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Mahlandt EK, Palacios Martínez S, Arts JJG, Tol S, van Buul JD, Goedhart J. Opto-RhoGEFs, an optimized optogenetic toolbox to reversibly control Rho GTPase activity on a global to subcellular scale, enabling precise control over vascular endothelial barrier strength. eLife 2023; 12:RP84364. [PMID: 37449837 PMCID: PMC10393062 DOI: 10.7554/elife.84364] [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] [Indexed: 07/18/2023] Open
Abstract
The inner layer of blood vessels consists of endothelial cells, which form the physical barrier between blood and tissue. This vascular barrier is tightly regulated and is defined by cell-cell contacts through adherens and tight junctions. To investigate the signaling that regulates vascular barrier strength, we focused on Rho GTPases, regulators of the actin cytoskeleton and known to control junction integrity. To manipulate Rho GTPase signaling in a temporal and spatial manner we applied optogenetics. Guanine-nucleotide exchange factor (GEF) domains from ITSN1, TIAM1, and p63RhoGEF, activating Cdc42, Rac, and Rho, respectively, were integrated into the optogenetic recruitment tool improved light-induced dimer (iLID). This tool allows for Rho GTPase activation at the subcellular level in a reversible and non-invasive manner by recruiting a GEF to a specific area at the plasma membrane, The membrane tag of iLID was optimized and a HaloTag was applied to gain more flexibility for multiplex imaging. The resulting optogenetically recruitable RhoGEFs (Opto-RhoGEFs) were tested in an endothelial cell monolayer and demonstrated precise temporal control of vascular barrier strength by a cell-cell overlap-dependent, VE-cadherin-independent, mechanism. Furthermore, Opto-RhoGEFs enabled precise optogenetic control in endothelial cells over morphological features such as cell size, cell roundness, local extension, and cell contraction. In conclusion, we have optimized and applied the optogenetic iLID GEF recruitment tool, that is Opto-RhoGEFs, to study the role of Rho GTPases in the vascular barrier of the endothelium and found that membrane protrusions at the junction region can rapidly increase barrier integrity independent of VE-cadherin.
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Affiliation(s)
- Eike K Mahlandt
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, Amsterdam, Netherlands
| | - Sebastián Palacios Martínez
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, Amsterdam, Netherlands
| | - Janine J G Arts
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, Amsterdam, Netherlands
- Molecular Cell Biology Lab at Dept. Molecular Hematology, Sanquin Research and Landsteiner Laboratory, Amsterdam, Netherlands
| | - Simon Tol
- Molecular Cell Biology Lab at Dept. Molecular Hematology, Sanquin Research and Landsteiner Laboratory, Amsterdam, Netherlands
| | - Jaap D van Buul
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, Amsterdam, Netherlands
- Molecular Cell Biology Lab at Dept. Molecular Hematology, Sanquin Research and Landsteiner Laboratory, Amsterdam, Netherlands
| | - Joachim Goedhart
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, Amsterdam, Netherlands
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2
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Saraswathibhatla A, Indana D, Chaudhuri O. Cell-extracellular matrix mechanotransduction in 3D. Nat Rev Mol Cell Biol 2023; 24:495-516. [PMID: 36849594 PMCID: PMC10656994 DOI: 10.1038/s41580-023-00583-1] [Citation(s) in RCA: 86] [Impact Index Per Article: 86.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2023] [Indexed: 03/01/2023]
Abstract
Mechanical properties of extracellular matrices (ECMs) regulate essential cell behaviours, including differentiation, migration and proliferation, through mechanotransduction. Studies of cell-ECM mechanotransduction have largely focused on cells cultured in 2D, on top of elastic substrates with a range of stiffnesses. However, cells often interact with ECMs in vivo in a 3D context, and cell-ECM interactions and mechanisms of mechanotransduction in 3D can differ from those in 2D. The ECM exhibits various structural features as well as complex mechanical properties. In 3D, mechanical confinement by the surrounding ECM restricts changes in cell volume and cell shape but allows cells to generate force on the matrix by extending protrusions and regulating cell volume as well as through actomyosin-based contractility. Furthermore, cell-matrix interactions are dynamic owing to matrix remodelling. Accordingly, ECM stiffness, viscoelasticity and degradability often play a critical role in regulating cell behaviours in 3D. Mechanisms of 3D mechanotransduction include traditional integrin-mediated pathways that sense mechanical properties and more recently described mechanosensitive ion channel-mediated pathways that sense 3D confinement, with both converging on the nucleus for downstream control of transcription and phenotype. Mechanotransduction is involved in tissues from development to cancer and is being increasingly harnessed towards mechanotherapy. Here we discuss recent progress in our understanding of cell-ECM mechanotransduction in 3D.
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Affiliation(s)
| | - Dhiraj Indana
- Department of Mechanical Engineering, Stanford University, Stanford, CA, USA
| | - Ovijit Chaudhuri
- Department of Mechanical Engineering, Stanford University, Stanford, CA, USA.
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA.
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3
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Mahlandt EK, Kreider-Letterman G, Chertkova AO, Garcia-Mata R, Goedhart J. Cell-based optimization and characterization of genetically encoded location-based biosensors for Cdc42 or Rac activity. J Cell Sci 2023; 136:jcs260802. [PMID: 37226883 PMCID: PMC10234108 DOI: 10.1242/jcs.260802] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 04/13/2023] [Indexed: 05/26/2023] Open
Abstract
Rac (herein referring to the Rac family) and Cdc42 are Rho GTPases that regulate the formation of lamellipoda and filopodia, and are therefore crucial in processes such as cell migration. Relocation-based biosensors for Rac and Cdc42 have not been characterized well in terms of their specificity or affinity. In this study, we identify relocation sensor candidates for both Rac and Cdc42. We compared their (1) ability to bind the constitutively active Rho GTPases, (2) specificity for Rac and Cdc42, and (3) relocation efficiency in cell-based assays. Subsequently, the relocation efficiency was improved by a multi-domain approach. For Rac1, we found a sensor candidate with low relocation efficiency. For Cdc42, we found several sensors with sufficient relocation efficiency and specificity. These optimized sensors enable the wider application of Rho GTPase relocation sensors, which was showcased by the detection of local endogenous Cdc42 activity at assembling invadopodia. Moreover, we tested several fluorescent proteins and HaloTag for their influence on the recruitment efficiency of the Rho location sensor, to find optimal conditions for a multiplexing experiment. This characterization and optimization of relocation sensors will broaden their application and acceptance.
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Affiliation(s)
- Eike K. Mahlandt
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | | | - Anna O. Chertkova
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Rafael Garcia-Mata
- Department of Biological Sciences, University of Toledo, Toledo, OH 43606, USA
| | - Joachim Goedhart
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
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4
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Kunida K, Takagi N, Aoki K, Ikeda K, Nakamura T, Sakumura Y. Decoding cellular deformation from pseudo-simultaneously observed Rho GTPase activities. Cell Rep 2023; 42:112071. [PMID: 36764299 DOI: 10.1016/j.celrep.2023.112071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 10/31/2022] [Accepted: 01/19/2023] [Indexed: 02/11/2023] Open
Abstract
Limitations in simultaneously observing the activity of multiple molecules in live cells prevent researchers from elucidating how these molecules coordinate the dynamic regulation of cellular functions. Here, we propose the motion-triggered average (MTA) algorithm to characterize pseudo-simultaneous dynamic changes in arbitrary cellular deformation and molecular activities. Using MTA, we successfully extract a pseudo-simultaneous time series from individually observed activities of three Rho GTPases: Cdc42, Rac1, and RhoA. To verify that this time series encoded information on cell-edge movement, we use a mathematical regression model to predict the edge velocity from the activities of the three molecules. The model accurately predicts the unknown edge velocity, providing numerical evidence that these Rho GTPases regulate edge movement. Data preprocessing using MTA combined with mathematical regression provides an effective strategy for reusing numerous individual observations of molecular activities.
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Affiliation(s)
- Katsuyuki Kunida
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 8916-5, Japan; School of Medicine, Fujita Health University, Toyoake, Aichi 470-1192, Japan
| | - Nobuhiro Takagi
- Graduate School of Information Science and Technology, Aichi Prefectural University, Nagakute, Aichi 480-1342, Japan
| | - Kazuhiro Aoki
- National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan; Exploratory Research Center on Life and Living Systems (ExCELLS), 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
| | - Kazushi Ikeda
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 8916-5, Japan; Data Science Center, Nara Institute of Science and Technology, Ikoma, Nara 8916-5, Japan; RIKEN Center for Advanced Intelligence Project (RIKEN AIP), Kyoto 619-0288, Japan
| | - Takeshi Nakamura
- Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Chiba 278-0022, Japan
| | - Yuichi Sakumura
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 8916-5, Japan; Data Science Center, Nara Institute of Science and Technology, Ikoma, Nara 8916-5, Japan.
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5
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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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6
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Förster resonance energy transfer biosensors for fluorescence and time-gated luminescence analysis of rac1 activity. Sci Rep 2022; 12:5291. [PMID: 35351946 PMCID: PMC8964680 DOI: 10.1038/s41598-022-09364-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/08/2022] [Indexed: 11/24/2022] Open
Abstract
Genetically encoded, Förster resonance energy transfer (FRET) biosensors enable live-cell optical imaging of signaling molecules. Small conformational changes often limit the dynamic range of biosensors that combine fluorescent proteins (FPs) and sensing domains into a single polypeptide. To address this, we developed FRET and lanthanide-based FRET (LRET) biosensors of Rac1 activation with two key features that enhance sensitivity and dynamic range. For one, alpha helical linker domains separate FRET partners and ensure a large conformational change and FRET increase when activated Rac1 at the biosensor C-terminus interacts with an amino-terminal Rac binding domain. Incorporation of a luminescent Tb(III) complex with long (~ ms) excited state lifetime as a LRET donor enabled time-gated luminescence measurements of Rac1 activity in cell lysates. The LRET dynamic range increased with ER/K linker length up to 1100% and enabled robust detection of Rac1 inhibition in 96-well plates. The ER/K linkers had a less pronounced, but still significant, effect on conventional FRET biosensors (with FP donors and acceptors), and we were able to dynamically image Rac1 activation at cell edges using fluorescence microscopy. The results herein highlight the potential of FRET and LRET biosensors with ER/K linkers for cell-based imaging and screening of protein activities.
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7
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Ebrahimi SB, Samanta D, Kusmierz CD, Mirkin CA. Protein transfection via spherical nucleic acids. Nat Protoc 2022; 17:327-357. [PMID: 35039669 DOI: 10.1038/s41596-021-00642-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 10/01/2021] [Indexed: 01/01/2023]
Abstract
The efficient transfection of functional proteins into cells can serve as a means for regulating cellular processes toward solving fundamental challenges in biology and medicine. However, the use of proteins as effective intracellular agents is hindered by their low cellular uptake and susceptibility to degradation. Over the past 15 years, our group has been developing spherical nucleic acids (SNAs), nanoparticles functionalized with a dense radially oriented shell of nucleic acids. These structures actively enter cells and have opened new frontiers in chemical sensing, biodiagnostics and therapeutics. Recently, we have shown that proteins can be used as structurally precise and homogeneous nanoparticle cores in SNAs. The resultant protein SNAs (ProSNAs) allow previously cell-impermeable proteins to actively enter cells, exhibit high degrees of stability and activity both in cell culture and in vivo, and show enhanced pharmacokinetics. Consequently, these modular structures constitute a plug-and-play platform in which the protein core and nucleic acid shell can be independently varied to achieve a desired function. Here, we describe the synthesis of ProSNAs through the chemical modification of solvent-accessible surface residues (3-5 d). We also discuss design considerations, strategies for characterization, and applications of ProSNAs in cellular transfection, biological sensing and functional enzyme delivery in vivo.
