1
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Conaway S, Huang W, Hernandez-Lara MA, Kane MA, Penn RB, Deshpande DA. Molecular mechanism of bitter taste receptor agonist-mediated relaxation of airway smooth muscle. FASEB J 2024; 38:e23842. [PMID: 39037554 PMCID: PMC11299423 DOI: 10.1096/fj.202400452r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 06/24/2024] [Accepted: 07/12/2024] [Indexed: 07/23/2024]
Abstract
G-protein-coupled receptors (GPCRs) belonging to the type 2 taste receptors (TAS2Rs) family are predominantly present in taste cells to allow the perception of bitter-tasting compounds. TAS2Rs have also been shown to be expressed in human airway smooth muscle (ASM), and TAS2R agonists relax ASM cells and bronchodilate airways despite elevating intracellular calcium. This calcium "paradox" (calcium mediates contraction by pro-contractile Gq-coupled GPCRs) and the mechanisms by which TAS2R agonists relax ASM remain poorly understood. To gain insight into pro-relaxant mechanisms effected by TAS2Rs, we employed an unbiased phosphoproteomic approach involving dual-mass spectrometry to determine differences in the phosphorylation of contractile-related proteins in ASM following the stimulation of cells with TAS2R agonists, histamine (an agonist of the Gq-coupled H1 histamine receptor) or isoproterenol (an agonist of the Gs-coupled β2-adrenoceptor) alone or in combination. Our study identified differential phosphorylation of proteins regulating contraction, including A-kinase anchoring protein (AKAP)2, AKAP12, and RhoA guanine nucleotide exchange factor (ARHGEF)12. Subsequent signaling analyses revealed RhoA and the T853 residue on myosin light chain phosphatase (MYPT)1 as points of mechanistic divergence between TAS2R and Gs-coupled GPCR pathways. Unlike Gs-coupled receptor signaling, which inhibits histamine-induced myosin light chain (MLC)20 phosphorylation via protein kinase A (PKA)-dependent inhibition of intracellular calcium mobilization, HSP20 and ERK1/2 activity, TAS2Rs are shown to inhibit histamine-induced pMLC20 via inhibition of RhoA activity and MYPT1 phosphorylation at the T853 residue. These findings provide insight into the TAS2R signaling in ASM by defining a distinct signaling mechanism modulating inhibition of pMLC20 to relax contracted ASM.
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Affiliation(s)
- Stanley Conaway
- Center for Translational Medicine, Jane and Leonard Korman Lung Center, Thomas Jefferson University, Philadelphia, PA, U.S.A., 19107
| | - Weiliang Huang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, U.S.A., 21201
| | - Miguel A. Hernandez-Lara
- Center for Translational Medicine, Jane and Leonard Korman Lung Center, Thomas Jefferson University, Philadelphia, PA, U.S.A., 19107
| | - Maureen A. Kane
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, U.S.A., 21201
| | - Raymond B. Penn
- Center for Translational Medicine, Jane and Leonard Korman Lung Center, Thomas Jefferson University, Philadelphia, PA, U.S.A., 19107
| | - Deepak A. Deshpande
- Center for Translational Medicine, Jane and Leonard Korman Lung Center, Thomas Jefferson University, Philadelphia, PA, U.S.A., 19107
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2
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Wojnacki J, Quassollo G, Bordenave MD, Unsain N, Martínez GF, Szalai AM, Pertz O, Gundersen GG, Bartolini F, Stefani FD, Cáceres A, Bisbal M. Dual spatio-temporal regulation of axon growth and microtubule dynamics by RhoA signaling pathways. J Cell Sci 2024; 137:jcs261970. [PMID: 38910449 DOI: 10.1242/jcs.261970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 06/17/2024] [Indexed: 06/25/2024] Open
Abstract
RhoA plays a crucial role in neuronal polarization, where its action restraining axon outgrowth has been thoroughly studied. We now report that RhoA has not only an inhibitory but also a stimulatory effect on axon development depending on when and where exerts its action and the downstream effectors involved. In cultured hippocampal neurons, FRET imaging revealed that RhoA activity selectively localized in growth cones of undifferentiated neurites, whereas in developing axons it displayed a biphasic pattern, being low in nascent axons and high in elongating ones. RhoA-Rho kinase (ROCK) signaling prevented axon initiation but had no effect on elongation, whereas formin inhibition reduced axon extension without significantly altering initial outgrowth. In addition, RhoA-mDia signaling promoted axon elongation by stimulating growth cone microtubule stability and assembly, as opposed to RhoA-ROCK signaling, which restrained growth cone microtubule assembly and protrusion.
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Affiliation(s)
- José Wojnacki
- Instituto de Investigación Médica Mercedes y Martín Ferreyra (INIMEC), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Córdoba, Córdoba 5016, Argentina
| | - Gonzalo Quassollo
- Instituto de Investigación Médica Mercedes y Martín Ferreyra (INIMEC), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Córdoba, Córdoba 5016, Argentina
| | - Martín D Bordenave
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, Ciudad Autónoma de Buenos Aires C1425FQD, Argentina
| | - Nicolás Unsain
- Instituto de Investigación Médica Mercedes y Martín Ferreyra (INIMEC), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Córdoba, Córdoba 5016, Argentina
- Instituto Universitario Ciencias Biomédicas de Córdoba (IUCBC), Córdoba 5016, Argentina
| | - Gaby F Martínez
- Instituto de Investigación Médica Mercedes y Martín Ferreyra (INIMEC), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Córdoba, Córdoba 5016, Argentina
| | - Alan M Szalai
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, Ciudad Autónoma de Buenos Aires C1425FQD, Argentina
| | - Olivier Pertz
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, Bern 3012, Switzerland
| | - Gregg G Gundersen
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Francesca Bartolini
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Fernando D Stefani
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, Ciudad Autónoma de Buenos Aires C1425FQD, Argentina
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Güiraldes 2620, Ciudad Autónoma de Buenos Aires C1428EHA, Argentina
| | - Alfredo Cáceres
- Centro Investigación Medicina Traslacional Severo R Amuchástegui (CIMETSA), Instituto Universitario Ciencias Biomédicas Córdoba (IUCBC), Av. Naciones Unidas 440, Córdoba 5016, Argentina
| | - Mariano Bisbal
- Instituto de Investigación Médica Mercedes y Martín Ferreyra (INIMEC), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Córdoba, Córdoba 5016, Argentina
- Instituto Universitario Ciencias Biomédicas de Córdoba (IUCBC), Córdoba 5016, Argentina
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3
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Qiao E, Fulmore CA, Schaffer DV, Kumar S. Substrate stress relaxation regulates neural stem cell fate commitment. Proc Natl Acad Sci U S A 2024; 121:e2317711121. [PMID: 38968101 PMCID: PMC11252819 DOI: 10.1073/pnas.2317711121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 05/17/2024] [Indexed: 07/07/2024] Open
Abstract
Adult neural stem cells (NSCs) reside in the dentate gyrus of the hippocampus, and their capacity to generate neurons and glia plays a role in learning and memory. In addition, neurodegenerative diseases are known to be caused by a loss of neurons and glial cells, resulting in a need to better understand stem cell fate commitment processes. We previously showed that NSC fate commitment toward a neuronal or glial lineage is strongly influenced by extracellular matrix stiffness, a property of elastic materials. However, tissues in vivo are not purely elastic and have varying degrees of viscous character. Relatively little is known about how the viscoelastic properties of the substrate impact NSC fate commitment. Here, we introduce a polyacrylamide-based cell culture platform that incorporates mismatched DNA oligonucleotide-based cross-links as well as covalent cross-links. This platform allows for tunable viscous stress relaxation properties via variation in the number of mismatched base pairs. We find that NSCs exhibit increased astrocytic differentiation as the degree of stress relaxation is increased. Furthermore, culturing NSCs on increasingly stress-relaxing substrates impacts cytoskeletal dynamics by decreasing intracellular actin flow rates and stimulating cyclic activation of the mechanosensitive protein RhoA. Additionally, inhibition of motor-clutch model components such as myosin II and focal adhesion kinase partially or completely reverts cells to lineage distributions observed on elastic substrates. Collectively, our results introduce a unique system for controlling matrix stress relaxation properties and offer insight into how NSCs integrate viscoelastic cues to direct fate commitment.
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Affiliation(s)
- Eric Qiao
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA94720
| | - Camille A. Fulmore
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - David V. Schaffer
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA94720
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
- Department of Bioengineering, University of California, Berkeley, CA94720
| | - Sanjay Kumar
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA94720
- Department of Bioengineering, University of California, Berkeley, CA94720
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA94143
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4
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Baek J, Kumar S, Schaffer DV. Dynamic light-responsive RhoA activity regulates mechanosensitive stem cell fate decision in 3D matrices. BIOMATERIALS ADVANCES 2024; 160:213836. [PMID: 38599042 DOI: 10.1016/j.bioadv.2024.213836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 03/05/2024] [Accepted: 03/19/2024] [Indexed: 04/12/2024]
Abstract
The behavior of stem cells is regulated by mechanical cues in their niche that continuously vary due to extracellular matrix (ECM) remodeling, pulsated mechanical stress exerted by blood flow, and/or cell migration. However, it is still unclear how dynamics of mechanical cues influence stem cell lineage commitment, especially in a 3D microenvironment where mechanosensing differs from that in a 2D microenvironment. In the present study, we investigated how temporally varying mechanical signaling regulates expression of the early growth response 1 gene (Egr1), which we recently discovered to be a 3D matrix-specific mediator of mechanosensitive neural stem cell (NSC) lineage commitment. Specifically, we temporally controlled the activity of Ras homolog family member A (RhoA), which is known to have a central role in mechanotransduction, using our previously developed Arabidopsis thaliana cryptochrome-2-based optoactivation system. Interestingly, pulsed RhoA activation induced Egr1 upregulation in stiff 3D gels only, whereas static light stimulation induced an increase in Egr1 expression across a wide range of 3D gel stiffnesses. Actin assembly inhibition limited Egr1 upregulation upon RhoA activation, implying that RhoA signaling requires an actin-involved process to upregulate Egr1. Consistently, static-light RhoA activation rather than pulsed-light activation restricted neurogenesis in soft gels. Our findings indicate that the dynamics of RhoA activation influence Egr1-mediated stem cell fate within 3D matrices in a matrix stiffness-dependent manner.
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Affiliation(s)
- Jieung Baek
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Bioengineering, University of California, Berkeley, CA 94720, USA; Division of Mechanical and Biomedical Engineering, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Sanjay Kumar
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Bioengineering, University of California, Berkeley, CA 94720, USA.
| | - David V Schaffer
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Bioengineering, University of California, Berkeley, CA 94720, USA; Helen Wills Neuroscience Institute, Berkeley, CA 94720, USA.
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5
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Rebeaud ME, Tiwari S, Fauvet B, Mohr A, Goloubinoff P, De Los Rios P. Autorepression of yeast Hsp70 cochaperones by intramolecular interactions involving their J-domains. Cell Stress Chaperones 2024; 29:338-348. [PMID: 38521349 PMCID: PMC10999819 DOI: 10.1016/j.cstres.2024.03.008] [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: 02/09/2024] [Revised: 03/19/2024] [Accepted: 03/19/2024] [Indexed: 03/25/2024] Open
Abstract
The 70 kDa heat shock protein (Hsp70) chaperones control protein homeostasis in all ATP-containing cellular compartments. J-domain proteins (JDPs) coevolved with Hsp70s to trigger ATP hydrolysis and catalytically upload various substrate polypeptides in need to be structurally modified by the chaperone. Here, we measured the protein disaggregation and refolding activities of the main yeast cytosolic Hsp70, Ssa1, in the presence of its most abundant JDPs, Sis1 and Ydj1, and two swap mutants, in which the J-domains have been interchanged. The observed differences by which the four constructs differently cooperate with Ssa1 and cooperate with each other, as well as their observed intrinsic ability to bind misfolded substrates and trigger Ssa1's ATPase, indicate the presence of yet uncharacterized intramolecular dynamic interactions between the J-domains and the remaining C-terminal segments of these proteins. Taken together, the data suggest an autoregulatory role to these intramolecular interactions within both type A and B JDPs, which might have evolved to reduce energy-costly ATPase cycles by the Ssa1-4 chaperones that are the most abundant Hsp70s in the yeast cytosol.
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Affiliation(s)
- Mathieu E Rebeaud
- Department of Plant Molecular Biology, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Vaud, Switzerland; Institute of Physics, School of Basic Sciences, École Polytechnique Fédérale de Lausanne - EPFL, 1015 Lausanne, Vaud, Switzerland
| | - Satyam Tiwari
- Institute of Physics, School of Basic Sciences, École Polytechnique Fédérale de Lausanne - EPFL, 1015 Lausanne, Vaud, Switzerland
| | - Bruno Fauvet
- Institute of Physics, School of Basic Sciences, École Polytechnique Fédérale de Lausanne - EPFL, 1015 Lausanne, Vaud, Switzerland
| | - Adelaïde Mohr
- Institute of Physics, School of Basic Sciences, École Polytechnique Fédérale de Lausanne - EPFL, 1015 Lausanne, Vaud, Switzerland
| | - Pierre Goloubinoff
- Department of Plant Molecular Biology, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Vaud, Switzerland.
| | - Paolo De Los Rios
- Institute of Physics, School of Basic Sciences, École Polytechnique Fédérale de Lausanne - EPFL, 1015 Lausanne, Vaud, Switzerland; Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne - EPFL, 1015 Lausanne, Vaud, Switzerland.
