to analyze the siRNA-based screening data. The hits identified in this analysis included specific genes of the ubiquitin proteasome system, and inhibition of ubiquitin-conjugating enzyme 2 N (UBE2N) with a specific antagonist, Bay 11-7082, indicated that UBE2N modulates parkin recruitment and downstream events in the mitophagy pathway. Screening of the compound library identified kenpaullone, an inhibitor of cyclin-dependent kinases and glycogen synthase kinase 3, as a modulator of parkin recruitment. Validation studies revealed that kenpaullone augments the mitochondrial network and protects against the complex I inhibitor MPP+. Finally, we used a microfluidics platform to assess the timing of parkin recruitment to depolarized mitochondria and its modulation by kenpaullone in real time and with single-cell resolution. We demonstrate that the high-content imaging-based assay presented here is suitable for both genetic and pharmacological screening approaches, and we also provide evidence that pharmacological compounds modulate PINK1-dependent parkin recruitment.
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Affiliation(s)
- Helen L Scott
- Bristol Medical School, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Nicola Buckner
- Bristol Medical School, University of Bristol, Bristol BS8 1TD, United Kingdom
| | | | - Elisa Pedone
- Department of Engineering and Mathematics, University of Bristol, Bristol BS8 1TD, United Kingdom; School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Lorena Postiglione
- Department of Engineering and Mathematics, University of Bristol, Bristol BS8 1TD, United Kingdom; School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Gongyu Shi
- Bristol Medical School, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Nicholas Allen
- School of Biosciences, Cardiff University, Cardiff CF10 3AX, United Kingdom
| | - Liang-Fong Wong
- Bristol Medical School, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Lorenzo Magini
- Bristol Medical School, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Lucia Marucci
- Department of Engineering and Mathematics, University of Bristol, Bristol BS8 1TD, United Kingdom; BrisSynBio, Bristol BS8 1QU, United Kingdom
| | - Gregory A O'Sullivan
- Takeda Cambridge Ltd., Cambridge Science Park, Cambridge CB4 0PZ, United Kingdom
| | - Sarah Cole
- Takeda Ventures, Inc., 61 Aldwych, London WC2B 4A, United Kingdom
| | - Justin Powell
- Takeda Cambridge Ltd., Cambridge Science Park, Cambridge CB4 0PZ, United Kingdom
| | - Peter Maycox
- Takeda Ventures, Inc., 61 Aldwych, London WC2B 4A, United Kingdom
| | - James B Uney
- Bristol Medical School, University of Bristol, Bristol BS8 1TD, United Kingdom.
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21
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Pedone E, Postiglione L, Aulicino F, Rocca DL, Montes-Olivas S, Khazim M, di Bernardo D, Pia Cosma M, Marucci L. A tunable dual-input system for on-demand dynamic gene expression regulation. Nat Commun 2019; 10:4481. [PMID: 31578371 PMCID: PMC6775159 DOI: 10.1038/s41467-019-12329-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 08/28/2019] [Indexed: 12/14/2022] Open
Abstract
Cellular systems have evolved numerous mechanisms to adapt to environmental stimuli, underpinned by dynamic patterns of gene expression. In addition to gene transcription regulation, modulation of protein levels, dynamics and localization are essential checkpoints governing cell functions. The introduction of inducible promoters has allowed gene expression control using orthogonal molecules, facilitating its rapid and reversible manipulation to study gene function. However, differing protein stabilities hinder the generation of protein temporal profiles seen in vivo. Here, we improve the Tet-On system integrating conditional destabilising elements at the post-translational level and permitting simultaneous control of gene expression and protein stability. We show, in mammalian cells, that adding protein stability control allows faster response times, fully tunable and enhanced dynamic range, and improved in silico feedback control of gene expression. Finally, we highlight the effectiveness of our dual-input system to modulate levels of signalling pathway components in mouse Embryonic Stem Cells.
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Affiliation(s)
- Elisa Pedone
- Department of Engineering Mathematics, University of Bristol, Bristol, BS8 1UB, UK.
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK.
| | - Lorena Postiglione
- Department of Engineering Mathematics, University of Bristol, Bristol, BS8 1UB, UK
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | - Francesco Aulicino
- BrisSynBio, Bristol, BS8 1TQ, UK
- Department of Biochemistry, Bristol, BS8 1TD, UK
| | - Dan L Rocca
- Department of Engineering Mathematics, University of Bristol, Bristol, BS8 1UB, UK.
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK.
- BrisSynBio, Bristol, BS8 1TQ, UK.
| | - Sandra Montes-Olivas
- Department of Engineering Mathematics, University of Bristol, Bristol, BS8 1UB, UK
| | - Mahmoud Khazim
- Department of Engineering Mathematics, University of Bristol, Bristol, BS8 1UB, UK
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | - Diego di Bernardo
- Telethon Institute of Genetics and Medicine Via Campi Flegrei 34, 80078, Pozzuoli, Italy
| | - Maria Pia Cosma
- Centre for Genomic Regulation (CRG), Dr Aiguader 88, 08002, Barcelona, Spain
- Universitati Pompeu Fabra (UPF), Barcelona, Spain
- ICREA, Pg. Luis Companys, 08010, Barcelona, Spain
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), 510005, Guangzhou, China
- Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Science, 510530, Guangzhou, China
| | - Lucia Marucci
- Department of Engineering Mathematics, University of Bristol, Bristol, BS8 1UB, UK.
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK.
- BrisSynBio, Bristol, BS8 1TQ, UK.