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Affiliation(s)
- Sasha B Ebrahimi
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- International Institute for Nanotechnology, Northwestern University, Evanston, IL, USA
| | - Devleena Samanta
- International Institute for Nanotechnology, Northwestern University, Evanston, IL, USA
- Department of Chemistry, Northwestern University, Evanston, IL, USA
| | - Caroline D Kusmierz
- International Institute for Nanotechnology, Northwestern University, Evanston, IL, USA
- Department of Chemistry, Northwestern University, Evanston, IL, USA
| | - Chad A Mirkin
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA.
- International Institute for Nanotechnology, Northwestern University, Evanston, IL, USA.
- Department of Chemistry, Northwestern University, Evanston, IL, USA.
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8
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Baker MJ, Kazanietz MG. The anti-Rac1-GTP antibody and the detection of active Rac1: a tool with a fundamental flaw. Small GTPases 2022; 13:136-140. [PMID: 33910489 PMCID: PMC9707529 DOI: 10.1080/21541248.2021.1920824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Rac1 is a member of the Rho GTPase family and is involved in many cellular processes, particularly the formation of actin-rich membrane protrusions, such as lamellipodia and ruffles. With such a widely studied protein, it is essential that the research community has reliable tools for detecting Rac1 activation both in cellular models and tissues. Using a series of cancer cellular models, we recently demonstrated that a widely used antibody for visualizing active Rac1 (Rac1-GTP) does not recognize Rac1 but instead recognizes vimentin filaments (Baker MJ, J. Biol. Chem. 295:13698-13710, 2020). We believe that this tool has misled the field and impose on the GTPase research community the need to validate published results using this antibody as well as to continue the development of new resources to visualize endogenous active Rac1.
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Affiliation(s)
- Martin J. Baker
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Marcelo G. Kazanietz
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA,CONTACT Marcelo G. Kazanietz Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, 1256 Biomedical Research Building II/III, 421 Curie Blvd., Philadelphia, PA19104-6160, USA
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9
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Yang JM, Chi WY, Liang J, Takayanagi S, Iglesias PA, Huang CH. Deciphering cell signaling networks with massively multiplexed biosensor barcoding. Cell 2021; 184:6193-6206.e14. [PMID: 34838160 PMCID: PMC8686192 DOI: 10.1016/j.cell.2021.11.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 09/27/2021] [Accepted: 11/03/2021] [Indexed: 12/27/2022]
Abstract
Genetically encoded fluorescent biosensors are powerful tools for monitoring biochemical activities in live cells, but their multiplexing capacity is limited by the available spectral space. We overcome this problem by developing a set of barcoding proteins that can generate over 100 barcodes and are spectrally separable from commonly used biosensors. Mixtures of barcoded cells expressing different biosensors are simultaneously imaged and analyzed by deep learning models to achieve massively multiplexed tracking of signaling events. Importantly, different biosensors in cell mixtures show highly coordinated activities, thus facilitating the delineation of their temporal relationship. Simultaneous tracking of multiple biosensors in the receptor tyrosine kinase signaling network reveals distinct mechanisms of effector adaptation, cell autonomous and non-autonomous effects of KRAS mutations, as well as complex interactions in the network. Biosensor barcoding presents a scalable method to expand multiplexing capabilities for deciphering the complexity of signaling networks and their interactions between cells.
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Affiliation(s)
- Jr-Ming Yang
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD 21205, USA.
| | - Wei-Yu Chi
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD 21205, USA
| | - Jessica Liang
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Saki Takayanagi
- XDBio Graduate Program, Johns Hopkins School of Medicine, MD 21205, USA
| | - Pablo A Iglesias
- Department of Electrical and Computer Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Chuan-Hsiang Huang
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD 21205, USA.
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10
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Kierzek M, Deal PE, Miller EW, Mukherjee S, Wachten D, Baumann A, Kaupp UB, Strünker T, Brenker C. Simultaneous recording of multiple cellular signaling events by frequency- and spectrally-tuned multiplexing of fluorescent probes. eLife 2021; 10:e63129. [PMID: 34859780 PMCID: PMC8700268 DOI: 10.7554/elife.63129] [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: 09/15/2020] [Accepted: 12/01/2021] [Indexed: 12/21/2022] Open
Abstract
Fluorescent probes that change their spectral properties upon binding to small biomolecules, ions, or changes in the membrane potential (Vm) are invaluable tools to study cellular signaling pathways. Here, we introduce a novel technique for simultaneous recording of multiple probes at millisecond time resolution: frequency- and spectrally-tuned multiplexing (FASTM). Different from present multiplexing approaches, FASTM uses phase-sensitive signal detection, which renders various combinations of common probes for Vm and ions accessible for multiplexing. Using kinetic stopped-flow fluorimetry, we show that FASTM allows simultaneous recording of rapid changes in Ca2+, pH, Na+, and Vm with high sensitivity and minimal crosstalk. FASTM is also suited for multiplexing using single-cell microscopy and genetically encoded FRET biosensors. Moreover, FASTM is compatible with optochemical tools to study signaling using light. Finally, we show that the exceptional time resolution of FASTM also allows resolving rapid chemical reactions. Altogether, FASTM opens new opportunities for interrogating cellular signaling.
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Affiliation(s)
- Michelina Kierzek
- Centre of Reproductive Medicine and Andrology, University of MünsterMünsterGermany
- CiM-IMPRS Graduate School, University of MünsterMünsterGermany
| | - Parker E Deal
- Department of Chemistry, University of California, BerkeleyBerkeleyUnited States
| | - Evan W Miller
- Department of Chemistry, University of California, BerkeleyBerkeleyUnited States
- Department of Molecular & Cell Biology, University of California, BerkeleyBerkeleyUnited States
- Helen Wills Neuroscience Institute, University of California, BerkeleyBerkeleyUnited States
| | - Shatanik Mukherjee
- Molecular Sensory Systems, Center of Advanced European Studies and ResearchBonnGermany
| | - Dagmar Wachten
- Institute of Innate Immunity, Department of Biophysical Imaging, Medical Faculty, University of BonnBonnGermany
| | - Arnd Baumann
- Institute of Biological Information Processing (IBI-1), Research Center JülichJülichGermany
| | - U Benjamin Kaupp
- Life & Medical Sciences Institute (LIMES), University of BonnBonnGermany
| | - Timo Strünker
- Centre of Reproductive Medicine and Andrology, University of MünsterMünsterGermany
- Cells in Motion Interfaculty Centre, University of MünsterMünsterGermany
| | - Christoph Brenker
- Centre of Reproductive Medicine and Andrology, University of MünsterMünsterGermany
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11
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Secilmis M, Altun HY, Pilic J, Erdogan YC, Cokluk Z, Ata BN, Sevimli G, Zaki AG, Yigit EN, Öztürk G, Malli R, Eroglu E. A Co-Culture-Based Multiparametric Imaging Technique to Dissect Local H 2O 2 Signals with Targeted HyPer7. BIOSENSORS 2021; 11:338. [PMID: 34562927 PMCID: PMC8466187 DOI: 10.3390/bios11090338] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/09/2021] [Accepted: 09/10/2021] [Indexed: 01/19/2023]
Abstract
Multispectral live-cell imaging is an informative approach that permits detecting biological processes simultaneously in the spatial and temporal domain by exploiting spectrally distinct biosensors. However, the combination of fluorescent biosensors with distinct spectral properties such as different sensitivities, and dynamic ranges can undermine accurate co-imaging of the same analyte in different subcellular locales. We advanced a single-color multiparametric imaging method, which allows simultaneous detection of hydrogen peroxide (H2O2) in multiple cell locales (nucleus, cytosol, mitochondria) using the H2O2 biosensor HyPer7. Co-culturing of endothelial cells stably expressing differentially targeted HyPer7 biosensors paved the way for co-imaging compartmentalized H2O2 signals simultaneously in neighboring cells in a single experimental setup. We termed this approach COMPARE IT, which is an acronym for co-culture-based multiparametric imaging technique. Employing this approach, we detected lower H2O2 levels in mitochondria of endothelial cells compared to the cell nucleus and cytosol under basal conditions. Upon administering exogenous H2O2, the cytosolic and nuclear-targeted probes displayed similarly slow and moderate HyPer7 responses, whereas the mitochondria-targeted HyPer7 signal plateaued faster and reached higher amplitudes. Our results indicate striking differences in mitochondrial H2O2 accumulation of endothelial cells. Here, we present the method's potential as a practicable and informative multiparametric live-cell imaging technique.
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Affiliation(s)
- Melike Secilmis
- Molecular Biology, Genetics and Bioengineering Program, Sabanci University, 34956 Istanbul, Turkey; (M.S.); (H.Y.A.); (Y.C.E.); (Z.C.); (B.N.A.); (G.S.); (A.G.Z.)
| | - Hamza Yusuf Altun
- Molecular Biology, Genetics and Bioengineering Program, Sabanci University, 34956 Istanbul, Turkey; (M.S.); (H.Y.A.); (Y.C.E.); (Z.C.); (B.N.A.); (G.S.); (A.G.Z.)
| | - Johannes Pilic
- Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, 8036 Graz, Austria;
| | - Yusuf Ceyhun Erdogan
- Molecular Biology, Genetics and Bioengineering Program, Sabanci University, 34956 Istanbul, Turkey; (M.S.); (H.Y.A.); (Y.C.E.); (Z.C.); (B.N.A.); (G.S.); (A.G.Z.)
- Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, 8036 Graz, Austria;
| | - Zeynep Cokluk
- Molecular Biology, Genetics and Bioengineering Program, Sabanci University, 34956 Istanbul, Turkey; (M.S.); (H.Y.A.); (Y.C.E.); (Z.C.); (B.N.A.); (G.S.); (A.G.Z.)
| | - Busra Nur Ata
- Molecular Biology, Genetics and Bioengineering Program, Sabanci University, 34956 Istanbul, Turkey; (M.S.); (H.Y.A.); (Y.C.E.); (Z.C.); (B.N.A.); (G.S.); (A.G.Z.)
| | - Gulsah Sevimli
- Molecular Biology, Genetics and Bioengineering Program, Sabanci University, 34956 Istanbul, Turkey; (M.S.); (H.Y.A.); (Y.C.E.); (Z.C.); (B.N.A.); (G.S.); (A.G.Z.)
| | - Asal Ghaffari Zaki
- Molecular Biology, Genetics and Bioengineering Program, Sabanci University, 34956 Istanbul, Turkey; (M.S.); (H.Y.A.); (Y.C.E.); (Z.C.); (B.N.A.); (G.S.); (A.G.Z.)
| | - Esra Nur Yigit
- Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, 34810 Istanbul, Turkey; (E.N.Y.); (G.Ö.)
- Department of Biotechnology, Gebze Technical University, 41400 Kocaeli, Turkey
| | - Gürkan Öztürk
- Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, 34810 Istanbul, Turkey; (E.N.Y.); (G.Ö.)