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6
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Bement WM, Goryachev AB, Miller AL, von Dassow G. Patterning of the cell cortex by Rho GTPases. Nat Rev Mol Cell Biol 2024; 25:290-308. [PMID: 38172611 DOI: 10.1038/s41580-023-00682-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/20/2023] [Indexed: 01/05/2024]
Abstract
The Rho GTPases - RHOA, RAC1 and CDC42 - are small GTP binding proteins that regulate basic biological processes such as cell locomotion, cell division and morphogenesis by promoting cytoskeleton-based changes in the cell cortex. This regulation results from active (GTP-bound) Rho GTPases stimulating target proteins that, in turn, promote actin assembly and myosin 2-based contraction to organize the cortex. This basic regulatory scheme, well supported by in vitro studies, led to the natural assumption that Rho GTPases function in vivo in an essentially linear matter, with a given process being initiated by GTPase activation and terminated by GTPase inactivation. However, a growing body of evidence based on live cell imaging, modelling and experimental manipulation indicates that Rho GTPase activation and inactivation are often tightly coupled in space and time via signalling circuits and networks based on positive and negative feedback. In this Review, we present and discuss this evidence, and we address one of the fundamental consequences of coupled activation and inactivation: the ability of the Rho GTPases to self-organize, that is, direct their own transition from states of low order to states of high order. We discuss how Rho GTPase self-organization results in the formation of diverse spatiotemporal cortical patterns such as static clusters, oscillatory pulses, travelling wave trains and ring-like waves. Finally, we discuss the advantages of Rho GTPase self-organization and pattern formation for cell function.
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Affiliation(s)
- William M Bement
- Center for Quantitative Cell Imaging, Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA.
| | - Andrew B Goryachev
- Center for Engineering Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
| | - Ann L Miller
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.
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7
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Zhang J, Zhang Y, Shang Q, Cheng Y, Su Y, Zhang J, Wang T, Ding J, Li Y, Xie Y, Xing Q. Gain-of-Function KIDINS220 Variants Disrupt Neuronal Development and Cause Cerebral Palsy. Mov Disord 2024; 39:498-509. [PMID: 38148610 DOI: 10.1002/mds.29694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/30/2023] [Accepted: 12/04/2023] [Indexed: 12/28/2023] Open
Abstract
BACKGROUND Kinase D-interacting substrate of 220 kDa (KIDINS220) is a multifunctional scaffolding protein essential for neuronal development. It has been implicated in neurological diseases with either autosomal dominant (AD) or autosomal recessive (AR) inheritance patterns. The molecular mechanisms underlying the AR/AD dual nature of KIDINS220 remain elusive, posing challenges to genetic interpretation and clinical interventions. Moreover, increased KIDINS220 exhibited neurotoxicity, but its role in neurodevelopment remains unclear. OBJECTIVE The aim was to investigate the genotype-phenotype correlations of KIDINS220 and elucidate its pathophysiological role in neuronal development. METHODS Whole-exome sequencing was performed in a four-generation family with cerebral palsy. CRISPR/Cas9 was used to generate KIDINS220 mutant cell lines. In utero electroporation was employed to investigate the effect of KIDINS220 variants on neurogenesis in vivo. RESULTS We identified in KIDINS220 a pathogenic nonsense variant (c.4177C > T, p.Q1393*) that associated with AD cerebral palsy. We demonstrated that the nonsense variants located in the terminal exon of KIDINS220 are gain-of-function (GoF) variants, which enable the mRNA to escape nonsense-mediated decay and produce a truncated yet functional KIDINS220 protein. The truncated protein exhibited significant resistance to calpain and consequently accumulated within cells, resulting in the hyperactivation of Rac1 and defects in neuronal development. CONCLUSIONS Our findings demonstrate that the location of variants within KIDINS220 plays a crucial role in determining inheritance patterns and corresponding clinical outcomes. The proposed interaction between Rac1 and KIDINS220 provides new insights into the pathogenesis of cerebral palsy, implying potential therapeutic perspectives. © 2023 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Jin Zhang
- Children's Hospital of Fudan University and Institutes of Biomedical Sciences of Fudan University, Shanghai, China
| | - Yandong Zhang
- Department of Anesthesia, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Zhongshan Hospital Fudan University, Shanghai, China
| | - Qing Shang
- Department of Pediatric Rehabilitation Medicine, Children's Hospital of Zhengzhou University and Henan Children's Hospital, Zhengzhou, China
| | - Ye Cheng
- Children's Hospital of Fudan University and Institutes of Biomedical Sciences of Fudan University, Shanghai, China
| | - Yu Su
- Children's Hospital of Fudan University and Institutes of Biomedical Sciences of Fudan University, Shanghai, China
| | - Junjie Zhang
- Children's Hospital of Fudan University and Institutes of Biomedical Sciences of Fudan University, Shanghai, China
| | - Ting Wang
- Children's Hospital of Fudan University and Institutes of Biomedical Sciences of Fudan University, Shanghai, China
| | - Jian Ding
- Children's Hospital of Fudan University and Institutes of Biomedical Sciences of Fudan University, Shanghai, China
| | - Yunqian Li
- Children's Hospital of Fudan University and Institutes of Biomedical Sciences of Fudan University, Shanghai, China
| | - Yunli Xie
- Department of Anesthesia, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Zhongshan Hospital Fudan University, Shanghai, China
| | - Qinghe Xing
- Children's Hospital of Fudan University and Institutes of Biomedical Sciences of Fudan University, Shanghai, China
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8
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Sanchez C, Ramirez A, Hodgson L. Unravelling molecular dynamics in living cells: Fluorescent protein biosensors for cell biology. J Microsc 2024. [PMID: 38357769 DOI: 10.1111/jmi.13270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/11/2024] [Accepted: 01/22/2024] [Indexed: 02/16/2024]
Abstract
Genetically encoded, fluorescent protein (FP)-based Förster resonance energy transfer (FRET) biosensors are microscopy imaging tools tailored for the precise monitoring and detection of molecular dynamics within subcellular microenvironments. They are characterised by their ability to provide an outstanding combination of spatial and temporal resolutions in live-cell microscopy. In this review, we begin by tracing back on the historical development of genetically encoded FP labelling for detection in live cells, which lead us to the development of early biosensors and finally to the engineering of single-chain FRET-based biosensors that have become the state-of-the-art today. Ultimately, this review delves into the fundamental principles of FRET and the design strategies underpinning FRET-based biosensors, discusses their diverse applications and addresses the distinct challenges associated with their implementation. We place particular emphasis on single-chain FRET biosensors for the Rho family of guanosine triphosphate hydrolases (GTPases), pointing to their historical role in driving our understanding of the molecular dynamics of this important class of signalling proteins and revealing the intricate relationships and regulatory mechanisms that comprise Rho GTPase biology in living cells.
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Affiliation(s)
- Colline Sanchez
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Andrea Ramirez
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Louis Hodgson
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, USA
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9
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Wang S, Chi WY, Au G, Huang CC, Yang JM, Huang CH. Reconstructing Signaling Networks Using Biosensor Barcoding. Methods Mol Biol 2024; 2800:189-202. [PMID: 38709485 PMCID: PMC11177205 DOI: 10.1007/978-1-0716-3834-7_13] [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: 05/07/2024]
Abstract
Understanding how signaling networks are regulated offers valuable insights into how cells and organisms react to internal and external stimuli and is crucial for developing novel strategies to treat diseases. To achieve this, it is necessary to delineate the intricate interactions between the nodes in the network, which can be accomplished by measuring the activities of individual nodes under perturbation conditions. To facilitate this, we have recently developed a biosensor barcoding technique that enables massively multiplexed tracking of numerous signaling activities in live cells using genetically encoded fluorescent biosensors. In this chapter, we detail how we employed this method to reconstruct the EGFR signaling network by systematically monitoring the activities of individual nodes under perturbations.
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Affiliation(s)
- Suyang Wang
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Wei-Yu Chi
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD, USA
- Weill Cornell Medicine, New York, NY, USA
| | - Gabriel Au
- Department of Biology, Krieger School of Arts and Sciences, Johns Hopkins University, Baltimore, MD, USA
| | - Cheng-Chieh Huang
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Jr-Ming Yang
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD, USA.
| | - Chuan-Hsiang Huang
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD, USA.
- Department of Cell Biology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA.
- Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD, USA.
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10
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Ram A, Murphy D, DeCuzzi N, Patankar M, Hu J, Pargett M, Albeck JG. A guide to ERK dynamics, part 1: mechanisms and models. Biochem J 2023; 480:1887-1907. [PMID: 38038974 PMCID: PMC10754288 DOI: 10.1042/bcj20230276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 11/02/2023] [Accepted: 11/06/2023] [Indexed: 12/02/2023]
Abstract
Extracellular signal-regulated kinase (ERK) has long been studied as a key driver of both essential cellular processes and disease. A persistent question has been how this single pathway is able to direct multiple cell behaviors, including growth, proliferation, and death. Modern biosensor studies have revealed that the temporal pattern of ERK activity is highly variable and heterogeneous, and critically, that these dynamic differences modulate cell fate. This two-part review discusses the current understanding of dynamic activity in the ERK pathway, how it regulates cellular decisions, and how these cell fates lead to tissue regulation and pathology. In part 1, we cover the optogenetic and live-cell imaging technologies that first revealed the dynamic nature of ERK, as well as current challenges in biosensor data analysis. We also discuss advances in mathematical models for the mechanisms of ERK dynamics, including receptor-level regulation, negative feedback, cooperativity, and paracrine signaling. While hurdles still remain, it is clear that higher temporal and spatial resolution provide mechanistic insights into pathway circuitry. Exciting new algorithms and advanced computational tools enable quantitative measurements of single-cell ERK activation, which in turn inform better models of pathway behavior. However, the fact that current models still cannot fully recapitulate the diversity of ERK responses calls for a deeper understanding of network structure and signal transduction in general.
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Affiliation(s)
- Abhineet Ram
- Department of Molecular and Cellular Biology, University of California, Davis, U.S.A
| | - Devan Murphy
- Department of Molecular and Cellular Biology, University of California, Davis, U.S.A
| | - Nicholaus DeCuzzi
- Department of Molecular and Cellular Biology, University of California, Davis, U.S.A
| | - Madhura Patankar
- Department of Molecular and Cellular Biology, University of California, Davis, U.S.A
| | - Jason Hu
- Department of Molecular and Cellular Biology, University of California, Davis, U.S.A
| | - Michael Pargett
- Department of Molecular and Cellular Biology, University of California, Davis, U.S.A
| | - John G. Albeck
- Department of Molecular and Cellular Biology, University of California, Davis, U.S.A
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11
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Conway JRW, Isomursu A, Follain G, Härmä V, Jou-Ollé E, Pasquier N, Välimäki EPO, Rantala JK, Ivaska J. Defined extracellular matrix compositions support stiffness-insensitive cell spreading and adhesion signaling. Proc Natl Acad Sci U S A 2023; 120:e2304288120. [PMID: 37844244 PMCID: PMC10614832 DOI: 10.1073/pnas.2304288120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 09/15/2023] [Indexed: 10/18/2023] Open
Abstract
Integrin-dependent adhesion to the extracellular matrix (ECM) mediates mechanosensing and signaling in response to altered microenvironmental conditions. In order to provide tissue- and organ-specific cues, the ECM is composed of many different proteins that temper the mechanical properties and provide the necessary structural diversity. Despite most human tissues being soft, the prevailing view from predominantly in vitro studies is that increased stiffness triggers effective cell spreading and activation of mechanosensitive signaling pathways. To address the functional coupling of ECM composition and matrix rigidity on compliant substrates, we developed a matrix spot array system to screen cell phenotypes against different ECM mixtures on defined substrate stiffnesses at high resolution. We applied this system to both cancer and normal cells and surprisingly identified ECM mixtures that support stiffness-insensitive cell spreading on soft substrates. Employing the motor-clutch model to simulate cell adhesion on biochemically distinct soft substrates, with varying numbers of available ECM-integrin-cytoskeleton (clutch) connections, we identified conditions in which spreading would be supported on soft matrices. Combining simulations and experiments, we show that cell spreading on soft is supported by increased clutch engagement on specific ECM mixtures and even augmented by the partial inhibition of actomyosin contractility. Thus, "stiff-like" spreading on soft is determined by a balance of a cell's contractile and adhesive machinery. This provides a fundamental perspective for in vitro mechanobiology studies, identifying a mechanism through which cells spread, function, and signal effectively on soft substrates.
