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Rahman SMT, Singh A, Lowe S, Aqdas M, Jiang K, Vaidehi Narayanan H, Hoffmann A, Sung MH. Co-imaging of RelA and c-Rel reveals features of NF-κB signaling for ligand discrimination. Cell Rep 2024; 43:113940. [PMID: 38483906 PMCID: PMC11015162 DOI: 10.1016/j.celrep.2024.113940] [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: 06/07/2023] [Revised: 12/11/2023] [Accepted: 02/23/2024] [Indexed: 04/02/2024] Open
Abstract
Individual cell sensing of external cues has evolved through the temporal patterns in signaling. Since nuclear factor κB (NF-κB) signaling dynamics have been examined using a single subunit, RelA, it remains unclear whether more information might be transmitted via other subunits. Using NF-κB double-knockin reporter mice, we monitored both canonical NF-κB subunits, RelA and c-Rel, simultaneously in single macrophages by quantitative live-cell imaging. We show that signaling features of RelA and c-Rel convey more information about the stimuli than those of either subunit alone. Machine learning is used to predict the ligand identity accurately based on RelA and c-Rel signaling features without considering the co-activated factors. Ligand discrimination is achieved through selective non-redundancy of RelA and c-Rel signaling dynamics, as well as their temporal coordination. These results suggest a potential role of c-Rel in fine-tuning immune responses and highlight the need for approaches that will elucidate the mechanisms regulating NF-κB subunit specificity.
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Affiliation(s)
- Shah Md Toufiqur Rahman
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Apeksha Singh
- Institute for Quantitative and Computational Biosciences and Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Sarina Lowe
- Institute for Quantitative and Computational Biosciences and Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Mohammad Aqdas
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Kevin Jiang
- Institute for Quantitative and Computational Biosciences and Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Haripriya Vaidehi Narayanan
- Institute for Quantitative and Computational Biosciences and Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Alexander Hoffmann
- Institute for Quantitative and Computational Biosciences and Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Myong-Hee Sung
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA.
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2
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Leemann S, Schneider-Warme F, Kleinlogel S. Cardiac optogenetics: shining light on signaling pathways. Pflugers Arch 2023; 475:1421-1437. [PMID: 38097805 PMCID: PMC10730638 DOI: 10.1007/s00424-023-02892-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 11/23/2023] [Accepted: 11/24/2023] [Indexed: 12/21/2023]
Abstract
In the early 2000s, the field of neuroscience experienced a groundbreaking transformation with the advent of optogenetics. This innovative technique harnesses the properties of naturally occurring and genetically engineered rhodopsins to confer light sensitivity upon target cells. The remarkable spatiotemporal precision offered by optogenetics has provided researchers with unprecedented opportunities to dissect cellular physiology, leading to an entirely new level of investigation. Initially revolutionizing neuroscience, optogenetics quickly piqued the interest of the wider scientific community, and optogenetic applications were expanded to cardiovascular research. Over the past decade, researchers have employed various optical tools to observe, regulate, and steer the membrane potential of excitable cells in the heart. Despite these advancements, achieving control over specific signaling pathways within the heart has remained an elusive goal. Here, we review the optogenetic tools suitable to control cardiac signaling pathways with a focus on GPCR signaling, and delineate potential applications for studying these pathways, both in healthy and diseased hearts. By shedding light on these exciting developments, we hope to contribute to the ongoing progress in basic cardiac research to facilitate the discovery of novel therapeutic possibilities for treating cardiovascular pathologies.
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Affiliation(s)
- Siri Leemann
- Institute of Physiology, University of Bern, Bern, Switzerland.
- Institute for Experimental Cardiovascular Medicine, University Heart Center Freiburg - Bad Krozingen, and Medical Faculty, University of Freiburg, Freiburg, Germany.
| | - Franziska Schneider-Warme
- Institute for Experimental Cardiovascular Medicine, University Heart Center Freiburg - Bad Krozingen, and Medical Faculty, University of Freiburg, Freiburg, Germany
| | - Sonja Kleinlogel
- Institute of Physiology, University of Bern, Bern, Switzerland
- F. Hoffmann-La Roche, Translational Medicine Neuroscience, Basel, Switzerland
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3
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Benman W, Datta S, Gonzalez-Martinez D, Lee G, Hooper J, Qian G, Leavitt G, Salloum L, Ho G, Mhatre S, Magaraci MS, Patterson M, Mannickarottu SG, Malani S, Avalos JL, Chow BY, Bugaj LJ. High-throughput feedback-enabled optogenetic stimulation and spectroscopy in microwell plates. Commun Biol 2023; 6:1192. [PMID: 38001175 PMCID: PMC10673842 DOI: 10.1038/s42003-023-05532-4] [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: 09/21/2023] [Accepted: 10/31/2023] [Indexed: 11/26/2023] Open
Abstract
The ability to perform sophisticated, high-throughput optogenetic experiments has been greatly enhanced by recent open-source illumination devices that allow independent programming of light patterns in single wells of microwell plates. However, there is currently a lack of instrumentation to monitor such experiments in real time, necessitating repeated transfers of the samples to stand-alone analytical instruments, thus limiting the types of experiments that could be performed. Here we address this gap with the development of the optoPlateReader (oPR), an open-source, solid-state, compact device that allows automated optogenetic stimulation and spectroscopy in each well of a 96-well plate. The oPR integrates an optoPlate illumination module with a module called the optoReader, an array of 96 photodiodes and LEDs that allows 96 parallel light measurements. The oPR was optimized for stimulation with blue light and for measurements of optical density and fluorescence. After calibration of all device components, we used the oPR to measure growth and to induce and measure fluorescent protein expression in E. coli. We further demonstrated how the optical read/write capabilities of the oPR permit computer-in-the-loop feedback control, where the current state of the sample can be used to adjust the optical stimulation parameters of the sample according to pre-defined feedback algorithms. The oPR will thus help realize an untapped potential for optogenetic experiments by enabling automated reading, writing, and feedback in microwell plates through open-source hardware that is accessible, customizable, and inexpensive.
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Affiliation(s)
- William Benman
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Saachi Datta
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | | | - Gloria Lee
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Juliette Hooper
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Grace Qian
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Gabrielle Leavitt
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Lana Salloum
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Gabrielle Ho
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Sharvari Mhatre
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Michael S Magaraci
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Michael Patterson
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | | | - Saurabh Malani
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, 08544, USA
| | - Jose L Avalos
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, 08544, USA
- The Andlinger Center for Energy and the Environment, Princeton, NJ, 08544, USA
- High Meadows Environmental Institute, Princeton, NJ, 08544, USA
| | - Brian Y Chow
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Lukasz J Bugaj
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Institute of Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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4
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Corre B, El Janati Elidrissi Y, Duval J, Quilhot M, Lefebvre G, Ecomard S, Lemaître F, Garcia Z, Bohineust A, Russo E, Bousso P. Integration of intermittent calcium signals in T cells revealed by temporally patterned optogenetics. iScience 2023; 26:106068. [PMID: 36824271 PMCID: PMC9942117 DOI: 10.1016/j.isci.2023.106068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 11/28/2022] [Accepted: 01/20/2023] [Indexed: 01/27/2023] Open
Abstract
T cells become activated following one or multiple contacts with antigen-presenting cells. Calcium influx is a key signaling event elicited during these cellular interactions; however, it is unclear whether T cells recall and integrate calcium signals elicited during temporally separated contacts. To study the integration of calcium signals, we designed a programmable, multiplex illumination strategy for temporally patterned optogenetics (TEMPO). We found that a single round of calcium elevation was insufficient to promote nuclear factor of activated T cells (NFAT) activity and cytokine production in a T cell line. However, robust responses were detected after a second identical stimulation even when signals were separated by several hours. Our results suggest the existence of a biochemical memory of calcium signals in T cells that favors signal integration during temporally separated contacts and promote cytokine production. As illustrated here, TEMPO is a versatile approach for dissecting temporal integration in defined signaling pathways.
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Affiliation(s)
- Béatrice Corre
- Dynamics of Immune Responses Unit, Institut Pasteur, Université Paris Cité, Inserm U1223, 75015 Paris, France
| | - Yassine El Janati Elidrissi
- Dynamics of Immune Responses Unit, Institut Pasteur, Université Paris Cité, Inserm U1223, 75015 Paris, France
| | - Justine Duval
- Dynamics of Immune Responses Unit, Institut Pasteur, Université Paris Cité, Inserm U1223, 75015 Paris, France
| | - Mailys Quilhot
- Dynamics of Immune Responses Unit, Institut Pasteur, Université Paris Cité, Inserm U1223, 75015 Paris, France
| | - Gaëtan Lefebvre
- Dynamics of Immune Responses Unit, Institut Pasteur, Université Paris Cité, Inserm U1223, 75015 Paris, France
| | - Solène Ecomard
- Dynamics of Immune Responses Unit, Institut Pasteur, Université Paris Cité, Inserm U1223, 75015 Paris, France
| | - Fabrice Lemaître
- Dynamics of Immune Responses Unit, Institut Pasteur, Université Paris Cité, Inserm U1223, 75015 Paris, France
| | - Zacarias Garcia
- Dynamics of Immune Responses Unit, Institut Pasteur, Université Paris Cité, Inserm U1223, 75015 Paris, France
| | - Armelle Bohineust
- Dynamics of Immune Responses Unit, Institut Pasteur, Université Paris Cité, Inserm U1223, 75015 Paris, France
| | - Erica Russo
- Dynamics of Immune Responses Unit, Institut Pasteur, Université Paris Cité, Inserm U1223, 75015 Paris, France
| | - Philippe Bousso
- Dynamics of Immune Responses Unit, Institut Pasteur, Université Paris Cité, Inserm U1223, 75015 Paris, France,Corresponding author
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5
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Streiff ME, Corbin AC, Ahmad AA, Hunter C, Sachse FB. TRPC1 channels underlie stretch-modulated sarcoplasmic reticulum calcium leak in cardiomyocytes. Front Physiol 2022; 13:1056657. [PMID: 36620209 PMCID: PMC9817106 DOI: 10.3389/fphys.2022.1056657] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 12/12/2022] [Indexed: 12/25/2022] Open
Abstract
Transient receptor potential canonical 1 (TRPC1) channels are Ca2+-permeable ion channels expressed in cardiomyocytes. An involvement of TRPC1 channels in cardiac diseases is widely established. However, the physiological role of TRPC1 channels and the mechanisms through which they contribute to disease development are still under investigation. Our prior work suggested that TRPC1 forms Ca2+ leak channels located in the sarcoplasmic reticulum (SR) membrane. Prior studies suggested that TRPC1 channels in the cell membrane are mechanosensitive, but this was not yet investigated in cardiomyocytes or for SR localized TRPC1 channels. We applied adenoviral transfection to overexpress or suppress TRPC1 expression in neonatal rat ventricular myocytes (NRVMs). Transfections were evaluated with RT-qPCR, western blot, and fluorescent imaging. Single-molecule localization microscopy revealed high colocalization of exogenously expressed TRPC1 and the sarco/endoplasmic reticulum Ca2+ ATPase (SERCA2). To test our hypothesis that TRPC1 channels contribute to mechanosensitive Ca2+ SR leak, we directly measured SR Ca2+ concentration ([Ca2+]SR) using adenoviral transfection with a novel ratiometric genetically encoded SR-targeting Ca2+ sensor. We performed fluorescence imaging to quantitatively assess [Ca2+]SR and leak through TRPC1 channels of NRVMs cultured on stretchable silicone membranes. [Ca2+]SR was increased in cells with suppressed TRPC1 expression vs. control and Transient receptor potential canonical 1-overexpressing cells. We also detected a significant reduction in [Ca2+]SR in cells with Transient receptor potential canonical 1 overexpression when 10% uniaxial stretch was applied. These findings indicate that TRPC1 channels underlie the mechanosensitive modulation of [Ca2+]SR. Our findings are critical for understanding the physiological role of TRPC1 channels and support the development of pharmacological therapies for cardiac diseases.
