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Yau E, Yang L, Chen Y, Umstead TM, Stanley AE, Halstead ES, Gandhi CK, Yewdell JW, Chroneos ZC. SP-R210 isoforms of Myosin18A modulate endosomal sorting and recognition of influenza A virus infection in macrophages. Microbes Infect 2024; 26:105280. [PMID: 38135024 PMCID: PMC10948314 DOI: 10.1016/j.micinf.2023.105280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 12/12/2023] [Accepted: 12/17/2023] [Indexed: 12/24/2023]
Abstract
Influenza A virus (IAV) infection causes acute and often lethal inflammation in the lung. The role of macrophages in this adverse inflammation is partially understood. The surfactant protein A receptor 210 (SP-R210) consists of two isoforms, a long (L) SP-R210L and a short (S) SP-R210S isoform encoded by alternative splicing of the myosin 18A gene. We reported that disruption of SP-R210L enhances cytosolic and endosomal antiviral response pathways. Here, we report that SP-R210L antagonizes type I interferon β (IFNβ), as depletion of SP-R210L potentiates IFNβ secretion. SP-R210 antibodies enhance and attenuate IFNβ secretion in SP-R210L replete and deficient macrophages, respectively, indicating that SP-R210 isoform stoichiometry alters macrophage function intrinsically. This reciprocal response is coupled to unopposed and restricted expression of viral genes in control and SP-R210L-deficient macrophages, respectively. Human monocytic cells with sub-stoichiometric expression of SP-R210L resist IAV infection, whereas alveolar macrophages with increased abundance of SP-R210L permit viral gene expression similar to murine macrophages. Uptake and membrane binding studies show that lack of SP-R210 isoforms does not impair IAV binding and internalization. Lack of SP-R210L, however, results in macropinocytic retention of the virus that depends on both SP-R210S and interferon-inducible transmembrane protein-3 (IFITM3). Mass spectrometry and Western blot analyses indicate that SP-R210 isoforms modulate differential recruitment of the Rho-family GTPase RAC1 and guanine nucleotide exchange factors. Our study suggests that SP-R210 isoforms modulate RAC-dependent macropinosomal sorting of IAV to discrete endosomal and lysosomal compartments that either permit or prevent endolysosomal escape and inflammatory sensing of viral genomes in macrophages.
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Affiliation(s)
- Eric Yau
- Department of Pediatrics, Division of Perinatal-Neonatal Medicine, Pulmonary Immunology and Physiology Laboratory, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Linlin Yang
- Department of Pediatrics, Division of Perinatal-Neonatal Medicine, Pulmonary Immunology and Physiology Laboratory, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Yan Chen
- Department of Pediatrics, Division of Perinatal-Neonatal Medicine, Pulmonary Immunology and Physiology Laboratory, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Todd M Umstead
- Department of Pediatrics, Division of Perinatal-Neonatal Medicine, Pulmonary Immunology and Physiology Laboratory, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Anne E Stanley
- Mass Spectrometry Core, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - E Scott Halstead
- Department of Pediatrics, Division of Perinatal-Neonatal Medicine, Pulmonary Immunology and Physiology Laboratory, Pennsylvania State University College of Medicine, Hershey, PA, USA; Department of Pediatrics, Division of Pediatric Critical Care Medicine, Pulmonary Immunology and Physiology Laboratory, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Chintan K Gandhi
- Department of Pediatrics, Division of Perinatal-Neonatal Medicine, Pulmonary Immunology and Physiology Laboratory, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Jonathan W Yewdell
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Zissis C Chroneos
- Department of Pediatrics, Division of Perinatal-Neonatal Medicine, Pulmonary Immunology and Physiology Laboratory, Pennsylvania State University College of Medicine, Hershey, PA, USA; Department of Microbiology and Immunology, Pennsylvania State University College of Medicine, Hershey, PA, USA.
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2
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Güler BE, Linnert J, Wolfrum U. Monitoring paxillin in astrocytes reveals the significance of the adhesion G protein coupled receptor VLGR1/ADGRV1 for focal adhesion assembly. Basic Clin Pharmacol Toxicol 2023; 133:301-312. [PMID: 36929698 DOI: 10.1111/bcpt.13860] [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: 01/03/2023] [Revised: 03/08/2023] [Accepted: 03/10/2023] [Indexed: 03/18/2023]
Abstract
VLGR1/ADGRV1 (very large G protein-coupled receptor-1) is the largest adhesion G protein-coupled receptor (aGPCR). Mutations in VLGR1/ADGRV1 are associated with human Usher syndrome, the most common form of deaf-blindness, and also with epilepsy in humans and mice. VLGR1 is expressed almost ubiquitously but is mainly found in the CNS and in the sensory cells of the eye and inner ear. Little is known about the pathogenesis of the diseases related to VLGR1. We previously identified VLGR1 as a vital component of focal adhesions (FAs) serving as a metabotropic mechanoreceptor controls cell spreading and migration. FAs are highly dynamic and turnover in response to internal and external signals. Here, we aimed to elucidate how VLGR1 participates in FA turnover. Nocodazole washouts and live cell imaging of paxillin-DsRed2 consistently showed that FA disassembly was not altered, but de novo assembly of FA was significantly delayed in Vlgr1-deficient astrocytes, indicating that VLGR1 is enrolled in FA assembly. In FRAP experiments, recovery rates were significantly reduced in Vlgr1-deficient FAs, indicating reduced turnover kinetics in VLGR1-deficient FAs. We showed that VLGR1 regulates cell migration by controlling the FA turnover during their assembly and expect novel insights into pathomechanisms related to pathogenic dysfunctions of VLGR1.
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Affiliation(s)
- Baran E Güler
- Institute of Molecular Physiology, Molecular Cell Biology, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Joshua Linnert
- Institute of Molecular Physiology, Molecular Cell Biology, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Uwe Wolfrum
- Institute of Molecular Physiology, Molecular Cell Biology, Johannes Gutenberg University Mainz, Mainz, Germany
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3
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Li Mow Chee F, Beernaert B, Griffith BGC, Loftus AEP, Kumar Y, Wills JC, Lee M, Valli J, Wheeler AP, Armstrong JD, Parsons M, Leigh IM, Proby CM, von Kriegsheim A, Bickmore WA, Frame MC, Byron A. Mena regulates nesprin-2 to control actin-nuclear lamina associations, trans-nuclear membrane signalling and gene expression. Nat Commun 2023; 14:1602. [PMID: 36959177 PMCID: PMC10036544 DOI: 10.1038/s41467-023-37021-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 02/21/2023] [Indexed: 03/25/2023] Open
Abstract
Interactions between cells and the extracellular matrix, mediated by integrin adhesion complexes, play key roles in fundamental cellular processes, including the sensing and transduction of mechanical cues. Here, we investigate systems-level changes in the integrin adhesome in patient-derived cutaneous squamous cell carcinoma cells and identify the actin regulatory protein Mena as a key node in the adhesion complex network. Mena is connected within a subnetwork of actin-binding proteins to the LINC complex component nesprin-2, with which it interacts and co-localises at the nuclear envelope. Moreover, Mena potentiates the interactions of nesprin-2 with the actin cytoskeleton and the nuclear lamina. CRISPR-mediated Mena depletion causes altered nuclear morphology, reduces tyrosine phosphorylation of the nuclear membrane protein emerin and downregulates expression of the immunomodulatory gene PTX3 via the recruitment of its enhancer to the nuclear periphery. We uncover an unexpected role for Mena at the nuclear membrane, where it controls nuclear architecture, chromatin repositioning and gene expression. Our findings identify an adhesion protein that regulates gene transcription via direct signalling across the nuclear envelope.
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Affiliation(s)
- Frederic Li Mow Chee
- Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - Bruno Beernaert
- Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, OX3 7DQ, UK
| | - Billie G C Griffith
- Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - Alexander E P Loftus
- Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - Yatendra Kumar
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Jimi C Wills
- Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - Martin Lee
- Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - Jessica Valli
- Edinburgh Super Resolution Imaging Consortium, Institute of Biological Chemistry, Biophysics and Bioengineering, School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh, EH14 4AS, UK
| | - Ann P Wheeler
- Advanced Imaging Resource, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - J Douglas Armstrong
- Simons Initiative for the Developing Brain, School of Informatics, University of Edinburgh, Edinburgh, EH8 9LE, UK
| | - Maddy Parsons
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, SE1 1UL, UK
| | - Irene M Leigh
- Division of Molecular and Clinical Medicine, School of Medicine, University of Dundee, Dundee, DD1 9SY, UK
- Institute of Dentistry, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, E1 2AT, UK
| | - Charlotte M Proby
- Division of Molecular and Clinical Medicine, School of Medicine, University of Dundee, Dundee, DD1 9SY, UK
| | - Alex von Kriegsheim
- Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - Wendy A Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Margaret C Frame
- Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - Adam Byron
- Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK.
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PT, UK.
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Byron A, Griffith BGC, Herrero A, Loftus AEP, Koeleman ES, Kogerman L, Dawson JC, McGivern N, Culley J, Grimes GR, Serrels B, von Kriegsheim A, Brunton VG, Frame MC. Characterisation of a nucleo-adhesome. Nat Commun 2022; 13:3053. [PMID: 35650196 PMCID: PMC9160004 DOI: 10.1038/s41467-022-30556-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 05/02/2022] [Indexed: 11/09/2022] Open
Abstract
In addition to central functions in cell adhesion signalling, integrin-associated proteins have wider roles at sites distal to adhesion receptors. In experimentally defined adhesomes, we noticed that there is clear enrichment of proteins that localise to the nucleus, and conversely, we now report that nuclear proteomes contain a class of adhesome components that localise to the nucleus. We here define a nucleo-adhesome, providing experimental evidence for a remarkable scale of nuclear localisation of adhesion proteins, establishing a framework for interrogating nuclear adhesion protein functions. Adding to nuclear FAK's known roles in regulating transcription, we now show that nuclear FAK regulates expression of many adhesion-related proteins that localise to the nucleus and that nuclear FAK binds to the adhesome component and nuclear protein Hic-5. FAK and Hic-5 work together in the nucleus, co-regulating a subset of genes transcriptionally. We demonstrate the principle that there are subcomplexes of nuclear adhesion proteins that cooperate to control transcription.