- Physiology Department, International School of Medicine, Istanbul Medipol University, 34810 Istanbul, Turkey
| | - Roland Malli
- Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, 8036 Graz, Austria;
- BioTechMed Graz, Mozartgasse 12/II, 8010 Graz, Austria
| | - Emrah Eroglu
- Molecular Biology, Genetics and Bioengineering Program, Sabanci University, 34956 Istanbul, Turkey; (M.S.); (H.Y.A.); (Y.C.E.); (Z.C.); (B.N.A.); (G.S.); (A.G.Z.)
- Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, 8036 Graz, Austria;
- Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, 34810 Istanbul, Turkey; (E.N.Y.); (G.Ö.)
- Nanotechnology Research and Application Center, Sabanci University, 34956 Istanbul, Turkey
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12
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Yoshii T, Oki C, Watahiki R, Nakamura A, Tahara K, Kuwata K, Furuta T, Tsukiji S. Chemo-optogenetic Protein Translocation System Using a Photoactivatable Self-Localizing Ligand. ACS Chem Biol 2021; 16:1557-1565. [PMID: 34339163 DOI: 10.1021/acschembio.1c00416] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Manipulating subcellular protein localization using light is a powerful approach for controlling signaling processes with high spatiotemporal precision. The most widely used strategy for this is based on light-induced protein heterodimerization. The use of small synthetic molecules that can control the localization of target proteins in response to light without the need for a second protein has several advantages. However, such methods have not been well established. Herein, we present a chemo-optogenetic approach for controlling protein localization using a photoactivatable self-localizing ligand (paSL). We developed a paSL that can recruit tag-fused proteins of interest from the cytoplasm to the plasma membrane within seconds upon light illumination. This paSL-induced protein translocation (paSLIPT) is reversible and enables the spatiotemporal control of signaling processes in living cells, even in a local region. paSLIPT can also be used to implement simultaneous optical stimulation and multiplexed imaging of molecular processes in a single cell, offering an attractive and novel chemo-optogenetic platform for interrogating and engineering dynamic cellular functions.
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Affiliation(s)
- Tatsuyuki Yoshii
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho,
Showa-ku, Nagoya 466-8555, Japan
- PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Choji Oki
- Department of Nanopharmaceutical Sciences, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Rei Watahiki
- Department of Biomolecular Science, Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi 274-8510, Japan
| | - Akinobu Nakamura
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho,
Showa-ku, Nagoya 466-8555, Japan
| | - Kai Tahara
- Department of Nanopharmaceutical Sciences, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Toshiaki Furuta
- Department of Biomolecular Science, Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi 274-8510, Japan
| | - Shinya Tsukiji
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho,
Showa-ku, Nagoya 466-8555, Japan
- Department of Nanopharmaceutical Sciences, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
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13
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Habif M, Corbat AA, Silberberg M, Grecco HE. CASPAM: A Triple-Modality Biosensor for Multiplexed Imaging of Caspase Network Activity. ACS Sens 2021; 6:2642-2653. [PMID: 34191492 DOI: 10.1021/acssensors.1c00554] [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] [Indexed: 01/20/2023]
Abstract
Understanding signal propagation across biological networks requires to simultaneously monitor the dynamics of several nodes to uncover correlations masked by inherent intercellular variability. To monitor the enzymatic activity of more than two components over short time scales has proven challenging. Exploiting the narrow spectral width of homo-FRET-based biosensors, up to three activities can be imaged through fluorescence polarization anisotropy microscopy. We introduce Caspase Activity Sensor by Polarization Anisotropy Multiplexing (CASPAM) a single-plasmid triple-modality reporter of key nodes of the apoptotic network. Apoptosis provides an ideal molecular framework to study interactions between its three composing pathways (intrinsic, extrinsic, and effector). We characterized the biosensor performance and demonstrated the advantages that equimolar expression has in both simplifying experimental procedure and reducing observable variation, thus enabling robust data-driven modeling. Tools like CASPAM become essential to analyze molecular pathways where multiple nodes need to be simultaneously monitored.
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Affiliation(s)
- Martín Habif
- Department of Physics, FCEN, University of Buenos Aires and IFIBA, CONICET, Buenos Aires C1428EHA, Argentina
| | - Agustín A. Corbat
- Department of Physics, FCEN, University of Buenos Aires and IFIBA, CONICET, Buenos Aires C1428EHA, Argentina
| | - Mauro Silberberg
- Department of Physics, FCEN, University of Buenos Aires and IFIBA, CONICET, Buenos Aires C1428EHA, Argentina
| | - Hernán E. Grecco
- Department of Physics, FCEN, University of Buenos Aires and IFIBA, CONICET, Buenos Aires C1428EHA, Argentina
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund 44227, Germany
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14
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Pham H, Miller LW. Lanthanide-based resonance energy transfer biosensors for live-cell applications. Methods Enzymol 2021; 651:291-311. [PMID: 33888207 DOI: 10.1016/bs.mie.2021.01.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Lanthanide-based, Förster resonance energy transfer (LRET) biosensors enable sensitive, time-gated luminescence (TGL) imaging or multiwell plate analysis of protein-protein interactions (PPIs) in living mammalian cells. LRET biosensors are polypeptides that consist of an alpha-helical linker sequence sandwiched between a lanthanide complex-binding domain and a fluorescent protein (FP) with two interacting domains residing at each terminus. Interaction between the terminal affinity domains brings the lanthanide complex and FP in close proximity such that lanthanide-to-FP, LRET-sensitized emission is increased. A recent proof-of-concept study examined model biosensors that incorporated the affinity partners FKBP12 and the rapamycin-binding domain of m-Tor (FRB) as well as p53 (1-92) and HDM2 (1-128). The sensors contained an Escherichia coli dihydrofolate reductase (eDHFR) domain that binds with high selectivity and affinity to Tb(III) complexes coupled to the ligand trimethoprim (TMP). When cell lines that stably expressed the sensors were treated with TMP-Tb(III), TGL microscopy revealed dramatic differences (>500%) in donor- or acceptor-denominated, Tb(III)-to-GFP LRET ratios between open (unbound) and closed (bound) states of the biosensors. Much larger signal changes (>2500%) and Z'-factors of 0.5 or more were observed when cells were grown in 96-well or 384-well plates and analyzed using a TGL plate reader. In this chapter, we elaborate on the design and performance of LRET biosensors and provide detailed protocols to guide their use for live-cell microscopic imaging studies and high-throughput library screening.
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Affiliation(s)
- Ha Pham
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, United States
| | - Lawrence W Miller
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, United States.
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15
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Chen T, Pham H, Mohamadi A, Miller LW. Single-Chain Lanthanide Luminescence Biosensors for Cell-Based Imaging and Screening of Protein-Protein Interactions. iScience 2020; 23:101533. [PMID: 33083762 PMCID: PMC7509216 DOI: 10.1016/j.isci.2020.101533] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 08/23/2020] [Accepted: 09/02/2020] [Indexed: 11/27/2022] Open
Abstract
Lanthanide-based, Förster resonance energy transfer (LRET) biosensors enabled sensitive, time-gated luminescence (TGL) imaging or multiwell plate analysis of protein-protein interactions (PPIs) in living cells. We prepared stable cell lines that expressed polypeptides composed of an alpha helical linker flanked by a Tb(III) complex-binding domain, GFP, and two interacting domains at each terminus. The PPIs examined included those between FKBP12 and the rapamycin-binding domain of m-Tor (FRB) and between p53 (1–92) and HDM2 (1–128). TGL microscopy revealed dramatic differences (>500%) in donor- or acceptor-denominated, Tb(III)-to-GFP LRET ratios between open (unbound) and closed (bound) states of the biosensors. We observed much larger signal changes (>2,500%) and Z′-factors of 0.5 or more when we grew cells in 96- or 384-well plates and analyzed PPI changes using a TGL plate reader. The modular design and exceptional dynamic range of lanthanide-based LRET biosensors will facilitate versatile imaging and cell-based screening of PPIs. Non-invasive, microscopic imaging or screening of protein-protein interactions Intracellular assembly of sensor polypeptides with luminescent Tb(III) complexes High dynamic range with time-gated detection of Tb(III)-to-GFP sensitized emission
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Affiliation(s)
- Ting Chen
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA
| | - Ha Pham
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA
| | - Ali Mohamadi
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA
| | - Lawrence W. Miller
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA
- Corresponding author
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16
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Baker MJ, Cooke M, Kreider-Letterman G, Garcia-Mata R, Janmey PA, Kazanietz MG. Evaluation of active Rac1 levels in cancer cells: A case of misleading conclusions from immunofluorescence analysis. J Biol Chem 2020; 295:13698-13710. [PMID: 32817335 DOI: 10.1074/jbc.ra120.013919] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 07/23/2020] [Indexed: 12/16/2022] Open
Abstract
A large number of aggressive cancer cell lines display elevated levels of activated Rac1, a small GTPase widely implicated in cytoskeleton reorganization, cell motility, and metastatic dissemination. A commonly accepted methodological approach for detecting Rac1 activation in cancer cells involves the use of a conformation-sensitive antibody that detects the active (GTP-bound) Rac1 without interacting with the GDP-bound inactive form. This antibody has been extensively used in fixed cell immunofluorescence and immunohistochemistry. Taking advantage of prostate and pancreatic cancer cell models known to have high basal Rac1-GTP levels, here we have established that this antibody does not recognize Rac1 but rather detects the intermediate filament protein vimentin. Indeed, Rac1-null PC3 prostate cancer cells or cancer models with low levels of Rac1 activation still show a high signal with the anti-Rac1-GTP antibody, which is lost upon silencing of vimentin expression. Moreover, this antibody was unable to detect activated Rac1 in membrane ruffles induced by epidermal growth factor stimulation. These results have profound implications for the study of this key GTPase in cancer, particularly because a large number of cancer cell lines with characteristic mesenchymal features show simultaneous up-regulation of vimentin and high basal Rac1-GTP levels when measured biochemically. This misleading correlation can lead to assumptions about the validity of this antibody and inaccurate conclusions that may affect the development of appropriate therapeutic approaches for targeting the Rac1 pathway.
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Affiliation(s)
- Martin J Baker
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
| | - Mariana Cooke
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Department of Medicine, Einstein Medical Center Philadelphia, Philadelphia, Pennsylvania, USA
| | | | | | - Paul A Janmey
- Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Marcelo G Kazanietz
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
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17
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Mogilner A, Barnhart EL, Keren K. Experiment, theory, and the keratocyte: An ode to a simple model for cell motility. Semin Cell Dev Biol 2020; 100:143-151. [DOI: 10.1016/j.semcdb.2019.10.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/27/2019] [Accepted: 10/31/2019] [Indexed: 01/20/2023]
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18
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Salazar-Cavazos E, Nitta CF, Mitra ED, Wilson BS, Lidke KA, Hlavacek WS, Lidke DS. Multisite EGFR phosphorylation is regulated by adaptor protein abundances and dimer lifetimes. Mol Biol Cell 2020; 31:695-708. [PMID: 31913761 PMCID: PMC7202077 DOI: 10.1091/mbc.e19-09-0548] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Differential epidermal growth factor receptor (EGFR) phosphorylation is thought to couple receptor activation to distinct signaling pathways. However, the molecular mechanisms responsible for biased signaling are unresolved due to a lack of insight into the phosphorylation patterns of full-length EGFR. We extended a single-molecule pull-down technique previously used to study protein-protein interactions to allow for robust measurement of receptor phosphorylation. We found that EGFR is predominantly phosphorylated at multiple sites, yet phosphorylation at specific tyrosines is variable and only a subset of receptors share phosphorylation at the same site, even with saturating ligand concentrations. We found distinct populations of receptors as soon as 1 min after ligand stimulation, indicating early diversification of function. To understand this heterogeneity, we developed a mathematical model. The model predicted that variations in phosphorylation are dependent on the abundances of signaling partners, while phosphorylation levels are dependent on dimer lifetimes. The predictions were confirmed in studies of cell lines with different expression levels of signaling partners, and in experiments comparing low- and high-affinity ligands and oncogenic EGFR mutants. These results reveal how ligand-regulated receptor dimerization dynamics and adaptor protein concentrations play critical roles in EGFR signaling.