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Affiliation(s)
- Molly E. Streiff
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, UT, United States,Department of Biomedical Engineering, University of Utah, Salt Lake City, UT, United States
| | - Andrea C. Corbin
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, UT, United States,Department of Biomedical Engineering, University of Utah, Salt Lake City, UT, United States
| | - Azmi A. Ahmad
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, UT, United States,Department of Biomedical Engineering, University of Utah, Salt Lake City, UT, United States
| | - Chris Hunter
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, UT, United States
| | - Frank B. Sachse
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, UT, United States,Department of Biomedical Engineering, University of Utah, Salt Lake City, UT, United States,*Correspondence: Frank B. Sachse,
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6
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LITOS: a versatile LED illumination tool for optogenetic stimulation. Sci Rep 2022; 12:13139. [PMID: 35907941 PMCID: PMC9338960 DOI: 10.1038/s41598-022-17312-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 07/25/2022] [Indexed: 01/18/2023] Open
Abstract
Optogenetics has become a key tool to manipulate biological processes with high spatio-temporal resolution. Recently, a number of commercial and open-source multi-well illumination devices have been developed to provide throughput in optogenetics experiments. However, available commercial devices remain expensive and lack flexibility, while open-source solutions require programming knowledge and/or include complex assembly processes. We present a LED Illumination Tool for Optogenetic Stimulation (LITOS) based on an assembled printed circuit board controlling a commercially available 32 × 64 LED matrix as illumination source. LITOS can be quickly assembled without any soldering, and includes an easy-to-use interface, accessible via a website hosted on the device itself. Complex light stimulation patterns can easily be programmed without coding expertise. LITOS can be used with different formats of multi-well plates, petri dishes, and flasks. We validated LITOS by measuring the activity of the MAPK/ERK signaling pathway in response to different dynamic light stimulation regimes using FGFR1 and Raf optogenetic actuators. LITOS can uniformly stimulate all the cells in a well and allows for flexible temporal stimulation schemes. LITOS’s affordability and ease of use aims at democratizing optogenetics in any laboratory.
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7
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A chemogenetic platform for controlling plasma membrane signaling and synthetic signal oscillation. Cell Chem Biol 2022; 29:1446-1464.e10. [PMID: 35835118 DOI: 10.1016/j.chembiol.2022.06.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/22/2022] [Accepted: 06/20/2022] [Indexed: 12/31/2022]
Abstract
Chemogenetic methods enabling the rapid translocation of specific proteins to the plasma membrane (PM) in a single protein-single ligand manner are useful tools in cell biology. We recently developed a technique, in which proteins fused to an Escherichia coli dihydrofolate reductase (eDHFR) variant carrying N-terminal hexalysine residues are recruited from the cytoplasm to the PM using the synthetic myristoyl-d-Cys-tethered trimethoprim (mDcTMP) ligand. However, this system achieved PM-specific translocation only when the eDHFR tag was fused to the N terminus of proteins, thereby limiting its application. In this report, we engineered a universal PM-targeting tag for mDcTMP-induced protein translocation by grafting the hexalysine motif into an intra-loop region of eDHFR. We demonstrate the broad applicability of the new loop-engineered eDHFR tag and mDcTMP pair for conditional PM recruitment and activation of various tag-fused signaling proteins with different fusion configurations and for reversibly and repeatedly controlling protein localization to generate synthetic signal oscillations.
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8
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Kumar S, Khammash M. Platforms for Optogenetic Stimulation and Feedback Control. Front Bioeng Biotechnol 2022; 10:918917. [PMID: 35757811 PMCID: PMC9213687 DOI: 10.3389/fbioe.2022.918917] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 05/06/2022] [Indexed: 11/13/2022] Open
Abstract
Harnessing the potential of optogenetics in biology requires methodologies from different disciplines ranging from biology, to mechatronics engineering, to control engineering. Light stimulation of a synthetic optogenetic construct in a given biological species can only be achieved via a suitable light stimulation platform. Emerging optogenetic applications entail a consistent, reproducible, and regulated delivery of light adapted to the application requirement. In this review, we explore the evolution of light-induction hardware-software platforms from simple illumination set-ups to sophisticated microscopy, microtiter plate and bioreactor designs, and discuss their respective advantages and disadvantages. Here, we examine design approaches followed in performing optogenetic experiments spanning different cell types and culture volumes, with induction capabilities ranging from single cell stimulation to entire cell culture illumination. The development of automated measurement and stimulation schemes on these platforms has enabled researchers to implement various in silico feedback control strategies to achieve computer-controlled living systems—a theme we briefly discuss in the last part of this review.
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Affiliation(s)
- Sant Kumar
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Basel, Switzerland
| | - Mustafa Khammash
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Basel, Switzerland
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9
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Towards 'end-to-end' analysis and understanding of biological timecourse data. Biochem J 2022; 479:1257-1263. [PMID: 35713413 PMCID: PMC9246344 DOI: 10.1042/bcj20220053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 11/17/2022]
Abstract
Petabytes of increasingly complex and multidimensional live cell and tissue imaging data are generated every year. These videos hold large promise for understanding biology at a deep and fundamental level, as they capture single-cell and multicellular events occurring over time and space. However, the current modalities for analysis and mining of these data are scattered and user-specific, preventing more unified analyses from being performed over different datasets and obscuring possible scientific insights. Here, we propose a unified pipeline for storage, segmentation, analysis, and statistical parametrization of live cell imaging datasets.
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10
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Miranda JG, Schleicher WE, Wells KL, Ramirez DG, Landgrave SP, Benninger RKP. Dynamic changes in β-cell [Ca 2+] regulate NFAT activation, gene transcription, and islet gap junction communication. Mol Metab 2022; 57:101430. [PMID: 34979329 PMCID: PMC8804269 DOI: 10.1016/j.molmet.2021.101430] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 12/28/2021] [Accepted: 12/29/2021] [Indexed: 11/23/2022] Open
Abstract
OBJECTIVE Diabetes occurs because of insufficient insulin secretion due to β-cell dysfunction within the islet of Langerhans. Elevated glucose levels trigger β-cell membrane depolarization, action potential generation, and slow sustained free-Ca2+ ([Ca2+]) oscillations, which trigger insulin release. Nuclear factor of activated T-cell (NFAT) is a transcription factor, which is regulated by the increases in [Ca2+] and calceineurin (CaN) activation. NFAT regulation links cell activity with gene transcription in many systems and regulates proliferation and insulin granule biogenesis within the β-cell. However, the link between the regulation of β-cell electrical activity and oscillatory [Ca2+] dynamics with NFAT activation and downstream transcription is poorly understood. Here, we tested whether dynamic changes to β-cell electrical activity and [Ca2+] regulate NFAT activation and downstream transcription. METHODS In cell lines, mouse islets, and human islets, including those from donors with type 2 diabetes, we applied both agonists/antagonists of ion channels together with optogenetics to modulate β-cell electrical activity. We measured the dynamics of [Ca2+] and NFAT activation as well as performed whole transcriptome and functional analyses. RESULTS Both glucose-induced membrane depolarization and optogenetic stimulation triggered NFAT activation as well as increased the transcription of NFAT targets and intermediate early genes (IEGs). Importantly, slow, sustained [Ca2+] oscillation conditions led to NFAT activation and downstream transcription. In contrast, in human islets from donors with type2 diabetes, NFAT activation by glucose was diminished, but rescued upon pharmacological stimulation of electrical activity. NFAT activation regulated GJD2 expression and increased Cx36 gap junction permeability upon elevated oscillatory [Ca2+] dynamics. However, it is unclear if NFAT directly binds the GJD2 gene to regulate expression. CONCLUSIONS This study provides an insight into the specific patterns of electrical activity that regulate NFAT activation, gene transcription, and islet function. In addition, it provides information on how these factors are disrupted in diabetes.
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Affiliation(s)
- Jose G Miranda
- Department of Bioengineering, University of Colorado Anschutz Medical Campus, Aurora CO, 80045, USA
| | - Wolfgang E Schleicher
- Department of Bioengineering, University of Colorado Anschutz Medical Campus, Aurora CO, 80045, USA
| | - Kristen L Wells
- Barbara Davis Center for Childhood Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - David G Ramirez
- Department of Bioengineering, University of Colorado Anschutz Medical Campus, Aurora CO, 80045, USA
| | - Samantha P Landgrave
- Program in Cell Biology, Stem Cell and Development, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Richard K P Benninger
- Department of Bioengineering, University of Colorado Anschutz Medical Campus, Aurora CO, 80045, USA; Program in Cell Biology, Stem Cell and Development, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA; Barbara Davis Center for Childhood Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.
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11
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Gao T, Gao C, Liu Z, Wang Y, Jia X, Tian H, Lu Q, Guo L. Inhibition of Noncanonical Ca 2+ Oscillation/Calcineurin/GSK-3β Pathway Contributes to Anti-Inflammatory Effect of Sigma-1 Receptor Activation. Neurochem Res 2022; 47:264-278. [PMID: 34468932 DOI: 10.1007/s11064-021-03439-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 08/23/2021] [Accepted: 08/26/2021] [Indexed: 11/29/2022]
Abstract
Further understanding the mechanism for microglia activation is necessary for developing novel anti-inflammatory strategies. Our previous study found that the activation of sigma-1 receptor can effectively inhibit the neuroinflammation, independent of the canonical mechanisms, such as NF-κB, JNK and ERK inflammatory pathways. Thus, it is reasonable that an un-identified, non-canonical pathway contributes to the activation of microglia. In the present study, we found that a sigma-1 receptor agonist of 2-morpholin-4-ylethyl 1-phenylcyclohexane-1-carboxylate (PRE-084) suppressed lipopolysaccharide (LPS) elevated nitric oxide (NO) content in BV-2 microglia culture supernatant and LPS-raised mRNA levels of tumor necrosis factor-α (TNF-α), interleukin-1β (IL-1β), inducible nitric oxide synthase (iNOS) in BV-2 microglia. Moreover, PRE-084 alleviated LPS-increased Ser 9 de-phosphorylation of glycogen synthase kinase-3 beta (GSK-3β), LPS-elevated catalytic activity of calcineurin, and LPS-raised percent and frequency of Ca2+ oscillatory BV-2 cells. We further found that the inhibitory effect of PRE-084 was reversed by a calcineurin activator of chlorogenic acid and a GSK-3β activator of pyrvinium. Moreover, an IP3 receptor inhibitor of 2-aminoethoxydiphenyl borate mimicked the anti-inflammatory activity of PRE-084. Thus, we identified a noncanonical pro-neuroinflammary pathway of Ca2+ oscillation/Calcineurin/GSK-3β and the inhibition of this pathway is necessary for the anti-inflammatory activity of sigma-1 receptor activation.