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Affiliation(s)
- Adam Byron
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK.
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK.
| | - Billie G C Griffith
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - Ana Herrero
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Cantabria, 39011, Santander, Spain
| | - Alexander E P Loftus
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - Emma S Koeleman
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK
- Leiden University Medical Center, 2333 ZC, Leiden, The Netherlands
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, 69120, Heidelberg, Germany
| | - Linda Kogerman
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - John C Dawson
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - Niamh McGivern
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK
- Almac Diagnostic Services, 19 Seagoe Industrial Estate, Craigavon, BT63 5QD, UK
| | - Jayne Culley
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - Graeme R Grimes
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Bryan Serrels
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK
- NanoString Technologies, Inc., Seattle, WA, 98109, USA
| | - Alex von Kriegsheim
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - Valerie G Brunton
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - Margaret C Frame
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK
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5
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Hight-Warburton W, Felix R, Burton A, Maple H, Chegkazi MS, Steiner RA, McGrath JA, Parsons M. α4/α9 Integrins Coordinate Epithelial Cell Migration Through Local Suppression of MAP Kinase Signaling Pathways. Front Cell Dev Biol 2021; 9:750771. [PMID: 34900996 PMCID: PMC8655878 DOI: 10.3389/fcell.2021.750771] [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: 07/31/2021] [Accepted: 10/31/2021] [Indexed: 11/18/2022] Open
Abstract
Adhesion of basal keratinocytes to the underlying extracellular matrix (ECM) plays a key role in the control of skin homeostasis and response to injury. Integrin receptors indirectly link the ECM to the cell cytoskeleton through large protein complexes called focal adhesions (FA). FA also function as intracellular biochemical signaling platforms to enable cells to respond to changing extracellular cues. The α4β1 and α9β1 integrins are both expressed in basal keratinocytes, share some common ECM ligands, and have been shown to promote wound healing in vitro and in vivo. However, their roles in maintaining epidermal homeostasis and relative contributions to pathological processes in the skin remain unclear. We found that α4β1 and α9β1 occupied distinct regions in monolayers of a basal keratinocyte cell line (NEB-1). During collective cell migration (CCM), α4 and α9 integrins co-localized along the leading edge. Pharmacological inhibition of α4β1 and α9β1 integrins increased keratinocyte proliferation and induced a dramatic change in cytoskeletal remodeling and FA rearrangement, detrimentally affecting CCM. Further analysis revealed that α4β1/α9β1 integrins suppress extracellular signal-regulated kinase (ERK1/2) activity to control migration through the regulation of downstream kinases including Mitogen and Stress Activated Kinase 1 (MSK1). This work demonstrates the roles of α4β1 and α9β1 in regulating migration in response to damage cues.
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Affiliation(s)
- Willow Hight-Warburton
- Parsons Group, Randall Centre for Cell and Molecular Biophysics, King's College London, London, United Kingdom
| | | | | | | | - Magda S Chegkazi
- Steiner Group, Randall Centre for Cell and Molecular Biophysics, King's College London, London, United Kingdom
| | - Roberto A Steiner
- Steiner Group, Randall Centre for Cell and Molecular Biophysics, King's College London, London, United Kingdom.,Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - John A McGrath
- St Johns Institute of Dermatology, King's College London, London, United Kingdom
| | - Maddy Parsons
- Parsons Group, Randall Centre for Cell and Molecular Biophysics, King's College London, London, United Kingdom
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6
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Daliri K, Pfannkuche K, Garipcan B. Effects of physicochemical properties of polyacrylamide (PAA) and (polydimethylsiloxane) PDMS on cardiac cell behavior. SOFT MATTER 2021; 17:1156-1172. [PMID: 33427281 DOI: 10.1039/d0sm01986k] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
In vitro cell culture is commonly applied in laboratories around the world. Cultured cells are either of primary origin or established cell lines. Such transformed cell lines are increasingly replaced by pluripotent stem cell derived organotypic cells with more physiological properties. The quality of the culture conditions and matrix environment is of considerable importance in this regard. In fact, mechanical cues of the extracellular matrix have substantial effects on the cellular physiology. This is especially true if contractile cells such as cardiomyocytes are cultured. Therefore, elastic biomaterials have been introduced as scaffolds in 2D and 3D culture models for different cell types, cardiac cells among them. In this review, key aspects of cell-matrix interaction are highlighted with focus on cardiomyocytes and chemical properties as well as strengths and potential pitfalls in using two commonly applied polymers for soft matrix engineering, polyacrylamide (PAA) and polydimethylsiloxane (PDMS) are discussed.
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Affiliation(s)
- Karim Daliri
- Institute for Neurophysiology, University of Cologne, Medical Faculty, Robert Koch Str. 39, 50931 Cologne, Germany.
| | - Kurt Pfannkuche
- Institute for Neurophysiology, University of Cologne, Medical Faculty, Robert Koch Str. 39, 50931 Cologne, Germany. and Department for Pediatric Cardiology, University Hospital Cologne, Cologne, Germany and Marga-and-Walter-Boll Laboratory for Cardiac Tissue Engineering, University of Cologne, Germany and Center for Molecular Medicine, University of Cologne, Germany
| | - Bora Garipcan
- Institute of Biomedical Engineering, Bogazici University, Cengelkoy, 34684, Istanbul, Turkey.
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Abstract
Cell-surface adhesion receptors mediate interactions with the extracellular matrix (ECM) to control many fundamental aspects of cell behavior, including cell migration, survival, and proliferation. Integrin adhesion receptors recruit structural and signaling proteins to form multimolecular adhesion complexes that link the plasma membrane to the actomyosin cytoskeleton. The assembly and turnover of adhesion complexes are tightly regulated, governed in part by the networks of physical protein interactions and functional signaling associations between components of the adhesome. Proteomic profiling of adhesion complexes has begun to reveal their molecular complexity and diversity. To interrogate the composition of cell-ECM adhesions, we detail herein an approach for the network analysis of adhesion complex proteomes. Integration of these proteomic data with adhesome databases in the context of predicted protein interactions enables the mapping of experimentally defined adhesion complex networks. Computational analysis of resultant network models can identify subnetworks of putative functionally linked adhesion protein communities. This approach provides a framework to predict functional adhesion protein relationships and generate new mechanistic hypotheses for further experimental testing.
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Affiliation(s)
- Frederic Li Mow Chee
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Adam Byron
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.
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8
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Single-Protein Tracking to Study Protein Interactions During Integrin-Based Migration. Methods Mol Biol 2021; 2217:85-113. [PMID: 33215379 DOI: 10.1007/978-1-0716-0962-0_8] [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: 12/03/2022]
Abstract
Cell migration is a complex biophysical process which involves the coordination of molecular assemblies including integrin-dependent adhesions, signaling networks and force-generating cytoskeletal structures incorporating both actin polymerization and myosin activity. During the last decades, proteomic studies have generated impressive protein-protein interaction maps, although the subcellular location, duration, strength, sequence, and nature of these interactions are still concealed. In this chapter we describe how recent developments in superresolution microscopy (SRM) and single-protein tracking (SPT) start to unravel protein interactions and actions in subcellular molecular assemblies driving cell migration.
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Abstract
The extracellular matrix (ECM) is the noncellular compartment of living organisms and is formed of a complex network of cross-linked proteins, which is collectively known as the matrisome. Apart from providing the structure for an organism, cells interact and thereby communicate with the ECM. Cells interact with their surrounding ECM using cell-surface receptors, such as integrins. Upon integrin engagement with the ECM, cytoskeletal proteins are recruited to integrins and form a molecular protein complex known as the integrin adhesome. Global descriptions of the matrisome and integrin adhesome have been proposed using in silico bioinformatics approaches, as well as through biochemical enrichment of matrisome and adhesome fractions coupled with mass spectrometry-based proteomic analyses, providing inventories of their compositions in different contexts. Here, methods are described for the computational downstream analyses of matrisome and adhesome mass spectrometry datasets that are accessible to wet lab biologists, which include comparing datasets to in silico descriptions, generating interaction networks and performing functional ontological analyses.
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10
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Randles MJ, Lausecker F, Humphries JD, Byron A, Clark SJ, Miner JH, Zent R, Humphries MJ, Lennon R. Basement membrane ligands initiate distinct signalling networks to direct cell shape. Matrix Biol 2020; 90:61-78. [PMID: 32147508 PMCID: PMC7327512 DOI: 10.1016/j.matbio.2020.02.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 02/29/2020] [Accepted: 02/29/2020] [Indexed: 01/09/2023]
Abstract
Cells have evolved mechanisms to sense the composition of their adhesive microenvironment. Although much is known about general mechanisms employed by adhesion receptors to relay signals between the extracellular environment and the cytoskeleton, the nuances of ligand-specific signalling remain undefined. Here, we investigated how glomerular podocytes, and four other basement membrane-associated cell types, respond morphologically to different basement membrane ligands. We defined the composition of the respective adhesion complexes using mass spectrometry-based proteomics. On type IV collagen, all epithelial cell types adopted a round morphology, with a single lamellipodium and large adhesion complexes rich in actin-binding proteins. On laminin (511 or 521), all cell types attached to a similar degree but were polygonal in shape with small adhesion complexes enriched in endocytic and microtubule-binding proteins. Consistent with their distinctive morphologies, cells on type IV collagen exhibited high Rac1 activity, while those on laminin had elevated PKCα. Perturbation of PKCα was able to interchange morphology consistent with a key role for this pathway in matrix ligand-specific signalling. Therefore, this study defines the switchable basement membrane adhesome and highlights two key signalling pathways within the systems that determine distinct cell morphologies. Proteomic data are availableviaProteomeXchange with identifier PXD017913.
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Affiliation(s)
- Michael J Randles
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Franziska Lausecker
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Jonathan D Humphries
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Adam Byron
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Simon J Clark
- Universitäts-Augenklinik Tübingen, Eberhard Karls University of Tübingen, Germany; The Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, UK
| | - Jeffrey H Miner
- Renal Division, Washington University School of Medicine, Saint Louis, MO, USA
| | - Roy Zent
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Martin J Humphries
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Rachel Lennon
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK; Department of Paediatric Nephrology, Royal Manchester Children's Hospital, Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK.