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Affiliation(s)
- James R. W. Conway
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, TurkuFI-20520, Finland
| | - Aleksi Isomursu
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, TurkuFI-20520, Finland
| | - Gautier Follain
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, TurkuFI-20520, Finland
| | - Ville Härmä
- Misvik Biology Oy, TurkuFI-20520, Finland
- Department of Oncology and Metabolism, University of Sheffield, SheffieldS10 2TN, United Kingdom
| | - Eva Jou-Ollé
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, TurkuFI-20520, Finland
| | - Nicolas Pasquier
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, TurkuFI-20520, Finland
| | | | - Juha K. Rantala
- Misvik Biology Oy, TurkuFI-20520, Finland
- Department of Oncology and Metabolism, University of Sheffield, SheffieldS10 2TN, United Kingdom
| | - Johanna Ivaska
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, TurkuFI-20520, Finland
- Department of Life Technologies, University of Turku, TurkuFI-20520, Finland
- InFLAMES Research Flagship, University of Turku, TurkuFI-20520, Finland
- Western Finnish Cancer Center, University of Turku, TurkuFI-20520, Finland
- Foundation for the Finnish Cancer Institute, HelsinkiFI-00014, Finland
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12
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Gasparski AN, Moissoglu K, Pallikkuth S, Meydan S, Guydosh NR, Mili S. mRNA location and translation rate determine protein targeting to dual destinations. Mol Cell 2023; 83:2726-2738.e9. [PMID: 37506697 PMCID: PMC10530421 DOI: 10.1016/j.molcel.2023.06.036] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 04/25/2023] [Accepted: 06/30/2023] [Indexed: 07/30/2023]
Abstract
Numerous proteins are targeted to two or multiple subcellular destinations where they exert distinct functional consequences. The balance between such differential targeting is thought to be determined post-translationally, relying on protein sorting mechanisms. Here, we show that mRNA location and translation rate can also determine protein targeting by modulating protein binding to specific interacting partners. Peripheral localization of the NET1 mRNA and fast translation lead to higher cytosolic retention of the NET1 protein by promoting its binding to the membrane-associated scaffold protein CASK. By contrast, perinuclear mRNA location and/or slower translation rate favor nuclear targeting by promoting binding to importins. This mRNA location-dependent mechanism is modulated by physiological stimuli and profoundly impacts NET1 function in cell motility. These results reveal that the location of protein synthesis and the rate of translation elongation act in coordination as a "partner-selection" mechanism that robustly influences protein distribution and function.
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Affiliation(s)
- Alexander N Gasparski
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Konstadinos Moissoglu
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Sandeep Pallikkuth
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Sezen Meydan
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA; National Institute of General Medical Sciences, NIH, Bethesda, MD 20892, USA
| | - Nicholas R Guydosh
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA
| | - Stavroula Mili
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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13
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Rohrer L, Spohr C, Beha C, Griffin R, Braun S, Halbach S, Brummer T. Analysis of RAS and drug induced homo- and heterodimerization of RAF and KSR1 proteins in living cells using split Nanoluc luciferase. Cell Commun Signal 2023; 21:136. [PMID: 37316874 DOI: 10.1186/s12964-023-01146-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 04/27/2023] [Indexed: 06/16/2023] Open
Abstract
The dimerization of RAF kinases represents a key event in their activation cycle and in RAS/ERK pathway activation. Genetic, biochemical and structural approaches provided key insights into this process defining RAF signaling output and the clinical efficacy of RAF inhibitors (RAFi). However, methods reporting the dynamics of RAF dimerization in living cells and in real time are still in their infancy. Recently, split luciferase systems have been developed for the detection of protein-protein-interactions (PPIs), incl. proof-of-concept studies demonstrating the heterodimerization of the BRAF and RAF1 isoforms. Due to their small size, the Nanoluc luciferase moieties LgBiT and SmBiT, which reconstitute a light emitting holoenzyme upon fusion partner promoted interaction, appear as well-suited to study RAF dimerization. Here, we provide an extensive analysis of the suitability of the Nanoluc system to study the homo- and heterodimerization of BRAF, RAF1 and the related KSR1 pseudokinase. We show that KRASG12V promotes the homo- and heterodimerization of BRAF, while considerable KSR1 homo- and KSR1/BRAF heterodimerization already occurs in the absence of this active GTPase and requires a salt bridge between the CC-SAM domain of KSR1 and the BRAF-specific region. We demonstrate that loss-of-function mutations impairing key steps of the RAF activation cycle can be used as calibrators to gauge the dynamics of heterodimerization. This approach identified the RAS-binding domains and the C-terminal 14-3-3 binding motifs as particularly critical for the reconstitution of RAF mediated LgBiT/SmBiT reconstitution, while the dimer interface was less important for dimerization but essential for downstream signaling. We show for the first time that BRAFV600E, the most common BRAF oncoprotein whose dimerization status is controversially portrayed in the literature, forms homodimers in living cells more efficiently than its wildtype counterpart. Of note, Nanoluc activity reconstituted by BRAFV600E homodimers is highly sensitive to the paradox-breaking RAFi PLX8394, indicating a dynamic and specific PPI. We report the effects of eleven ERK pathway inhibitors on RAF dimerization, incl. third-generation compounds that are less-defined in terms of their dimer promoting abilities. We identify Naporafenib as a potent and long-lasting dimerizer and show that the split Nanoluc approach discriminates between type I, I1/2 and II RAFi. Video Abstract.
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Affiliation(s)
- Lino Rohrer
- Institute of Molecular Medicine and Cell Research (IMMZ), Zentrum für Biochemie und Molekulare Zellforschung (ZBMZ), Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, Freiburg, 79104, Germany
| | - Corinna Spohr
- Institute of Molecular Medicine and Cell Research (IMMZ), Zentrum für Biochemie und Molekulare Zellforschung (ZBMZ), Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, Freiburg, 79104, Germany
| | - Carina Beha
- Institute of Molecular Medicine and Cell Research (IMMZ), Zentrum für Biochemie und Molekulare Zellforschung (ZBMZ), Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, Freiburg, 79104, Germany
| | - Ricarda Griffin
- Institute of Molecular Medicine and Cell Research (IMMZ), Zentrum für Biochemie und Molekulare Zellforschung (ZBMZ), Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, Freiburg, 79104, Germany
| | - Sandra Braun
- Institute of Molecular Medicine and Cell Research (IMMZ), Zentrum für Biochemie und Molekulare Zellforschung (ZBMZ), Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, Freiburg, 79104, Germany
| | - Sebastian Halbach
- Institute of Molecular Medicine and Cell Research (IMMZ), Zentrum für Biochemie und Molekulare Zellforschung (ZBMZ), Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, Freiburg, 79104, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Tilman Brummer
- Institute of Molecular Medicine and Cell Research (IMMZ), Zentrum für Biochemie und Molekulare Zellforschung (ZBMZ), Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, Freiburg, 79104, Germany.
- German Cancer Consortium (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany.
- Comprehensive Cancer Center Freiburg (CCCF), Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, 79106, Germany.
- Center for Biological Signalling Studies BIOSS, University of Freiburg, Freiburg, 79104, Germany.
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14
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Sampayo RG, Sakamoto M, Wang M, Kumar S, Schaffer DV. Mechanosensitive stem cell fate choice is instructed by dynamic fluctuations in activation of Rho GTPases. Proc Natl Acad Sci U S A 2023; 120:e2219854120. [PMID: 37216516 PMCID: PMC10235963 DOI: 10.1073/pnas.2219854120] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 04/24/2023] [Indexed: 05/24/2023] Open
Abstract
During the intricate process by which cells give rise to tissues, embryonic and adult stem cells are exposed to diverse mechanical signals from the extracellular matrix (ECM) that influence their fate. Cells can sense these cues in part through dynamic generation of protrusions, modulated and controlled by cyclic activation of Rho GTPases. However, it remains unclear how extracellular mechanical signals regulate Rho GTPase activation dynamics and how such rapid, transient activation dynamics are integrated to yield long-term, irreversible cell fate decisions. Here, we report that ECM stiffness cues alter not only the magnitude but also the temporal frequency of RhoA and Cdc42 activation in adult neural stem cells (NSCs). Using optogenetics to control the frequency of RhoA and Cdc42 activation, we further demonstrate that these dynamics are functionally significant, where high- vs. low-frequency activation of RhoA and Cdc42 drives astrocytic vs. neuronal differentiation, respectively. In addition, high-frequency Rho GTPase activation induces sustained phosphorylation of the TGFβ pathway effector SMAD1, which in turn drives the astrocytic differentiation. By contrast, under low-frequency Rho GTPase stimulation, cells fail to accumulate SMAD1 phosphorylation and instead undergo neurogenesis. Our findings reveal the temporal patterning of Rho GTPase signaling and the resulting accumulation of an SMAD1 signal as a critical mechanism through which ECM stiffness cues regulate NSC fate.
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Affiliation(s)
- Rocío G. Sampayo
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA94720
- Department of Bioengineering, University of California, Berkeley, CA94720
| | - Mason Sakamoto
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA94720
- Department of Bioengineering, University of California, Berkeley, CA94720
| | - Madeline Wang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA94720
- Department of Bioengineering, University of California, Berkeley, CA94720
| | - Sanjay Kumar
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA94720
- Department of Bioengineering, University of California, Berkeley, CA94720
| | - David V. Schaffer
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA94720
- Department of Bioengineering, University of California, Berkeley, CA94720
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15
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Saldanha DJ, Cai A, Dorval Courchesne NM. The Evolving Role of Proteins in Wearable Sweat Biosensors. ACS Biomater Sci Eng 2023; 9:2020-2047. [PMID: 34491052 DOI: 10.1021/acsbiomaterials.1c00699] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Sweat is an increasingly popular biological medium for fitness monitoring and clinical diagnostics. It contains an abundance of biological information and is available continuously and noninvasively. Sweat-sensing devices often employ proteins in various capacities to create skin-friendly matrices that accurately extract valuable and time-sensitive information from sweat. Proteins were first used in sensors as biorecognition elements in the form of enzymes and antibodies, which are now being tuned to operate at ranges relevant for sweat. In addition, a range of structural proteins, sometimes assembled in conjunction with polymers, can provide flexible and compatible matrices for skin sensors. Other proteins also naturally possess a range of functionalities─as adhesives, charge conductors, fluorescence emitters, and power generators─that can make them useful components in wearable devices. Here, we examine the four main components of wearable sweat sensors─the biorecognition element, the transducer, the scaffold, and the adhesive─and the roles that proteins have played so far, or promise to play in the future, in each component. On a case-by-case basis, we analyze the performance characteristics of existing protein-based devices, their applicable ranges of detection, their transduction mechanism and their mechanical properties. Thereby, we review and compare proteins that can readily be used in sweat sensors and others that will require further efforts to overcome design, stability or scalability challenges. Incorporating proteins in one or multiple components of sweat sensors could lead to the development and deployment of tunable, greener, and safer biosourced devices.
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Affiliation(s)
- Dalia Jane Saldanha
- Department of Chemical Engineering, McGill University, Montréal, Québec, Canada H3A 0C5
| | - Anqi Cai
- Department of Chemical Engineering, McGill University, Montréal, Québec, Canada H3A 0C5
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16
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Gasparski AN, Moissoglu K, Pallikkuth S, Meydan S, Guydosh NR, Mili S. mRNA Location and Translation Rate Determine Protein Targeting to Dual Destinations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.24.538105. [PMID: 37163129 PMCID: PMC10168211 DOI: 10.1101/2023.04.24.538105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Numerous proteins are targeted to two or multiple subcellular destinations where they exert distinct functional consequences. The balance between such differential targeting is thought to be determined post-translationally, relying on protein sorting mechanisms. Here, we show that protein targeting can additionally be determined by mRNA location and translation rate, through modulating protein binding to specific interacting partners. Peripheral localization of the NET1 mRNA and fast translation lead to higher cytosolic retention of the NET1 protein, through promoting its binding to the membrane-associated scaffold protein CASK. By contrast, perinuclear mRNA location and/or slower translation rate favor nuclear targeting, through promoting binding to importins. This mRNA location-dependent mechanism is modulated by physiological stimuli and profoundly impacts NET1 function in cell motility. These results reveal that the location of protein synthesis and the rate of translation elongation act in coordination as a 'partner-selection' mechanism that robustly influences protein distribution and function.
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Affiliation(s)
- Alexander N. Gasparski
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, NIH, Bethesda, 20892, MD, USA
| | - Konstadinos Moissoglu
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, NIH, Bethesda, 20892, MD, USA
| | - Sandeep Pallikkuth
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, NIH, Bethesda, 20892, MD, USA
| | - Sezen Meydan
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, 20892, MD, USA
- National Institute of General Medical Sciences, NIH, Bethesda, 20892, MD, USA
| | - Nicholas R. Guydosh
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, 20892, MD, USA
| | - Stavroula Mili
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, NIH, Bethesda, 20892, MD, USA
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17
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Oh SC, Kim SE, Jang IH, Kim SM, Lee SY, Lee S, Chu IS, Yoon SR, Jung H, Choi I, Doh J, Kim TD. NgR1 is an NK cell inhibitory receptor that destabilizes the immunological synapse. Nat Immunol 2023; 24:463-473. [PMID: 36624164 DOI: 10.1038/s41590-022-01394-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 11/22/2022] [Indexed: 01/10/2023]
Abstract
The formation of an immunological synapse (IS) is essential for natural killer (NK) cells to eliminate target cells. Despite an advanced understanding of the characteristics of the IS and its formation processes, the mechanisms that regulate its stability via the cytoskeleton are unclear. Here, we show that Nogo receptor 1 (NgR1) has an important function in modulating NK cell-mediated killing by destabilization of IS formation. NgR1 deficiency or blockade resulted in improved tumor control of NK cells by enhancing NK-to-target cell contact stability and regulating F-actin dynamics during IS formation. Patients with tumors expressing abundant NgR1 ligand had poor prognosis despite high levels of NK cell infiltration. Thus, our study identifies NgR1 as an immune checkpoint in IS formation and indicates a potential approach to improve the cytolytic function of NK cells in cancer immunotherapy.