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Affiliation(s)
- Tianyu Gao
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221000, Jiangsu Province, China
- Department of Pharmacy, The Affiliated Hospital of Xuzhou Medical University, 99 West Huai-hai Road, Xuzhou, 221004, Jiangsu Province, China
| | - Ce Gao
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221000, Jiangsu Province, China
- Department of Pharmacy, The Affiliated Hospital of Xuzhou Medical University, 99 West Huai-hai Road, Xuzhou, 221004, Jiangsu Province, China
| | - Zhidong Liu
- Department of Pharmacy, The Affiliated Hospital of Xuzhou Medical University, 99 West Huai-hai Road, Xuzhou, 221004, Jiangsu Province, China
| | - Yun Wang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221000, Jiangsu Province, China
| | - Xiaoxia Jia
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221000, Jiangsu Province, China
| | - Hao Tian
- Agro-Products Processing Research Institute, Yunnan Academy of Agricultural Sciences, 2238 Beijing Road, Kunming, 650000, Yunnan Province, China
| | - Qian Lu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221000, Jiangsu Province, China.
| | - Lin Guo
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221000, Jiangsu Province, China.
- Department of Pharmacy, The Affiliated Hospital of Xuzhou Medical University, 99 West Huai-hai Road, Xuzhou, 221004, Jiangsu Province, China.
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12
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Maltan L, Najjar H, Tiffner A, Derler I. Deciphering Molecular Mechanisms and Intervening in Physiological and Pathophysiological Processes of Ca 2+ Signaling Mechanisms Using Optogenetic Tools. Cells 2021; 10:3340. [PMID: 34943850 PMCID: PMC8699489 DOI: 10.3390/cells10123340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/17/2021] [Accepted: 11/22/2021] [Indexed: 11/16/2022] Open
Abstract
Calcium ion channels are involved in numerous biological functions such as lymphocyte activation, muscle contraction, neurotransmission, excitation, hormone secretion, gene expression, cell migration, memory, and aging. Therefore, their dysfunction can lead to a wide range of cellular abnormalities and, subsequently, to diseases. To date various conventional techniques have provided valuable insights into the roles of Ca2+ signaling. However, their limited spatiotemporal resolution and lack of reversibility pose significant obstacles in the detailed understanding of the structure-function relationship of ion channels. These drawbacks could be partially overcome by the use of optogenetics, which allows for the remote and well-defined manipulation of Ca2+-signaling. Here, we review the various optogenetic tools that have been used to achieve precise control over different Ca2+-permeable ion channels and receptors and associated downstream signaling cascades. We highlight the achievements of optogenetics as well as the still-open questions regarding the resolution of ion channel working mechanisms. In addition, we summarize the successes of optogenetics in manipulating many Ca2+-dependent biological processes both in vitro and in vivo. In summary, optogenetics has significantly advanced our understanding of Ca2+ signaling proteins and the used tools provide an essential basis for potential future therapeutic application.
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Affiliation(s)
| | | | | | - Isabella Derler
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, A-4020 Linz, Austria; (L.M.); (H.N.); (A.T.)
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13
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Progress and challenges in understanding the regulation and function of p53 dynamics. Biochem Soc Trans 2021; 49:2123-2131. [PMID: 34495325 PMCID: PMC8765192 DOI: 10.1042/bst20210148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/20/2021] [Accepted: 08/23/2021] [Indexed: 02/01/2023]
Abstract
The dynamics of p53 expression provide a mechanism to increase differentiation between cellular stresses and specificity in appropriate responses. Here, we review recent advances in our understanding of the molecular mechanisms regulating p53 dynamics and the functions of the dynamics in the regulation of p53-dependent cell stress responses. We also compare dynamic encoding in the p53 system with that found in other important cell signaling systems, many of which can interact with the p53 network. Finally, we highlight some of the current challenges in understanding dynamic cell signaling within a larger cellular network context.
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14
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Abstract
T cells experience complex temporal patterns of stimulus via receptor-ligand-binding interactions with surrounding cells. From these temporal patterns, T cells are able to pick out antigenic signals while establishing self-tolerance. Although features such as duration of antigen binding have been examined, our understanding of how T cells interpret signals with different frequencies or temporal stimulation patterns is relatively unexplored. We engineered T cells to respond to light as a stimulus by building an optogenetically controlled chimeric antigen receptor (optoCAR). We discovered that T cells respond to minute-scale oscillations of activation signal by stimulating optoCAR T cells with tunable pulse trains of light. Systematically scanning signal oscillation period from 1 to 150 min revealed that expression of CD69, a T cell activation marker, reached a local minimum at a period of ∼25 min (corresponding to 5 to 15 min pulse widths). A combination of inhibitors and genetic knockouts suggest that this frequency filtering mechanism lies downstream of the Erk signaling branch of the T cell response network and may involve a negative feedback loop that diminishes Erk activity. The timescale of CD69 filtering corresponds with the duration of T cell encounters with self-peptide-presenting APCs observed via intravital imaging in mice, indicating a potential functional role for temporal filtering in vivo. This study illustrates that the T cell signaling machinery is tuned to temporally filter and interpret time-variant input signals in discriminatory ways.
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15
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Farahani PE, Reed EH, Underhill EJ, Aoki K, Toettcher JE. Signaling, Deconstructed: Using Optogenetics to Dissect and Direct Information Flow in Biological Systems. Annu Rev Biomed Eng 2021; 23:61-87. [PMID: 33722063 PMCID: PMC10436267 DOI: 10.1146/annurev-bioeng-083120-111648] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cells receive enormous amounts of information from their environment. How they act on this information-by migrating, expressing genes, or relaying signals to other cells-comprises much of the regulatory and self-organizational complexity found across biology. The "parts list" involved in cell signaling is generally well established, but how do these parts work together to decode signals and produce appropriate responses? This fundamental question is increasingly being addressed with optogenetic tools: light-sensitive proteins that enable biologists to manipulate the interaction, localization, and activity state of proteins with high spatial and temporal precision. In this review, we summarize how optogenetics is being used in the pursuit of an answer to this question, outlining the current suite of optogenetic tools available to the researcher and calling attention to studies that increase our understanding of and improve our ability to engineer biology.
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Affiliation(s)
- Payam E Farahani
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, USA
| | - Ellen H Reed
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
- International Research Collaboration Center (IRCC), National Institutes of Natural Sciences, Tokyo 105-0001, Japan
| | - Evan J Underhill
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, USA
| | - Kazuhiro Aoki
- International Research Collaboration Center (IRCC), National Institutes of Natural Sciences, Tokyo 105-0001, Japan
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8787, Japan
| | - Jared E Toettcher
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
- International Research Collaboration Center (IRCC), National Institutes of Natural Sciences, Tokyo 105-0001, Japan
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16
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Repina NA, McClave T, Johnson HJ, Bao X, Kane RS, Schaffer DV. Engineered Illumination Devices for Optogenetic Control of Cellular Signaling Dynamics. Cell Rep 2021; 31:107737. [PMID: 32521262 PMCID: PMC9357365 DOI: 10.1016/j.celrep.2020.107737] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 03/09/2020] [Accepted: 05/14/2020] [Indexed: 10/31/2022] Open
Abstract
Spatially and temporally varying patterns of morphogen signals during development drive cell fate specification at the proper location and time. However, current in vitro methods typically do not allow for precise, dynamic spatiotemporal control of morphogen signaling and are thus insufficient to readily study how morphogen dynamics affect cell behavior. Here, we show that optogenetic Wnt/β-catenin pathway activation can be controlled at user-defined intensities, temporal sequences, and spatial patterns using engineered illumination devices for optogenetic photostimulation and light activation at variable amplitudes (LAVA). By patterning human embryonic stem cell (hESC) cultures with varying light intensities, LAVA devices enabled dose-responsive control of optoWnt activation and Brachyury expression. Furthermore, time-varying and spatially localized patterns of light revealed tissue patterning that models the embryonic presentation of Wnt signals in vitro. LAVA devices thus provide a low-cost, user-friendly method for high-throughput and spatiotemporal optogenetic control of cell signaling for applications in developmental and cell biology.
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Affiliation(s)
- Nicole A Repina
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA; Graduate Program in Bioengineering, University of California, San Francisco, San Francisco, CA, USA; Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Thomas McClave
- Department of Physics, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Hunter J Johnson
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA; Graduate Program in Bioengineering, University of California, San Francisco, San Francisco, CA, USA; Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Xiaoping Bao
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Ravi S Kane
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.
| | - David V Schaffer
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA; Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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17
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Bounds AD, Bailey RD, Adams CT, Callaghan DC, Girkin JM. LightBox: A multiwell plate illumination system for photoactive molecule characterization. JOURNAL OF BIOPHOTONICS 2021; 14:e202000481. [PMID: 33576569 DOI: 10.1002/jbio.202000481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/20/2021] [Accepted: 01/28/2021] [Indexed: 06/12/2023]
Abstract
Multiwell plates (MWPs) are the workhorses of the life sciences. However, biophotonics research with MWPs is limited, in part due to the lack of equipment suitable for photo-irradiation of photoactive molecules in a MWP-suitable, high-throughput manner, either commercially or through open-source MWP systems. Here we present "LightBox", a calibrated controllable MWP illumination system with broad applications including screening of photoactive molecules and characterization of photocatalytic chemicals. LightBox is a high intensity, accurately controllable, uniform illumination system designed for MWPs with electronics and a control unit that provides a simple and intuitive interface. LightBox can reach intensities of 0.23 mW/mm2 at wavelengths of 405 nm with variance between well sites of <5%. The usefulness of LightBox is demonstrated by assessing the IC50 of a photosensitizing compound using a live/dead assay following simultaneous irradiation of the sample at a range of concentrations, eliminating uncontrolled variables between concentrations and drastically increasing assessment speed.
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Affiliation(s)
- A D Bounds
- Centre for Advanced Instrumentation, Department of Physics, Durham University, Durham, DH1 3LE, UK
| | - R D Bailey
- Centre for Advanced Instrumentation, Department of Physics, Durham University, Durham, DH1 3LE, UK
| | - C T Adams
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
| | - D C Callaghan
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
| | - J M Girkin
- Centre for Advanced Instrumentation, Department of Physics, Durham University, Durham, DH1 3LE, UK
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18
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Bondar A, Lazar J. Optical sensors of heterotrimeric G protein signaling. FEBS J 2020; 288:2570-2584. [DOI: 10.1111/febs.15655] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/26/2020] [Accepted: 12/03/2020] [Indexed: 01/14/2023]
Affiliation(s)
- Alexey Bondar
- Center for Nanobiology and Structural Biology Institute of Microbiology of the Czech Academy of Sciences Nove Hrady Czech Republic
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Prague Czech Republic
- Faculty of Science University of South Bohemia Ceske Budejovice Czech Republic
| | - Josef Lazar
- Center for Nanobiology and Structural Biology Institute of Microbiology of the Czech Academy of Sciences Nove Hrady Czech Republic
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Prague Czech Republic
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19
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Meng X, Wu X, Zheng Y, Shang K, Jing R, Jiao P, Zhou C, Zhou J, Sun J. Exploiting Ca 2+ signaling in T cells to advance cancer immunotherapy. Semin Immunol 2020; 49:101434. [PMID: 33272900 DOI: 10.1016/j.smim.2020.101434] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 11/10/2020] [Accepted: 11/18/2020] [Indexed: 12/17/2022]
Abstract
Decades of basic research has established the importance of Ca2+ to various T cell functions, such as cytotoxicity, proliferation, differentiation and cytokine secretion. We now have a good understanding of how proximal TCR signaling initiates Ca2+ influx and how this influx subsequently changes transcriptional activities in T cells. As chimeric antigen receptor (CAR)-T therapy has achieved great clinical success, is it possible to harness Ca2+ signaling to further advance CAR-T research? How is CAR signaling different from TCR signaling? How can functional CARs be identified in a high-throughput way? Quantification of various Ca2+ signals downstream of CAR/TCR activation might help answer these questions. Here we first summarized recent studies that used Ca2+ dye, genetically-encoded Ca2+ indicators (GECI) or transcriptional activity reporters to understand CAR activation in vitro and in vivo. We next reviewed several proof-of-concept reports that manipulate Ca2+ signaling by light or ultrasound to achieve precise spatiotemporal control of T cell functions. These efforts, though preliminary, opened up new avenues to solve the on-target/off-tumor problem of therapeutic T cells. Other modalities to regulate Ca2+ signaling, such as radio wave and electrical pulse, were also discussed. Thus, monitoring or manipulating Ca2+ signaling in T cells provides us many opportunities to advance cancer immunotherapy.