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Calcium in Cell-Extracellular Matrix Interactions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1131:1079-1102. [PMID: 31646546 DOI: 10.1007/978-3-030-12457-1_43] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In multicellular organisms, the cells are surrounded by persistent, dynamic extracellular matrix (ECM), the largest calcium reservoir in animals. ECM regulates several aspects of cell behavior including cell migration and adhesion, survival, gene expression and differentiation, thus playing a significant role in health and disease. Calcium is reported to be important in the assembly of ECM, where it binds to many ECM proteins. While serving as a calcium reservoir, ECM macromolecules can directly interact with cell surface receptors resulting in calcium transport across the membrane. This chapter mainly focusses on the role of cell-ECM interactions in cellular calcium regulation and how calcium itself mediates these interactions.
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12
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Casals C, García-Fojeda B, Minutti CM. Soluble defense collagens: Sweeping up immune threats. Mol Immunol 2019; 112:291-304. [DOI: 10.1016/j.molimm.2019.06.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 06/12/2019] [Accepted: 06/13/2019] [Indexed: 12/14/2022]
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13
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Singh K, Lin J, Zhong Y, Burčul A, Mohan P, Jiang M, Sun L, Yong-Gonzalez V, Viale A, Cross JR, Hendrickson RC, Rätsch G, Ouyang Z, Wendel HG. c-MYC regulates mRNA translation efficiency and start-site selection in lymphoma. J Exp Med 2019; 216:1509-1524. [PMID: 31142587 PMCID: PMC6605752 DOI: 10.1084/jem.20181726] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 02/22/2019] [Accepted: 04/19/2019] [Indexed: 12/24/2022] Open
Abstract
The oncogenic c-MYC (MYC) transcription factor has broad effects on gene expression and cell behavior. We show that MYC alters the efficiency and quality of mRNA translation into functional proteins. Specifically, MYC drives the translation of most protein components of the electron transport chain in lymphoma cells, and many of these effects are independent from proliferation. Specific interactions of MYC-sensitive RNA-binding proteins (e.g., SRSF1/RBM42) with 5'UTR sequence motifs mediate many of these changes. Moreover, we observe a striking shift in translation initiation site usage. For example, in low-MYC conditions, lymphoma cells initiate translation of the CD19 mRNA from a site in exon 5. This results in the truncation of all extracellular CD19 domains and facilitates escape from CD19-directed CAR-T cell therapy. Together, our findings reveal MYC effects on the translation of key metabolic enzymes and immune receptors in lymphoma cells.
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Affiliation(s)
- Kamini Singh
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jianan Lin
- The Jackson Laboratory for Genomic Medicine, Farmington, CT
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT
| | - Yi Zhong
- Computational Biology Department, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Antonija Burčul
- Computational Biology Department, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Prathibha Mohan
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Man Jiang
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Liping Sun
- Integrated Genomics Operation, Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Vladimir Yong-Gonzalez
- Donald B. and Catherine C. Marron Cancer Metabolism Center, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Agnes Viale
- Integrated Genomics Operation, Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Justin R Cross
- Donald B. and Catherine C. Marron Cancer Metabolism Center, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ronald C Hendrickson
- Proteomics and Microchemistry, Memorial Sloan- Kettering Cancer Center, New York, NY
| | - Gunnar Rätsch
- Computational Biology Department, Memorial Sloan Kettering Cancer Center, New York, NY
- Biomedical Informatics, Department of Computer Science, Swiss Federal Institute of Technology, Zürich, Switzerland
| | - Zhengqing Ouyang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT
- Department of Genetics and Genome Sciences and Institute for System Genomics, University of Connecticut Health Center, Farmington, CT
| | - Hans-Guido Wendel
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY
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14
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Leiphart RJ, Chen D, Peredo AP, Loneker AE, Janmey PA. Mechanosensing at Cellular Interfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:7509-7519. [PMID: 30346180 DOI: 10.1021/acs.langmuir.8b02841] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
At the plasma membrane interface, cells use various adhesions to sense their extracellular environment. These adhesions facilitate the transmission of mechanical signals that dictate cell behavior. This review discusses the mechanisms by which these mechanical signals are transduced through cell-matrix and cell-cell adhesions and how this mechanotransduction influences cell processes. Cell-matrix adhesions require the activation of and communication between various transmembrane protein complexes such as integrins. These links at the plasma membrane affect how a cell senses and responds to its matrix environment. Cells also communicate with each other through cell-cell adhesions, which further regulate cell behavior on a single- and multicellular scale. Coordination and competition between cell-cell and cell-matrix adhesions in multicellular aggregates can, to a significant extent, be modeled by differential adhesion analyses between the different interfaces even without knowing the details of cellular signaling. In addition, cell-matrix and cell-cell adhesions are connected by an intracellular cytoskeletal network that allows for direct communication between these distinct adhesions and activation of specific signaling pathways. Other membrane-embedded protein complexes, such as growth factor receptors and ion channels, play additional roles in mechanotransduction. Overall, these mechanoactive elements show the dynamic interplay between the cell, its matrix, and neighboring cells and how these relationships affect cellular function.
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Affiliation(s)
- Ryan J Leiphart
- Department of Bioengineering , University of Pennsylvania , 210 S 33rd St , Philadelphia , Pennsylvania 19104 , United States
- McKay Orthopedic Research Laboratory , University of Pennsylvania , Philadelphia , Pennsylvania , United States
| | - Dongning Chen
- Department of Bioengineering , University of Pennsylvania , 210 S 33rd St , Philadelphia , Pennsylvania 19104 , United States
- Center for Engineering Mechanobiology , University of Pennsylvania , Philadelphia , Pennsylvania , United States
| | - Ana P Peredo
- Department of Bioengineering , University of Pennsylvania , 210 S 33rd St , Philadelphia , Pennsylvania 19104 , United States
- McKay Orthopedic Research Laboratory , University of Pennsylvania , Philadelphia , Pennsylvania , United States
| | - Abigail E Loneker
- Department of Bioengineering , University of Pennsylvania , 210 S 33rd St , Philadelphia , Pennsylvania 19104 , United States
- Center for Engineering Mechanobiology , University of Pennsylvania , Philadelphia , Pennsylvania , United States
| | - Paul A Janmey
- Department of Bioengineering , University of Pennsylvania , 210 S 33rd St , Philadelphia , Pennsylvania 19104 , United States
- Institute for Medicine and Engineering, Department of Physiology , University of Pennsylvania , 3340 Smith Walk , Philadelphia , Pennsylvania 19104 , United States
- Center for Engineering Mechanobiology , University of Pennsylvania , Philadelphia , Pennsylvania , United States
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15
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Orré T, Rossier O, Giannone G. The inner life of integrin adhesion sites: From single molecules to functional macromolecular complexes. Exp Cell Res 2019; 379:235-244. [DOI: 10.1016/j.yexcr.2019.03.036] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 03/07/2019] [Accepted: 03/27/2019] [Indexed: 12/31/2022]
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16
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Abstract
It is increasingly clear that mechanotransduction pathways play important roles in regulating fundamental cellular functions. Of the basic mechanical functions, the determination of cellular morphology is critical. Cells typically use many mechanosensitive steps and different cell states to achieve a polarized shape through repeated testing of the microenvironment. Indeed, morphology is determined by the microenvironment through periodic activation of motility, mechanotesting, and mechanoresponse functions by hormones, internal clocks, and receptor tyrosine kinases. Patterned substrates and controlled environments with defined rigidities limit the range of cell behavior and influence cell state decisions and are thus very useful for studying these steps. The recently defined rigidity sensing process provides a good example of how cells repeatedly test their microenvironment and is also linked to cancer. In general, aberrant extracellular matrix mechanosensing is associated with numerous conditions, including cardiovascular disease, aging, and fibrosis, that correlate with changes in tissue morphology and matrix composition. Hence, detailed descriptions of the steps involved in sensing and responding to the microenvironment are needed to better understand both the mechanisms of tissue homeostasis and the pathomechanisms of human disease.
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Affiliation(s)
- Haguy Wolfenson
- Department of Genetics and Developmental Biology, Rappaport Faculty of Medicine, Technion Israel Institute of Technology, Haifa, Israel 31096;
| | - Bo Yang
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore;
| | - Michael P Sheetz
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore; .,Department of Biological Sciences, Columbia University, New York, NY 10027, USA
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17
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Kayser K, Degenhardt F, Holzapfel S, Horpaopan S, Peters S, Spier I, Morak M, Vangala D, Rahner N, von Knebel-Doeberitz M, Schackert HK, Engel C, Büttner R, Wijnen J, Doerks T, Bork P, Moebus S, Herms S, Fischer S, Hoffmann P, Aretz S, Steinke-Lange V. Copy number variation analysis and targeted NGS in 77 families with suspected Lynch syndrome reveals novel potential causative genes. Int J Cancer 2018; 143:2800-2813. [PMID: 29987844 DOI: 10.1002/ijc.31725] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 03/10/2018] [Accepted: 03/26/2018] [Indexed: 12/22/2022]
Abstract
In many families with suspected Lynch syndrome (LS), no germline mutation in the causative mismatch repair (MMR) genes is detected during routine diagnostics. To identify novel causative genes for LS, the present study investigated 77 unrelated, mutation-negative patients with clinically suspected LS and a loss of MSH2 in tumor tissue. An analysis for genomic copy number variants (CNV) was performed, with subsequent next generation sequencing (NGS) of selected candidate genes in a subgroup of the cohort. Genomic DNA was genotyped using Illumina's HumanOmniExpress Bead Array. After quality control and filtering, 25 deletions and 16 duplications encompassing 73 genes were identified in 28 patients. No recurrent CNV was detected, and none of the CNVs affected the regulatory regions of MSH2. A total of 49 candidate genes from genomic regions implicated by the present CNV analysis and 30 known or assumed risk genes for colorectal cancer (CRC) were then sequenced in a subset of 38 patients using a customized NGS gene panel and Sanger sequencing. Single nucleotide variants were identified in 14 candidate genes from the CNV analysis. The most promising of these candidate genes were: (i) PRKCA, PRKDC, and MCM4, as a functional relation to MSH2 is predicted by network analysis, and (ii) CSMD1, as this is commonly mutated in CRC. Furthermore, six patients harbored POLE variants outside the exonuclease domain, suggesting that these might be implicated in hereditary CRC. Analyses in larger cohorts of suspected LS patients recruited via international collaborations are warranted to verify the present findings.