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Affiliation(s)
| | | | - Eshan D Mitra
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545
| | | | - Keith A Lidke
- Comprehensive Cancer Center, and.,Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM 87131
| | - William S Hlavacek
- Comprehensive Cancer Center, and.,Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Diane S Lidke
- Department of Pathology.,Comprehensive Cancer Center, and
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19
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Shu X. Imaging dynamic cell signaling in vivo with new classes of fluorescent reporters. Curr Opin Chem Biol 2019; 54:1-9. [PMID: 31678813 DOI: 10.1016/j.cbpa.2019.09.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/08/2019] [Accepted: 09/19/2019] [Indexed: 12/27/2022]
Abstract
Dynamical features of cell signaling are the essence of living organisms. To understand animal development, it is fundamental to investigate signaling dynamics in vivo. Robust reporters are required to visualize spatial and temporal dynamics of enzyme activities and protein-protein interactions involved in signaling pathways. In this review, we summarize recent development in the design of new classes of fluorescent reporters for imaging dynamic activities of proteases, kinases, and protein-protein interactions. These reporters operate on new physical and/or chemical principles; achieve large dynamic range, high brightness, and fast kinetics; and reveal spatiotemporal dynamics of signaling that is correlated with developmental events such as embryonic morphogenesis in live animals including Drosophila and zebrafish. Therefore, many of these reporters are great tools for biological discovery and mechanistic understanding of animal development and disease progression.
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Affiliation(s)
- Xiaokun Shu
- Department of Pharmaceutical Chemistry, University of California - San Francisco, San Francisco, CA, United States; Cardiovascular Research Institute, University of California - San Francisco, San Francisco, CA, United States.
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20
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Senoo H, Kamimura Y, Kimura R, Nakajima A, Sawai S, Sesaki H, Iijima M. Phosphorylated Rho-GDP directly activates mTORC2 kinase towards AKT through dimerization with Ras-GTP to regulate cell migration. Nat Cell Biol 2019; 21:867-878. [PMID: 31263268 PMCID: PMC6650273 DOI: 10.1038/s41556-019-0348-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 05/29/2019] [Indexed: 11/19/2022]
Abstract
mTORC2 plays critical roles in metabolism, cell survival and actin cytoskeletal dynamics through the phosphorylation of AKT. Despite its importance to biology and medicine, it is unclear how mTORC2-mediated AKT phosphorylation is controlled. Here, we identify an unforeseen principle by which a GDP-bound form of the conserved small G protein Rho GTPase directly activates mTORC2 in AKT phosphorylation in social amoebae (Dictyostelium discoideum) cells. Using biochemical reconstitution with purified proteins, we demonstrate that Rho-GDP promotes AKT phosphorylation by assembling a supercomplex with Ras-GTP and mTORC2. This supercomplex formation is controlled by the chemoattractant-induced phosphorylation of Rho-GDP at S192 by GSK-3. Furthermore, Rho-GDP rescues defects in both mTORC2-mediated AKT phosphorylation and directed cell migration in Rho-null cells in a manner dependent on phosphorylation of S192. Thus, in contrast to the prevailing view that the GDP-bound forms of G proteins are inactive, our study reveals that mTORC2-AKT signalling is activated by Rho-GDP.
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Affiliation(s)
- Hiroshi Senoo
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Yoichiro Kamimura
- Laboratory for Cell Signaling Dynamics, Quantitative Biology Center, RIKEN, Suita, Japan
| | - Reona Kimura
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Akihiko Nakajima
- Department of Basic Science, Graduate School of Arts and Sciences, University of Tokyo, Tokyo, Japan
| | - Satoshi Sawai
- Department of Basic Science, Graduate School of Arts and Sciences, University of Tokyo, Tokyo, Japan
| | - Hiromi Sesaki
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Miho Iijima
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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21
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MacNevin CJ, Watanabe T, Weitzman M, Gulyani A, Fuehrer S, Pinkin NK, Tian X, Liu F, Jin J, Hahn KM. Membrane-Permeant, Environment-Sensitive Dyes Generate Biosensors within Living Cells. J Am Chem Soc 2019; 141:7275-7282. [PMID: 30994345 DOI: 10.1021/jacs.8b09841] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Dyes with environment-sensitive fluorescence have proven useful to study the spatiotemporal dynamics of protein activity in living cells. When attached to proteins, their fluorescence can reflect protein conformational changes, post-translational modifications, or protein interactions. However, the utility of such dye-protein conjugates has been limited because it is difficult to load them into cells. They usually must be introduced using techniques that perturb cell physiology, limit throughput, or generate fluorescent vesicles (e.g., electroporation, microinjection, or membrane transduction peptides). Here we circumvent these problems by modifying a proven, environment-sensitive biosensor fluorophore so that it can pass through cell membranes without staining intracellular compartments and can be attached to proteins within living cells using unnatural amino acid (UAA) mutagenesis. Reactive groups were incorporated for attachment to UAAs or small molecules (mero166, azide; mero167, alkyne; mero76, carboxylic acid). These dyes are bright and fluoresce at long wavelengths (reaching ε = 100 000 M-1 cm-1, ϕ = 0.24, with excitation 565 nm and emission 594 nm). The utility of mero166 was demonstrated by in-cell labeling of a UAA to generate a biosensor for the small GTPase Cdc42. In addition, conjugation of mero166 to a small molecule produced a membrane-permeable probe that reported the localization of the DNA methyltransferase G9a in cells. This approach provides a strategy to access biosensors for many targets and to more practically harness the varied environmental sensitivities of synthetic dyes.
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Affiliation(s)
- Christopher J MacNevin
- Department of Pharmacology, School of Medicine , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Takashi Watanabe
- Department of Pharmacology, School of Medicine , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Matthew Weitzman
- Department of Pharmacology, School of Medicine , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Akash Gulyani
- Department of Pharmacology, School of Medicine , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Sheryl Fuehrer
- Department of Pharmacology, School of Medicine , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Nicholas K Pinkin
- Department of Pharmacology, School of Medicine , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Xu Tian
- Department of Pharmacology, School of Medicine , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Feng Liu
- Center for Integrative Chemical Biology and Drug Discovery, School of Pharmacy , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Jian Jin
- Center for Integrative Chemical Biology and Drug Discovery, School of Pharmacy , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Klaus M Hahn
- Department of Pharmacology, School of Medicine , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
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22
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Intensiometric biosensors visualize the activity of multiple small GTPases in vivo. Nat Commun 2019; 10:211. [PMID: 30643148 PMCID: PMC6331645 DOI: 10.1038/s41467-018-08217-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 12/22/2018] [Indexed: 01/21/2023] Open
Abstract
Ras and Rho small GTPases are critical for numerous cellular processes including cell division, migration, and intercellular communication. Despite extensive efforts to visualize the spatiotemporal activity of these proteins, achieving the sensitivity and dynamic range necessary for in vivo application has been challenging. Here, we present highly sensitive intensiometric small GTPase biosensors visualizing the activity of multiple small GTPases in single cells in vivo. Red-shifted sensors combined with blue light-controllable optogenetic modules achieved simultaneous monitoring and manipulation of protein activities in a highly spatiotemporal manner. Our biosensors revealed spatial dynamics of Cdc42 and Ras activities upon structural plasticity of single dendritic spines, as well as a broad range of subcellular Ras activities in the brains of freely behaving mice. Thus, these intensiometric small GTPase sensors enable the spatiotemporal dissection of complex protein signaling networks in live animals. FRET sensors hardly achieve visualization of spatiotemporal dynamics of protein activity in vivo. Here the authors present intensiometric small GTPase biosensors based on dimerization-dependent fluorescent proteins that enable monitoring of activity of small GTPases in the brains of behaving mice at a single spine resolution.
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23
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Greenwald EC, Mehta S, Zhang J. Genetically Encoded Fluorescent Biosensors Illuminate the Spatiotemporal Regulation of Signaling Networks. Chem Rev 2018; 118:11707-11794. [PMID: 30550275 PMCID: PMC7462118 DOI: 10.1021/acs.chemrev.8b00333] [Citation(s) in RCA: 302] [Impact Index Per Article: 50.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cellular signaling networks are the foundation which determines the fate and function of cells as they respond to various cues and stimuli. The discovery of fluorescent proteins over 25 years ago enabled the development of a diverse array of genetically encodable fluorescent biosensors that are capable of measuring the spatiotemporal dynamics of signal transduction pathways in live cells. In an effort to encapsulate the breadth over which fluorescent biosensors have expanded, we endeavored to assemble a comprehensive list of published engineered biosensors, and we discuss many of the molecular designs utilized in their development. Then, we review how the high temporal and spatial resolution afforded by fluorescent biosensors has aided our understanding of the spatiotemporal regulation of signaling networks at the cellular and subcellular level. Finally, we highlight some emerging areas of research in both biosensor design and applications that are on the forefront of biosensor development.
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Affiliation(s)
- Eric C Greenwald
- University of California , San Diego, 9500 Gilman Drive, BRFII , La Jolla , CA 92093-0702 , United States
| | - Sohum Mehta
- University of California , San Diego, 9500 Gilman Drive, BRFII , La Jolla , CA 92093-0702 , United States
| | - Jin Zhang
- University of California , San Diego, 9500 Gilman Drive, BRFII , La Jolla , CA 92093-0702 , United States
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24
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Kim J, Heo WD. Synergistic Ensemble of Optogenetic Actuators and Dynamic Indicators in Cell Biology. Mol Cells 2018; 41:809-817. [PMID: 30157546 PMCID: PMC6182222 DOI: 10.14348/molcells.2018.0295] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 08/07/2018] [Indexed: 12/13/2022] Open
Abstract
Discovery of the naturally evolved fluorescent proteins and their genetically engineered biosensors have enormously contributed to current bioimaging techniques. These reporters to trace dynamic changes of intracellular protein activities have continuously transformed according to the various demands in biological studies. Along with that, light-inducible optogenetic technologies have offered scientists to perturb, control and analyze the function of intracellular machineries in spatiotemporal manner. In this review, we present an overview of the molecular strategies that have been exploited for producing genetically encoded protein reporters and various optogenetic modules. Finally, in particular, we discuss the current efforts for combined use of these reporters and optogenetic modules as a powerful tactic for the control and imaging of signaling events in cells and tissues.