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Affiliation(s)
- Xianhui Meng
- Bone Marrow Transplantation Center of the First Affiliated Hospital, Department of Cell Biology, Zhejiang University School of Medicine, Zhejiang, China
| | - Xiaoyan Wu
- Bone Marrow Transplantation Center of the First Affiliated Hospital, Department of Cell Biology, Zhejiang University School of Medicine, Zhejiang, China
| | - Yuyuan Zheng
- School of Public Health, and Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Zhejiang, China
| | - Kai Shang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, Department of Cell Biology, Zhejiang University School of Medicine, Zhejiang, China; Institute of Hematology, Zhejiang University, Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Zhejiang, China; Zhejiang Laboratory for Systems and Precision Medicine, Zhejiang University Medical Center, Zhejiang, China
| | - Ruirui Jing
- Bone Marrow Transplantation Center of the First Affiliated Hospital, Department of Cell Biology, Zhejiang University School of Medicine, Zhejiang, China; Institute of Hematology, Zhejiang University, Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Zhejiang, China; Zhejiang Laboratory for Systems and Precision Medicine, Zhejiang University Medical Center, Zhejiang, China
| | - Peng Jiao
- Bone Marrow Transplantation Center of the First Affiliated Hospital, Department of Cell Biology, Zhejiang University School of Medicine, Zhejiang, China; Institute of Hematology, Zhejiang University, Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Zhejiang, China; Zhejiang Laboratory for Systems and Precision Medicine, Zhejiang University Medical Center, Zhejiang, China
| | - Chun Zhou
- School of Public Health, and Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Zhejiang, China
| | - Jing Zhou
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, China.
| | - Jie Sun
- Bone Marrow Transplantation Center of the First Affiliated Hospital, Department of Cell Biology, Zhejiang University School of Medicine, Zhejiang, China.
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20
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Lai YS, Chang YH, Chen YY, Xu J, Yu CS, Chang SJ, Chen PS, Tsai SJ, Chiu WT. Ca 2+ -regulated cell migration revealed by optogenetically engineered Ca 2+ oscillations. J Cell Physiol 2020; 236:4681-4693. [PMID: 33244795 PMCID: PMC8048425 DOI: 10.1002/jcp.30190] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 11/16/2020] [Accepted: 11/18/2020] [Indexed: 01/05/2023]
Abstract
The ability of a single Ca2+ ion to play an important role in cell biology is highlighted by the need for cells to form Ca2+ signals in the dimensions of space, time, and amplitude. Thus, spatial and temporal changes in intracellular Ca2+ concentration are important for determining cell fate. Optogenetic technology has been developed to provide more precise and targeted stimulation of cells. Here, U2OS cells overexpressing Ca2+ translocating channelrhodopsin (CatCh) were used to mediate Ca2+ influx through blue light illumination with various parameters, such as intensity, frequency, duty cycle, and duration. We identified that several Ca2+‐dependent transcription factors and certain kinases can be activated by specific Ca2+ waves. Using a wound‐healing assay, we found that low‐frequency Ca2+ oscillations increased cell migration through the activation of NF‐κB. This study explores the regulation of cell migration by Ca2+ signals. Thus, we can choose optical parameters to modulate Ca2+ waves and achieve activation of specific signaling pathways. This novel methodology can be applied to clarify related cell‐signaling mechanisms in the future.
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Affiliation(s)
- Yi-Shyun Lai
- Department of Biomedical Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Ya-Han Chang
- Department of Biomedical Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Yong-Yi Chen
- Department of Biomedical Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Jixuan Xu
- Department of Biomedical Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Chi-Sian Yu
- Department of Biomedical Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Su-Jing Chang
- Department of Biomedical Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Pai-Sheng Chen
- Department of Medical Laboratory Science and Biotechnology, National Cheng Kung University, Tainan, Taiwan
| | - Shaw-Jenq Tsai
- Department of Physiology, National Cheng Kung University, Tainan, Taiwan
| | - Wen-Tai Chiu
- Department of Biomedical Engineering, National Cheng Kung University, Tainan, Taiwan.,Medical Device Innovation Center, National Cheng Kung University, Tainan, Taiwan
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21
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Ayad O, Al Sayed ZR, Sebille S, Magaud C, Chapotte-Baldacci CA, Jayle C, Faivre JF, Gaborit N, Chatelier A, Bois P. In vitro differentiation of W8B2 + human cardiac stem cells: gene expression of ionic channels and spontaneous calcium activity. Cell Mol Biol Lett 2020; 25:50. [PMID: 33292162 PMCID: PMC7646077 DOI: 10.1186/s11658-020-00242-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 10/29/2020] [Indexed: 11/18/2022] Open
Abstract
Background Human cardiac stem cells expressing the W8B2 marker (W8B2+ CSCs) were recently identified and proposed as a new model of multipotent CSCs capable of differentiating into smooth muscle cells, endothelial cells and immature myocytes. Nevertheless, no characterization of ion channel or calcium activity during the differentiation of these stem cells has been reported. Methods The objectives of this study were thus to analyze (using the TaqMan Low-Density Array technique) the gene profile of W8B2+ CSCs pertaining to the regulation of ion channels, transporters and other players involved in the calcium homeostasis of these cells. We also analyzed spontaneous calcium activity (via the GCaMP calcium probe) during the in vitro differentiation of W8B2+ CSCs into cardiac myocytes. Results Our results show an entirely different electrophysiological genomic profile between W8B2+ CSCs before and after differentiation. Some specific nodal genes, such as Tbx3, HCN, ICaT, L, KV, and NCX, are overexpressed after this differentiation. In addition, we reveal spontaneous calcium activity or a calcium clock whose kinetics change during the differentiation process. A pharmacological study carried out on differentiated W8B2+ CSCs showed that the NCX exchanger and IP3 stores play a fundamental role in the generation of these calcium oscillations. Conclusions Taken together, the present results provide important information on ion channel expression and intrinsic calcium dynamics during the differentiation process of stem cells expressing the W8B2 marker.
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Affiliation(s)
- Oualid Ayad
- University of Poitiers Signalisation et Transports Ioniques Membranaires, EA7349, Poitiers Cedex 09, France
| | - Zeina R Al Sayed
- CNRS, INSERM, l'institut du thorax, Université de Nantes, 44000, Nantes, France
| | - Stéphane Sebille
- University of Poitiers Signalisation et Transports Ioniques Membranaires, EA7349, Poitiers Cedex 09, France
| | - Christophe Magaud
- University of Poitiers Signalisation et Transports Ioniques Membranaires, EA7349, Poitiers Cedex 09, France
| | | | - Christophe Jayle
- CHU of Poitiers chirurgie cardiaque et thoracique, , Poitiers Cedex 09, France
| | - Jean-François Faivre
- University of Poitiers Signalisation et Transports Ioniques Membranaires, EA7349, Poitiers Cedex 09, France
| | - Nathalie Gaborit
- CNRS, INSERM, l'institut du thorax, Université de Nantes, 44000, Nantes, France
| | - Aurélien Chatelier
- University of Poitiers Signalisation et Transports Ioniques Membranaires, EA7349, Poitiers Cedex 09, France
| | - Patrick Bois
- University of Poitiers Signalisation et Transports Ioniques Membranaires, EA7349, Poitiers Cedex 09, France.
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22
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Qi H, Li X, Jin Z, Simmen T, Shuai J. The Oscillation Amplitude, Not the Frequency of Cytosolic Calcium, Regulates Apoptosis Induction. iScience 2020; 23:101671. [PMID: 33196017 PMCID: PMC7644924 DOI: 10.1016/j.isci.2020.101671] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 08/15/2020] [Accepted: 10/08/2020] [Indexed: 01/06/2023] Open
Abstract
Although a rising concentration of cytosolic Ca2+ has long been recognized as an essential signal for apoptosis, the dynamical mechanisms by which Ca2+ regulates apoptosis are not clear yet. To address this, we constructed a computational model that integrates known biochemical reactions and can reproduce the dynamical behaviors of Ca2+-induced apoptosis as observed in experiments. Model analysis shows that oscillating Ca2+ signals first convert into gradual signals and eventually transform into a switch-like apoptotic response. Via the two processes, the apoptotic signaling pathway filters the frequency of Ca2+ oscillations effectively but instead responds acutely to their amplitude. Collectively, our results suggest that Ca2+ regulates apoptosis mainly via oscillation amplitude, rather than frequency, modulation. This study not only provides a comprehensive understanding of how oscillatory Ca2+ dynamically regulates the complex apoptotic signaling network but also presents a typical example of how Ca2+ controls cellular responses through amplitude modulation.
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Affiliation(s)
- Hong Qi
- Complex Systems Research Center, Shanxi University, Taiyuan 030006, China.,Shanxi Key Laboratory of Mathematical Techniques and Big Data Analysis on Disease Control and Prevention, Shanxi University, Taiyuan 030006, China
| | - Xiang Li
- Department of Physics, Xiamen University, Xiamen 361005, China.,State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, Xiamen University, Xiamen 361102, China.,National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen 361102, China
| | - Zhen Jin
- Complex Systems Research Center, Shanxi University, Taiyuan 030006, China.,Shanxi Key Laboratory of Mathematical Techniques and Big Data Analysis on Disease Control and Prevention, Shanxi University, Taiyuan 030006, China
| | - Thomas Simmen
- Faculty of Medicine and Dentistry, Department of Cell Biology, University of Alberta, Edmonton, AB T6G2H7, Canada
| | - Jianwei Shuai
- Department of Physics, Xiamen University, Xiamen 361005, China.,State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, Xiamen University, Xiamen 361102, China.,National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen 361102, China
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23
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Nguyen NT, Ma G, Zhou Y, Jing J. Optogenetic approaches to control Ca 2+-modulated physiological processes. CURRENT OPINION IN PHYSIOLOGY 2020; 17:187-196. [PMID: 33184610 DOI: 10.1016/j.cophys.2020.08.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
As a versatile intracellular second messenger, calcium ion (Ca2+) regulates a plethora of physiological processes. To achieve precise control over Ca2+ signals in living cells and organisms, a set of optogenetic tools have recently been crafted by engineering photosensitive domains into intracellular signaling proteins, G-protein coupled receptors (GPCRs), receptor tyrosine kinases (RTKs), and Ca2+ channels. We highlight herein the optogenetic engineering strategies, kinetic properties, advantages and limitations of these genetically-encoded Ca2+ channel actuators (GECAs) and modulators. In parallel, we present exemplary applications in both excitable and non-excitable cells and tissues. Furthermore, we briefly discuss potential solutions for wireless optogenetics to accelerate the in vivo applications of GECAs under physiological conditions, with an emphasis on integrating near-infrared (NIR) light-excitable upconversion nanoparticles (UCNPs) and bioluminescence with optogenetics.