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Affiliation(s)
- Katrin Kayser
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Franziska Degenhardt
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany
| | - Stefanie Holzapfel
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Center for Hereditary Tumor Syndromes, University of Bonn, Bonn, Germany
| | - Sukanya Horpaopan
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Anatomy, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | - Sophia Peters
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany
| | - Isabel Spier
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Center for Hereditary Tumor Syndromes, University of Bonn, Bonn, Germany
| | - Monika Morak
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Munich, Germany.,Medical Genetics Center (MGZ), Munich, Germany
| | - Deepak Vangala
- Department of Internal Medicine, Knappschaftskrankenhaus, Ruhr-University Bochum, Bochum, Germany
| | - Nils Rahner
- Institute of Human Genetics, University of Düsseldorf, Düsseldorf, Germany
| | - Magnus von Knebel-Doeberitz
- Department of Applied Tumor Biology, Institute of Pathology, University Hospital of Heidelberg, Heidelberg, Germany.,Cooperation Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hans K Schackert
- Department of Surgical Research, Technische Universität Dresden, Dresden, Germany
| | - Christoph Engel
- Institute of Medical Informatics, Statistics, and Epidemiology, University of Leipzig, Leipzig, Germany
| | | | - Juul Wijnen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Tobias Doerks
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Susanne Moebus
- Centre for Urban Epidemiology, University Hospital of Duisburg-Essen, University of Duisburg-Essen, Essen, Germany
| | - Stefan Herms
- Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany.,Human Genomics Research Group, Department of Biomedicine, University of Basel, Basel, Switzerland.,Insitute of Medical Genetics and Pathology, University Hospital of Basel, Basel, Switzerland
| | - Sascha Fischer
- Human Genomics Research Group, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany.,Human Genomics Research Group, Department of Biomedicine, University of Basel, Basel, Switzerland.,Insitute of Medical Genetics and Pathology, University Hospital of Basel, Basel, Switzerland
| | - Stefan Aretz
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Center for Hereditary Tumor Syndromes, University of Bonn, Bonn, Germany
| | - Verena Steinke-Lange
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Munich, Germany.,Medical Genetics Center (MGZ), Munich, Germany
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18
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Massimino ML, Simonato M, Spolaore B, Franchin C, Arrigoni G, Marin O, Monturiol-Gross L, Fernández J, Lomonte B, Tonello F. Cell surface nucleolin interacts with and internalizes Bothrops asper Lys49 phospholipase A 2 and mediates its toxic activity. Sci Rep 2018; 8:10619. [PMID: 30006575 PMCID: PMC6045611 DOI: 10.1038/s41598-018-28846-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 06/20/2018] [Indexed: 01/01/2023] Open
Abstract
Phospholipases A2 are a major component of snake venoms. Some of them cause severe muscle necrosis through an unknown mechanism. Phospholipid hydrolysis is a possible explanation of their toxic action, but catalytic and toxic properties of PLA2s are not directly connected. In addition, viperid venoms contain PLA2-like proteins, which are very toxic even if they lack catalytic activity due to a critical mutation in position 49. In this work, the PLA2-like Bothrops asper myotoxin-II, conjugated with the fluorophore TAMRA, was found to be internalized in mouse myotubes, and in RAW264.7 cells. Through experiments of protein fishing and mass spectrometry analysis, using biotinylated Mt-II as bait, we found fifteen proteins interacting with the toxin and among them nucleolin, a nucleolar protein present also on cell surface. By means of confocal microscopy, Mt-II and nucleolin were shown to colocalise, at 4 °C, on cell membrane where they form Congo-red sensitive assemblies, while at 37 °C, 20 minutes after the intoxication, they colocalise in intracellular spots going from plasmatic membrane to paranuclear and nuclear area. Finally, nucleolin antagonists were found to inhibit the Mt-II internalization and toxic activity and were used to identify the nucleolin regions involved in the interaction with the toxin.
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Affiliation(s)
| | - Morena Simonato
- Istituto di Neuroscienze, CNR, Via Ugo Bassi 58/B, 35131, Padova, Italy
| | - Barbara Spolaore
- Dipartimento di Scienze del Farmaco, Università di Padova, Via F. Marzolo, 5, 35131, Padova, Italy
| | - Cinzia Franchin
- Dipartimento di Scienze Biomediche, Università di Padova, Via Ugo Bassi 58/B, 35131, Padova, Italy
- Centro di Proteomica, Università di Padova e Azienda Ospedaliera di Padova, Via G. Orus 2/B, 35129, Padova, Italy
| | - Giorgio Arrigoni
- Dipartimento di Scienze Biomediche, Università di Padova, Via Ugo Bassi 58/B, 35131, Padova, Italy
- Centro di Proteomica, Università di Padova e Azienda Ospedaliera di Padova, Via G. Orus 2/B, 35129, Padova, Italy
| | - Oriano Marin
- Dipartimento di Scienze Biomediche, Università di Padova, Via Ugo Bassi 58/B, 35131, Padova, Italy
| | - Laura Monturiol-Gross
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, 11501, San José, Costa Rica
| | - Julián Fernández
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, 11501, San José, Costa Rica
| | - Bruno Lomonte
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, 11501, San José, Costa Rica
| | - Fiorella Tonello
- Istituto di Neuroscienze, CNR, Via Ugo Bassi 58/B, 35131, Padova, Italy.
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19
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Abstract
Cell adhesion to components of the cellular microenvironment via cell-surface adhesion receptors controls many aspects of cell behavior in a range of physiological and pathological processes. Multimolecular complexes of scaffolding and signaling proteins are recruited to the intracellular domains of adhesion receptors such as integrins, and these adhesion complexes tether the cytoskeleton to the plasma membrane and compartmentalize cellular signaling events. Integrin adhesion complexes are highly dynamic, and their assembly is tightly regulated. Comprehensive, unbiased, quantitative analyses of the composition of different adhesion complexes over the course of their formation will enable better understanding of how the dynamics of adhesion protein recruitment influence the functions of adhesion complexes in fundamental cellular processes. Here, a pipeline is detailed integrating biochemical isolation of integrin adhesion complexes during a time course, quantitative proteomic analysis of isolated adhesion complexes, and computational analysis of temporal proteomic data. This approach enables the characterization of adhesion complex composition and dynamics during complex assembly.
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Affiliation(s)
- Adam Byron
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.
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20
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Wasik AA, Schiller HB. Functional proteomics of cellular mechanosensing mechanisms. Semin Cell Dev Biol 2017; 71:118-128. [DOI: 10.1016/j.semcdb.2017.06.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 06/23/2017] [Accepted: 06/25/2017] [Indexed: 10/19/2022]
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21
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Vidotto A, Morais ATS, Ribeiro MR, Pacca CC, Terzian ACB, Gil LHVG, Mohana-Borges R, Gallay P, Nogueira ML. Systems Biology Reveals NS4B-Cyclophilin A Interaction: A New Target to Inhibit YFV Replication. J Proteome Res 2017; 16:1542-1555. [PMID: 28317380 DOI: 10.1021/acs.jproteome.6b00933] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Yellow fever virus (YFV) replication is highly dependent on host cell factors. YFV NS4B is reported to be involved in viral replication and immune evasion. Here interactions between NS4B and human proteins were determined using a GST pull-down assay and analyzed using 1-DE and LC-MS/MS. We present a total of 207 proteins confirmed using Scaffold 3 Software. Cyclophilin A (CypA), a protein that has been shown to be necessary for the positive regulation of flavivirus replication, was identified as a possible NS4B partner. 59 proteins were found to be significantly increased when compared with a negative control, and CypA exhibited the greatest difference, with a 22-fold change. Fisher's exact test was significant for 58 proteins, and the p value of CypA was the most significant (0.000000019). The Ingenuity Systems software identified 16 pathways, and this analysis indicated sirolimus, an mTOR pathway inhibitor, as a potential inhibitor of CypA. Immunofluorescence and viral plaque assays showed a significant reduction in YFV replication using sirolimus and cyclosporine A (CsA) as inhibitors. Furthermore, YFV replication was strongly inhibited in cells treated with both inhibitors using reporter BHK-21-rep-YFV17D-LucNeoIres cells. Taken together, these data suggest that CypA-NS4B interaction regulates YFV replication. Finally, we present the first evidence that YFV inhibition may depend on NS4B-CypA interaction.