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Affiliation(s)
- Se-Chan Oh
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea.,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon, Republic of Korea
| | - Seong-Eun Kim
- Department of Mechanical Engineering, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - In-Hwan Jang
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea.,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon, Republic of Korea
| | - Seok-Min Kim
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea.,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon, Republic of Korea
| | - Soo Yun Lee
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Sunyoung Lee
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea.,Department of Life Sciences, Korea University, Seoul, Republic of Korea
| | - In-Sun Chu
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea.,Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon, Republic of Korea
| | - Suk Ran Yoon
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea.,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon, Republic of Korea
| | - Haiyoung Jung
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea.,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon, Republic of Korea
| | - Inpyo Choi
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Junsang Doh
- Department of Materials Science and Engineering, Research Institute of Advanced Materials, Institute of Engineering Research, Bio-MAX Institute, Soft Foundry Institute, Seoul National University, Seoul, Republic of Korea.
| | - Tae-Don Kim
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea. .,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon, Republic of Korea. .,Biomedical Mathematics Group, Institute for Basic Science, Daejeon, Republic of Korea. .,Department of Biopharmaceutical Convergence, School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea.
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18
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Gohil K, Wu SY, Takahashi-Yamashiro K, Shen Y, Campbell RE. Biosensor Optimization Using a Förster Resonance Energy Transfer Pair Based on mScarlet Red Fluorescent Protein and an mScarlet-Derived Green Fluorescent Protein. ACS Sens 2023; 8:587-597. [PMID: 36693235 DOI: 10.1021/acssensors.2c01730] [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: 01/26/2023]
Abstract
Genetically encoded biosensors based on Förster resonance energy transfer (FRET) are indispensable tools for monitoring biochemical changes in cells. Green and red fluorescent protein-based FRET pairs offer advantages over the classically employed cyan and yellow fluorescent protein pairs, such as better spectral separation, lower phototoxicity, and less autofluorescence. Here, we describe the development of an mScarlet-derived green fluorescent protein (designated as mWatermelon) and its use as a FRET donor to the red fluorescent protein mScarlet-I as a FRET acceptor. We tested the functionality of this FRET pair by engineering biosensors for the detection of protease activity, Ca2+, and K+. Furthermore, we described a strategy to enhance the FRET efficiency of these biosensors by modulating the intramolecular association between mWatermelon and mScarlet-I.
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Affiliation(s)
- Khyati Gohil
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Sheng-Yi Wu
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | | | - Yi Shen
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Robert E Campbell
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada.,Department of Chemistry, The University of Tokyo, Tokyo 113-0033, Japan
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19
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de Seze J, Gatin J, Coppey M. RhoA regulation in space and time. FEBS Lett 2023; 597:836-849. [PMID: 36658753 DOI: 10.1002/1873-3468.14578] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 12/22/2022] [Accepted: 12/29/2022] [Indexed: 01/21/2023]
Abstract
RhoGTPases are well known for being controllers of cell cytoskeleton and share common features in the way they act and are controlled. These include their switch from GDP to GTP states, their regulations by different guanine exchange factors (GEFs), GTPase-activating proteins and guanosine dissociation inhibitors (GDIs), and their similar structure of active sites/membrane anchors. These very similar features often lead to the common consideration that the differences in their biological effects mainly arise from the different types of regulators and specific effectors associated with each GTPase. Focusing on data obtained through biosensors, live cell microscopy and recent optogenetic approaches, we highlight in this review that the regulation of RhoA appears to depart from Cdc42 and Rac1 modes of regulation through its enhanced lability at the plasma membrane. RhoA presents a high dynamic turnover at the membrane that is regulated not only by GDIs but also by GEFs, effectors and a possible soluble conformational state. This peculiarity of RhoA regulation may be important for the specificities of its functions, such as the existence of activity waves or its putative dual role in the initiation of protrusions and contractions.
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Affiliation(s)
- Jean de Seze
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico-Chimie Curie, Paris, France
| | - Joséphine Gatin
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico-Chimie Curie, Paris, France
| | - Mathieu Coppey
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico-Chimie Curie, Paris, France
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20
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Law RA, Kiepas A, Desta HE, Perez Ipiña E, Parlani M, Lee SJ, Yankaskas CL, Zhao R, Mistriotis P, Wang N, Gu Z, Kalab P, Friedl P, Camley BA, Konstantopoulos K. Cytokinesis machinery promotes cell dissociation from collectively migrating strands in confinement. SCIENCE ADVANCES 2023; 9:eabq6480. [PMID: 36630496 PMCID: PMC9833664 DOI: 10.1126/sciadv.abq6480] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Cells tune adherens junction dynamics to regulate epithelial integrity in diverse (patho)physiological processes, including cancer metastasis. We hypothesized that the spatially confining architecture of peritumor stroma promotes metastatic cell dissemination by remodeling cell-cell adhesive interactions. By combining microfluidics with live-cell imaging, FLIM/FRET biosensors, and optogenetic tools, we show that confinement induces leader cell dissociation from cohesive ensembles. Cell dissociation is triggered by myosin IIA (MIIA) dismantling of E-cadherin cell-cell junctions, as recapitulated by a mathematical model. Elevated MIIA contractility is controlled by RhoA/ROCK activation, which requires distinct guanine nucleotide exchange factors (GEFs). Confinement activates RhoA via nucleocytoplasmic shuttling of the cytokinesis-regulatory proteins RacGAP1 and Ect2 and increased microtubule dynamics, which results in the release of active GEF-H1. Thus, confining microenvironments are sufficient to induce cell dissemination from primary tumors by remodeling E-cadherin cell junctions via the interplay of microtubules, nuclear trafficking, and RhoA/ROCK/MIIA pathway and not by down-regulating E-cadherin expression.
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Affiliation(s)
- Robert A. Law
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Johns Hopkins Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Alexander Kiepas
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Johns Hopkins Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Habben E. Desta
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Johns Hopkins Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Emiliano Perez Ipiña
- William H. Miller III Department of Physics and Astronomy, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Maria Parlani
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Se Jong Lee
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Johns Hopkins Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Christopher L. Yankaskas
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Johns Hopkins Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Runchen Zhao
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Johns Hopkins Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Panagiotis Mistriotis
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Johns Hopkins Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Chemical Engineering, Auburn University, Auburn, AL 36849, USA
| | - Nianchao Wang
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Johns Hopkins Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Zhizhan Gu
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Johns Hopkins Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
- Corresponding author. (K.K.); (Z.G.)
| | - Petr Kalab
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Peter Friedl
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
- Cancer Genomics Center, 3584 Utrecht, Netherlands
| | - Brian A. Camley
- William H. Miller III Department of Physics and Astronomy, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Konstantinos Konstantopoulos
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Johns Hopkins Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
- Corresponding author. (K.K.); (Z.G.)
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21
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Tiwari S, Fauvet B, Assenza S, De Los Rios P, Goloubinoff P. A fluorescent multi-domain protein reveals the unfolding mechanism of Hsp70. Nat Chem Biol 2023; 19:198-205. [PMID: 36266349 PMCID: PMC9889267 DOI: 10.1038/s41589-022-01162-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 09/06/2022] [Indexed: 02/04/2023]
Abstract
Detailed understanding of the mechanism by which Hsp70 chaperones protect cells against protein aggregation is hampered by the lack of a comprehensive characterization of the aggregates, which are typically heterogeneous. Here we designed a reporter chaperone substrate, MLucV, composed of a stress-labile luciferase flanked by stress-resistant fluorescent domains, which upon denaturation formed a discrete population of small aggregates. Combining Förster resonance energy transfer and enzymatic activity measurements provided unprecedented details on the aggregated, unfolded, Hsp70-bound and native MLucV conformations. The Hsp70 mechanism first involved ATP-fueled disaggregation and unfolding of the stable pre-aggregated substrate, which stretched MLucV beyond simply unfolded conformations, followed by native refolding. The ATP-fueled unfolding and refolding action of Hsp70 on MLucV aggregates could accumulate native MLucV species under elevated denaturing temperatures highly adverse to the native state. These results unambiguously exclude binding and preventing of aggregation from the non-equilibrium mechanism by which Hsp70 converts stable aggregates into metastable native proteins.
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Affiliation(s)
- Satyam Tiwari
- grid.9851.50000 0001 2165 4204Department of Plant Molecular Biology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland ,grid.5333.60000000121839049Institute of Physics, School of Basic Sciences, École Polytechnique Fédérale de Lausanne - EPFL, Lausanne, Switzerland
| | - Bruno Fauvet
- grid.5333.60000000121839049Institute of Physics, School of Basic Sciences, École Polytechnique Fédérale de Lausanne - EPFL, Lausanne, Switzerland
| | - Salvatore Assenza
- grid.5515.40000000119578126Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, Spain ,grid.5515.40000000119578126Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, Madrid, Spain ,grid.5515.40000000119578126Instituto Nicolás Cabrera, Universidad Autónoma de Madrid, Madrid, Spain
| | - Paolo De Los Rios
- Institute of Physics, School of Basic Sciences, École Polytechnique Fédérale de Lausanne - EPFL, Lausanne, Switzerland. .,Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne - EPFL, Lausanne, Switzerland.
| | - Pierre Goloubinoff
- Department of Plant Molecular Biology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland. .,School of Plant Sciences and Food Security, Tel-Aviv University, Tel Aviv, Israel.
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22
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Müller PM, Rocks O. A screening-compatible live cell fluorescence resonance energy transfer-based assay for modulation of Rho GTPase activity. STAR Protoc 2022; 3:101705. [PMID: 36149795 PMCID: PMC9508600 DOI: 10.1016/j.xpro.2022.101705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/08/2022] [Accepted: 08/23/2022] [Indexed: 01/25/2023] Open
Abstract
Rho family GTPases are central regulators of cytoskeletal dynamics controlled by guanine nucleotide exchange factors (RhoGEFs) and GTPase-activating proteins (RhoGAPs). This protocol presents a workflow for a robust high-throughput compatible biosensor assay to analyze changes in Rho GTPase activity by these proteins in the native cellular environment. The procedure can be used for semi-quantitative comparison of GEF/GAP function and extended for analysis of additional modulators. The experimental design is applicable also to other monomolecular ratiometric FRET sensors. For complete details on the use and execution of this protocol, please refer to Müller et al. (2020).
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Affiliation(s)
- Paul Markus Müller
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany,Corresponding author
| | - Oliver Rocks
- Institute of Biochemistry, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany,Corresponding author
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23
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Phuyal S, Djaerff E, Le Roux A, Baker MJ, Fankhauser D, Mahdizadeh SJ, Reiterer V, Parizadeh A, Felder E, Kahlhofer JC, Teis D, Kazanietz MG, Geley S, Eriksson L, Roca‐Cusachs P, Farhan H. Mechanical strain stimulates COPII-dependent secretory trafficking via Rac1. EMBO J 2022; 41:e110596. [PMID: 35938214 PMCID: PMC9475550 DOI: 10.15252/embj.2022110596] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 06/29/2022] [Accepted: 07/05/2022] [Indexed: 12/13/2022] Open
Abstract
Cells are constantly exposed to various chemical and physical stimuli. While much has been learned about the biochemical factors that regulate secretory trafficking from the endoplasmic reticulum (ER), much less is known about whether and how this trafficking is subject to regulation by mechanical signals. Here, we show that subjecting cells to mechanical strain both induces the formation of ER exit sites (ERES) and accelerates ER-to-Golgi trafficking. We found that cells with impaired ERES function were less capable of expanding their surface area when placed under mechanical stress and were more prone to develop plasma membrane defects when subjected to stretching. Thus, coupling of ERES function to mechanotransduction appears to confer resistance of cells to mechanical stress. Furthermore, we show that the coupling of mechanotransduction to ERES formation was mediated via a previously unappreciated ER-localized pool of the small GTPase Rac1. Mechanistically, we show that Rac1 interacts with the small GTPase Sar1 to drive budding of COPII carriers and stimulates ER-to-Golgi transport. This interaction therefore represents an unprecedented link between mechanical strain and export from the ER.