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Affiliation(s)
- Jihoon Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141,
Korea
| | - Won Do Heo
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141,
Korea
- Center for Cognition and Sociality, Institute for Basic Science (IBS), Daejeon 34141,
Korea
- KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141,
Korea
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25
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Co-imaging extrinsic, intrinsic and effector caspase activity by fluorescence anisotropy microscopy. Redox Biol 2018; 19:210-217. [PMID: 30176560 PMCID: PMC6120609 DOI: 10.1016/j.redox.2018.07.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 07/23/2018] [Accepted: 07/31/2018] [Indexed: 01/08/2023] Open
Abstract
In order to overcome intercellular variability and thereby effectively assess signal propagation in biological networks it is imperative to simultaneously quantify multiple biological observables in single living cells. While fluorescent biosensors have been the tool of choice to monitor the dynamics of protein interaction and enzymatic activity, co-measuring more than two of them has proven challenging. In this work, we designed three spectrally separated anisotropy-based Förster Resonant Energy Transfer (FRET) biosensors to overcome this difficulty. We demonstrate this principle by monitoring the activation of extrinsic, intrinsic and effector caspases upon apoptotic stimulus. Together with modelling and simulations we show that time of maximum activity for each caspase can be derived from the anisotropy of the corresponding biosensor. Such measurements correlate relative activation times and refine existing models of biological signalling networks, providing valuable insight into signal propagation.
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26
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Alexandrov Y, Nikolic DS, Dunsby C, French PMW. Quantitative time domain analysis of lifetime-based Förster resonant energy transfer measurements with fluorescent proteins: Static random isotropic fluorophore orientation distributions. JOURNAL OF BIOPHOTONICS 2018; 11:e201700366. [PMID: 29582566 DOI: 10.1002/jbio.201700366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 03/23/2018] [Indexed: 06/08/2023]
Abstract
Förster resonant energy transfer (FRET) measurements are widely used to obtain information about molecular interactions and conformations through the dependence of FRET efficiency on the proximity of donor and acceptor fluorophores. Fluorescence lifetime measurements can provide quantitative analysis of FRET efficiency and interacting population fraction. Many FRET experiments exploit the highly specific labelling of genetically expressed fluorescent proteins, applicable in live cells and organisms. Unfortunately, the typical assumption of fast randomization of fluorophore orientations in the analysis of fluorescence lifetime-based FRET readouts is not valid for fluorescent proteins due to their slow rotational mobility compared to their upper state lifetime. Here, previous analysis of effectively static isotropic distributions of fluorophore dipoles on FRET measurements is incorporated into new software for fitting donor emission decay profiles. Calculated FRET parameters, including molar population fractions, are compared for the analysis of simulated and experimental FRET data under the assumption of static and dynamic fluorophores and the intermediate regimes between fully dynamic and static fluorophores, and mixtures within FRET pairs, is explored. Finally, a method to correct the artefact resulting from fitting the emission from static FRET pairs with isotropic angular distributions to the (incorrect) typically assumed dynamic FRET decay model is presented.
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Affiliation(s)
- Yuriy Alexandrov
- Photonics Group, Department of Physics, Imperial College London, London, UK
- Light Microscopy, Francis Crick Institute, London, UK
| | - Dino S Nikolic
- Quantum Physics and Information Technology Group, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Christopher Dunsby
- Photonics Group, Department of Physics, Imperial College London, London, UK
- Light Microscopy, Francis Crick Institute, London, UK
- Centre for Pathology, Imperial College London, London, UK
| | - Paul M W French
- Photonics Group, Department of Physics, Imperial College London, London, UK
- Light Microscopy, Francis Crick Institute, London, UK
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27
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Leopold AV, Chernov KG, Verkhusha VV. Optogenetically controlled protein kinases for regulation of cellular signaling. Chem Soc Rev 2018; 47:2454-2484. [PMID: 29498733 DOI: 10.1039/c7cs00404d] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Protein kinases are involved in the regulation of many cellular processes including cell differentiation, survival, migration, axon guidance and neuronal plasticity. A growing set of optogenetic tools, termed opto-kinases, allows activation and inhibition of different protein kinases with light. The optogenetic regulation enables fast, reversible and non-invasive manipulation of protein kinase activities, complementing traditional methods, such as treatment with growth factors, protein kinase inhibitors or chemical dimerizers. In this review, we summarize the properties of the existing optogenetic tools for controlling tyrosine kinases and serine-threonine kinases. We discuss how the opto-kinases can be applied for studies of spatial and temporal aspects of protein kinase signaling in cells and organisms. We compare approaches for chemical and optogenetic regulation of protein kinase activity and present guidelines for selection of opto-kinases and equipment to control them with light. We also describe strategies to engineer novel opto-kinases on the basis of various photoreceptors.
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Affiliation(s)
- Anna V Leopold
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki 00290, Finland
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28
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Reinhard NR, Mastop M, Yin T, Wu Y, Bosma EK, Gadella TWJ, Goedhart J, Hordijk PL. The balance between Gα i-Cdc42/Rac and Gα 12/ 13-RhoA pathways determines endothelial barrier regulation by sphingosine-1-phosphate. Mol Biol Cell 2017; 28:3371-3382. [PMID: 28954861 PMCID: PMC5687037 DOI: 10.1091/mbc.e17-03-0136] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 09/14/2017] [Accepted: 09/19/2017] [Indexed: 01/18/2023] Open
Abstract
The bioactive sphingosine-1-phosphatephosphate (S1P) is present in plasma, bound to carrier proteins, and involved in many physiological processes, including angiogenesis, inflammatory responses, and vascular stabilization. S1P can bind to several G-protein-coupled receptors (GPCRs) activating a number of different signaling networks. At present, the dynamics and relative importance of signaling events activated immediately downstream of GPCR activation are unclear. To examine these, we used a set of fluorescence resonance energy transfer-based biosensors for different RhoGTPases (Rac1, RhoA/B/C, and Cdc42) as well as for heterotrimeric G-proteins in a series of live-cell imaging experiments in primary human endothelial cells. These experiments were accompanied by biochemical GTPase activity assays and transendothelial resistance measurements. We show that S1P promotes cell spreading and endothelial barrier function through S1PR1-Gαi-Rac1 and S1PR1-Gαi-Cdc42 pathways. In parallel, a S1PR2-Gα12/13-RhoA pathway is activated that can induce cell contraction and loss of barrier function, but only if Gαi-mediated signaling is suppressed. Our results suggest that Gαq activity is not involved in S1P-mediated regulation of barrier integrity. Moreover, we show that early activation of RhoA by S1P inactivates Rac1 but not Cdc42, and vice versa. Together, our data show that the rapid S1P-induced increase in endothelial integrity is mediated by a S1PR1-Gαi-Cdc42 pathway.
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Affiliation(s)
- Nathalie R Reinhard
- van Leeuwenhoek Centre for Advanced Microscopy, Molecular Cytology, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, Netherlands
- Molecular Cell Biology and
- University of Amsterdam Academic Medical Centre-Landsteiner Laboratory, Sanquin Research, 1066 CX Amsterdam, Netherlands
| | - Marieke Mastop
- van Leeuwenhoek Centre for Advanced Microscopy, Molecular Cytology, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, Netherlands
| | - Taofei Yin
- Center for Cell Analysis and Modeling, University of Connecticut Health Center, Farmington, CT 06030
| | - Yi Wu
- Center for Cell Analysis and Modeling, University of Connecticut Health Center, Farmington, CT 06030
| | - Esmeralda K Bosma
- van Leeuwenhoek Centre for Advanced Microscopy, Molecular Cytology, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, Netherlands
| | - Theodorus W J Gadella
- van Leeuwenhoek Centre for Advanced Microscopy, Molecular Cytology, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, Netherlands
| | - Joachim Goedhart
- van Leeuwenhoek Centre for Advanced Microscopy, Molecular Cytology, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, Netherlands
| | - Peter L Hordijk
- van Leeuwenhoek Centre for Advanced Microscopy, Molecular Cytology, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, Netherlands
- Molecular Cell Biology and
- University of Amsterdam Academic Medical Centre-Landsteiner Laboratory, Sanquin Research, 1066 CX Amsterdam, Netherlands
- Department of Physiology, Free University Medical Center, 1081 HZ Amsterdam, Netherlands
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29
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Pu J, Dewey JA, Hadji A, LaBelle JL, Dickinson BC. RNA Polymerase Tags To Monitor Multidimensional Protein-Protein Interactions Reveal Pharmacological Engagement of Bcl-2 Proteins. J Am Chem Soc 2017; 139:11964-11972. [PMID: 28767232 PMCID: PMC5828006 DOI: 10.1021/jacs.7b06152] [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] [Indexed: 01/10/2023]
Abstract
We report the development of a new technology for monitoring multidimensional protein-protein interactions (PPIs) inside live mammalian cells using split RNA polymerase (RNAP) tags. In this new system, a protein-of-interest is tagged with an N-terminal split RNAP (RNAPN), and multiple potential binding partners are each fused to orthogonal C-terminal RNAPs (RNAPC). Assembly of RNAPN with each RNAPC is highly dependent on interactions between the tagged proteins. Each PPI-mediated RNAPN-RNAPC assembly transcribes from a separate promoter on a supplied DNA substrate, thereby generating a unique RNA output signal for each PPI. We develop and validate this new approach in the context of the Bcl-2 family of proteins. These key regulators of apoptosis are important cancer mediators, but are challenging to therapeutically target due to imperfect selectivity that leads to either off-target toxicity or tumor resistance. We demonstrate binary (1 × 1) and ternary (1 × 2) Bcl-2 PPI analyses by imaging fluorescent protein translation from mRNA outputs. Next, we perform a 1 × 4 PPI network analysis by direct measurement of four unique RNA signals via RT-qPCR. Finally, we use these new tools to monitor pharmacological engagement of Bcl-2 protein inhibitors, and uncover inhibitor-dependent competitive PPIs. The split RNAP tags improve upon other protein fragment complementation (PFC) approaches by offering both multidimensionality and sensitive detection using nucleic acid amplification and analysis techniques. Furthermore, this technology opens new opportunities for synthetic biology applications due to the versatility of RNA outputs for cellular engineering applications.