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Affiliation(s)
- Alessandra Vidotto
- Laboratório de Virologia, Faculdade de Medicina de José do Rio Preto , São José do Rio Preto, São Paulo 15090-000, Brazil
| | - Ana T S Morais
- Laboratório de Virologia, Faculdade de Medicina de José do Rio Preto , São José do Rio Preto, São Paulo 15090-000, Brazil
| | - Milene R Ribeiro
- Laboratório de Virologia, Faculdade de Medicina de José do Rio Preto , São José do Rio Preto, São Paulo 15090-000, Brazil
| | - Carolina C Pacca
- Laboratório de Virologia, Faculdade de Medicina de José do Rio Preto , São José do Rio Preto, São Paulo 15090-000, Brazil
| | - Ana C B Terzian
- Laboratório de Virologia, Faculdade de Medicina de José do Rio Preto , São José do Rio Preto, São Paulo 15090-000, Brazil
| | - Laura H V G Gil
- Departamento de Virologia, Centro de Pesquisa Aggeu Magalhães , Fundação Oswaldo Cruz (FIOCRUZ) - Recife, Pernambuco 50740-465, Brazil
| | - Ronaldo Mohana-Borges
- Laboratório de Genômica Estrutural, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro - UFRJ , Rio de Janeiro RJ 21941-902, Brazil
| | - Philippe Gallay
- Department of Immunology & Microbial Science, The Scripps Research Institute - La Jolla , San Diego, California 92037, United States
| | - Mauricio L Nogueira
- Laboratório de Virologia, Faculdade de Medicina de José do Rio Preto , São José do Rio Preto, São Paulo 15090-000, Brazil
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22
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Millon-Frémillon A, Aureille J, Guilluy C. Analyzing Cell Surface Adhesion Remodeling in Response to Mechanical Tension Using Magnetic Beads. J Vis Exp 2017:55330. [PMID: 28362397 PMCID: PMC5408950 DOI: 10.3791/55330] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Mechanosensitive cell surface adhesion complexes allow cells to sense the mechanical properties of their surroundings. Recent studies have identified both force-sensing molecules at adhesion sites, and force-dependent transcription factors that regulate lineage-specific gene expression and drive phenotypic outputs. However, the signaling networks converting mechanical tension into biochemical pathways have remained elusive. To explore the signaling pathways engaged upon mechanical tension applied to cell surface receptor, superparamagnetic microbeads can be used. Here we present a protocol for using magnetic beads to apply forces to cell surface adhesion proteins. Using this approach, it is possible to investigate not only force-dependent cytoplasmic signaling pathways by various biochemical approaches, but also adhesion remodeling by magnetic isolation of adhesion complexes attached to the ligand-coated beads. This protocol includes the preparation of ligand-coated superparamagnetic beads, and the application of define tensile forces followed by biochemical analyses. Additionally, we provide a representative sample of data demonstrating that tension applied to integrin-based adhesion triggers adhesion remodeling and alters protein tyrosine phosphorylation.
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Affiliation(s)
| | - Julien Aureille
- Institute for Advanced Biosciences, Centre de recherche UGA - INSERM U1209 - CNRS UMR
| | - Christophe Guilluy
- Institute for Advanced Biosciences, Centre de recherche UGA - INSERM U1209 - CNRS UMR;
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23
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Integrin signaling in atherosclerosis. Cell Mol Life Sci 2017; 74:2263-2282. [PMID: 28246700 DOI: 10.1007/s00018-017-2490-4] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 01/24/2017] [Accepted: 02/15/2017] [Indexed: 02/07/2023]
Abstract
Atherosclerosis, a chronic lipid-driven inflammatory disease affecting large arteries, represents the primary cause of cardiovascular disease in the world. The local remodeling of the vessel intima during atherosclerosis involves the modulation of vascular cell phenotype, alteration of cell migration and proliferation, and propagation of local extracellular matrix remodeling. All of these responses represent targets of the integrin family of cell adhesion receptors. As such, alterations in integrin signaling affect multiple aspects of atherosclerosis, from the earliest induction of inflammation to the development of advanced fibrotic plaques. Integrin signaling has been shown to regulate endothelial phenotype, facilitate leukocyte homing, affect leukocyte function, and drive smooth muscle fibroproliferative remodeling. In addition, integrin signaling in platelets contributes to the thrombotic complications that typically drive the clinical manifestation of cardiovascular disease. In this review, we examine the current literature on integrin regulation of atherosclerotic plaque development and the suitability of integrins as potential therapeutic targets to limit cardiovascular disease and its complications.
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24
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Thomas MP, Erneux C, Potter BVL. SHIP2: Structure, Function and Inhibition. Chembiochem 2017; 18:233-247. [DOI: 10.1002/cbic.201600541] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Mark P. Thomas
- Department of Pharmacy and Pharmacology; University of Bath; Claverton Down Bath BA2 7AY UK
| | - Christophe Erneux
- I.R.I.B.H.M.; Université Libre de Bruxelles; Campus Erasme 808 Route de Lennik 1070 Brussels Belgium
| | - Barry V. L. Potter
- Drug Discovery and Medicinal Chemistry; Department of Pharmacology; University of Oxford; Mansfield Road Oxford OX1 3QT UK
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25
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Robertson J, Humphries JD, Paul NR, Warwood S, Knight D, Byron A, Humphries MJ. Characterization of the Phospho-Adhesome by Mass Spectrometry-Based Proteomics. Methods Mol Biol 2017; 1636:235-251. [PMID: 28730483 DOI: 10.1007/978-1-4939-7154-1_15] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Integrin adhesion receptors engage with their extracellular matrix (ECM) ligands, initiating intracellular signaling pathways that regulate a range of fundamental cell functions. Protein kinases and phosphatases play an integral role in integrin adhesion-mediated signaling. However, until recently, knowledge of the phosphorylation sites regulated downstream of integrin ligation was limited to candidate-based approaches and did not support a system-level understanding of the molecular mechanisms through which ECM engagement influences cell behavior. Here, we describe a mass spectrometry (MS)-based phosphoproteomic protocol that enables the global characterization of phosphorylation-based signaling networks activated by integrin-mediated adhesion. To analyze specifically integrin-proximal signaling, the phosphoproteomic workflow involves the affinity-based isolation and analysis of integrin-associated complexes (IACs) rather than proteins solubilized from whole-cell lysates , which are typically used for global phosphoproteomic studies. The detection of phosphorylation sites from IAC proteins was optimized at various stages of the workflow, including IAC isolation, proteolytic digestion, and MS-based data acquisition strategies. The protocol permits the identification and quantification of IAC components by both Western blotting and MS. Notably, compared to phosphoproteomic analyses of cell lysates, the workflow described here enables an improved detection of phosphorylation sites from well-defined IAC proteins, including many known components of the signaling pathways activated by adhesion to the ECM.
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Affiliation(s)
- Joseph Robertson
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
- Department of Molecular Microbiology, Oslo University Hospital, 0027, Oslo, Norway
| | - Jonathan D Humphries
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Nikki R Paul
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
- CRUK Beatson Institute, Glasgow, G61 1BD, UK
| | - Stacey Warwood
- Biological Mass Spectrometry Core Facility, Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK
| | - David Knight
- Biological Mass Spectrometry Core Facility, Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK
| | - Adam Byron
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
- Edinburgh Cancer Research UK Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - Martin J Humphries
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK.
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26
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Manninen A, Varjosalo M. A proteomics view on integrin-mediated adhesions. Proteomics 2016; 17. [PMID: 27723259 DOI: 10.1002/pmic.201600022] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 09/05/2016] [Accepted: 10/06/2016] [Indexed: 01/15/2023]
Abstract
Individual cells in multicellular organisms constantly explore their microenvironment, or niche, to obtain spatial information that is used to regulate cell behavior to maintain tissue integrity. The extracellular matrix (ECM) is an important source of such spatial information. Binding of the integrin family receptors to the ECM triggers formation of integrin adhesion complexes (IACs) that link the ECM network to cellular cytoskeleton via remarkably large multiprotein complexes collectively referred to as the integrin adhesome. Recent advances in proteomics have enabled researchers to study the IAC composition in detail. Various biochemical IAC isolation methods and culture conditions have been employed to study the composition and dynamics of integrin-mediated adhesions mainly in fibroblasts and lymphoblasts. These studies have led to identification of daunting lists of potential IAC components. This review focuses on the current status of proteomics-driven research seeking to understand integrin functions by comprehensive analysis of IAC components. These systems level approaches have revealed the complexity of biochemical and biomechanical signals that are processed at IACs and provide a novel insight into how these signals are conveyed to regulate cellular behavior.
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Affiliation(s)
- Aki Manninen
- Biocenter Oulu, Oulu Center for Cell-Matrix Research, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Markku Varjosalo
- Institute of Biotechnology, Biocenter 3, University of Helsinki, Helsinki, Finland
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27
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Horton ER, Humphries JD, James J, Jones MC, Askari JA, Humphries MJ. The integrin adhesome network at a glance. J Cell Sci 2016; 129:4159-4163. [PMID: 27799358 PMCID: PMC5117201 DOI: 10.1242/jcs.192054] [Citation(s) in RCA: 132] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The adhesion nexus is the site at which integrin receptors bridge intracellular cytoskeletal and extracellular matrix networks. The connection between integrins and the cytoskeleton is mediated by a dynamic integrin adhesion complex (IAC), the components of which transduce chemical and mechanical signals to control a multitude of cellular functions. In this Cell Science at a Glance article and the accompanying poster, we integrate the consensus adhesome, a set of 60 proteins that have been most commonly identified in isolated IAC proteomes, with the literature-curated adhesome, a theoretical network that has been assembled through scholarly analysis of proteins that localise to IACs. The resulting IAC network, which comprises four broad signalling and actin-bridging axes, provides a platform for future studies of the regulation and function of the adhesion nexus in health and disease.
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Affiliation(s)
- Edward R Horton
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Jonathan D Humphries
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Jenny James
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Matthew C Jones
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Janet A Askari
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Martin J Humphries
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
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Byron A, Frame MC. Adhesion protein networks reveal functions proximal and distal to cell-matrix contacts. Curr Opin Cell Biol 2016; 39:93-100. [PMID: 26930633 PMCID: PMC5094910 DOI: 10.1016/j.ceb.2016.02.013] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 02/09/2016] [Accepted: 02/09/2016] [Indexed: 12/15/2022]
Abstract
Cell adhesion to the extracellular matrix is generally mediated by integrin receptors, which bind to intracellular adhesion proteins that form multi-molecular scaffolding and signalling complexes. The networks of proteins, and their interactions, are dynamic, mechanosensitive and extremely complex. Recent efforts to characterise adhesions using a variety of technologies, including imaging, proteomics and bioinformatics, have provided new insights into their composition, organisation and how they are regulated, and have also begun to reveal unexpected roles for so-called adhesion proteins in other cellular compartments (for example, the nucleus or centrosomes) in diseases such as cancer. We believe this is opening a new chapter on understanding the wider functions of adhesion proteins, both proximal and distal to cell-matrix contacts.