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Affiliation(s)
- Santosh Phuyal
- Institute of Basic Medical SciencesUniversity of OsloOsloNorway
| | - Elena Djaerff
- Institute of Basic Medical SciencesUniversity of OsloOsloNorway
| | - Anabel‐Lise Le Roux
- Institute for Bioengineering of Catalonia (IBEC)the Barcelona Institute of Technology (BIST)BarcelonaSpain
| | - Martin J Baker
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Daniela Fankhauser
- Institute of PathophysiologyMedical University of InnsbruckInnsbruckAustria
| | | | - Veronika Reiterer
- Institute of PathophysiologyMedical University of InnsbruckInnsbruckAustria
| | | | - Edward Felder
- Institute of General PhysiologyUniversity of UlmUlmGermany
| | | | - David Teis
- Institute of Cell BiologyMedical University of InnsbruckInnsbruckAustria
| | - Marcelo G Kazanietz
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Stephan Geley
- Institute of PathophysiologyMedical University of InnsbruckInnsbruckAustria
| | - Leif Eriksson
- Department of chemistry and molecular biologyUniversity of GothenburgGothenburgSweden
| | - Pere Roca‐Cusachs
- Institute for Bioengineering of Catalonia (IBEC)the Barcelona Institute of Technology (BIST)BarcelonaSpain
- Universitat de BarcelonaBarcelonaSpain
| | - Hesso Farhan
- Institute of Basic Medical SciencesUniversity of OsloOsloNorway
- Institute of PathophysiologyMedical University of InnsbruckInnsbruckAustria
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24
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Imaging and analysis for simultaneous tracking of fluorescent biosensors in barcoded cells. STAR Protoc 2022; 3:101611. [PMID: 36042884 PMCID: PMC9420398 DOI: 10.1016/j.xpro.2022.101611] [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] [Indexed: 11/30/2022] Open
Abstract
We recently developed a biosensor barcoding approach for highly multiplexed tracking of molecular activities in live cells. In this protocol, we detail the labeling of cells expressing different genetically encoded fluorescent biosensors with a pair of barcoding proteins and parallel imaging. Signals from cells with the same barcodes are then pooled together to obtain the dynamics of the corresponding biosensor activity. We describe the steps involved in cell barcoding, image acquisition, and analysis by deep learning models. For complete details on the use and execution of this protocol, please refer to Yang et al. (2021). Cells expressing different biosensors can be barcoded for simultaneous imaging Spectral imaging is used to resolve multiple red barcoding proteins Deep learning models accelerate barcode reading during image analysis
Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.
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25
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Anijs M, Devanna P, Vernes SC. ARHGEF39, a Gene Implicated in Developmental Language Disorder, Activates RHOA and Is Involved in Cell De-Adhesion and Neural Progenitor Cell Proliferation. Front Mol Neurosci 2022; 15:941494. [PMID: 35959104 PMCID: PMC9359124 DOI: 10.3389/fnmol.2022.941494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 06/21/2022] [Indexed: 11/13/2022] Open
Abstract
ARHGEF39 was previously implicated in developmental language disorder (DLD) via a functional polymorphism that can disrupt post-transcriptional regulation by microRNAs. ARHGEF39 is part of the family of Rho guanine nucleotide exchange factors (RhoGEFs) that activate small Rho GTPases to regulate a wide variety of cellular processes. However, little is known about the function of ARHGEF39, or how its function might contribute to neurodevelopment or related disorders. Here, we explore the molecular function of ARHGEF39 and show that it activates the Rho GTPase RHOA and that high ARHGEF39 expression in cell cultures leads to an increase of detached cells. To explore its role in neurodevelopment, we analyse published single cell RNA-sequencing data and demonstrate that ARHGEF39 is a marker gene for proliferating neural progenitor cells and that it is co-expressed with genes involved in cell division. This suggests a role for ARHGEF39 in neurogenesis in the developing brain. The co-expression of ARHGEF39 with other RHOA-regulating genes supports RHOA as substrate of ARHGEF39 in neural cells, and the involvement of RHOA in neuropsychiatric disorders highlights a potential link between ARHGEF39 and neurodevelopment and disorder. Understanding the GTPase substrate, co-expression network, and processes downstream of ARHGEF39 provide new avenues for exploring the mechanisms by which altered expression levels of ARHGEF39 may contribute to neurodevelopment and associated disorders.
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26
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Grubisha MJ, DeGiosio RA, Wills ZP, Sweet RA. Trio and Kalirin as unique enactors of Rho/Rac spatiotemporal precision. Cell Signal 2022; 98:110416. [PMID: 35872089 DOI: 10.1016/j.cellsig.2022.110416] [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: 06/22/2022] [Revised: 07/18/2022] [Accepted: 07/19/2022] [Indexed: 12/18/2022]
Abstract
Rac1 and RhoA are among the most widely studied small GTPases. The classic dogma surrounding their biology has largely focused on their activity as an "on/off switch" of sorts. However, the advent of more sophisticated techniques, such as genetically-encoded FRET-based sensors, has afforded the ability to delineate the spatiotemporal regulation of Rac1 and RhoA. As a result, there has been a shift from this simplistic global view to one incorporating the precision of spatiotemporal modularity. This review summarizes emerging data surrounding the roles of Rac1 and RhoA as cytoskeletal regulators and examines how these new data have led to a revision of the traditional dogma which placed Rac1 and RhoA in antagonistic pathways. This more recent evidence suggests that rather than absolute activity levels, it is the tight spatiotemporal regulation of Rac1 and RhoA across multiple roles, from oppositional to complementary, that is necessary to execute coordinated cytoskeletal processes affecting cell structure, function, and migration. We focus on how Kalirin and Trio, as dual GEFs that target Rac1 and RhoA, are uniquely designed to provide the spatiotemporally-precise shifts in Rac/Rho balance which mediate changes in neuronal structure and function, particularly by way of cytoskeletal rearrangements. Finally, we review how alterations in Trio and/or Kalirin function are associated with cellular abnormalities and neuropsychiatric disease.
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Affiliation(s)
- M J Grubisha
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - R A DeGiosio
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Z P Wills
- Department of Neurobiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - R A Sweet
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA; Department of Neurology, University of Pittsburgh, Pittsburgh, PA, USA.
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27
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Lee SH, Hou JC, Hamidzadeh A, Yousafzai MS, Ajeti V, Chang H, Odde DJ, Murrell M, Levchenko A. A molecular clock controls periodically driven cell migration in confined spaces. Cell Syst 2022; 13:514-529.e10. [PMID: 35679858 DOI: 10.1016/j.cels.2022.05.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 09/10/2021] [Accepted: 05/13/2022] [Indexed: 01/25/2023]
Abstract
Navigation through a dense, physically confining extracellular matrix is common in invasive cell spread and tissue reorganization but is still poorly understood. Here, we show that this migration is mediated by cyclic changes in the activity of a small GTPase RhoA, which is dependent on the oscillatory changes in the activity and abundance of the RhoA guanine nucleotide exchange factor, GEF-H1, and triggered by a persistent increase in the intracellular Ca2+ levels. We show that the molecular clock driving these cyclic changes is mediated by two coupled negative feedback loops, dependent on the microtubule dynamics, with a frequency that can be experimentally modulated based on a predictive mathematical model. We further demonstrate that an increasing frequency of the clock translates into a faster cell migration within physically confining spaces. This work lays the foundation for a better understanding of the molecular mechanisms dynamically driving cell migration in complex environments.
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Affiliation(s)
- Sung Hoon Lee
- Yale Systems Biology Institute, Yale University, West Haven, CT 06516, USA; Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Jay C Hou
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Archer Hamidzadeh
- Yale Systems Biology Institute, Yale University, West Haven, CT 06516, USA; Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - M Sulaiman Yousafzai
- Yale Systems Biology Institute, Yale University, West Haven, CT 06516, USA; Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA; Department of Physics, Yale University, New Haven, CT 06520, USA
| | - Visar Ajeti
- Yale Systems Biology Institute, Yale University, West Haven, CT 06516, USA; Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA; Department of Physics, Yale University, New Haven, CT 06520, USA; Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, CT 06032, USA
| | - Hao Chang
- Yale Systems Biology Institute, Yale University, West Haven, CT 06516, USA; Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - David J Odde
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Michael Murrell
- Yale Systems Biology Institute, Yale University, West Haven, CT 06516, USA; Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA; Department of Physics, Yale University, New Haven, CT 06520, USA
| | - Andre Levchenko
- Yale Systems Biology Institute, Yale University, West Haven, CT 06516, USA; Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA.
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28
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Ju J, Lee HN, Ning L, Ryu H, Zhou XX, Chun H, Lee YW, Lee-Richerson AI, Jeong C, Lin MZ, Seong J. Optical regulation of endogenous RhoA reveals selection of cellular responses by signal amplitude. Cell Rep 2022; 40:111080. [PMID: 35830815 DOI: 10.1016/j.celrep.2022.111080] [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: 09/27/2021] [Revised: 05/19/2022] [Accepted: 06/21/2022] [Indexed: 11/15/2022] Open
Abstract
How protein signaling networks respond to different input strengths is an important but poorly understood problem in cell biology. For example, RhoA can promote focal adhesion (FA) growth or disassembly, but how RhoA activity mediates these opposite outcomes is not clear. Here, we develop a photoswitchable RhoA guanine nucleotide exchange factor (GEF), psRhoGEF, to precisely control endogenous RhoA activity. Using this optical tool, we discover that peak FA disassembly selectively occurs upon activation of RhoA to submaximal levels. We also find that Src activation at FAs selectively occurs upon submaximal RhoA activation, identifying Src as an amplitude-dependent RhoA effector. Finally, a pharmacological Src inhibitor reverses the direction of the FA response to RhoA activation from disassembly to growth, demonstrating that Src functions to suppress FA growth upon RhoA activation. Thus, rheostatic control of RhoA activation by psRhoGEF reveals that cells can use signal amplitude to produce multiple responses to a single biochemical signal.
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Affiliation(s)
- Jeongmin Ju
- Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Republic of Korea
| | - Hae Nim Lee
- Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Department of Converging Science and Technology, Kyung Hee University, Seoul 02453, Republic of Korea
| | - Lin Ning
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Neurobiology, Stanford University, Stanford, CA 94305, USA
| | - Hyunjoo Ryu
- Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Xin X Zhou
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Neurobiology, Stanford University, Stanford, CA 94305, USA
| | - Hyeyeon Chun
- Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Yong Woo Lee
- Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | | | - Cherlhyun Jeong
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, South Korea
| | - Michael Z Lin
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Neurobiology, Stanford University, Stanford, CA 94305, USA.
| | - Jihye Seong
- Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Republic of Korea; Department of Converging Science and Technology, Kyung Hee University, Seoul 02453, Republic of Korea; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
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29
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Grazon C, Chern M, Lally P, Baer RC, Fan A, Lecommandoux S, Klapperich C, Dennis AM, Galagan JE, Grinstaff MW. The quantum dot vs. organic dye conundrum for ratiometric FRET-based biosensors: which one would you chose? Chem Sci 2022; 13:6715-6731. [PMID: 35756504 PMCID: PMC9172442 DOI: 10.1039/d1sc06921g] [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: 12/11/2021] [Accepted: 05/04/2022] [Indexed: 11/21/2022] Open
Abstract
Förster resonance energy transfer (FRET) is a widely used and ideal transduction modality for fluorescent based biosensors as it offers high signal to noise with a visibly detectable signal. While intense efforts are ongoing to improve the limit of detection and dynamic range of biosensors based on biomolecule optimization, the selection of and relative location of the dye remains understudied. Herein, we describe a combined experimental and computational study to systematically compare the nature of the dye, i.e., organic fluorophore (Cy5 or Texas Red) vs. inorganic nanoparticle (QD), and the position of the FRET donor or acceptor on the biomolecular components. Using a recently discovered transcription factor (TF)-deoxyribonucleic acid (DNA) biosensor for progesterone, we examine four different biosensor configurations and report the quantum yield, lifetime, FRET efficiency, IC50, and limit of detection. Fitting the computational models to the empirical data identifies key molecular parameters driving sensor performance in each biosensor configuration. Finally, we provide a set of design parameters to enable one to select the fluorophore system for future intermolecular biosensors using FRET-based conformational regulation in in vitro assays and new diagnostic devices.
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Affiliation(s)
- Chloé Grazon
- Department of Chemistry, Boston University Boston MA 02215 USA .,University Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629 F-33600 Pessac France .,University Bordeaux, CNRS, Bordeaux INP, ISM, UMR 5255 F-33400 Talence France
| | - Margaret Chern
- Division of Materials Science and Engineering, Boston University Boston MA 02215 USA
| | - Patrick Lally
- Department of Biomedical Engineering, Boston University Boston MA 02215 USA
| | - R. C. Baer
- Department of Microbiology, Boston UniversityBostonMA 02118USA,National Emerging Infectious Diseases Laboratories, Boston UniversityBostonMA 02118USA
| | - Andy Fan
- Department of Biomedical Engineering, Boston University Boston MA 02215 USA
| | | | | | - Allison M. Dennis
- Division of Materials Science and Engineering, Boston UniversityBostonMA 02215USA,Department of Biomedical Engineering, Boston UniversityBostonMA 02215USA
| | - James E. Galagan
- Department of Microbiology, Boston UniversityBostonMA 02118USA,Department of Biomedical Engineering, Boston UniversityBostonMA 02215USA,National Emerging Infectious Diseases Laboratories, Boston UniversityBostonMA 02118USA
| | - Mark W. Grinstaff
- Department of Chemistry, Boston UniversityBostonMA 02215USA,Division of Materials Science and Engineering, Boston UniversityBostonMA 02215USA,Department of Biomedical Engineering, Boston UniversityBostonMA 02215USA
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30
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Molecular sensors for detection of tumor-stroma crosstalk. Adv Cancer Res 2022; 154:47-91. [PMID: 35459472 DOI: 10.1016/bs.acr.2022.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In most solid tumors, malignant cells coexist with non-cancerous host tissue comprised of a variety of extracellular matrix components and cell types, notably fibroblasts, immune cells, and endothelial cells. It is becoming increasingly evident that the non-cancerous host tissue, often referred to as the tumor stroma or the tumor microenvironment, wields tremendous influence in the proliferation, survival, and metastatic ability of cancer cells. The tumor stroma has an active biological role in the transmission of signals, such as growth factors and chemokines that activate oncogenic signaling pathways by autocrine and paracrine mechanisms. Moreover, the constituents of the stroma define the mechanical properties and the physical features of solid tumors, which influence cancer progression and response to therapy. Inspired by the emerging importance of tumor-stroma crosstalk and oncogenic physical forces, numerous biosensors, or advanced imaging and analysis techniques have been developed and applied to investigate complex and challenging questions in cancer research. These techniques facilitate measurements and biological readouts at scales ranging from subcellular to tissue-level with unprecedented level of spatial and temporal precision. Here we examine the application of biosensor technology for studying the complex and dynamic multiscale interactions of the tumor-host system.