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Affiliation(s)
- Nhung T Nguyen
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA
| | - Guolin Ma
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA
| | - Yubin Zhou
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA.,Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX 77030, USA
| | - Ji Jing
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA
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24
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Ca 2+ Release via IP 3 Receptors Shapes the Cardiac Ca 2+ Transient for Hypertrophic Signaling. Biophys J 2020; 119:1178-1192. [PMID: 32871099 DOI: 10.1016/j.bpj.2020.08.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 06/16/2020] [Accepted: 08/04/2020] [Indexed: 12/27/2022] Open
Abstract
Calcium (Ca2+) plays a central role in mediating both contractile function and hypertrophic signaling in ventricular cardiomyocytes. L-type Ca2+ channels trigger release of Ca2+ from ryanodine receptors for cellular contraction, whereas signaling downstream of G-protein-coupled receptors stimulates Ca2+ release via inositol 1,4,5-trisphosphate receptors (IP3Rs), engaging hypertrophic signaling pathways. Modulation of the amplitude, duration, and duty cycle of the cytosolic Ca2+ contraction signal and spatial localization have all been proposed to encode this hypertrophic signal. Given current knowledge of IP3Rs, we develop a model describing the effect of functional interaction (cross talk) between ryanodine receptor and IP3R channels on the Ca2+ transient and examine the sensitivity of the Ca2+ transient shape to properties of IP3R activation. A key result of our study is that IP3R activation increases Ca2+ transient duration for a broad range of IP3R properties, but the effect of IP3R activation on Ca2+ transient amplitude is dependent on IP3 concentration. Furthermore we demonstrate that IP3-mediated Ca2+ release in the cytosol increases the duty cycle of the Ca2+ transient, the fraction of the cycle for which [Ca2+] is elevated, across a broad range of parameter values and IP3 concentrations. When coupled to a model of downstream transcription factor (NFAT) activation, we demonstrate that there is a high correspondence between the Ca2+ transient duty cycle and the proportion of activated NFAT in the nucleus. These findings suggest increased cytosolic Ca2+ duty cycle as a plausible mechanism for IP3-dependent hypertrophic signaling via Ca2+-sensitive transcription factors such as NFAT in ventricular cardiomyocytes.
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25
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Ghilardi SJ, O'Reilly BM, Sgro AE. Intracellular signaling dynamics and their role in coordinating tissue repair. WILEY INTERDISCIPLINARY REVIEWS. SYSTEMS BIOLOGY AND MEDICINE 2020; 12:e1479. [PMID: 32035001 PMCID: PMC7187325 DOI: 10.1002/wsbm.1479] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 12/20/2019] [Accepted: 12/31/2019] [Indexed: 12/11/2022]
Abstract
Tissue repair is a complex process that requires effective communication and coordination between cells across multiple tissues and organ systems. Two of the initial intracellular signals that encode injury signals and initiate tissue repair responses are calcium and extracellular signal-regulated kinase (ERK). However, calcium and ERK signaling control a variety of cellular behaviors important for injury repair including cellular motility, contractility, and proliferation, as well as the activity of several different transcription factors, making it challenging to relate specific injury signals to their respective repair programs. This knowledge gap ultimately hinders the development of new wound healing therapies that could take advantage of native cellular signaling programs to more effectively repair tissue damage. The objective of this review is to highlight the roles of calcium and ERK signaling dynamics as mechanisms that link specific injury signals to specific cellular repair programs during epithelial and stromal injury repair. We detail how the signaling networks controlling calcium and ERK can now also be dissected using classical signal processing techniques with the advent of new biosensors and optogenetic signal controllers. Finally, we advocate the importance of recognizing calcium and ERK dynamics as key links between injury detection and injury repair programs that both organize and execute a coordinated tissue repair response between cells across different tissues and organs. This article is categorized under: Models of Systems Properties and Processes > Mechanistic Models Biological Mechanisms > Cell Signaling Laboratory Methods and Technologies > Imaging Models of Systems Properties and Processes > Organ, Tissue, and Physiological Models.
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Affiliation(s)
- Samuel J. Ghilardi
- Department of Biomedical Engineering and the Biological Design CenterBoston UniversityBostonMassachusetts
| | - Breanna M. O'Reilly
- Department of Biomedical Engineering and the Biological Design CenterBoston UniversityBostonMassachusetts
| | - Allyson E. Sgro
- Department of Biomedical Engineering and the Biological Design CenterBoston UniversityBostonMassachusetts
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26
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Ahmad AA, Streiff ME, Hunter C, Sachse FB. Modulation of Calcium Transients in Cardiomyocytes by Transient Receptor Potential Canonical 6 Channels. Front Physiol 2020; 11:44. [PMID: 32116757 DOI: 10.3389/fphys.2020.00044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 01/20/2020] [Indexed: 11/13/2022] Open
Abstract
Transient receptor potential canonical 6 (TRPC6) channels are non-selective cation channels that are thought to underlie mechano-modulation of calcium signaling in cardiomyocytes. TRPC6 channels are involved in development of cardiac hypertrophy and related calcineurin-nuclear factor of activated T cells (NFAT) signaling. However, the exact location and roles of TRPC6 channels remain ill-defined in cardiomyocytes. We used an expression system based on neonatal rat ventricular myocytes (NRVMs) to investigate the location of TRPC6 channels and their role in calcium signaling. NRVMs isolated from 1- to 2-day-old animals were cultured and infected with an adenoviral vector to express enhanced-green fluorescent protein (eGFP) or TRPC6-eGFP. After 3 days, NRVMs were fixed, immunolabeled, and imaged with confocal and super-resolution microscopy to determine TRPC6 localization. Cytosolic calcium transients at 0.5 and 1 Hz pacing rates were recorded in NRVMs using indo-1, a ratio-metric calcium dye. Confocal and super-resolution microscopy suggested that TRPC6-eGFP localized to the sarcolemma. NRVMs infected with TRPC6-eGFP exhibited higher diastolic and systolic cytosolic calcium concentration as well as increased sarcoplasmic reticulum (SR) calcium load compared to eGFP infected cells. We applied a computer model comprising sarcolemmal TRPC6 current to explain our experimental findings. Altogether, our studies indicate that TRPC6 channels play a role in sarcolemmal and intracellular calcium signaling in cardiomyocytes. Our findings support the hypothesis that upregulation or activation of TRPC6 channels, e.g., in disease, leads to sustained elevation of the cytosolic calcium concentration, which is thought to activate calcineurin-NFAT signaling and cardiac hypertrophic remodeling. Also, our findings support the hypothesis that mechanosensitivity of TRPC6 channels modulates cytosolic calcium transients and SR calcium load.
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Affiliation(s)
- Azmi A Ahmad
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, UT, United States.,Department of Biomedical Engineering, University of Utah, Salt Lake City, UT, United States
| | - Molly E Streiff
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, UT, United States.,Department of Biomedical Engineering, University of Utah, Salt Lake City, UT, United States
| | - Chris Hunter
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, UT, United States
| | - Frank B Sachse
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, UT, United States.,Department of Biomedical Engineering, University of Utah, Salt Lake City, UT, United States
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27
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Johnson HE, Toettcher JE. Signaling Dynamics Control Cell Fate in the Early Drosophila Embryo. Dev Cell 2019; 48:361-370.e3. [PMID: 30753836 DOI: 10.1016/j.devcel.2019.01.009] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 11/27/2018] [Accepted: 01/04/2019] [Indexed: 12/12/2022]
Abstract
The Erk mitogen-activated protein kinase plays diverse roles in animal development. Its widespread reuse raises a conundrum: when a single kinase like Erk is activated, how does a developing cell know which fate to adopt? We combine optogenetic control with genetic perturbations to dissect Erk-dependent fates in the early Drosophila embryo. We find that Erk activity is sufficient to "posteriorize" 88% of the embryo, inducing gut endoderm-like gene expression and morphogenetic movements in all cells within this region. Gut endoderm fate adoption requires at least 1 h of signaling, whereas a 30-min Erk pulse specifies a distinct ectodermal cell type, intermediate neuroblasts. We find that the endoderm-ectoderm cell fate switch is controlled by the cumulative load of Erk activity, not the duration of a single pulse. The fly embryo thus harbors a classic example of dynamic control, where the temporal profile of Erk signaling selects between distinct physiological outcomes.
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Affiliation(s)
- Heath E Johnson
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Jared E Toettcher
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
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28
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Bugaj LJ, Lim WA. High-throughput multicolor optogenetics in microwell plates. Nat Protoc 2019; 14:2205-2228. [PMID: 31235951 DOI: 10.1038/s41596-019-0178-y] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 04/09/2019] [Indexed: 12/27/2022]
Abstract
Optogenetic probes can be powerful tools for dissecting complexity in cell biology, but there is a lack of instrumentation to exploit their potential for automated, high-information-content experiments. This protocol describes the construction and use of the optoPlate-96, a platform for high-throughput three-color optogenetics experiments that allows simultaneous manipulation of common red- and blue-light-sensitive optogenetic probes. The optoPlate-96 enables illumination of individual wells in 96-well microwell plates or in groups of wells in 384-well plates. Its design ensures that there will be no cross-illumination between microwells in 96-well plates, and an active cooling system minimizes sample heating during light-intensive experiments. This protocol details the steps to assemble, test, and use the optoPlate-96. The device can be fully assembled without specialized equipment beyond a 3D printer and a laser cutter, starting from open-source design files and commercially available components. We then describe how to perform a typical optogenetics experiment using the optoPlate-96 to stimulate adherent mammalian cells. Although optoPlate-96 experiments are compatible with any plate-based readout, we describe analysis using quantitative single-cell immunofluorescence. This workflow thus allows complex optogenetics experiments (independent control of stimulation colors, intensity, dynamics, and time points) with high-dimensional outputs at single-cell resolution. Starting from 3D-printed and laser-cut components, assembly and testing of the optoPlate-96 can be accomplished in 3-4 h, at a cost of ~$600. A full optoPlate-96 experiment with immunofluorescence analysis can be performed within ~24 h, but this estimate is variable depending on the cell type and experimental parameters.
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Affiliation(s)
- Lukasz J Bugaj
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA. .,Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA.
| | - Wendell A Lim
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA.,Center for Systems and Synthetic Biology, University of California, San Francisco, San Francisco, CA, USA
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29
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Zi Z. Molecular Engineering of the TGF-β Signaling Pathway. J Mol Biol 2019; 431:2644-2654. [PMID: 31121181 DOI: 10.1016/j.jmb.2019.05.022] [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: 01/30/2019] [Revised: 05/05/2019] [Accepted: 05/13/2019] [Indexed: 12/19/2022]
Abstract
Transforming growth factor beta (TGF-β) is an important growth factor that plays essential roles in regulating tissue development and homeostasis. Dysfunction of TGF-β signaling is a hallmark of many human diseases. Therefore, targeting TGF-β signaling presents broad therapeutic potential. Since the discovery of the TGF-β ligand, a collection of engineered signaling proteins have been developed to probe and manipulate TGF-β signaling responses. In this review, we highlight recent progress in the engineering of TGF-β signaling for different applications and discuss how molecular engineering approaches can advance our understanding of this important pathway. In addition, we provide a future outlook on the opportunities and challenges in the engineering of the TGF-β signaling pathway from a quantitative perspective.
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Affiliation(s)
- Zhike Zi
- Otto-Warburg Laboratory, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany.