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Affiliation(s)
- Adam Byron
- Edinburgh Cancer Research UK Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom.
| | - Margaret C Frame
- Edinburgh Cancer Research UK Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
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29
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Richens JL, Spencer HL, Butler M, Cantlay F, Vere KA, Bajaj N, Morgan K, O'Shea P. Rationalising the role of Keratin 9 as a biomarker for Alzheimer's disease. Sci Rep 2016; 6:22962. [PMID: 26973255 PMCID: PMC4789650 DOI: 10.1038/srep22962] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 02/19/2016] [Indexed: 02/07/2023] Open
Abstract
Keratin 9 was recently identified as an important component of a biomarker panel which demonstrated a high diagnostic accuracy (87%) for Alzheimer's disease (AD). Understanding how a protein which is predominantly expressed in palmoplantar epidermis is implicated in AD may shed new light on the mechanisms underlying the disease. Here we use immunoassays to examine blood plasma expression patterns of Keratin 9 and its relationship to other AD-associated proteins. We correlate this with the use of an in silico analysis tool VisANT to elucidate possible pathways through which the involvement of Keratin 9 may take place. We identify possible links with Dickkopf-1, a negative regulator of the wnt pathway, and propose that the abnormal expression of Keratin 9 in AD blood and cerebrospinal fluid may be a result of blood brain barrier dysregulation and disruption of the ubiquitin proteasome system. Our findings suggest that dysregulated Keratin 9 expression is a consequence of AD pathology but, as it interacts with a broad range of proteins, it may have other, as yet uncharacterized, downstream effects which could contribute to AD onset and progression.
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Affiliation(s)
- Joanna L Richens
- Cell Biophysics Group, School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Hannah L Spencer
- Cell Biophysics Group, School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Molly Butler
- Cell Biophysics Group, School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Fiona Cantlay
- Cell Biophysics Group, School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Kelly-Ann Vere
- Cell Biophysics Group, School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Nin Bajaj
- Department of Neurology, Nottingham University Hospitals NHS Trust, Queen's Medical Centre, Nottingham, United Kingdom
| | - Kevin Morgan
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom
| | - Paul O'Shea
- Cell Biophysics Group, School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
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30
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Horton ER, Humphries JD, Stutchbury B, Jacquemet G, Ballestrem C, Barry ST, Humphries MJ. Modulation of FAK and Src adhesion signaling occurs independently of adhesion complex composition. J Cell Biol 2016; 212:349-64. [PMID: 26833789 PMCID: PMC4739608 DOI: 10.1083/jcb.201508080] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 01/06/2016] [Indexed: 01/15/2023] Open
Abstract
Integrin adhesion complexes (IACs) form mechanochemical connections between the extracellular matrix and actin cytoskeleton and mediate phenotypic responses via posttranslational modifications. Here, we investigate the modularity and robustness of the IAC network to pharmacological perturbation of the key IAC signaling components focal adhesion kinase (FAK) and Src. FAK inhibition using AZ13256675 blocked FAK(Y397) phosphorylation but did not alter IAC composition, as reported by mass spectrometry. IAC composition was also insensitive to Src inhibition using AZD0530 alone or in combination with FAK inhibition. In contrast, kinase inhibition substantially reduced phosphorylation within IACs, cell migration and proliferation. Furthermore using fluorescence recovery after photobleaching, we found that FAK inhibition increased the exchange rate of a phosphotyrosine (pY) reporter (dSH2) at IACs. These data demonstrate that kinase-dependent signal propagation through IACs is independent of gross changes in IAC composition. Together, these findings demonstrate a general separation between the composition of IACs and their ability to relay pY-dependent signals.
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Affiliation(s)
- Edward R Horton
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, England, UK
| | - Jonathan D Humphries
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, England, UK
| | - Ben Stutchbury
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, England, UK
| | - Guillaume Jacquemet
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, England, UK
| | - Christoph Ballestrem
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, England, UK
| | - Simon T Barry
- Oncology iMed, AstraZeneca, Cheshire SK10 4TG, England, UK
| | - Martin J Humphries
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, England, UK
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31
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Ouanouki A, Desrosiers RR. The enzyme l-isoaspartyl (d-aspartyl) methyltransferase is required for VEGF-dependent endothelial cell migration and tubulogenesis. Mol Cell Biochem 2016; 413:37-46. [DOI: 10.1007/s11010-015-2637-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Accepted: 12/23/2015] [Indexed: 02/08/2023]
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Horton ER, Byron A, Askari JA, Ng DHJ, Millon-Frémillon A, Robertson J, Koper EJ, Paul NR, Warwood S, Knight D, Humphries JD, Humphries MJ. Definition of a consensus integrin adhesome and its dynamics during adhesion complex assembly and disassembly. Nat Cell Biol 2015; 17:1577-1587. [PMID: 26479319 PMCID: PMC4663675 DOI: 10.1038/ncb3257] [Citation(s) in RCA: 369] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 09/18/2015] [Indexed: 12/14/2022]
Abstract
Integrin receptor activation initiates the formation of integrin adhesion complexes (IACs) at the cell membrane that transduce adhesion-dependent signals to control a multitude of cellular functions. Proteomic analyses of isolated IACs have revealed an unanticipated molecular complexity; however, a global view of the consensus composition and dynamics of IACs is lacking. Here, we have integrated several IAC proteomes and generated a 2,412-protein integrin adhesome. Analysis of this data set reveals the functional diversity of proteins in IACs and establishes a consensus adhesome of 60 proteins. The consensus adhesome is likely to represent a core cell adhesion machinery, centred around four axes comprising ILK-PINCH-kindlin, FAK-paxillin, talin-vinculin and α-actinin-zyxin-VASP, and includes underappreciated IAC components such as Rsu-1 and caldesmon. Proteomic quantification of IAC assembly and disassembly detailed the compositional dynamics of the core cell adhesion machinery. The definition of this consensus view of integrin adhesome components provides a resource for the research community.
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Affiliation(s)
- Edward R. Horton
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Adam Byron
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
- Edinburgh Cancer Research UK Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XR, UK
| | - Janet A. Askari
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Daniel H. J. Ng
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Angélique Millon-Frémillon
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Joseph Robertson
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Ewa J. Koper
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Nikki R. Paul
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Stacey Warwood
- Biological Mass Spectrometry Core Facility, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - David Knight
- Biological Mass Spectrometry Core Facility, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Jonathan D. Humphries
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Martin J. Humphries
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
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33
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Mechanosensitivity of integrin adhesion complexes: role of the consensus adhesome. Exp Cell Res 2015; 343:7-13. [PMID: 26515553 DOI: 10.1016/j.yexcr.2015.10.025] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 10/23/2015] [Indexed: 12/17/2022]
Abstract
Cell and tissue stiffness have been known to contribute to both developmental and pathological signalling for some time, but the underlying mechanisms remain elusive. Integrins and their associated adhesion signalling complexes (IACs), which form a nexus between the cell cytoskeleton and the extracellular matrix, act as a key force sensing and transducing unit in cells. Accordingly, there has been much interest in obtaining a systems-level understanding of IAC composition. Proteomic approaches have revealed the complexity of IACs and identified a large number of components that are regulated by cytoskeletal force. Here we review the function of the consensus adhesome, an assembly of core IAC proteins that emerged from a meta-analysis of multiple proteomic datasets, in the context of mechanosensing. As IAC components have been linked to a variety of diseases involved with rigidity sensing, the field is now in a position to define the mechanosensing function of individual IAC proteins and elucidate their mechanisms of action.
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34
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Manninen A. Epithelial polarity – Generating and integrating signals from the ECM with integrins. Exp Cell Res 2015; 334:337-49. [DOI: 10.1016/j.yexcr.2015.01.003] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 01/08/2015] [Accepted: 01/09/2015] [Indexed: 01/20/2023]
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SP-R210 (Myo18A) Isoforms as Intrinsic Modulators of Macrophage Priming and Activation. PLoS One 2015; 10:e0126576. [PMID: 25965346 PMCID: PMC4428707 DOI: 10.1371/journal.pone.0126576] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 04/06/2015] [Indexed: 11/19/2022] Open
Abstract
The surfactant protein (SP-A) receptor SP-R210 has been shown to increase phagocytosis of SP-A-bound pathogens and to modulate cytokine secretion by immune cells. SP-A plays an important role in pulmonary immunity by enhancing opsonization and clearance of pathogens and by modulating macrophage inflammatory responses. Alternative splicing of the Myo18A gene results in two isoforms: SP-R210S and SP-R210L, with the latter predominantly expressed in alveolar macrophages. In this study we show that SP-A is required for optimal expression of SP-R210L on alveolar macrophages. Interestingly, pre-treatment with SP-A prepared by different methods either enhances or suppresses responsiveness to LPS, possibly due to differential co-isolation of SP-B or other proteins. We also report that dominant negative disruption of SP-R210L augments expression of receptors including SR-A, CD14, and CD36, and enhances macrophages' inflammatory response to TLR stimulation. Finally, because SP-A is known to modulate CD14, we used a variety of techniques to investigate how SP-R210 mediates the effect of SP-A on CD14. These studies revealed a novel physical association between SP-R210S, CD14, and SR-A leading to an enhanced response to LPS, and found that SP-R210L and SP-R210S regulate internalization of CD14 via distinct macropinocytosis-like mechanisms. Together, our findings support a model in which SP-R210 isoforms differentially regulate trafficking, expression, and activation of innate immune receptors on macrophages.