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31
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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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32
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Hu J, Gong X, Strömblad S. Local temporal Rac1-GTP nadirs and peaks restrict cell protrusions and retractions. SCIENCE ADVANCES 2022; 8:eabl3667. [PMID: 35319996 PMCID: PMC8942371 DOI: 10.1126/sciadv.abl3667] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
Cells probe their microenvironment using membrane protrusion-retraction cycles. Spatiotemporal coordination of Rac1 and RhoA GTP-binding activities initiates and reinforces protrusions and retractions, but the control of their finite lifetime remains unclear. We examined the relations of Rac1 and RhoA GTP-binding levels to key protrusion and retraction events, as well as to cell-ECM traction forces at physiologically relevant ECM stiffness. High RhoA-GTP preceded retractions and Rac1-GTP elevation before protrusions. Notable temporal Rac1-GTP nadirs and peaks occurred at the maximal edge velocity of local membrane protrusions and retractions, respectively, followed by declined edge velocity. Moreover, altered local Rac1-GTP consistently preceded similarly altered traction force. Local optogenetic Rac1-GTP perturbations defined a function of Rac1 in restricting protrusions and retractions and in promoting local traction force. Together, we show that Rac1 plays a fundamental role in restricting the size and durability of protrusions and retractions, plausibly in part through controlling traction forces.
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33
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Guerra P, Vuillemenot LA, Rae B, Ladyhina V, Milias-Argeitis A. Systematic In Vivo Characterization of Fluorescent Protein Maturation in Budding Yeast. ACS Synth Biol 2022; 11:1129-1141. [PMID: 35180343 PMCID: PMC8938947 DOI: 10.1021/acssynbio.1c00387] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Fluorescent protein
(FP) maturation can limit the accuracy with
which dynamic intracellular processes are captured and reduce the in vivo brightness of a given FP in fast-dividing cells.
The knowledge of maturation timescales can therefore help users determine
the appropriate FP for each application. However, in vivo maturation rates can greatly deviate from in vitro estimates that are mostly available. In this work, we present the
first systematic study of in vivo maturation for
12 FPs in budding yeast. To overcome the technical limitations of
translation inhibitors commonly used to study FP maturation, we implemented
a new approach based on the optogenetic stimulations of FP expression
in cells grown under constant nutrient conditions. Combining the rapid
and orthogonal induction of FP transcription with a mathematical model
of expression and maturation allowed us to accurately estimate maturation
rates from microscopy data in a minimally invasive manner. Besides
providing a useful resource for the budding yeast community, we present
a new joint experimental and computational approach for characterizing
FP maturation, which is applicable to a wide range of organisms.
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Affiliation(s)
- Paolo Guerra
- Molecular Systems Biology, Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, Netherlands
| | - Luc-Alban Vuillemenot
- Molecular Systems Biology, Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, Netherlands
| | - Brady Rae
- Molecular Systems Biology, Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, Netherlands
| | - Valeriia Ladyhina
- Molecular Systems Biology, Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, Netherlands
| | - Andreas Milias-Argeitis
- Molecular Systems Biology, Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, Netherlands
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34
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Bourque K, Hawey C, Jiang A, Mazarura GR, Hébert TE. Biosensor-based profiling to track cellular signalling in patient-derived models of dilated cardiomyopathy. Cell Signal 2022; 91:110239. [PMID: 34990783 DOI: 10.1016/j.cellsig.2021.110239] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/06/2021] [Accepted: 12/29/2021] [Indexed: 12/18/2022]
Abstract
Dilated cardiomyopathies (DCM) represent a diverse group of cardiovascular diseases impacting the structure and function of the myocardium. To better treat these diseases, we need to understand the impact of such cardiomyopathies on critical signalling pathways that drive disease progression downstream of receptors we often target therapeutically. Our understanding of cellular signalling events has progressed substantially in the last few years, in large part due to the design, validation and use of biosensor-based approaches to studying such events in cells, tissues and in some cases, living animals. Another transformative development has been the use of human induced pluripotent stem cells (hiPSCs) to generate disease-relevant models from individual patients. We highlight the importance of going beyond monocellular cultures to incorporate the influence of paracrine signalling mediators. Finally, we discuss the recent coalition of these approaches in the context of DCM. We discuss recent work in generating patient-derived models of cardiomyopathies and the utility of using signalling biosensors to track disease progression and test potential therapeutic strategies that can be later used to inform treatment options in patients.
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Affiliation(s)
- Kyla Bourque
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec H3G 1Y6, Canada
| | - Cara Hawey
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec H3G 1Y6, Canada
| | - Alyson Jiang
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec H3G 1Y6, Canada
| | - Grace R Mazarura
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec H3G 1Y6, Canada
| | - Terence E Hébert
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec H3G 1Y6, Canada.
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35
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Dobrzyński M, Jacques MA, Pertz O. Mining of Single-Cell Signaling Time-Series for Dynamic Phenotypes with Clustering. Methods Mol Biol 2022; 2488:183-206. [PMID: 35347690 DOI: 10.1007/978-1-0716-2277-3_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Fluorescent live cell time-lapse microscopy is steadily contributing to our better understanding of the relationship between cell signaling and fate. However, large volumes of time-series data generated in these experiments and the heterogenous nature of signaling responses due to cell-cell variability hinder the exploration of such datasets. The population averages insufficiently describe the dynamics, yet finding prototypic dynamic patterns that relate to different cell fates is difficult when mining thousands of time-series. Here we demonstrate a protocol where we identify such dynamic phenotypes in a population of PC-12 cells that respond to a range of sustained growth factor perturbations. We use Time-Course Inspector, a free R/Shiny web application to explore and cluster single-cell time-series.
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Affiliation(s)
| | | | - Olivier Pertz
- Institute of Cell Biology, University of Bern, Bern, Switzerland
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36
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Koh SP, Pham NP, Piekny A. Seeing is believing: tools to study the role of Rho GTPases during cytokinesis. Small GTPases 2022; 13:211-224. [PMID: 34405757 PMCID: PMC9707540 DOI: 10.1080/21541248.2021.1957384] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Cytokinesis is required to cleave the daughter cells at the end of mitosis and relies on the spatiotemporal control of RhoA GTPase. Cytokinesis failure can lead to changes in cell fate or aneuploidy, which can be detrimental during development and/or can lead to cancer. However, our knowledge of the pathways that regulate RhoA during cytokinesis is limited, and the role of other Rho family GTPases is not clear. This is largely because the study of Rho GTPases presents unique challenges using traditional cell biological and biochemical methods, and they have pleiotropic functions making genetic studies difficult to interpret. The recent generation of optogenetic tools and biosensors that control and detect active Rho has overcome some of these challenges and is helping to elucidate the role of RhoA in cytokinesis. However, improvements are needed to reveal the role of other Rho GTPases in cytokinesis, and to identify the molecular mechanisms that control Rho activity. This review examines some of the outstanding questions in cytokinesis, and explores tools for the imaging and control of Rho GTPases.
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Affiliation(s)
- Su Pin Koh
- Department of Biology, Concordia University, Montreal, QC, Canada
| | - Nhat Phi Pham
- Department of Biology, Concordia University, Montreal, QC, Canada
| | - Alisa Piekny
- Department of Biology, Concordia University, Montreal, QC, Canada,CONTACT Alisa Piekny Department of Biology, Concordia University, 7141 Sherbrooke St. W, Montreal, QC, Canada
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37
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Zhang YW, Torsilieri HM, Casanova JE. Quantitation of RhoA activation: differential binding to downstream effectors. Small GTPases 2022; 13:296-306. [PMID: 35950594 PMCID: PMC9377269 DOI: 10.1080/21541248.2022.2111945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 07/29/2022] [Accepted: 08/05/2022] [Indexed: 10/15/2022] Open
Abstract
The small GTPase RhoA controls many important cellular processes through its ability to activate multiple downstream effector pathways. Most RhoA effectors contain a Rho-binding domain (RBD), and interaction between active RhoA and the RBD typically induces a conformational change in effectors that stimulates their recruitment or activity. Isolated GTPase binding domains fused to GST have been widely used in so-called pulldown assays to measure the activation state of other GTPases in cell lysates. Similarly, GST fusions containing the RBD of the RhoA effector Rhotekin have been widely adopted as a standardized tool for the measurement of RhoA activation. RBDs have also been used to generate fluorescent reporter constructs to localize sites of GTPase activation in intact cells. In this report, we demonstrate that not all forms of active RhoA are capable of interacting with the Rhotekin RBD. A constitutively active RhoA-G14V mutant, which interacted with the RBDs of ROCK2 and mDIA1, was unable to bind the Rhotekin RBD as evidenced by both conventional GST pulldown assay and our newly established BRET assay. Furthermore, active RhoA induced by different stimuli in cells also displayed binding preference for its diverse effectors. Our data demonstrate that RhoA may undergo effector-specific activation for differential regulation of its downstream pathways, and that RhoA activation should not be defined solely by its interaction with Rhotekin.
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Affiliation(s)
- Yu-Wen Zhang
- Department of Cell Biology, University of Virginia, School of Medicine, Charlottesville, VA22908USA
| | - Holly M. Torsilieri
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, School of Medicine, Charlottesville, VA22908, USA
| | - James E. Casanova
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, School of Medicine, Charlottesville, VA22908, USA
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38
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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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39
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Grubisha MJ, Sun T, Eisenman L, Erickson SL, Chou S, Helmer CD, Trudgen MT, Ding Y, Homanics GE, Penzes P, Wills ZP, Sweet RA. A Kalirin missense mutation enhances dendritic RhoA signaling and leads to regression of cortical dendritic arbors across development. Proc Natl Acad Sci U S A 2021; 118:e2022546118. [PMID: 34848542 PMCID: PMC8694055 DOI: 10.1073/pnas.2022546118] [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: 11/05/2020] [Accepted: 09/15/2021] [Indexed: 11/26/2022] Open
Abstract
Normally, dendritic size is established prior to adolescence and then remains relatively constant into adulthood due to a homeostatic balance between growth and retraction pathways. However, schizophrenia is characterized by accelerated reductions of cerebral cortex gray matter volume and onset of clinical symptoms during adolescence, with reductions in layer 3 pyramidal neuron dendritic length, complexity, and spine density identified in multiple cortical regions postmortem. Nogo receptor 1 (NGR1) activation of the GTPase RhoA is a major pathway restricting dendritic growth in the cerebral cortex. We show that the NGR1 pathway is stimulated by OMGp and requires the Rho guanine nucleotide exchange factor Kalirin-9 (KAL9). Using a genetically encoded RhoA sensor, we demonstrate that a naturally occurring missense mutation in Kalrn, KAL-PT, that was identified in a schizophrenia cohort, confers enhanced RhoA activitation in neuronal dendrites compared to wild-type KAL. In mice containing this missense mutation at the endogenous locus, there is an adolescent-onset reduction in dendritic length and complexity of layer 3 pyramidal neurons in the primary auditory cortex. Spine density per unit length of dendrite is unaffected. Early adult mice with these structural deficits exhibited impaired detection of short gap durations. These findings provide a neuropsychiatric model of disease capturing how a mild genetic vulnerability may interact with normal developmental processes such that pathology only emerges around adolescence. This interplay between genetic susceptibility and normal adolescent development, both of which possess inherent individual variability, may contribute to heterogeneity seen in phenotypes in human neuropsychiatric disease.