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30
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Jeknić S, Kudo T, Covert MW. Techniques for Studying Decoding of Single Cell Dynamics. Front Immunol 2019; 10:755. [PMID: 31031756 PMCID: PMC6470274 DOI: 10.3389/fimmu.2019.00755] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 03/21/2019] [Indexed: 12/21/2022] Open
Abstract
Cells must be able to interpret signals they encounter and reliably generate an appropriate response. It has long been known that the dynamics of transcription factor and kinase activation can play a crucial role in selecting an individual cell's response. The study of cellular dynamics has expanded dramatically in the last few years, with dynamics being discovered in novel pathways, new insights being revealed about the importance of dynamics, and technological improvements increasing the throughput and capabilities of single cell measurements. In this review, we highlight the important developments in this field, with a focus on the methods used to make new discoveries. We also include a discussion on improvements in methods for engineering and measuring single cell dynamics and responses. Finally, we will briefly highlight some of the many challenges and avenues of research that are still open.
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Affiliation(s)
- Stevan Jeknić
- Department of Bioengineering, Stanford University, Stanford, CA, United States.,Allen Discovery Center for Systems Modeling of Infection, Stanford, CA, United States
| | - Takamasa Kudo
- Allen Discovery Center for Systems Modeling of Infection, Stanford, CA, United States.,Department of Chemical and Systems Biology, Stanford University, Stanford, CA, United States
| | - Markus W Covert
- Department of Bioengineering, Stanford University, Stanford, CA, United States.,Allen Discovery Center for Systems Modeling of Infection, Stanford, CA, United States.,Department of Chemical and Systems Biology, Stanford University, Stanford, CA, United States
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31
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Optically inducible membrane recruitment and signaling systems. Curr Opin Struct Biol 2019; 57:84-92. [PMID: 30884362 DOI: 10.1016/j.sbi.2019.01.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 01/12/2019] [Accepted: 01/28/2019] [Indexed: 02/06/2023]
Abstract
Optical induction of intracellular signaling by membrane-associated and integral membrane proteins allows spatiotemporally precise control over second messenger signaling and cytoskeletal rearrangements that are important to cell migration, development, and proliferation. Optogenetic membrane recruitment of a protein-of-interest to control its signaling by altering subcellular localization is a versatile means to these ends. Here, we summarize the signaling characteristics and underlying structure-function of RGS-LOV photoreceptors as single-component membrane recruitment tools that rapidly, reversibly, and efficiently carry protein cargo from the cytoplasm to the plasma membrane by a light-regulated electrostatic interaction with the membrane itself. We place the technology-relevant features of these recently described natural photosensory proteins in context of summarized protein engineering and design strategies for optically controlling membrane protein signaling.
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32
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Yang Y, Wu M. Rhythmicity and waves in the cortex of single cells. Philos Trans R Soc Lond B Biol Sci 2019; 373:rstb.2017.0116. [PMID: 29632268 PMCID: PMC5904302 DOI: 10.1098/rstb.2017.0116] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/30/2017] [Indexed: 12/15/2022] Open
Abstract
Emergence of dynamic patterns in the form of oscillations and waves on the cortex of single cells is a fascinating and enigmatic phenomenon. Here we outline various theoretical frameworks used to model pattern formation with the goal of reducing complex, heterogeneous patterns into key parameters that are biologically tractable. We also review progress made in recent years on the quantitative and molecular definitions of these terms, which we believe have begun to transform single-cell dynamic patterns from a purely observational and descriptive subject to more mechanistic studies. Specifically, we focus on the nature of local excitable and oscillation events, their spatial couplings leading to propagating waves and the role of active membrane. Instead of arguing for their functional importance, we prefer to consider such patterns as basic properties of dynamic systems. We discuss how knowledge of these patterns could be used to dissect the structure of cellular organization and how the network-centric view could help define cellular functions as transitions between different dynamical states. Last, we speculate on how these patterns could encode temporal and spatial information. This article is part of the theme issue ‘Self-organization in cell biology’.
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Affiliation(s)
- Yang Yang
- Department of Biological Sciences, Centre for Bioimaging Sciences, Mechanobiology Institute, National University of Singapore, Singapore
| | - Min Wu
- Department of Biological Sciences, Centre for Bioimaging Sciences, Mechanobiology Institute, National University of Singapore, Singapore
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33
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Zhao B, Wang Y, Tan X, Zheng X, Wang F, Ke K, Zhang C, Liao N, Dang Y, Shi Y, Zheng Y, Gao Y, Li Q, Liu X, Liu J. An Optogenetic Controllable T Cell System for Hepatocellular Carcinoma Immunotherapy. Theranostics 2019; 9:1837-1850. [PMID: 31037142 PMCID: PMC6485282 DOI: 10.7150/thno.27051] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 01/08/2019] [Indexed: 12/16/2022] Open
Abstract
Rationale: T-cell based immunotherapy increasingly shows broad application prospects in cancer treatment, but its performance in solid tumors is far from our expectation, partly due to the re-inhibition of infiltrated T cells by immunosuppressive tumor microenvironment. Here we presented an artificial synthetic optogenetic circuit to control the immune responses of engineered T cells on demand for promoting and enhancing the therapeutic efficiency of cancer immunotherapy. Methods: We designed and synthesized blue-light inducible artificial immune signaling circuit and transgene expression system. The blue light triggered transgene expression was investigated by luciferase activity assay, qPCR and ELISA. The in vitro cytotoxicity and proliferation assays were carried out on engineered T cells. The in vivo anti-tumor activity of engineered T cells was investigated on xenograft model of human hepatocellular carcinoma. Results: Blue light stimulation could spatiotemporally control gene expression of specific cytokines (IL2, IL15, and TNF-α) in both engineered 293T cells and human primary T cells. This optogenetic engineering strategy significantly enhanced the expansion ability and cytolytic activity of primary T cells upon light irradiation, and the light activated T cells showed high-efficiency of elimination against xenograft of hepatocellular carcinoma cells. Conclusions: The current study represented an engineered remotely control T cell system for solid tumor treatment, and provided a potential strategy to partially overcome the intrinsic shortages of current immune cell therapy.
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Affiliation(s)
- Bixing Zhao
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, P. R. China
- The Liver Center of Fujian Province, Fujian Medical University, Fuzhou 350025, P. R. China
| | - Yingchao Wang
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, P. R. China
- The Liver Center of Fujian Province, Fujian Medical University, Fuzhou 350025, P. R. China
| | - Xionghong Tan
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, P. R. China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, P.R. China
| | - Xiaoyuan Zheng
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, P. R. China
- The Liver Center of Fujian Province, Fujian Medical University, Fuzhou 350025, P. R. China
| | - Fei Wang
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, P. R. China
- The Liver Center of Fujian Province, Fujian Medical University, Fuzhou 350025, P. R. China
| | - Kun Ke
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, P. R. China
- Liver Disease Center, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, P. R. China
- The Liver Center of Fujian Province, Fujian Medical University, Fuzhou 350025, P. R. China
| | - Cuilin Zhang
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, P. R. China
- The Liver Center of Fujian Province, Fujian Medical University, Fuzhou 350025, P. R. China
| | - Naishun Liao
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, P. R. China
- The Liver Center of Fujian Province, Fujian Medical University, Fuzhou 350025, P. R. China
| | - Yuan Dang
- Department of Comparative, Fuzhou General Hospital, Xiamen University Medical College, 156 Road Xi'erhuanbei, Fuzhou 350025, Fujian, P.R. China
| | - Yingjun Shi
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, P. R. China
- The Liver Center of Fujian Province, Fujian Medical University, Fuzhou 350025, P. R. China
| | - Youshi Zheng
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, P. R. China
- The Liver Center of Fujian Province, Fujian Medical University, Fuzhou 350025, P. R. China
| | - Yunzhen Gao
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, P. R. China
- The Liver Center of Fujian Province, Fujian Medical University, Fuzhou 350025, P. R. China
| | - Qin Li
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, P. R. China
| | - Xiaolong Liu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, P. R. China
- The Liver Center of Fujian Province, Fujian Medical University, Fuzhou 350025, P. R. China
| | - Jingfeng Liu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, P. R. China
- Liver Disease Center, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, P. R. China
- The Liver Center of Fujian Province, Fujian Medical University, Fuzhou 350025, P. R. China
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34
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Moayedi Y, Greenberg SA, Jenkins BA, Marshall KL, Dimitrov LV, Nelson AM, Owens DM, Lumpkin EA. Camphor white oil induces tumor regression through cytotoxic T cell-dependent mechanisms. Mol Carcinog 2019; 58:722-734. [PMID: 30582219 DOI: 10.1002/mc.22965] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 12/18/2018] [Accepted: 12/20/2018] [Indexed: 12/11/2022]
Abstract
Bioactive derivatives from the camphor laurel tree, Cinnamomum camphora, are posited to exhibit chemopreventive properties but the efficacy and mechanism of these natural products are not fully understood. We tested an essential-oil derivative, camphor white oil (CWO), for anti-tumor activity in a mouse model of keratinocyte-derived skin cancer. Daily topical treatment with CWO induced dramatic regression of pre-malignant skin tumors and a two-fold reduction in cutaneous squamous cell carcinomas. We next investigated underlying cellular and molecular mechanisms. In cultured keratinocytes, CWO stimulated calcium signaling, resulting in calcineurin-dependent activation of nuclear factor of activated T cells (NFAT). In vivo, CWO induced transcriptional changes in immune-related genes identified by RNA-sequencing, resulting in cytotoxic T cell-dependent tumor regression. Finally, we identified chemical constituents of CWO that recapitulated effects of the admixture. Together, these studies identify T cell-mediated tumor regression as a mechanism through which a plant-derived essential oil diminishes established tumor burden.
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Affiliation(s)
- Yalda Moayedi
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, New York
| | - Sophie A Greenberg
- Department of Dermatology, Columbia University Irving Medical Center, New York, New York
| | - Blair A Jenkins
- Medical Scientist Training Program, Columbia University Irving Medical Center, New York, New York
| | - Kara L Marshall
- Department of Dermatology, Columbia University Irving Medical Center, New York, New York
| | - Lina V Dimitrov
- Program in Neuroscience and Behavior, Barnard College, Columbia University, New York, New York
| | - Aislyn M Nelson
- Department of Dermatology, Columbia University Irving Medical Center, New York, New York.,Department of Neuroscience, Baylor College of Medicine, Houston, Texas
| | - David M Owens
- Department of Dermatology, Columbia University Irving Medical Center, New York, New York.,Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York
| | - Ellen A Lumpkin
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, New York.,Department of Dermatology, Columbia University Irving Medical Center, New York, New York
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35
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Szymula KP, Magaraci MS, Patterson M, Clark A, Mannickarottu SG, Chow BY. An Open-Source Plate Reader. Biochemistry 2018; 58:468-473. [PMID: 30511843 DOI: 10.1021/acs.biochem.8b00952] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Microplate readers are foundational instruments in experimental biology and bioengineering that enable multiplexed spectrophotometric measurements. To enhance their accessibility, we here report the design, construction, validation, and benchmarking of an open-source microplate reader. The system features full-spectrum absorbance and fluorescence emission detection, in situ optogenetic stimulation, and stand-alone touch screen programming of automated assay protocols. The total system costs less than $3500, a fraction of the cost of commercial plate readers, and can detect the fluorescence of common dyes at concentrations as low as ∼10 nM. Functional capabilities were demonstrated in the context of synthetic biology, optogenetics, and photosensory biology: by steady-state measurements of ligand-induced reporter gene expression in a model of bacterial quorum sensing and by flavin photocycling kinetic measurements of a LOV (light-oxygen-voltage) domain photoreceptor used for optogenetic transcriptional activation. Fully detailed guides for assembling the device and automating it using the custom Python-based API (Application Program Interface) are provided. This work contributes a key technology to the growing community-wide infrastructure of open-source biology-focused hardware, whose creation is facilitated by rapid prototyping capabilities and low-cost electronics, optoelectronics, and microcomputers.