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36
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Scifo E, Szwajda A, Soliymani R, Pezzini F, Bianchi M, Dapkunas A, Dębski J, Uusi-Rauva K, Dadlez M, Gingras AC, Tyynelä J, Simonati A, Jalanko A, Baumann MH, Lalowski M. Proteomic analysis of the palmitoyl protein thioesterase 1 interactome in SH-SY5Y human neuroblastoma cells. J Proteomics 2015; 123:42-53. [PMID: 25865307 DOI: 10.1016/j.jprot.2015.03.038] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 03/12/2015] [Accepted: 03/31/2015] [Indexed: 12/20/2022]
Abstract
UNLABELLED Neuronal ceroid lipofuscinoses (NCL) are a group of inherited progressive childhood disorders, characterized by early accumulation of autofluorescent storage material in lysosomes of neurons or other cells. Clinical symptoms of NCL include: progressive loss of vision, mental and motor deterioration, epileptic seizures and premature death. CLN1 disease (MIM#256730) is caused by mutations in the CLN1 gene, which encodes palmitoyl protein thioesterase 1 (PPT1). In this study, we utilised single step affinity purification coupled to mass spectrometry (AP-MS) to unravel the in vivo substrates of human PPT1 in the brain neuronal cells. Protein complexes were isolated from human PPT1 expressing SH-SY5Y stable cells, subjected to filter-aided sample preparation (FASP) and analysed on a Q Exactive Hybrid Quadrupole-Orbitrap mass spectrometer. A total of 23 PPT1 interacting partners (IP) were identified from label free quantitation of the MS data by SAINT platform. Three of the identified PPT1 IP, namely CRMP1, DBH, and MAP1B are predicted to be palmitoylated. Our proteomic analysis confirmed previously suggested roles of PPT1 in axon guidance and lipid metabolism, yet implicates the enzyme in novel roles including: involvement in neuronal migration and dopamine receptor mediated signalling pathway. BIOLOGICAL SIGNIFICANCE The significance of this work lies in the unravelling of putative in vivo substrates of human CLN1 or PPT1 in brain neuronal cells. Moreover, the PPT1 IP implicate the enzyme in novel roles including: involvement in neuronal migration and dopamine receptor mediated signalling pathway.
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Affiliation(s)
- Enzo Scifo
- Meilahti Clinical Proteomics Core Facility, Institute of Biomedicine/Biochemistry and Developmental Biology, University of Helsinki, Helsinki, Finland; Doctoral Program Brain & Mind, University of Helsinki, Helsinki, Finland.
| | - Agnieszka Szwajda
- Institute for Molecular Medicine (FIMM), University of Helsinki, Helsinki, Finland
| | - Rabah Soliymani
- Meilahti Clinical Proteomics Core Facility, Institute of Biomedicine/Biochemistry and Developmental Biology, University of Helsinki, Helsinki, Finland
| | - Francesco Pezzini
- Department of Neurological and Movement Sciences, University of Verona, Verona, Italy
| | - Marzia Bianchi
- Department of Neurological and Movement Sciences, University of Verona, Verona, Italy; Unit for Neuromuscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Arvydas Dapkunas
- Meilahti Clinical Proteomics Core Facility, Institute of Biomedicine/Biochemistry and Developmental Biology, University of Helsinki, Helsinki, Finland
| | - Janusz Dębski
- Mass Spectrometry Laboratory, Department of Biophysics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Kristiina Uusi-Rauva
- Folkhälsan Institute of Genetics, Helsinki, Finland; National Institute for Health and Welfare, Public Health Genomics Unit, Helsinki, Finland
| | - Michał Dadlez
- Mass Spectrometry Laboratory, Department of Biophysics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Anne-Claude Gingras
- Centre for Systems Biology, Samuel Lunenfeld Research Institute at Mount Sinai Hospital, Toronto, Canada; Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Jaana Tyynelä
- Meilahti Clinical Proteomics Core Facility, Institute of Biomedicine/Biochemistry and Developmental Biology, University of Helsinki, Helsinki, Finland
| | - Alessandro Simonati
- Department of Neurological and Movement Sciences, University of Verona, Verona, Italy
| | - Anu Jalanko
- Institute for Molecular Medicine (FIMM), University of Helsinki, Helsinki, Finland; National Institute for Health and Welfare, Public Health Genomics Unit, Helsinki, Finland
| | - Marc H Baumann
- Meilahti Clinical Proteomics Core Facility, Institute of Biomedicine/Biochemistry and Developmental Biology, University of Helsinki, Helsinki, Finland
| | - Maciej Lalowski
- Meilahti Clinical Proteomics Core Facility, Institute of Biomedicine/Biochemistry and Developmental Biology, University of Helsinki, Helsinki, Finland; Folkhälsan Institute of Genetics, Helsinki, Finland.
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Emerging properties of adhesion complexes: what are they and what do they do? Trends Cell Biol 2015; 25:388-97. [PMID: 25824971 DOI: 10.1016/j.tcb.2015.02.008] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 02/13/2015] [Accepted: 02/24/2015] [Indexed: 02/07/2023]
Abstract
The regulation of cell adhesion machinery is central to a wide variety of developmental and pathological processes and occurs primarily within integrin-associated adhesion complexes. Here, we review recent advances that have furthered our understanding of the composition, organisation, and dynamics of these complexes, and provide an updated view on their emerging functions. Key findings are that adhesion complexes contain both core and non-canonical components. As a result of the dramatic increase in the range of components observed in adhesion complexes by proteomics, we comment on newly emerging functions for adhesion signalling. We conclude that, from a cellular or tissue systems perspective, adhesion signalling should be viewed as an emergent property of both the core and non-canonical adhesion complex components.
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Jones MC, Humphries JD, Byron A, Millon-Frémillon A, Robertson J, Paul NR, Ng DHJ, Askari JA, Humphries MJ. Isolation of integrin-based adhesion complexes. CURRENT PROTOCOLS IN CELL BIOLOGY 2015; 66:9.8.1-9.8.15. [PMID: 25727331 PMCID: PMC4402726 DOI: 10.1002/0471143030.cb0908s66] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The integration of cells with their extracellular environment is facilitated by cell surface adhesion receptors, such as integrins, which play important roles in both normal development and the onset of pathologies. Engagement of integrins with their ligands in the extracellular matrix, or counter-receptors on other cells, initiates the intracellular assembly of a wide variety of proteins into adhesion complexes such as focal contacts, focal adhesions, and fibrillar adhesions. The proteins recruited to these complexes mediate bidirectional signaling across the plasma membrane, and, as such, help to coordinate and/or modulate the multitude of physical and chemical signals to which the cell is subjected. The protocols in this unit describe two approaches for the isolation or enrichment of proteins contained within integrin-associated adhesion complexes, together with their local plasma membrane/cytosolic environments, from cells in culture. In the first protocol, integrin-associated adhesion structures are affinity isolated using microbeads coated with extracellular ligands or antibodies. The second protocol describes the isolation of ventral membrane preparations that are enriched for adhesion complex structures. The protocols permit the determination of adhesion complex components via subsequent downstream analysis by western blotting or mass spectrometry.
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Affiliation(s)
- Matthew C. Jones
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Jonathan D. Humphries
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Adam Byron
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Angelique Millon-Frémillon
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Joseph Robertson
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Nikki R. Paul
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Daniel H. J. Ng
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Janet A. Askari
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Martin J. Humphries
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
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Robertson J, Jacquemet G, Byron A, Jones MC, Warwood S, Selley JN, Knight D, Humphries JD, Humphries MJ. Defining the phospho-adhesome through the phosphoproteomic analysis of integrin signalling. Nat Commun 2015; 6:6265. [PMID: 25677187 PMCID: PMC4338609 DOI: 10.1038/ncomms7265] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 01/09/2015] [Indexed: 01/09/2023] Open
Abstract
Cell–extracellular matrix (ECM) adhesion is a fundamental requirement for multicellular existence due to roles in positioning, proliferation and differentiation. Phosphorylation plays a major role in adhesion signalling; however, a full understanding of the phosphorylation events that occur at sites of adhesion is lacking. Here we report a proteomic and phosphoproteomic analysis of adhesion complexes isolated from cells spread on fibronectin. We identify 1,174 proteins, 499 of which are phosphorylated (1,109 phosphorylation sites), including both well-characterized and novel adhesion-regulated phosphorylation events. Immunoblotting suggests that two classes of phosphorylated residues are found at adhesion sites—those induced by adhesion and those constitutively phosphorylated but recruited in response to adhesion. Kinase prediction analysis identifies novel kinases with putative roles in adhesion signalling including CDK1, inhibition of which reduces adhesion complex formation. This phospho-adhesome data set constitutes a valuable resource to improve our understanding of the signalling mechanisms through which cell–ECM interactions control cell behaviour. Protein phosphorylation is known to play an important role in cell adhesion signalling. Robertson et al. present a proteomic resource mapping the phosphorylation states of proteins isolated from adhesion complexes and, taking advantage of this data set, show that the cell cycle kinase CDK1 may influence cell adhesion.
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Affiliation(s)
- Joseph Robertson
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Guillaume Jacquemet
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Adam Byron
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Matthew C Jones
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Stacey Warwood
- Biological Mass Spectrometry Core Facility, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Julian N Selley
- Biological Mass Spectrometry Core Facility, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - David Knight
- Biological Mass Spectrometry Core Facility, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Jonathan D Humphries
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Martin J Humphries
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
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40
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A proteomic approach reveals integrin activation state-dependent control of microtubule cortical targeting. Nat Commun 2015; 6:6135. [PMID: 25609142 PMCID: PMC4317495 DOI: 10.1038/ncomms7135] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 12/15/2014] [Indexed: 12/13/2022] Open
Abstract
Integrin activation, which is regulated by allosteric changes in receptor conformation, enables cellular responses to the chemical, mechanical and topological features of the extracellular microenvironment. A global view of how activation state converts the molecular composition of the region proximal to integrins into functional readouts is, however, lacking. Here, using conformation-specific monoclonal antibodies, we report the isolation of integrin activation state-dependent complexes and their characterization by mass spectrometry. Quantitative comparisons, integrating network, clustering, pathway and image analyses, define multiple functional protein modules enriched in a conformation-specific manner. Notably, active integrin complexes are specifically enriched for proteins associated with microtubule-based functions. Visualization of microtubules on micropatterned surfaces and live cell imaging demonstrate that active integrins establish an environment that stabilizes microtubules at the cell periphery. These data provide a resource for the interrogation of the global molecular connections that link integrin activation to adhesion signalling. Integrins are activated by many extracellular cues and respond by assembling diverse signalling complexes. Byron et al. use activation state-specific antibodies to proteomically characterize these complexes, and provide insight into integrin-dependent microtubule stabilization.