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Affiliation(s)
- Jinyue Pu
- Department of Chemistry, The University of Chicago, Chicago, IL 60637
| | - Jeffrey A. Dewey
- Department of Chemistry, The University of Chicago, Chicago, IL 60637
| | - Abbas Hadji
- Section of Hematology, Oncology, Stem Cell Transplantation, Department of Pediatrics, The University of Chicago, Comer Children’s Hospital, Chicago, IL, 60637
| | - James L. LaBelle
- Section of Hematology, Oncology, Stem Cell Transplantation, Department of Pediatrics, The University of Chicago, Comer Children’s Hospital, Chicago, IL, 60637
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30
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Mohan K, Nosbisch JL, Elston TC, Bear JE, Haugh JM. A Reaction-Diffusion Model Explains Amplification of the PLC/PKC Pathway in Fibroblast Chemotaxis. Biophys J 2017; 113:185-194. [PMID: 28700916 DOI: 10.1016/j.bpj.2017.05.035] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 05/18/2017] [Accepted: 05/25/2017] [Indexed: 12/20/2022] Open
Abstract
During the proliferative phase of cutaneous wound healing, dermal fibroblasts are recruited into the clotted wound by a concentration gradient of platelet-derived growth factor (PDGF), together with other spatial cues. Despite the importance of this chemotactic process, the mechanisms controlling the directed migration of slow-moving mesenchymal cells such as fibroblasts are not well understood. Here, we develop and analyze a reaction-diffusion model of phospholipase C/protein kinase C (PKC) signaling, which was recently identified as a requisite PDGF-gradient-sensing pathway, with the goal of identifying mechanisms that can amplify its sensitivity in the shallow external gradients typical of chemotaxis experiments. We show that phosphorylation of myristoylated alanine-rich C kinase substrate by membrane-localized PKC constitutes a positive feedback that is sufficient for local pathway amplification. The release of phosphorylated myristoylated alanine-rich C kinase substrate and its subsequent diffusion and dephosphorylation in the cytosol also serves to suppress the pathway in down-gradient regions of the cell. By itself, this mechanism only weakly amplifies signaling in a shallow PDGF gradient, but it synergizes with other feedback mechanisms to enhance amplification. This model offers a framework for a mechanistic understanding of phospholipase C/PKC signaling in chemotactic gradient sensing and can guide the design of experiments to assess the roles of putative feedback loops.
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Affiliation(s)
- Krithika Mohan
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina
| | - Jamie L Nosbisch
- Biomathematics Graduate Program, North Carolina State University, Raleigh, North Carolina
| | - Timothy C Elston
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - James E Bear
- Department of Cell Biology and Physiology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Jason M Haugh
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina.
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31
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Lossless Three-Dimensional Parallelization in Digitally Scanned Light-Sheet Fluorescence Microscopy. Sci Rep 2017; 7:9332. [PMID: 28839150 PMCID: PMC5570909 DOI: 10.1038/s41598-017-08113-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 07/10/2017] [Indexed: 12/19/2022] Open
Abstract
We introduce a concept that enables parallelized three-dimensional imaging throughout large volumes with isotropic 300–350 nm resolution. By staggering high aspect ratio illumination beams laterally and axially within the depth of focus of a digitally scanned light-sheet fluorescence microscope (LSFM), multiple image planes can be simultaneously imaged with minimal cross-talk and light loss. We present a first demonstration of this concept for parallelized imaging by synthesizing two light-sheets with nonlinear Bessel beams and perform volumetric imaging of fluorescent beads and invasive breast cancer cells. This work demonstrates that in principle any digitally scanned LSFM can be parallelized in a lossless manner, enabling drastically faster volumetric image acquisition rates for a given sample brightness and detector technology.
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32
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Pomeroy JE, Nguyen HX, Hoffman BD, Bursac N. Genetically Encoded Photoactuators and Photosensors for Characterization and Manipulation of Pluripotent Stem Cells. Theranostics 2017; 7:3539-3558. [PMID: 28912894 PMCID: PMC5596442 DOI: 10.7150/thno.20593] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Accepted: 07/14/2017] [Indexed: 12/28/2022] Open
Abstract
Our knowledge of pluripotent stem cell biology has advanced considerably in the past four decades, but it has yet to deliver on the great promise of regenerative medicine. The slow progress can be mainly attributed to our incomplete understanding of the complex biologic processes regulating the dynamic developmental pathways from pluripotency to fully-differentiated states of functional somatic cells. Much of the difficulty arises from our lack of specific tools to query, or manipulate, the molecular scale circuitry on both single-cell and organismal levels. Fortunately, the last two decades of progress in the field of optogenetics have produced a variety of genetically encoded, light-mediated tools that enable visualization and control of the spatiotemporal regulation of cellular function. The merging of optogenetics and pluripotent stem cell biology could thus be an important step toward realization of the clinical potential of pluripotent stem cells. In this review, we have surveyed available genetically encoded photoactuators and photosensors, a rapidly expanding toolbox, with particular attention to those with utility for studying pluripotent stem cells.
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Affiliation(s)
- Jordan E. Pomeroy
- Department of Biomedical Engineering, Duke University, 101 Science Drive, Room 1427, Fitzpatrick CIEMAS, Durham, North Carolina 27708, USA
- Division of Cardiology, Department of Medicine, Duke University Health System, Durham, North Carolina, USA
| | - Hung X. Nguyen
- Department of Biomedical Engineering, Duke University, 101 Science Drive, Room 1427, Fitzpatrick CIEMAS, Durham, North Carolina 27708, USA
| | - Brenton D. Hoffman
- Department of Biomedical Engineering, Duke University, 101 Science Drive, Room 1427, Fitzpatrick CIEMAS, Durham, North Carolina 27708, USA
| | - Nenad Bursac
- Department of Biomedical Engineering, Duke University, 101 Science Drive, Room 1427, Fitzpatrick CIEMAS, Durham, North Carolina 27708, USA
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33
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Integrin-Dependent Regulation of Small GTPases: Role in Cell Migration. J Indian Inst Sci 2017. [DOI: 10.1007/s41745-016-0010-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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34
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Matson JP, Cook JG. Cell cycle proliferation decisions: the impact of single cell analyses. FEBS J 2017; 284:362-375. [PMID: 27634578 PMCID: PMC5296213 DOI: 10.1111/febs.13898] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 08/23/2016] [Accepted: 09/13/2016] [Indexed: 12/16/2022]
Abstract
Cell proliferation is a fundamental requirement for organismal development and homeostasis. The mammalian cell division cycle is tightly controlled to ensure complete and precise genome duplication and segregation of replicated chromosomes to daughter cells. The onset of DNA replication marks an irreversible commitment to cell division, and the accumulated efforts of many decades of molecular and cellular studies have probed this cellular decision, commonly called the restriction point. Despite a long-standing conceptual framework of the restriction point for progression through G1 phase into S phase or exit from G1 phase to quiescence (G0), recent technical advances in quantitative single cell analysis of mammalian cells have provided new insights. Significant intercellular heterogeneity revealed by single cell studies and the discovery of discrete subpopulations in proliferating cultures suggests the need for an even more nuanced understanding of cell proliferation decisions. In this review, we describe some of the recent developments in the cell cycle field made possible by quantitative single cell experimental approaches.
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Affiliation(s)
- Jacob P. Matson
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill. Chapel Hill, North Carolina 27599
| | - Jeanette G. Cook
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill. Chapel Hill, North Carolina 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill. Chapel Hill, North Carolina 27599
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35
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Görlitz F, Kelly DJ, Warren SC, Alibhai D, West L, Kumar S, Alexandrov Y, Munro I, Garcia E, McGinty J, Talbot C, Serwa RA, Thinon E, da Paola V, Murray EJ, Stuhmeier F, Neil MAA, Tate EW, Dunsby C, French PMW. Open Source High Content Analysis Utilizing Automated Fluorescence Lifetime Imaging Microscopy. J Vis Exp 2017:55119. [PMID: 28190060 PMCID: PMC5352269 DOI: 10.3791/55119] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
We present an open source high content analysis instrument utilizing automated fluorescence lifetime imaging (FLIM) for assaying protein interactions using Förster resonance energy transfer (FRET) based readouts of fixed or live cells in multiwell plates. This provides a means to screen for cell signaling processes read out using intramolecular FRET biosensors or intermolecular FRET of protein interactions such as oligomerization or heterodimerization, which can be used to identify binding partners. We describe here the functionality of this automated multiwell plate FLIM instrumentation and present exemplar data from our studies of HIV Gag protein oligomerization and a time course of a FRET biosensor in live cells. A detailed description of the practical implementation is then provided with reference to a list of hardware components and a description of the open source data acquisition software written in µManager. The application of FLIMfit, an open source MATLAB-based client for the OMERO platform, to analyze arrays of multiwell plate FLIM data is also presented. The protocols for imaging fixed and live cells are outlined and a demonstration of an automated multiwell plate FLIM experiment using cells expressing fluorescent protein-based FRET constructs is presented. This is complemented by a walk-through of the data analysis for this specific FLIM FRET data set.
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Affiliation(s)
- Frederik Görlitz
- Photonics Group, Department of Physics, Imperial College London;
| | - Douglas J Kelly
- Photonics Group, Department of Physics, Imperial College London
| | - Sean C Warren
- Photonics Group, Department of Physics, Imperial College London
| | - Dominic Alibhai
- Institute for Chemical Biology, Department of Chemistry, Imperial College London
| | - Lucien West
- MRC Clinical Sciences Centre, Hammersmith Hospital
| | - Sunil Kumar
- Photonics Group, Department of Physics, Imperial College London
| | | | - Ian Munro
- Photonics Group, Department of Physics, Imperial College London
| | - Edwin Garcia
- Photonics Group, Department of Physics, Imperial College London
| | - James McGinty
- Photonics Group, Department of Physics, Imperial College London
| | - Clifford Talbot
- Photonics Group, Department of Physics, Imperial College London
| | - Remigiusz A Serwa
- Chemical Biology Section, Department of Chemistry, Imperial College London
| | - Emmanuelle Thinon
- Chemical Biology Section, Department of Chemistry, Imperial College London
| | | | | | - Frank Stuhmeier
- Pfizer Global Research and Development, Pfizer Limited, Sandwich, Kent, UK
| | - Mark A A Neil
- Photonics Group, Department of Physics, Imperial College London
| | - Edward W Tate
- Chemical Biology Section, Department of Chemistry, Imperial College London
| | - Christopher Dunsby
- Photonics Group, Department of Physics, Imperial College London; Centre for Histopathology, Imperial College London
| | - Paul M W French
- Photonics Group, Department of Physics, Imperial College London
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36
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Affiliation(s)
- Rick Horwitz
- Allen Institute for Cell Science, Seattle, Washington.
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37
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Time-lapse 3-D measurements of a glucose biosensor in multicellular spheroids by light sheet fluorescence microscopy in commercial 96-well plates. Sci Rep 2016; 6:37777. [PMID: 27886235 PMCID: PMC5122899 DOI: 10.1038/srep37777] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 11/01/2016] [Indexed: 11/08/2022] Open
Abstract
Light sheet fluorescence microscopy has previously been demonstrated on a commercially available inverted fluorescence microscope frame using the method of oblique plane microscopy (OPM). In this paper, OPM is adapted to allow time-lapse 3-D imaging of 3-D biological cultures in commercially available glass-bottomed 96-well plates using a stage-scanning OPM approach (ssOPM). Time-lapse 3-D imaging of multicellular spheroids expressing a glucose Förster resonance energy transfer (FRET) biosensor is demonstrated in 16 fields of view with image acquisition at 10 minute intervals. As a proof-of-principle, the ssOPM system is also used to acquire a dose response curve with the concentration of glucose in the culture medium being varied across 42 wells of a 96-well plate with the whole acquisition taking 9 min. The 3-D image data enable the FRET ratio to be measured as a function of distance from the surface of the spheroid. Overall, the results demonstrate the capability of the OPM system to measure spatio-temporal changes in FRET ratio in 3-D in multicellular spheroids over time in a multi-well plate format.