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22
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Eilenberger C, Spitz S, Bachmann BEM, Ehmoser EK, Ertl P, Rothbauer M. The Usual Suspects 2019: of Chips, Droplets, Synthesis, and Artificial Cells. MICROMACHINES 2019; 10:E285. [PMID: 31035574 PMCID: PMC6562886 DOI: 10.3390/mi10050285] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 04/24/2019] [Accepted: 04/26/2019] [Indexed: 12/03/2022]
Abstract
Synthetic biology aims to understand fundamental biological processes in more detail than possible for actual living cells. Synthetic biology can combat decomposition and build-up of artificial experimental models under precisely controlled and defined environmental and biochemical conditions. Microfluidic systems can provide the tools to improve and refine existing synthetic systems because they allow control and manipulation of liquids on a micro- and nanoscale. In addition, chip-based approaches are predisposed for synthetic biology applications since they present an opportune technological toolkit capable of fully automated high throughput and content screening under low reagent consumption. This review critically highlights the latest updates in microfluidic cell-free and cell-based protein synthesis as well as the progress on chip-based artificial cells. Even though progress is slow for microfluidic synthetic biology, microfluidic systems are valuable tools for synthetic biology and may one day help to give answers to long asked questions of fundamental cell biology and life itself.
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Affiliation(s)
- Christoph Eilenberger
- Institute of Applied Synthetic Chemistry, Institute of Chemical Technologies and Analytics, Faculty of Technical Chemistry, Vienna University of Technology, A-1060 Vienna, Austria.
| | - Sarah Spitz
- Institute of Applied Synthetic Chemistry, Institute of Chemical Technologies and Analytics, Faculty of Technical Chemistry, Vienna University of Technology, A-1060 Vienna, Austria.
| | - Barbara Eva Maria Bachmann
- Austrian Cluster for Tissue Regeneration, Vienna, Austria; Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, Allgemeine Unfallversicherungsanstalt (AUVA) Research Centre, A-1200 Vienna, Austria.
| | - Eva Kathrin Ehmoser
- Institute of Synthetic Bioarchitectures, Department of Nanobiotechnology, University of Natural Resources and Life Sciences Vienna, A-1190 Vienna, Austria.
| | - Peter Ertl
- Institute of Applied Synthetic Chemistry, Institute of Chemical Technologies and Analytics, Faculty of Technical Chemistry, Vienna University of Technology, A-1060 Vienna, Austria.
| | - Mario Rothbauer
- Institute of Applied Synthetic Chemistry, Institute of Chemical Technologies and Analytics, Faculty of Technical Chemistry, Vienna University of Technology, A-1060 Vienna, Austria.
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23
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Pedone E, Marucci L. Role of β-Catenin Activation Levels and Fluctuations in Controlling Cell Fate. Genes (Basel) 2019; 10:genes10020176. [PMID: 30823613 PMCID: PMC6410200 DOI: 10.3390/genes10020176] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 02/18/2019] [Indexed: 12/12/2022] Open
Abstract
Cells have developed numerous adaptation mechanisms to external cues by controlling signaling-pathway activity, both qualitatively and quantitatively. The Wnt/β-catenin pathway is a highly conserved signaling pathway involved in many biological processes, including cell proliferation, differentiation, somatic cell reprogramming, development, and cancer. The activity of the Wnt/β-catenin pathway and the temporal dynamics of its effector β-catenin are tightly controlled by complex regulations. The latter encompass feedback loops within the pathway (e.g., a negative feedback loop involving Axin2, a β-catenin transcriptional target) and crosstalk interactions with other signaling pathways. Here, we provide a review shedding light on the coupling between Wnt/β-catenin activation levels and fluctuations across processes and cellular systems; in particular, we focus on development, in vitro pluripotency maintenance, and cancer. Possible mechanisms originating Wnt/β-catenin dynamic behaviors and consequently driving different cellular responses are also reviewed, and new avenues for future research are suggested.
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Affiliation(s)
- Elisa Pedone
- Department of Engineering Mathematics, University of Bristol, Bristol, BS8 1UB, UK.
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK.
| | - Lucia Marucci
- Department of Engineering Mathematics, University of Bristol, Bristol, BS8 1UB, UK.
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK.
- BrisSynBio, Bristol, BS8 1TQ, UK.
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24
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Lugagne JB, Dunlop MJ. Cell-machine interfaces for characterizing gene regulatory network dynamics. ACTA ACUST UNITED AC 2019; 14:1-8. [PMID: 31579842 DOI: 10.1016/j.coisb.2019.01.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Gene regulatory networks and the dynamic responses they produce offer a wealth of information about how biological systems process information about their environment. Recently, researchers interested in dissecting these networks have been outsourcing various parts of their experimental workflow to computers. Here we review how, using microfluidic or optogenetic tools coupled with fluorescence imaging, it is now possible to interface cells and computers. These platforms enable scientists to perform informative dynamic stimulations of genetic pathways and monitor their reaction. It is also possible to close the loop and regulate genes in real time, providing an unprecedented view of how signals propagate through the network. Finally, we outline new tools that can be used within the framework of cell-machine interfaces.
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Affiliation(s)
- Jean-Baptiste Lugagne
- Department of Biomedical Engineering, Boston University, Boston, MA, USA.,Biological Design Center, Boston University, Boston, MA, USA
| | - Mary J Dunlop
- Department of Biomedical Engineering, Boston University, Boston, MA, USA.,Biological Design Center, Boston University, Boston, MA, USA
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25
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Khazim M, Postiglione L, Pedone E, Rocca DL, Zahra C, Marucci L. Towards automated control of embryonic stem cell pluripotency. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.ifacol.2019.12.240] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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