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Affiliation(s)
- Karol P Szymula
- Department of Bioengineering , University of Pennsylvania , 210 South 33rd Street , Philadelphia , Pennsylvania 19104 , United States
| | - Michael S Magaraci
- Department of Bioengineering , University of Pennsylvania , 210 South 33rd Street , Philadelphia , Pennsylvania 19104 , United States
| | - Michael Patterson
- Department of Bioengineering , University of Pennsylvania , 210 South 33rd Street , Philadelphia , Pennsylvania 19104 , United States
| | - Andrew Clark
- Department of Bioengineering , University of Pennsylvania , 210 South 33rd Street , Philadelphia , Pennsylvania 19104 , United States
| | - Sevile G Mannickarottu
- Department of Bioengineering , University of Pennsylvania , 210 South 33rd Street , Philadelphia , Pennsylvania 19104 , United States
| | - Brian Y Chow
- Department of Bioengineering , University of Pennsylvania , 210 South 33rd Street , Philadelphia , Pennsylvania 19104 , United States
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36
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Ravindran PT, Wilson MZ. Lighting Up Cancer Dynamics. Trends Cancer 2018; 4:657-659. [PMID: 30292348 DOI: 10.1016/j.trecan.2018.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 06/05/2018] [Indexed: 12/22/2022]
Abstract
Live-cell microscopy has revealed that signaling pathways carry elaborate time-varying activities. Yet, the connection between these dynamics and cellular disease has remained elusive. Recent work leverages cellular optogenetics to analyze the Ras-to-Erk transfer function in cancer cells. These analyses reveal how changes to the filtering properties of a pathway lead to the misperception of extracellular events. Overall, these studies suggest that mutations do not simply hyperactivate pathways but rather can also change their transmission properties in more subtle ways.
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Affiliation(s)
- Pavithran T Ravindran
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Maxwell Z Wilson
- Department of Molecular, Cellular, and Developmental Biology, University of California-Santa Barbara, Santa Barbara, CA 93106, USA.
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37
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Design and validation of an open-source modular Microplate Photoirradiation System for high-throughput photobiology experiments. PLoS One 2018; 13:e0203597. [PMID: 30289930 PMCID: PMC6173374 DOI: 10.1371/journal.pone.0203597] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 08/23/2018] [Indexed: 01/09/2023] Open
Abstract
Research in photobiology is currently limited by a lack of devices capable of delivering precise and tunable irradiation to cells in a high-throughput format. This limits researchers to using expensive commercially available or custom-built light sources which make it difficult to replicate, standardize, optimize, and scale experiments. Here we present an open-source Microplate Photoirradiation System (MPS) developed to enable high-throughput light experiments in standard 96 and 24-well microplates for a variety of applications in photobiology research. This open-source system features 96 independently controlled LEDs (4 LEDs per well in 24-well), Wi-Fi connected control and programmable graphical user interface (GUI) for control and programming, automated calibration GUI, and modular control and LED boards for maximum flexibility. A web-based GUI generates light program files containing irradiation parameters for groups of LEDs. These parameters are then uploaded wirelessly, stored and used on the MPS to run photoirradiation experiments inside any incubator. A rapid and semi-quantitative porphyrin metabolism assay was also developed to validate the system in wild-type fibroblasts. Protoporphyrin IX (PpIX) fluorescence accumulation was induced by incubation with 5-aminolevulinic acid (ALA), a photosensitization method leveraged clinically to destroy malignant cell types in a process termed photodynamic therapy (PDT), and cells were irradiated with 405nm light with varying irradiance, duration and pulsation parameters. Immediately after light treatment with the MPS, subsequent photobleaching was measured in live, adherent cells in both 96-well and a 24-well microplates using a microplate reader. Results demonstrate the utility and reliability of the Microplate Photoirradiation System to irradiate cells with precise irradiance and timing parameters in order to measure PpIx photobleaching kinetics in live adherent cells and perform comparable experiments with both 24 and 96 well microplate formats. The high-throughput capability of the MPS enabled measurement of enough irradiance conditions in a single microplate to fit PpIX fluorescence to a bioexponential decay model of photobleaching, as well as reveal a dependency of photobleaching on duty-cycle-but not frequency-in a pulsed irradiance regimen.
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Directly light-regulated binding of RGS-LOV photoreceptors to anionic membrane phospholipids. Proc Natl Acad Sci U S A 2018; 115:E7720-E7727. [PMID: 30065115 PMCID: PMC6099885 DOI: 10.1073/pnas.1802832115] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Light–oxygen–voltage (LOV) domain photoreceptors are found ubiquitously in nature and possess highly diverse signaling roles and mechanisms. Here, we show that a class of fungal LOV proteins dynamically associates with anionic plasma membrane phospholipids by a blue light-switched electrostatic interaction. This reversible association is rapidly triggered by blue light and ceases within seconds when illumination ceases. Within the native host, we predict that these proteins regulate G-protein signaling by the controlled recruitment of fused regulator of G-protein signaling (RGS) domains; in applied contexts, we anticipate that engineered chimeric versions of such proteins will be useful for rapid optogenetic membrane localization of fused proteins through direct interaction with the membrane itself, without requiring additional components to direct subcellular localization. We report natural light–oxygen–voltage (LOV) photoreceptors with a blue light-switched, high-affinity (KD ∼ 10−7 M), and direct electrostatic interaction with anionic phospholipids. Membrane localization of one such photoreceptor, BcLOV4 from Botrytis cinerea, is directly coupled to its flavin photocycle, and is mediated by a polybasic amphipathic helix in the linker region between the LOV sensor and its C-terminal domain of unknown function (DUF), as revealed through a combination of bioinformatics, computational protein modeling, structure–function studies, and optogenetic assays in yeast and mammalian cell line expression systems. In model systems, BcLOV4 rapidly translocates from the cytosol to plasma membrane (∼1 second). The reversible electrostatic interaction is nonselective among anionic phospholipids, exhibiting binding strengths dependent on the total anionic content of the membrane without preference for a specific headgroup. The in vitro and cellular responses were also observed with a BcLOV4 homolog and thus are likely to be general across the dikarya LOV class, whose members are associated with regulator of G-protein signaling (RGS) domains. Natural photoreceptors are not previously known to directly associate with membrane phospholipids in a light-dependent manner, and thus this work establishes both a photosensory signal transmission mode and a single-component optogenetic tool with rapid membrane localization kinetics that approaches the diffusion limit.
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Hannanta-anan P, Chow BY. Optogenetic Inhibition of Gα q Protein Signaling Reduces Calcium Oscillation Stochasticity. ACS Synth Biol 2018; 7:1488-1495. [PMID: 29792810 PMCID: PMC6311707 DOI: 10.1021/acssynbio.8b00065] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
As fast terminators of G-protein coupled receptor (GPCR) signaling, regulators of G-protein signaling (RGS) serve critical roles in fine-tuning second messenger levels and, consequently, cellular responses to external stimuli. Here, we report the creation of an optogenetic RGS2 (opto-RGS2) that suppresses agonist-evoked calcium oscillations by the inactivation of Gαq protein. In this system, cryptochrome-mediated heterodimerization of the catalytic RGS2-box with its N-terminal amphipathic helix reconstitutes a functional membrane-localized complex that can dynamically suppress store-operated release of calcium. Engineered opto-RGS2 cell lines were used to establish the role of RGS2 as a key inhibitory feedback regulator of the stochasticity of the Gαq-mediated calcium spike timing. RGS2 reduced the stochasticity of carbachol-stimulated calcium oscillations, and the feedback inhibition was coupled to the global calcium elevation by calmodulin/RGS2 interactions. The identification of a critical negative feedback circuit exemplifies the utility of optogenetic approaches for interrogating RGS/GPCR biology and calcium encoding principles through temporally precise molecular gain-of-function.
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Affiliation(s)
| | - Brian Y. Chow
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104
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Abstract
Decoding how tissue properties emerge across multiple spatial and temporal scales from the integration of local signals is a grand challenge in quantitative biology. For example, the collective behavior of epithelial cells is critical for shaping developing embryos. Understanding how epithelial cells interpret a diverse range of local signals to coordinate tissue-level processes requires a systems-level understanding of development. Integration of multiple signaling pathways that specify cell signaling information requires second messengers such as calcium ions. Increasingly, specific roles have been uncovered for calcium signaling throughout development. Calcium signaling regulates many processes including division, migration, death, and differentiation. However, the pleiotropic and ubiquitous nature of calcium signaling implies that many additional functions remain to be discovered. Here we review a selection of recent studies to highlight important insights into how multiple signals are transduced by calcium transients in developing epithelial tissues. Quantitative imaging and computational modeling have provided important insights into how calcium signaling integration occurs. Reverse-engineering the conserved features of signal integration mediated by calcium signaling will enable novel approaches in regenerative medicine and synthetic control of morphogenesis.
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Affiliation(s)
- Pavel A. Brodskiy
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, 205 McCourtney Hall, Notre Dame, IN 46556, USA
| | - Jeremiah J. Zartman
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, 205 McCourtney Hall, Notre Dame, IN 46556, USA
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41
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Pchelintseva E, Djamgoz MBA. Mesenchymal stem cell differentiation: Control by calcium-activated potassium channels. J Cell Physiol 2017; 233:3755-3768. [PMID: 28776687 DOI: 10.1002/jcp.26120] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 08/01/2017] [Indexed: 12/12/2022]
Abstract
Mesenchymal stem cells (MSCs) are widely used in modern medicine for which understanding the mechanisms controlling their differentiation is fundamental. Ion channels offer novel insights to this process because of their role in modulating membrane potential and intracellular milieu. Here, we evaluate the contribution of calcium-activated potassium (KCa ) channels to the three main components of MSC differentiation: initiation, proliferation, and migration. First, we demonstrate the importance of the membrane potential (Vm ) and the apparent association of hyperpolarization with differentiation. Of KCa subtypes, most evidence points to activity of big-conductance channels in inducing initiation. On the other hand, intermediate-conductance currents have been shown to promote progression through the cell cycle. While there is no information on the role of KCa channels in migration of MSCs, work from other stem cells and cancer cells suggest that intermediate-conductance and to a lesser extent big-conductance channels drive migration. In all cases, these effects depend on species, tissue origin and lineage. Finally, we present a conceptual model that demonstrates how KCa activity could influence differentiation by regulating Vm and intracellular Ca2+ oscillations. We conclude that KCa channels have significant involvement in MSC differentiation and could potentially enable novel tissue engineering approaches and therapies.
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Affiliation(s)
- Ekaterina Pchelintseva
- Department of Life Sciences, Imperial College London, South Kensington Campus, Neuroscience Solution to Cancer Research Group, London, UK.,Department of Bioengineering, Imperial College London, South Kensington Campus, London, UK
| | - Mustafa B A Djamgoz
- Department of Life Sciences, Imperial College London, South Kensington Campus, Neuroscience Solution to Cancer Research Group, London, UK
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Wilson MZ, Ravindran PT, Lim WA, Toettcher JE. Tracing Information Flow from Erk to Target Gene Induction Reveals Mechanisms of Dynamic and Combinatorial Control. Mol Cell 2017; 67:757-769.e5. [PMID: 28826673 DOI: 10.1016/j.molcel.2017.07.016] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 06/12/2017] [Accepted: 07/13/2017] [Indexed: 10/19/2022]
Abstract
Cell signaling networks coordinate specific patterns of protein expression in response to external cues, yet the logic by which signaling pathway activity determines the eventual abundance of target proteins is complex and poorly understood. Here, we describe an approach for simultaneously controlling the Ras/Erk pathway and monitoring a target gene's transcription and protein accumulation in single live cells. We apply our approach to dissect how Erk activity is decoded by immediate early genes (IEGs). We find that IEG transcription decodes Erk dynamics through a shared band-pass filtering circuit; repeated Erk pulses transcribe IEGs more efficiently than sustained Erk inputs. However, despite highly similar transcriptional responses, each IEG exhibits dramatically different protein-level accumulation, demonstrating a high degree of post-transcriptional regulation by combinations of multiple pathways. Our results demonstrate that the Ras/Erk pathway is decoded by both dynamic filters and logic gates to shape target gene responses in a context-specific manner.