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38
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Nordenfelt P, Elliott HL, Springer TA. Coordinated integrin activation by actin-dependent force during T-cell migration. Nat Commun 2016; 7:13119. [PMID: 27721490 PMCID: PMC5062559 DOI: 10.1038/ncomms13119] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 09/05/2016] [Indexed: 12/28/2022] Open
Abstract
For a cell to move forward it must convert chemical energy into mechanical propulsion. Force produced by actin polymerization can generate traction across the plasma membrane by transmission through integrins to their ligands. However, the role this force plays in integrin activation is unknown. Here we show that integrin activity and cytoskeletal dynamics are reciprocally linked, where actin-dependent force itself appears to regulate integrin activity. We generated fluorescent tension-sensing constructs of integrin αLβ2 (LFA-1) to visualize intramolecular tension during cell migration. Using quantitative imaging of migrating T cells, we correlate tension in the αL or β2 subunit with cell and actin dynamics. We find that actin engagement produces tension within the β2 subunit to induce and stabilize an active integrin conformational state and that this requires intact talin and kindlin motifs. This supports a general mechanism where localized actin polymerization can coordinate activation of the complex machinery required for cell migration. The role of force in activating integrin cell adhesion receptors is not known. Here the authors develop fluorescent tension sensors for αL and β2 integrins and show that in migrating T cells force is transduced across the β2 integrin, and that this correlates with an active conformational state.
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Affiliation(s)
- Pontus Nordenfelt
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Program in Cellular and Molecular Medicine, Children's Hospital Boston, 3 Blackfan Circle, Boston, Massachusetts 02115, USA.,Image and Data Analysis Core, Harvard Medical School, 240 Longwood Ave., Boston, Massachusetts 02115, USA.,Department of Clinical Sciences, Division of Infection Medicine, Faculty of Medicine, Lund University, BMC, B14, Sölvegatan 19, 22362 Lund, Sweden
| | - Hunter L Elliott
- Image and Data Analysis Core, Harvard Medical School, 240 Longwood Ave., Boston, Massachusetts 02115, USA
| | - Timothy A Springer
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Program in Cellular and Molecular Medicine, Children's Hospital Boston, 3 Blackfan Circle, Boston, Massachusetts 02115, USA
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39
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Afsari HS, Cardoso Dos Santos M, Lindén S, Chen T, Qiu X, van Bergen en Henegouwen PMP, Jennings TL, Susumu K, Medintz IL, Hildebrandt N, Miller LW. Time-gated FRET nanoassemblies for rapid and sensitive intra- and extracellular fluorescence imaging. SCIENCE ADVANCES 2016; 2:e1600265. [PMID: 27386579 PMCID: PMC4928903 DOI: 10.1126/sciadv.1600265] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 05/19/2016] [Indexed: 05/20/2023]
Abstract
Time-gated Förster resonance energy transfer (FRET) using the unique material combination of long-lifetime terbium complexes (Tb) and semiconductor quantum dots (QDs) provides many advantages for highly sensitive and multiplexed biosensing. Although time-gated detection can efficiently suppress sample autofluorescence and background fluorescence from directly excited FRET acceptors, Tb-to-QD FRET has rarely been exploited for biomolecular imaging. We demonstrate Tb-to-QD time-gated FRET nanoassemblies that can be applied for intra- and extracellular imaging. Immunostaining of different epitopes of the epidermal growth factor receptor (EGFR) with Tb- and QD-conjugated antibodies and nanobodies allowed for efficient Tb-to-QD FRET on A431 cell membranes. The broad usability of Tb-to-QD FRET was further demonstrated by intracellular Tb-to-QD FRET and Tb-to-QD-to-dye FRET using microinjection as well as cell-penetrating peptide-mediated endocytosis with HeLa cells. Effective brightness enhancement by FRET from several Tb to the same QD, the use of low nanomolar concentrations, and the quick and sensitive detection void of FRET acceptor background fluorescence are important advantages for advanced intra- and extracellular imaging of biomolecular interactions.
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Affiliation(s)
- Hamid Samareh Afsari
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, IL 60607–7061, USA
| | - Marcelina Cardoso Dos Santos
- NanoBioPhotonics (www.nanofret.com), Institut d’Electronique Fondamentale, Université Paris-Saclay, Université Paris-Sud, CNRS, 91405 Orsay Cedex, France
| | - Stina Lindén
- NanoBioPhotonics (www.nanofret.com), Institut d’Electronique Fondamentale, Université Paris-Saclay, Université Paris-Sud, CNRS, 91405 Orsay Cedex, France
| | - Ting Chen
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, IL 60607–7061, USA
| | - Xue Qiu
- NanoBioPhotonics (www.nanofret.com), Institut d’Electronique Fondamentale, Université Paris-Saclay, Université Paris-Sud, CNRS, 91405 Orsay Cedex, France
| | | | | | - Kimihiro Susumu
- Optical Sciences Division, Code 5611, U.S. Naval Research Laboratory, Washington, DC 20375, USA
- Sotera Defense Solutions, Columbia, MD 21046, USA
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, USA
| | - Niko Hildebrandt
- NanoBioPhotonics (www.nanofret.com), Institut d’Electronique Fondamentale, Université Paris-Saclay, Université Paris-Sud, CNRS, 91405 Orsay Cedex, France
| | - Lawrence W. Miller
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, IL 60607–7061, USA
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40
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Marinović M, Šoštar M, Filić V, Antolović V, Weber I. Quantitative imaging of Rac1 activity in Dictyostelium cells with a fluorescently labelled GTPase-binding domain from DPAKa kinase. Histochem Cell Biol 2016; 146:267-79. [DOI: 10.1007/s00418-016-1440-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/19/2016] [Indexed: 02/06/2023]
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41
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Abstract
Probes and biosensors that incorporate luminescent Tb(III) or Eu(III) complexes are promising for cellular imaging because time-gated microscopes can detect their long-lifetime (approximately milliseconds) emission without interference from short-lifetime (approximately nanoseconds) fluorescence background. Moreover, the discrete, narrow emission bands of Tb(III) complexes make them uniquely suited for multiplexed imaging applications because they can serve as Förster resonance energy transfer (FRET) donors to two or more differently colored acceptors. However, lanthanide complexes have low photon emission rates that can limit the image signal/noise ratio, which has a square-root dependence on photon counts. This work describes the performance of a wide-field, time-gated microscope with respect to its ability to image Tb(III) luminescence and Tb(III)-mediated FRET in cultured mammalian cells. The system employed a UV-emitting LED for low-power, pulsed excitation and an intensified CCD camera for gated detection. Exposure times of ∼1 s were needed to collect 5-25 photons per pixel from cells that contained micromolar concentrations of a Tb(III) complex. The observed photon counts matched those predicted by a theoretical model that incorporated the photophysical properties of the Tb(III) probe and the instrument's light-collection characteristics. Despite low photon counts, images of Tb(III)/green fluorescent protein FRET with a signal/noise ratio ≥ 7 were acquired, and a 90% change in the ratiometric FRET signal was measured. This study shows that the sensitivity and precision of lanthanide-based cellular microscopy can approach that of conventional FRET microscopy with fluorescent proteins. The results should encourage further development of lanthanide biosensors that can measure analyte concentration, enzyme activation, and protein-protein interactions in live cells.
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42
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Doucette J, Zhao Z, Geyer RJ, Barra MM, Balunas MJ, Zweifach A. Flow Cytometry Enables Multiplexed Measurements of Genetically Encoded Intramolecular FRET Sensors Suitable for Screening. ACTA ACUST UNITED AC 2016; 21:535-47. [DOI: 10.1177/1087057116634007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 01/31/2016] [Indexed: 11/16/2022]
Abstract
Genetically encoded sensors based on intramolecular FRET between CFP and YFP are used extensively in cell biology research. Flow cytometry has been shown to offer a means to measure CFP-YFP FRET; we suspected it would provide a unique way to conduct multiplexed measurements from cells expressing different FRET sensors, which is difficult to do with microscopy, and that this could be used for screening. We confirmed that flow cytometry accurately measures FRET signals using cells transiently transfected with an ERK activity reporter, comparing responses measured with imaging and cytometry. We created polyclonal long-term transfectant lines, each expressing a different intramolecular FRET sensor, and devised a way to bar-code four distinct populations of cells. We demonstrated the feasibility of multiplexed measurements and determined that robust multiplexed measurements can be conducted in plate format. To validate the suitability of the method for screening, we measured responses from a plate of bacterial extracts that in unrelated experiments we had determined contained the protein kinase C (PKC)–activating compound teleocidin A-1. The multiplexed assay correctly identifying the teleocidin A-1-containing well. We propose that multiplexed cytometric FRET measurements will be useful for analyzing cellular function and for screening compound collections.
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Affiliation(s)
- Jaimee Doucette
- Department of Molecular and Cell Biology, University of Connecticut at Storrs, Storrs, CT
| | - Ziyan Zhao
- Department of Molecular and Cell Biology, University of Connecticut at Storrs, Storrs, CT
| | - Rory J. Geyer
- Department of Molecular and Cell Biology, University of Connecticut at Storrs, Storrs, CT
| | - Melanie M. Barra
- Department of Molecular and Cell Biology, University of Connecticut at Storrs, Storrs, CT
| | - Marcy J. Balunas
- Division of Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Connecticut at Storrs, Storrs, CT
| | - Adam Zweifach
- Department of Molecular and Cell Biology, University of Connecticut at Storrs, Storrs, CT
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43
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Roukos DH. Crossroad between linear and nonlinear transcription concepts in the discovery of next-generation sequencing systems-based anticancer therapies. Drug Discov Today 2016; 21:663-73. [PMID: 26912452 DOI: 10.1016/j.drudis.2016.02.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 01/20/2016] [Accepted: 02/11/2016] [Indexed: 01/06/2023]
Abstract
The unprecedented potential of standard and new next-generation sequencing applications and methods to explore cancer genome evolution and tumor heterogeneity as well as transcription networks in time and space shapes the development of next-generation therapeutics. However, biomedical and pharmaceutical research for overcoming heterogeneity-based therapeutic resistance is at an important crossroads. Focus on linear transcription-based drug development targeting dynamics of simple intrapatient structured genome diversity represents a realistic medium-term goal. By contrast, the discovery of nonlinear transcription drugs for targeting structural and functional genome and transcriptome heterogeneity represents a long-term rational strategy. This review compares effectiveness, challenges and expectations between linear and nonlinear drugs targeting simple intrapatient variation and aberrant transcriptional biocircuits, respectively.
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Affiliation(s)
- Dimitrios H Roukos
- Centre for Biosystems and Genomic Network Medicine and Research & Innovation Commission of Ioannina University, School of Medicine, Ioannina, Greece; Hellenic Genomic Center and Systems Biology Unit of Biomedical Research Foundation of the Academy of Athens (BRFAA), Athens, Greece.
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44
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Gordonov S, Hwang MK, Wells A, Gertler FB, Lauffenburger DA, Bathe M. Time series modeling of live-cell shape dynamics for image-based phenotypic profiling. Integr Biol (Camb) 2016; 8:73-90. [PMID: 26658688 PMCID: PMC5058786 DOI: 10.1039/c5ib00283d] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Live-cell imaging can be used to capture spatio-temporal aspects of cellular responses that are not accessible to fixed-cell imaging. As the use of live-cell imaging continues to increase, new computational procedures are needed to characterize and classify the temporal dynamics of individual cells. For this purpose, here we present the general experimental-computational framework SAPHIRE (Stochastic Annotation of Phenotypic Individual-cell Responses) to characterize phenotypic cellular responses from time series imaging datasets. Hidden Markov modeling is used to infer and annotate morphological state and state-switching properties from image-derived cell shape measurements. Time series modeling is performed on each cell individually, making the approach broadly useful for analyzing asynchronous cell populations. Two-color fluorescent cells simultaneously expressing actin and nuclear reporters enabled us to profile temporal changes in cell shape following pharmacological inhibition of cytoskeleton-regulatory signaling pathways. Results are compared with existing approaches conventionally applied to fixed-cell imaging datasets, and indicate that time series modeling captures heterogeneous dynamic cellular responses that can improve drug classification and offer additional important insight into mechanisms of drug action. The software is available at http://saphire-hcs.org.