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Affiliation(s)
- Melanie J Grubisha
- Department of Psychiatry, Translational Neuroscience Program, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
| | - Tao Sun
- Department of Biostatistics, University of Pittsburgh, PA 15261
| | - Leanna Eisenman
- Department of Neurobiology, University of Pittsburgh, Pittsburgh, PA 15261
| | - Susan L Erickson
- Department of Psychiatry, Translational Neuroscience Program, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
| | - Shinnyi Chou
- Department of Psychiatry, Translational Neuroscience Program, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
| | - Cassandra D Helmer
- Department of Psychiatry, Translational Neuroscience Program, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
| | - Melody T Trudgen
- Department of Psychiatry, Translational Neuroscience Program, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
| | - Ying Ding
- Department of Biostatistics, University of Pittsburgh, PA 15261
| | - Gregg E Homanics
- Department of Neurobiology, University of Pittsburgh, Pittsburgh, PA 15261
- Department of Anesthesiology and Perioperative Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
| | - Peter Penzes
- Department of Psychiatry and Behavioral Sciences, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Zachary P Wills
- Department of Neurobiology, University of Pittsburgh, Pittsburgh, PA 15261
| | - Robert A Sweet
- Department of Psychiatry, Translational Neuroscience Program, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213;
- Department of Neurology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
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40
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Barbera S, Raucci L, Lugano R, Tosi GM, Dimberg A, Santucci A, Galvagni F, Orlandini M. CD93 Signaling via Rho Proteins Drives Cytoskeletal Remodeling in Spreading Endothelial Cells. Int J Mol Sci 2021; 22:ijms222212417. [PMID: 34830297 PMCID: PMC8622518 DOI: 10.3390/ijms222212417] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 10/29/2021] [Accepted: 11/13/2021] [Indexed: 11/16/2022] Open
Abstract
During angiogenesis, cell adhesion molecules expressed on the endothelial cell surface promote the growth and survival of newly forming vessels. Hence, elucidation of the signaling pathways activated by cell-to-matrix adhesion may assist in the discovery of new targets to be used in antiangiogenic therapy. In proliferating endothelial cells, the single-pass transmembrane glycoprotein CD93 has recently emerged as an important endothelial cell adhesion molecule regulating vascular maturation. In this study, we unveil a signaling pathway triggered by CD93 that regulates actin cytoskeletal dynamics responsible of endothelial cell adhesion. We show that the Src-dependent phosphorylation of CD93 and the adaptor protein Cbl leads to the recruitment of Crk, which works as a downstream integrator in the CD93-mediated signaling. Moreover, confocal microscopy analysis of FRET-based biosensors shows that CD93 drives the coordinated activation of Rac1 and RhoA at the cell edge of spreading cells, thus promoting the establishment of cell polarity and adhesion required for cell motility.
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Affiliation(s)
- Stefano Barbera
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy; (S.B.); (L.R.); (A.S.); (F.G.)
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Rudbeck Laboratory, SE-75185 Uppsala, Sweden; (R.L.); (A.D.)
| | - Luisa Raucci
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy; (S.B.); (L.R.); (A.S.); (F.G.)
| | - Roberta Lugano
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Rudbeck Laboratory, SE-75185 Uppsala, Sweden; (R.L.); (A.D.)
| | - Gian Marco Tosi
- Ophthalmology Unit, Department of Medicine, Surgery and Neuroscience, University of Siena, 53100 Siena, Italy;
| | - Anna Dimberg
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Rudbeck Laboratory, SE-75185 Uppsala, Sweden; (R.L.); (A.D.)
| | - Annalisa Santucci
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy; (S.B.); (L.R.); (A.S.); (F.G.)
| | - Federico Galvagni
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy; (S.B.); (L.R.); (A.S.); (F.G.)
| | - Maurizio Orlandini
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy; (S.B.); (L.R.); (A.S.); (F.G.)
- Correspondence:
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41
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Sipieter F, Cappe B, Leray A, De Schutter E, Bridelance J, Hulpiau P, Van Camp G, Declercq W, Héliot L, Vincent P, Vandenabeele P, Riquet FB. Characteristic ERK1/2 signaling dynamics distinguishes necroptosis from apoptosis. iScience 2021; 24:103074. [PMID: 34568795 PMCID: PMC8449238 DOI: 10.1016/j.isci.2021.103074] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 05/21/2021] [Accepted: 08/30/2021] [Indexed: 12/15/2022] Open
Abstract
ERK1/2 involvement in cell death remains unclear, although many studies have demonstrated the importance of ERK1/2 dynamics in determining cellular responses. To untangle how ERK1/2 contributes to two cell death programs, we investigated ERK1/2 signaling dynamics during hFasL-induced apoptosis and TNF-induced necroptosis in L929 cells. We observed that ERK1/2 inhibition sensitizes cells to apoptosis while delaying necroptosis. By monitoring ERK1/2 activity by live-cell imaging using an improved ERK1/2 biosensor (EKAR4.0), we reported differential ERK1/2 signaling dynamics between cell survival, apoptosis, and necroptosis. We also decrypted a temporally shifted amplitude- and frequency-modulated (AM/FM) ERK1/2 activity profile in necroptosis versus apoptosis. ERK1/2 inhibition, which disrupted ERK1/2 signaling dynamics, prevented TNF and IL-6 gene expression increase during TNF-induced necroptosis. Using an inducible cell line for activated MLKL, the final executioner of necroptosis, we showed ERK1/2 and its distinctive necroptotic ERK1/2 activity dynamics to be positioned downstream of MLKL.
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Affiliation(s)
- François Sipieter
- Molecular Signaling and Cell Death Unit, Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.,Molecular Signaling and Cell Death Unit, VIB Center for Inflammation Research, Technologiepark 71, Zwijnaarde, 9052 Ghent, Belgium.,Université de Lille, Lille, France
| | - Benjamin Cappe
- Molecular Signaling and Cell Death Unit, Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.,Molecular Signaling and Cell Death Unit, VIB Center for Inflammation Research, Technologiepark 71, Zwijnaarde, 9052 Ghent, Belgium
| | - Aymeric Leray
- Laboratoire Interdisciplinaire Carnot De Bourgogne, UMR 6303 CNRS-Université de Bourgogne Franche-Comté, 21078 Dijon, France
| | - Elke De Schutter
- Molecular Signaling and Cell Death Unit, Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.,Molecular Signaling and Cell Death Unit, VIB Center for Inflammation Research, Technologiepark 71, Zwijnaarde, 9052 Ghent, Belgium.,Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43/6, Edegem, 2650 Antwerp, Belgium
| | - Jolien Bridelance
- Molecular Signaling and Cell Death Unit, Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.,Molecular Signaling and Cell Death Unit, VIB Center for Inflammation Research, Technologiepark 71, Zwijnaarde, 9052 Ghent, Belgium
| | - Paco Hulpiau
- Data Mining and Modeling for Biomedicine (DaMBi), VIB Center for Inflammation Research, Ghent, Belgium
| | - Guy Van Camp
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43/6, Edegem, 2650 Antwerp, Belgium.,Center for Oncological Research, University of Antwerp and Antwerp University Hospital, Universiteitsplein 1, Wilrijk, 2610 Antwerp, Belgium
| | - Wim Declercq
- Molecular Signaling and Cell Death Unit, Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.,Molecular Signaling and Cell Death Unit, VIB Center for Inflammation Research, Technologiepark 71, Zwijnaarde, 9052 Ghent, Belgium
| | - Laurent Héliot
- Team Biophotonique Cellulaire Fonctionnelle, Laboratoire de Physique des Lasers, Atomes et Molécules (PhLAM), CNRS UMR 8523, 59655 Villeneuve d'Ascq, France
| | - Pierre Vincent
- Sorbonne Université, CNRS, Neurobiology of Adaptative Processes, UMR8256, 75005 Paris, France
| | - Peter Vandenabeele
- Molecular Signaling and Cell Death Unit, Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.,Molecular Signaling and Cell Death Unit, VIB Center for Inflammation Research, Technologiepark 71, Zwijnaarde, 9052 Ghent, Belgium
| | - Franck B Riquet
- Molecular Signaling and Cell Death Unit, Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.,Molecular Signaling and Cell Death Unit, VIB Center for Inflammation Research, Technologiepark 71, Zwijnaarde, 9052 Ghent, Belgium.,Université de Lille, Lille, France
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42
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The RhoGEF Trio: A Protein with a Wide Range of Functions in the Vascular Endothelium. Int J Mol Sci 2021; 22:ijms221810168. [PMID: 34576329 PMCID: PMC8467920 DOI: 10.3390/ijms221810168] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/16/2021] [Accepted: 09/17/2021] [Indexed: 12/29/2022] Open
Abstract
Many cellular processes are controlled by small GTPases, which can be activated by guanine nucleotide exchange factors (GEFs). The RhoGEF Trio contains two GEF domains that differentially activate the small GTPases such as Rac1/RhoG and RhoA. These small RhoGTPases are mainly involved in the remodeling of the actin cytoskeleton. In the endothelium, they regulate junctional stabilization and play a crucial role in angiogenesis and endothelial barrier integrity. Multiple extracellular signals originating from different vascular processes can influence the activity of Trio and thereby the regulation of the forementioned small GTPases and actin cytoskeleton. This review elucidates how various signals regulate Trio in a distinct manner, resulting in different functional outcomes that are crucial for endothelial cell function in response to inflammation.
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43
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Kim Y, Song J, Lee Y, Cho S, Kim S, Lee SR, Park S, Shin Y, Jeon NL. High-throughput injection molded microfluidic device for single-cell analysis of spatiotemporal dynamics. LAB ON A CHIP 2021; 21:3150-3158. [PMID: 34180916 DOI: 10.1039/d0lc01245a] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Single-cell level analysis of various cellular behaviors has been aided by recent developments in microfluidic technology. Polydimethylsiloxane (PDMS)-based microfluidic devices have been widely used to elucidate cell differentiation and migration under spatiotemporal stimulation. However, microfluidic devices fabricated with PDMS have inherent limitations due to material issues and non-scalable fabrication process. In this study, we designed and fabricated an injection molded microfluidic device that enables real-time chemical profile control. This device is made of polystyrene (PS), engineered with channel dimensions optimized for injection molding to achieve functionality and compatibility with single cell observation. We demonstrated the spatiotemporal dynamics in the device with computational simulation and experiments. In temporal dynamics, we observed extracellular signal-regulated kinase (ERK) activation of PC12 cells by stimulating the cells with growth factors (GFs). Also, we confirmed yes-associated protein (YAP) phase separation of HEK293 cells under stimulation using sorbitol. In spatial dynamics, we observed the migration of NIH 3T3 cells (transfected with Lifeact-GFP) under different spatiotemporal stimulations of PDGF. Using the injection molded plastic devices, we obtained comprehensive data more easily than before while using less time compared to previous PDMS models. This easy-to-use plastic microfluidic device promises to open a new approach for investigating the mechanisms of cell behavior at the single-cell level.
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Affiliation(s)
- Youngtaek Kim
- Department of Mechanical Engineering, Seoul National University, Seoul, Republic of Korea.
| | - Jiyoung Song
- Department of Mechanical Engineering, Seoul National University, Seoul, Republic of Korea.
| | - Younggyun Lee
- Department of Mechanical Engineering, Seoul National University, Seoul, Republic of Korea.
| | - Sunghyun Cho
- Department of Mechanical Engineering, Seoul National University, Seoul, Republic of Korea.
| | - Suryong Kim
- Department of Mechanical Engineering, Seoul National University, Seoul, Republic of Korea.
| | - Seung-Ryeol Lee
- Department of Mechanical Engineering, Seoul National University, Seoul, Republic of Korea.
| | - Seonghyuk Park
- Department of Mechanical Engineering, Seoul National University, Seoul, Republic of Korea.
| | - Yongdae Shin
- Department of Mechanical Engineering, Seoul National University, Seoul, Republic of Korea. and Institute of BioEngineering, Seoul National University, Seoul, Republic of Korea
| | - Noo Li Jeon
- Department of Mechanical Engineering, Seoul National University, Seoul, Republic of Korea. and Institute of BioEngineering, Seoul National University, Seoul, Republic of Korea and Institute of Advanced Machinery and Design, Seoul National University, Seoul, Republic of Korea
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44
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Liu L, Limsakul P, Meng X, Huang Y, Harrison RES, Huang TS, Shi Y, Yu Y, Charupanit K, Zhong S, Lu S, Zhang J, Chien S, Sun J, Wang Y. Integration of FRET and sequencing to engineer kinase biosensors from mammalian cell libraries. Nat Commun 2021; 12:5031. [PMID: 34413312 PMCID: PMC8376904 DOI: 10.1038/s41467-021-25323-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 07/30/2021] [Indexed: 01/01/2023] Open
Abstract
The limited sensitivity of Förster Resonance Energy Transfer (FRET) biosensors hinders their broader applications. Here, we develop an approach integrating high-throughput FRET sorting and next-generation sequencing (FRET-Seq) to identify sensitive biosensors with varying substrate sequences from large-scale libraries directly in mammalian cells, utilizing the design of self-activating FRET (saFRET) biosensor. The resulting biosensors of Fyn and ZAP70 kinases exhibit enhanced performance and enable the dynamic imaging of T-cell activation mediated by T cell receptor (TCR) or chimeric antigen receptor (CAR), revealing a highly organized ZAP70 subcellular activity pattern upon TCR but not CAR engagement. The ZAP70 biosensor elucidates the role of immunoreceptor tyrosine-based activation motif (ITAM) in affecting ZAP70 activation to regulate CAR functions. A saFRET biosensor-based high-throughput drug screening (saFRET-HTDS) assay further enables the identification of an FDA-approved cancer drug, Sunitinib, that can be repurposed to inhibit ZAP70 activity and autoimmune-disease-related T-cell activation.