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Affiliation(s)
- Maxwell Z Wilson
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Pavithran T Ravindran
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Wendell A Lim
- Howard Hughes Medical Institute; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jared E Toettcher
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
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Ma G, Wen S, He L, Huang Y, Wang Y, Zhou Y. Optogenetic toolkit for precise control of calcium signaling. Cell Calcium 2017; 64:36-46. [PMID: 28104276 PMCID: PMC5457325 DOI: 10.1016/j.ceca.2017.01.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 01/10/2017] [Accepted: 01/10/2017] [Indexed: 12/19/2022]
Abstract
Calcium acts as a second messenger to regulate a myriad of cell functions, ranging from short-term muscle contraction and cell motility to long-term changes in gene expression and metabolism. To study the impact of Ca2+-modulated 'ON' and 'OFF' reactions in mammalian cells, pharmacological tools and 'caged' compounds are commonly used under various experimental conditions. The use of these reagents for precise control of Ca2+ signals, nonetheless, is impeded by lack of reversibility and specificity. The recently developed optogenetic tools, particularly those built upon engineered Ca2+ release-activated Ca2+ (CRAC) channels, provide exciting opportunities to remotely and non-invasively modulate Ca2+ signaling due to their superior spatiotemporal resolution and rapid reversibility. In this review, we briefly summarize the latest advances in the development of optogenetic tools (collectively termed as 'genetically encoded Ca2+ actuators', or GECAs) that are tailored for the interrogation of Ca2+ signaling, as well as their applications in remote neuromodulation and optogenetic immunomodulation. Our goal is to provide a general guide to choosing appropriate GECAs for optical control of Ca2+ signaling in cellulo, and in parallel, to stimulate further thoughts on evolving non-opsin-based optogenetics into a fully fledged technology for the study of Ca2+-dependent activities in vivo.
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Affiliation(s)
- Guolin Ma
- Center for Translational Cancer Research, Institute of Biosciences and Technology Texas A&M University, Houston, TX 77030, USA
| | - Shufan Wen
- Center for Translational Cancer Research, Institute of Biosciences and Technology Texas A&M University, Houston, TX 77030, USA
| | - Lian He
- Center for Translational Cancer Research, Institute of Biosciences and Technology Texas A&M University, Houston, TX 77030, USA
| | - Yun Huang
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA; Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University, Bryan, TX 77807, USA
| | - Youjun Wang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China.
| | - Yubin Zhou
- Center for Translational Cancer Research, Institute of Biosciences and Technology Texas A&M University, Houston, TX 77030, USA; Department of Medical Physiology, College of Medicine Texas A&M University, Temple, TX 76504, USA, USA.
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Cooper S, Bakal C. Accelerating Live Single-Cell Signalling Studies. Trends Biotechnol 2017; 35:422-433. [PMID: 28161141 DOI: 10.1016/j.tibtech.2017.01.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 12/24/2016] [Accepted: 01/06/2017] [Indexed: 12/21/2022]
Abstract
The dynamics of signalling networks that couple environmental conditions with cellular behaviour can now be characterised in exquisite detail using live single-cell imaging experiments. Recent improvements in our abilities to introduce fluorescent sensors into cells, coupled with advances in pipelines for quantifying and extracting single-cell data, mean that high-throughput systematic analyses of signalling dynamics are becoming possible. In this review, we consider current technologies that are driving progress in the scale and range of such studies. Moreover, we discuss novel approaches that are allowing us to explore how pathways respond to changes in inputs and even predict the fate of a cell based upon its signalling history and state.
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Affiliation(s)
- Sam Cooper
- The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK; Department of Computational Systems Medicine, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK.
| | - Chris Bakal
- The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
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Determining the Limitations and Benefits of Noise in Gene Regulation and Signal Transduction through Single Cell, Microscopy-Based Analysis. J Mol Biol 2017; 429:1143-1154. [PMID: 28288800 DOI: 10.1016/j.jmb.2017.03.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 03/02/2017] [Accepted: 03/06/2017] [Indexed: 12/22/2022]
Abstract
Stochastic fluctuations, termed "noise," in the level of biological molecules can greatly impact cellular functions. While biological noise can sometimes be detrimental, recent studies have provided an increasing number of examples in which biological noise can be functionally beneficial. Rather than provide an exhaustive review of the growing literature in this field, in this review, we focus on single-cell studies based on quantitative microscopy that have generated a deeper understanding of the sources, characteristics, limitations, and benefits of biological noise. Specifically, we highlight studies showing how noise can help coordinate the expression of multiple downstream target genes, impact the channel capacity of signaling networks, and interact synergistically with oscillatory dynamics to enhance the sensitivity of signal processing. We conclude with a discussion of current challenges and future opportunities.
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46
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Bugaj LJ, O'Donoghue GP, Lim WA. Interrogating cellular perception and decision making with optogenetic tools. J Cell Biol 2016; 216:25-28. [PMID: 28003330 PMCID: PMC5223619 DOI: 10.1083/jcb.201612094] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
In this Viewpoint article, Wendell A. Lim and colleagues examine the ways by which optogenetic tools and techniques are being used to query cellular signaling and function. Optogenetics promises to deepen our understanding of how cells perceive and respond to complex and dynamic signals and how this perception regulates normal and abnormal function. In this study, we present our vision for how these nascent tools may transform our view of fundamental cell biological processes.
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Affiliation(s)
- Lukasz J Bugaj
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158
| | - Geoff P O'Donoghue
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158
| | - Wendell A Lim
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158 .,Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158.,Center for Systems and Synthetic Biology, University of California, San Francisco, San Francisco, CA 94158
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Mackay L, Mikolajewicz N, Komarova SV, Khadra A. Systematic Characterization of Dynamic Parameters of Intracellular Calcium Signals. Front Physiol 2016; 7:525. [PMID: 27891096 PMCID: PMC5102910 DOI: 10.3389/fphys.2016.00525] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 10/24/2016] [Indexed: 12/14/2022] Open
Abstract
Dynamic processes, such as intracellular calcium signaling, are hallmark of cellular biology. As real-time imaging modalities become widespread, a need for analytical tools to reliably characterize time-series data without prior knowledge of the nature of the recordings becomes more pressing. The goal of this study is to develop a signal-processing algorithm for MATLAB that autonomously computes the parameters characterizing prominent single transient responses (TR) and/or multi-peaks responses (MPR). The algorithm corrects for signal contamination and decomposes experimental recordings into contributions from drift, TRs, and MPRs. It subsequently provides numerical estimates for the following parameters: time of onset after stimulus application, activation time (time for signal to increase from 10 to 90% of peak), and amplitude of response. It also provides characterization of the (i) TRs by quantifying their area under the curve (AUC), response duration (time between 1/2 amplitude on ascent and descent of the transient), and decay constant of the exponential decay region of the deactivation phase of the response, and (ii) MPRs by quantifying the number of peaks, mean peak magnitude, mean periodicity, standard deviation of periodicity, oscillatory persistence (time between first and last discernable peak), and duty cycle (fraction of period during which system is active) for all the peaks in the signal, as well as coherent oscillations (i.e., deterministic spikes). We demonstrate that the signal detection performance of this algorithm is in agreement with user-mediated detection and that parameter estimates obtained manually and algorithmically are correlated. We then apply this algorithm to study how metabolic acidosis affects purinergic (P2) receptor-mediated calcium signaling in osteoclast precursor cells. Our results reveal that acidosis significantly attenuates the amplitude and AUC calcium responses at high ATP concentrations. Collectively, our data validated this algorithm as a general framework for comprehensively analyzing dynamic time-series.
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Affiliation(s)
- Laurent Mackay
- Department of Physiology, McGill University Montreal, QC, Canada
| | - Nicholas Mikolajewicz
- Faculty of Dentistry, McGill UniversityMontreal, QC, Canada; Shriners Hospital for Children-CanadaMontreal, QC, Canada
| | - Svetlana V Komarova
- Faculty of Dentistry, McGill UniversityMontreal, QC, Canada; Shriners Hospital for Children-CanadaMontreal, QC, Canada
| | - Anmar Khadra
- Department of Physiology, McGill University Montreal, QC, Canada
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48
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An open-hardware platform for optogenetics and photobiology. Sci Rep 2016; 6:35363. [PMID: 27805047 PMCID: PMC5096413 DOI: 10.1038/srep35363] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 09/28/2016] [Indexed: 12/27/2022] Open
Abstract
In optogenetics, researchers use light and genetically encoded photoreceptors to control biological processes with unmatched precision. However, outside of neuroscience, the impact of optogenetics has been limited by a lack of user-friendly, flexible, accessible hardware. Here, we engineer the Light Plate Apparatus (LPA), a device that can deliver two independent 310 to 1550 nm light signals to each well of a 24-well plate with intensity control over three orders of magnitude and millisecond resolution. Signals are programmed using an intuitive web tool named Iris. All components can be purchased for under $400 and the device can be assembled and calibrated by a non-expert in one day. We use the LPA to precisely control gene expression from blue, green, and red light responsive optogenetic tools in bacteria, yeast, and mammalian cells and simplify the entrainment of cyanobacterial circadian rhythm. The LPA dramatically reduces the entry barrier to optogenetics and photobiology experiments.
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Tan P, He L, Han G, Zhou Y. Optogenetic Immunomodulation: Shedding Light on Antitumor Immunity. Trends Biotechnol 2016; 35:215-226. [PMID: 27692897 DOI: 10.1016/j.tibtech.2016.09.002] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 09/02/2016] [Accepted: 09/06/2016] [Indexed: 12/28/2022]
Abstract
Microbial opsin-based optogenetic tools have been transformative for neuroscience. To extend optogenetic approaches to the immune system to remotely control immune responses with superior spatiotemporal precision, pioneering tools have recently been crafted to modulate lymphocyte trafficking, inflammasome activation, dendritic cell (DC) maturation, and antitumor immunity through the photoactivation of engineered chemokine receptors and calcium release-activated calcium channels. We highlight herein some conceptual design strategies for installing light sensitivities into the immune signaling network and, in parallel, we propose potential solutions for in vivo optogenetic applications in living organisms with near-infrared light-responsive upconversion nanomaterials. Moreover, to move beyond proof-of-concept into translational applications, we discuss future prospects for integrating personalized immunoengineering with optogenetics to overcome critical hurdles in cancer immunotherapy.
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Affiliation(s)
- Peng Tan
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, TX 77030, USA
| | - Lian He
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, TX 77030, USA
| | - Gang Han
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
| | - Yubin Zhou
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, TX 77030, USA; Department of Medical Physiology, College of Medicine, Texas A&M University Health Science Center, Temple, TX 76504, USA.
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The Duty of an Intracellular Signal: Illuminating Calcium's Role in Transcriptional Control. Cell Syst 2016; 2:223-4. [PMID: 27135534 DOI: 10.1016/j.cels.2016.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
An optogenetic approach reveals how cells encode external information in complex patterns of protein activity.
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