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Affiliation(s)
- Simon Gordonov
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- The David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | - Mun Kyung Hwang
- The David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | - Alan Wells
- Department of Pathology, University of Pittsburgh, and Pittsburgh VA Health System, Pittsburgh, PA, USA
| | - Frank B. Gertler
- The David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Douglas A. Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- The David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
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45
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González-Vera JA, Morris MC. Fluorescent Reporters and Biosensors for Probing the Dynamic Behavior of Protein Kinases. Proteomes 2015; 3:369-410. [PMID: 28248276 PMCID: PMC5217393 DOI: 10.3390/proteomes3040369] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 09/30/2015] [Accepted: 10/23/2015] [Indexed: 12/20/2022] Open
Abstract
Probing the dynamic activities of protein kinases in real-time in living cells constitutes a major challenge that requires specific and sensitive tools tailored to meet the particular demands associated with cellular imaging. The development of genetically-encoded and synthetic fluorescent biosensors has provided means of monitoring protein kinase activities in a non-invasive fashion in their native cellular environment with high spatial and temporal resolution. Here, we review existing technologies to probe different dynamic features of protein kinases and discuss limitations where new developments are required to implement more performant tools, in particular with respect to infrared and near-infrared fluorescent probes and strategies which enable improved signal-to-noise ratio and controlled activation of probes.
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Affiliation(s)
- Juan A González-Vera
- Cell Cycle Biosensors & Inhibitors, Department of Amino Acids, Peptides and Proteins, Institute of Biomolecules Max Mousseron (IBMM) CNRS-UMR 5247, 15 Avenue Charles Flahault, Montpellier 34093, France.
| | - May C Morris
- Cell Cycle Biosensors & Inhibitors, Department of Amino Acids, Peptides and Proteins, Institute of Biomolecules Max Mousseron (IBMM) CNRS-UMR 5247, 15 Avenue Charles Flahault, Montpellier 34093, France.
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46
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Kamiyama D, McGorty R, Kamiyama R, Kim MD, Chiba A, Huang B. Specification of Dendritogenesis Site in Drosophila aCC Motoneuron by Membrane Enrichment of Pak1 through Dscam1. Dev Cell 2015; 35:93-106. [PMID: 26460947 PMCID: PMC4626010 DOI: 10.1016/j.devcel.2015.09.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 07/07/2015] [Accepted: 09/11/2015] [Indexed: 01/11/2023]
Abstract
Precise positioning of dendritic branches is a critical step in the establishment of neuronal circuitry. However, there is limited knowledge on how environmental cues translate into dendrite initiation or branching at a specific position. Here, through a combination of mutation, RNAi, and imaging experiments, we found that a Dscam-Dock-Pak1 hierarchical interaction defines the stereotypical dendrite growth site in the Drosophila aCC motoneuron. This interaction localizes the Cdc42 effector Pak1 to the plasma membrane at the dendrite initiation site before the activation of Cdc42. Ectopic expression of membrane-anchored Pak1 overrides this spatial specification of dendritogenesis, confirming its function in guiding Cdc42 signaling. We further discovered that Dscam1 localization in aCC occurs through an inter-neuronal contact that involves Dscam1 in the partner MP1 neuron. These findings elucidate a mechanism by which Dscam1 controls neuronal morphogenesis through spatial regulation of Cdc42 signaling and, subsequently, cytoskeletal remodeling.
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MESH Headings
- Adaptor Proteins, Signal Transducing/genetics
- Adaptor Proteins, Signal Transducing/metabolism
- Animals
- Animals, Genetically Modified/genetics
- Animals, Genetically Modified/growth & development
- Animals, Genetically Modified/metabolism
- Cell Adhesion Molecules
- Cell Differentiation
- Cell Membrane/metabolism
- Cells, Cultured
- Cytoskeleton/metabolism
- Dendrites/physiology
- Drosophila/genetics
- Drosophila/growth & development
- Drosophila/metabolism
- Drosophila Proteins/antagonists & inhibitors
- Drosophila Proteins/genetics
- Drosophila Proteins/metabolism
- Embryo, Nonmammalian/cytology
- Embryo, Nonmammalian/metabolism
- GTP-Binding Proteins/genetics
- GTP-Binding Proteins/metabolism
- Gene Expression Regulation, Developmental
- Immunoenzyme Techniques
- Interneurons/cytology
- Interneurons/metabolism
- Morphogenesis/physiology
- Motor Neurons/cytology
- Motor Neurons/metabolism
- Nerve Tissue Proteins/genetics
- Nerve Tissue Proteins/metabolism
- Neural Cell Adhesion Molecules/antagonists & inhibitors
- Neural Cell Adhesion Molecules/genetics
- Neural Cell Adhesion Molecules/metabolism
- RNA, Small Interfering/genetics
- p21-Activated Kinases/genetics
- p21-Activated Kinases/metabolism
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Affiliation(s)
- Daichi Kamiyama
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - Ryan McGorty
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Rie Kamiyama
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Michael D Kim
- Miami Institute of Molecular Imaging and Computation, Coral Gables, FL 33146, USA; Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Akira Chiba
- Department of Biology, University of Miami, Coral Gables, FL 33146, USA; Miami Institute of Molecular Imaging and Computation, Coral Gables, FL 33146, USA
| | - Bo Huang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.
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47
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Sustarsic M, Kapanidis AN. Taking the ruler to the jungle: single-molecule FRET for understanding biomolecular structure and dynamics in live cells. Curr Opin Struct Biol 2015; 34:52-9. [DOI: 10.1016/j.sbi.2015.07.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2015] [Accepted: 07/02/2015] [Indexed: 12/29/2022]
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48
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Cheng Z, Taylor B, Ourthiague DR, Hoffmann A. Distinct single-cell signaling characteristics are conferred by the MyD88 and TRIF pathways during TLR4 activation. Sci Signal 2015; 8:ra69. [PMID: 26175492 DOI: 10.1126/scisignal.aaa5208] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Toll-like receptors (TLRs) recognize specific pathogen-associated molecular patterns and initiate innate immune responses through signaling pathways that depend on the adaptor proteins MyD88 (myeloid differentiation marker 88) or TRIF (TIR domain-containing adaptor protein-inducing interferon-β). TLR4, in particular, uses both adaptor proteins to activate the transcription factor nuclear factor κB (NF-κB); however, the specificity and redundancy of these two pathways remain to be elucidated. We developed a mathematical model to show how each pathway encodes distinct dynamical features of NF-κB activity and makes distinct contributions to the high variability observed in single-cell measurements. The assembly of a macromolecular signaling platform around MyD88 associated with receptors at the cell surface determined the timing of initial responses to generate a reliable, digital NF-κB signal. In contrast, ligand-induced receptor internalization into endosomes produced noisy, delayed, yet sustained NF-κB signals through TRIF. With iterative mathematical model development, we predicted the molecular mechanisms by which the MyD88- and TRIF-mediated pathways provide ligand concentration-dependent signaling dynamics that transmit information about the pathogen threat.
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Affiliation(s)
- Zhang Cheng
- Institute for Quantitative and Computational Biosciences and Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90025, USA. San Diego Center for Systems Biology and Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Brooks Taylor
- Institute for Quantitative and Computational Biosciences and Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90025, USA. San Diego Center for Systems Biology and Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Diana R Ourthiague
- San Diego Center for Systems Biology and Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, 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 90025, USA. San Diego Center for Systems Biology and Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
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49
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Heemskerk N, van Rijssel J, van Buul JD. Rho-GTPase signaling in leukocyte extravasation: an endothelial point of view. Cell Adh Migr 2015; 8:67-75. [PMID: 24621576 PMCID: PMC4049863 DOI: 10.4161/cam.28244] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Leukocyte transendothelial migration (TEM) is one of the crucial steps during inflammation. A better understanding of the key molecules that regulate leukocyte extravasation aids to the development of novel therapeutics for treatment of inflammation-based diseases, such as atherosclerosis and rheumatoid arthritis. The adhesion molecules ICAM-1 and VCAM-1 are known as central mediators of TEM. Clustering of these molecules by their leukocytic integrins initiates the activation of several signaling pathways within the endothelium, including a rise in intracellular Ca (2+), activation of several kinase cascades, and the activation of Rho-GTPases. Activation of Rho-GTPases has been shown to control adhesion molecule clustering and the formation of apical membrane protrusions that embrace adherent leukocytes during TEM. Here, we discuss the potential regulatory mechanisms of leukocyte extravasation from an endothelial point of view, with specific focus on the role of the Rho-GTPases.
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Affiliation(s)
- Niels Heemskerk
- Department of Molecular Cell Biology; Sanquin Research and Landsteiner Laboratory; Academic Medical Center; University of Amsterdam; Amsterdam, the Netherlands
| | - Jos van Rijssel
- Department of Molecular Cell Biology; Sanquin Research and Landsteiner Laboratory; Academic Medical Center; University of Amsterdam; Amsterdam, the Netherlands
| | - Jaap D van Buul
- Department of Molecular Cell Biology; Sanquin Research and Landsteiner Laboratory; Academic Medical Center; University of Amsterdam; Amsterdam, the Netherlands
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50
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Lewis OL, Guy RD, Allard JF. Actin-myosin spatial patterns from a simplified isotropic viscoelastic model. Biophys J 2015; 107:863-70. [PMID: 25140421 DOI: 10.1016/j.bpj.2014.06.041] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 05/28/2014] [Accepted: 06/16/2014] [Indexed: 11/30/2022] Open
Abstract
F-actin networks are involved in cell mechanical processes ranging from motility to endocytosis. The mesoscale architecture of assemblies of individual F-actin polymers that gives rise to micrometer-scale rheological properties is poorly understood, despite numerous in vivo and vitro studies. In vitro networks have been shown to organize into spatial patterns when spatially confined, including dense spherical shells inside spherical emulsion droplets. Here we develop a simplified model of an isotropic, compressible, viscoelastic material continually assembling and disassembling. We demonstrate that spherical shells emerge naturally when the strain relaxation rate (corresponding to internal network reorganization) is slower than the disassembly rate (corresponding to F-actin depolymerization). These patterns are consistent with recent experiments, including a collapse of shells to a central high-density focus of F-actin when either assembly or disassembly is reduced with drugs. Our results demonstrate how complex spatio-temporal patterns can emerge without spatially distributed force generation, polar alignment of F-actin polymers, or spatially nonuniform regulation of F-actin by upstream biochemical networks.
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Affiliation(s)
- Owen L Lewis
- Department of Mathematics, University of California at Davis, Davis, California
| | - Robert D Guy
- Department of Mathematics, University of California at Davis, Davis, California
| | - Jun F Allard
- Department of Mathematics, Department of Physics and Astronomy, Center for Complex Biological Systems, University of California at Irvine, Irvine, California.
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