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Affiliation(s)
- Longwei Liu
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, CA, USA
| | - Praopim Limsakul
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, CA, USA
- Center of Excellence for Trace Analysis and Biosensor, Division of Physical Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Xianhui Meng
- Department of Cell Biology and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, P.R. China
| | - Yan Huang
- Department of Chemistry and Chemical Engineering, Hunan University, Changsha, P.R. China
| | - Reed E S Harrison
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, CA, USA
| | - Tse-Shun Huang
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, CA, USA
- BioLegend, San Diego, CA, USA
| | - Yiwen Shi
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, CA, USA
| | - Yiyan Yu
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, CA, USA
| | - Krit Charupanit
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| | - Sheng Zhong
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, CA, USA
| | - Shaoying Lu
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, CA, USA
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, CA, USA
| | - Shu Chien
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, CA, USA
- Department of Medicine, University of California, San Diego, CA, USA
| | - Jie Sun
- Department of Cell Biology and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, P.R. China.
| | - Yingxiao Wang
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, CA, USA.
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45
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Mahlandt EK, Arts JJG, van der Meer WJ, van der Linden FH, Tol S, van Buul JD, Gadella TWJ, Goedhart J. Visualizing endogenous Rho activity with an improved localization-based, genetically encoded biosensor. J Cell Sci 2021; 134:272101. [PMID: 34357388 PMCID: PMC8445605 DOI: 10.1242/jcs.258823] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 07/26/2021] [Indexed: 12/05/2022] Open
Abstract
Rho GTPases are regulatory proteins, which orchestrate cell features such as morphology, polarity and movement. Therefore, probing Rho GTPase activity is key to understanding processes such as development and cell migration. Localization-based reporters for active Rho GTPases are attractive probes to study Rho GTPase-mediated processes in real time with subcellular resolution in living cells and tissue. Until now, relocation Rho biosensors (sensors that relocalize to the native location of active Rho GTPase) seem to have been only useful in certain organisms and have not been characterized well. In this paper, we systematically examined the contribution of the fluorescent protein and Rho-binding peptides on the performance of localization-based sensors. To test the performance, we compared relocation efficiency and specificity in cell-based assays. We identified several improved localization-based, genetically encoded fluorescent biosensors for detecting endogenous Rho activity. This enables a broader application of Rho relocation biosensors, which was demonstrated by using the improved biosensor to visualize Rho activity during several cellular processes, such as cell division, migration and G protein-coupled receptor signaling. Owing to the improved avidity of the new biosensors for Rho activity, cellular processes regulated by Rho can be better understood. This article has an associated First Person interview with the first author of the paper. Summary: The dT-2xrGBD location-based Rho biosensor relocalizes more efficiently than other sensors of this type, and this sensor enables the observation of endogenous Rho activity in cultured cells.
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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
| | - Janine J G Arts
- 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.,Molecular Cell Biology Lab at Dept. Molecular Hematology, Sanquin Research and Landsteiner Laboratory, Amsterdam, The Netherlands
| | - Werner J van der Meer
- 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
| | - Franka H van der Linden
- 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
| | - Simon Tol
- Molecular Cell Biology Lab at Dept. Molecular Hematology, Sanquin Research and Landsteiner Laboratory, Amsterdam, The Netherlands
| | - Jaap D van Buul
- 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.,Molecular Cell Biology Lab at Dept. Molecular Hematology, Sanquin Research and Landsteiner Laboratory, Amsterdam, The Netherlands
| | - Theodorus W J Gadella
- 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
| | - 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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46
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Nakamura A, Goto Y, Kondo Y, Aoki K. Shedding light on developmental ERK signaling with genetically encoded biosensors. Development 2021; 148:271153. [PMID: 34338283 DOI: 10.1242/dev.199767] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The extracellular signal-regulated kinase (ERK) pathway governs cell proliferation, differentiation and migration, and therefore plays key roles in various developmental and regenerative processes. Recent advances in genetically encoded fluorescent biosensors have unveiled hitherto unrecognized ERK activation dynamics in space and time and their functional importance mainly in cultured cells. However, ERK dynamics during embryonic development have still only been visualized in limited numbers of model organisms, and we are far from a sufficient understanding of the roles played by developmental ERK dynamics. In this Review, we first provide an overview of the biosensors used for visualization of ERK activity in live cells. Second, we highlight the applications of the biosensors to developmental studies of model organisms and discuss the current understanding of how ERK dynamics are encoded and decoded for cell fate decision-making.
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Affiliation(s)
- Akinobu Nakamura
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan.,Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| | - Yuhei Goto
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan.,Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan.,Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| | - Yohei Kondo
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan.,Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan.,Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| | - Kazuhiro Aoki
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan.,Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan.,Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan.,IRCC International Research Collaboration Center, National Institutes of Natural Sciences, 4-3-13 Toranomon, Minato-ku, Tokyo 105-0001, Japan
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47
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Masner M, Lujea N, Bisbal M, Acosta C, Kunda P. Linoleic and oleic acids enhance cell migration by altering the dynamics of microtubules and the remodeling of the actin cytoskeleton at the leading edge. Sci Rep 2021; 11:14984. [PMID: 34294745 PMCID: PMC8298526 DOI: 10.1038/s41598-021-94399-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 06/30/2021] [Indexed: 01/22/2023] Open
Abstract
Fatty acids (FA) have a multitude of biological actions on living cells. A target of their action is cell motility, a process of critical importance during cancer cell dissemination. Here, we studied the effect of unsaturated FA on ovarian cancer cell migration in vitro and its role in regulating cytoskeleton structures that are essential for cell motility. Scratch wound assays on human ovary cancer SKOV-3 cell monolayers revealed that low doses (16 μM) of linoleic acid (LA, 18:2 ω6) and oleic acid (OA; 18:1 ω9) promoted migration, while α-linolenic acid (ALA, 18:3 ω3), showed a migration rate similar to that of the control group. Single cell tracking demonstrated that LA and OA-treated cells migrated faster and were more orientated towards the wound closure than control. In vitro addition of those FA resulted in an increased number, length and protrusion speed of filopodia and also in a prominent and dynamic lamellipodia at the cell leading edge. Using time-lapse video-microscopy and FRAP we observed an increase in both the speed and frequency of actin waves associated with more mobile actin and augmented Rac1 activity. We also observed that FA induced microtubule-organizing center (MTOC)-orientation towards the cell front and affected the dynamics of microtubules (MT) in the direction of cell migration. We propose that environmental cues such as OA and LA present in ascitic fluid, should be taken into account as key factors for the regulation of cell migration.
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Affiliation(s)
- M Masner
- Centro de Investigación en Medicina Traslacional "Severo Amuchástegui" (CIMETSA), Instituto Universitario Ciencias Biomédicas Córdoba (IUCBC), Naciones Unidas 420, Córdoba, Argentina
| | - N Lujea
- Centro de Investigación en Medicina Traslacional "Severo Amuchástegui" (CIMETSA), Instituto Universitario Ciencias Biomédicas Córdoba (IUCBC), Naciones Unidas 420, Córdoba, Argentina
| | - M Bisbal
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, INIMEC-CONICET-Universidad Nacional de Córdoba, Córdoba, Argentina
| | - C Acosta
- Instituto de Histología y Embriología de Mendoza (IHEM), Facultad de Ciencias Médicas, Universidad Nacional de Cuyo, Mendoza, Argentina
| | - Patricia Kunda
- Centro de Investigación en Medicina Traslacional "Severo Amuchástegui" (CIMETSA), Instituto Universitario Ciencias Biomédicas Córdoba (IUCBC), Naciones Unidas 420, Córdoba, Argentina.
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48
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Kull T, Schroeder T. Analyzing signaling activity and function in hematopoietic cells. J Exp Med 2021; 218:e20201546. [PMID: 34129015 PMCID: PMC8210623 DOI: 10.1084/jem.20201546] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/14/2020] [Accepted: 01/07/2021] [Indexed: 11/25/2022] Open
Abstract
Cells constantly sense their environment, allowing the adaption of cell behavior to changing needs. Fine-tuned responses to complex inputs are computed by signaling pathways, which are wired in complex connected networks. Their activity is highly context-dependent, dynamic, and heterogeneous even between closely related individual cells. Despite lots of progress, our understanding of the precise implementation, relevance, and possible manipulation of cellular signaling in health and disease therefore remains limited. Here, we discuss the requirements, potential, and limitations of the different current technologies for the analysis of hematopoietic stem and progenitor cell signaling and its effect on cell fates.
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Affiliation(s)
| | - Timm Schroeder
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule Zurich, Basel, Switzerland
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49
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Barbera S, Lugano R, Pedalina A, Mongiat M, Santucci A, Tosi GM, Dimberg A, Galvagni F, Orlandini M. The C-type lectin CD93 controls endothelial cell migration via activation of the Rho family of small GTPases. Matrix Biol 2021; 99:1-17. [PMID: 34062268 DOI: 10.1016/j.matbio.2021.05.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/19/2021] [Accepted: 05/24/2021] [Indexed: 02/07/2023]
Abstract
Endothelial cell migration is essential to angiogenesis, enabling the outgrowth of new blood vessels both in physiological and pathological contexts. Migration requires the activation of several signaling pathways, the elucidation of which expands the opportunity to develop new drugs to be used in antiangiogenic therapy. In the proliferating endothelium, the interaction between the transmembrane glycoprotein CD93 and the extracellular matrix activates signaling pathways that regulate cell adhesion, migration, and vascular maturation. Here we identify a pathway, comprising CD93, the adaptor proteins Cbl and Crk, and the small GTPases Rac1, Cdc42, and RhoA, which we propose acts as a regulator of cytoskeletal movements responsible for endothelial cell migration. In this framework, phosphorylation of Cbl on tyrosine 774 leads to the interaction with Crk, which acts as a downstream integrator in the CD93-mediated signaling regulating cell polarity and migration. Moreover, confocal microscopy analyses of GTPase biosensors show that CD93 drives coordinated activation of Rho-proteins at the cell edge of migratory endothelial cells. In conclusion, together with the demonstration of the key contribution of CD93 to the migratory process in living cells, these findings suggest that the signaling triggered by CD93 converges to the activation and modulation of the Rho GTPase signaling pathways regulating cell dynamics.
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Affiliation(s)
- Stefano Barbera
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Italy; Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Rudbeck Laboratory, Uppsala, Sweden
| | - Roberta Lugano
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Rudbeck Laboratory, Uppsala, Sweden
| | - Alessia Pedalina
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Italy
| | - Maurizio Mongiat
- Department of Research and Diagnosis, Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Italy
| | - Annalisa Santucci
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Italy
| | - Gian Marco Tosi
- Department of Medicine, Surgery and Neuroscience, Ophthalmology Unit, University of Siena, Italy
| | - Anna Dimberg
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Rudbeck Laboratory, Uppsala, Sweden
| | - Federico Galvagni
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Italy
| | - Maurizio Orlandini
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Italy.
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50
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Lauri A, Fasano G, Venditti M, Dallapiccola B, Tartaglia M. In vivo Functional Genomics for Undiagnosed Patients: The Impact of Small GTPases Signaling Dysregulation at Pan-Embryo Developmental Scale. Front Cell Dev Biol 2021; 9:642235. [PMID: 34124035 PMCID: PMC8194860 DOI: 10.3389/fcell.2021.642235] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/12/2021] [Indexed: 12/24/2022] Open
Abstract
While individually rare, disorders affecting development collectively represent a substantial clinical, psychological, and socioeconomic burden to patients, families, and society. Insights into the molecular mechanisms underlying these disorders are required to speed up diagnosis, improve counseling, and optimize management toward targeted therapies. Genome sequencing is now unveiling previously unexplored genetic variations in undiagnosed patients, which require functional validation and mechanistic understanding, particularly when dealing with novel nosologic entities. Functional perturbations of key regulators acting on signals' intersections of evolutionarily conserved pathways in these pathological conditions hinder the fine balance between various developmental inputs governing morphogenesis and homeostasis. However, the distinct mechanisms by which these hubs orchestrate pathways to ensure the developmental coordinates are poorly understood. Integrative functional genomics implementing quantitative in vivo models of embryogenesis with subcellular precision in whole organisms contribute to answering these questions. Here, we review the current knowledge on genes and mechanisms critically involved in developmental syndromes and pediatric cancers, revealed by genomic sequencing and in vivo models such as insects, worms and fish. We focus on the monomeric GTPases of the RAS superfamily and their influence on crucial developmental signals and processes. We next discuss the effectiveness of exponentially growing functional assays employing tractable models to identify regulatory crossroads. Unprecedented sophistications are now possible in zebrafish, i.e., genome editing with single-nucleotide precision, nanoimaging, highly resolved recording of multiple small molecules activity, and simultaneous monitoring of brain circuits and complex behavioral response. These assets permit accurate real-time reporting of dynamic small GTPases-controlled processes in entire organisms, owning the potential to tackle rare disease mechanisms.
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Affiliation(s)
- Antonella Lauri
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | | | | | | | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
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