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Schlesinger M, Bendas G. Contribution of very late antigen-4 (VLA-4) integrin to cancer progression and metastasis. Cancer Metastasis Rev 2015; 34:575-91. [DOI: 10.1007/s10555-014-9545-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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42
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Hsu RM, Hsieh YJ, Yang TH, Chiang YC, Kan CY, Lin YT, Chen JT, Yu JS. Binding of the extreme carboxyl-terminus of PAK-interacting exchange factor β (βPIX) to myosin 18A (MYO18A) is required for epithelial cell migration. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:2513-27. [PMID: 25014165 DOI: 10.1016/j.bbamcr.2014.06.023] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 06/30/2014] [Indexed: 10/25/2022]
Abstract
The PAK2/βPIX/GIT1 (p21-activated kinase 2/PAK-interacting exchange factor-β/G protein-coupled receptor kinase-interactor 1) complex has been shown to distribute to both membrane ruffles and focal adhesions of cells, where it plays an important role in regulating focal adhesion turnover. However, the detailed mechanism underlying this regulation is largely unknown. We previously reported that MYO18Aα interacts via its carboxyl terminus with the PAK2/βPIX/GIT1 complex through direct binding to βPIX, and that knockdown of MYO18Aα in epithelial cells causes accumulation of the complex in focal adhesions and decreased cell migration ability (Hsu et al., 2010). The current study characterized the detailed MYO18Aα-βPIX interaction mechanism and the biological significance of this interaction. We found that deletion of the carboxyl-terminal globular domain of MYO18Aα profoundly altered the cellular localization of βPIX and inhibited cell migration. βPIX interacts through its most carboxyl-terminus, PAWDETNL (639-646), with MYO18Aα and partially colocalized with MYO18Aα in membrane ruffles of cells, whereas βPIX(1-638), a mutant with deletion of PAWDETNL, accumulated in focal adhesions. Both focal adhesion numbers and area in βPIX(1-638)-expressing cells were greater than those in cells expressing wild-type βPIX(FL). Further experiments using deletion mutants of MYO18A and βPIX showed that disruption of MYO18A-βPIX interaction not only impaired cell motility but also decreased Rac1 activity. Collectively, our data unravel the interaction regions between MYO18A and βPIX and provide evidence for the critical role of this interaction in regulating cellular localization of βPIX, Rac1 activity, and adhesion and migration in epithelial cells.
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Affiliation(s)
- Rae-Mann Hsu
- Department of Cell and Molecular Biology, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan, ROC
| | - Ya-Ju Hsieh
- Molecular Medicine Research Center, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan, ROC
| | - Tsung-Han Yang
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan, ROC
| | - Yi-Chien Chiang
- Department of Cell and Molecular Biology, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan, ROC
| | - Chih-Yen Kan
- Department of Cell and Molecular Biology, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan, ROC
| | - Yu-Tsuen Lin
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan, ROC
| | - Jeng-Ting Chen
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan, ROC
| | - Jau-Song Yu
- Department of Cell and Molecular Biology, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan, ROC; Molecular Medicine Research Center, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan, ROC; Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan, ROC.
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Lennon R, Randles MJ, Humphries MJ. The importance of podocyte adhesion for a healthy glomerulus. Front Endocrinol (Lausanne) 2014; 5:160. [PMID: 25352829 PMCID: PMC4196579 DOI: 10.3389/fendo.2014.00160] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 09/21/2014] [Indexed: 12/23/2022] Open
Abstract
Podocytes are specialized epithelial cells that cover the outer surfaces of glomerular capillaries. Unique cell junctions, known as slit diaphragms, which feature nephrin and Neph family proteins in addition to components of adherens, tight, and gap junctions, connect adjacent podocyte foot processes. Single gene disorders affecting the slit diaphragm result in nephrotic syndrome in humans, characterized by massive loss of protein across the capillary wall. In addition to specialized cell junctions, interconnecting podocytes also adhere to the glomerular basement membrane (GBM) of the capillary wall. The GBM is a dense network of secreted, extracellular matrix (ECM) components and contains tissue-restricted isoforms of collagen IV and laminin in addition to other structural proteins and ECM regulators such as proteases and growth factors. The specialized niche of the GBM provides a scaffold for endothelial cells and podocytes to support their unique functions and human genetic mutations in GBM components lead to renal failure, thus highlighting the importance of cell-matrix interactions in the glomerulus. Cells adhere to ECM via adhesion receptors, including integrins, syndecans, and dystroglycan and in particular the integrin heterodimer α3β1 is required to maintain barrier integrity. Therefore, the sophisticated function of glomerular filtration relies on podocyte adhesion both at cell junctions and at the interface with the ECM. In health, the podocyte coordinates signals from cell junctions and cell-matrix interactions, in response to environmental cues in order to regulate filtration and as our understanding of mechanisms that control cell adhesion in the glomerulus develops, then insight into the effects of disease will improve. The ultimate goal will be to develop targeted therapies to prevent or repair defects in the filtration barrier and to restore glomerular function.
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Affiliation(s)
- Rachel Lennon
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, The University of Manchester, Manchester, UK
- Institute of Human Development, Faculty of Medical and Human Sciences, The University of Manchester, Manchester, UK
- Department of Paediatric Nephrology, Manchester Academic Health Science Centre, Central Manchester University Hospitals NHS Foundation Trust, Manchester, UK
- *Correspondence: Rachel Lennon, Wellcome Trust Centre for Cell-Matrix Research, The University of Manchester, Michael Smith Building, Manchester M13 9PT, UK e-mail:
| | - Michael J. Randles
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, The University of Manchester, Manchester, UK
- Institute of Human Development, Faculty of Medical and Human Sciences, The University of Manchester, Manchester, UK
| | - Martin J. Humphries
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, The University of Manchester, Manchester, UK
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Quantitative proteomic dissection of a native 14-3-3ε interacting protein complex associated with hepatocellular carcinoma. Amino Acids 2013; 46:841-52. [DOI: 10.1007/s00726-013-1644-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Accepted: 12/11/2013] [Indexed: 12/18/2022]
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Aladowicz E, Ferro L, Vitali GC, Venditti E, Fornasari L, Lanfrancone L. Molecular networks in melanoma invasion and metastasis. Future Oncol 2013; 9:713-26. [PMID: 23647299 DOI: 10.2217/fon.13.9] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Metastatic melanoma accounts for approximately 80% of skin cancer-related deaths. Up to now there has been no effective treatment for stage IV melanoma patients due to the complexity and dissemination potential of this disease. Melanomas are heterogeneous tumors in which conventional therapies fail to improve overall survival. Targeted therapies are being developed, but the final outcome can be hampered by the incomplete knowledge of the process of melanoma progression. Even if the intracellular pathways are similar, the interaction of the cells with the surrounding environment should be taken into consideration. This article seeks to highlight some of the advances in the understanding of the molecular mechanisms underlying melanoma dissemination.
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Affiliation(s)
- Ewa Aladowicz
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, Milan, Italy
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46
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Elad N, Volberg T, Patla I, Hirschfeld-Warneken V, Grashoff C, Spatz JP, Fässler R, Geiger B, Medalia O. The role of integrin-linked kinase in the molecular architecture of focal adhesions. J Cell Sci 2013; 126:4099-107. [PMID: 23843624 DOI: 10.1242/jcs.120295] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Integrin-mediated focal adhesions (FAs) are large, multi-protein complexes that link the actin cytoskeleton to the extracellular matrix and take part in adhesion-mediated signaling. These adhesions are highly complex and diverse at the molecular level; thus, assigning particular structural or signaling functions to specific components is highly challenging. Here, we combined functional, structural and biophysical approaches to assess the role of a major FA component, namely, integrin-linked kinase (ILK), in adhesion formation. We show here that ILK plays a key role in the formation of focal complexes, early forms of integrin adhesions, and confirm its involvement in the assembly of fibronectin-bound fibrillar adhesions. Examination of ILK-null fibroblasts by cryo-electron tomography pointed to major structural changes in their FAs, manifested as disarray of the associated actin filaments and an increase in the packing density of FA-related particles. Interestingly, adhesion of the mutant cells to the substrate required a higher ligand density than in control cells. These data indicate that ILK has a key role in integrin adhesion assembly and sub-structure, and in the regulation of the FA-associated cytoskeleton.
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Affiliation(s)
- Nadav Elad
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben Gurion University of the Negev, Beer-Sheva 84120, Israel
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47
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Ulyanova T, Jiang Y, Padilla SM, Papayannopoulou T. Erythroid cells generated in the absence of specific β1-integrin heterodimers accumulate reactive oxygen species at homeostasis and are unable to mount effective antioxidant defenses. Haematologica 2013; 98:1769-77. [PMID: 23812936 DOI: 10.3324/haematol.2013.087577] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
We have previously reported that β1(Δ/Δ) mice have a markedly impaired response to hemolytic stress, but the mechanisms of this were unclear. In the present study we explored in detail quantitative, phenotypic and functional aspects of erythropoiesis at homeostasis in a large number of animals for each of 3 murine models with specific β1 heterodimer integrin deficiencies. We found that, at homeostasis, β1-deficient mice have a modest uncompensated anemia with ineffective erythropoiesis and decreased red blood cell survival. Mice lacking only α4 integrins (α4β1/α4β7) do not share this phenotype. There is an increased tendency for reactive oxygen species accumulation in β1(Δ/Δ) erythroid cells with decreased anti-oxidant defenses at homeostasis which are exaggerated after stress. Furthermore, expansion of erythroid cells in spleen post-stress is dependent on α5β1, likely through mechanisms activating focal adhesion kinase complexes that are distinct from α4β1-mediated responses. In vivo inhibition of focal adhesion kinase activation partially recapitulates the β1(Δ/Δ) stress response. Mice lacking all α4 and β1 integrins (double knockouts) had, at homeostasis, the most severe phenotype with selective impairment of erythroid responses. The fact that integrins participate in mitigating stress in erythroid cells through redox activation of distinct signaling pathways by specific integrin heterodimers is a link that has not been appreciated until now.
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Joshi P, Quach OL, Giguere SSB, Cristea IM. A Functional Proteomics Perspective of DBC1 as a Regulator of Transcription. JOURNAL OF PROTEOMICS & BIOINFORMATICS 2013; Suppl 2:002. [PMID: 24273392 PMCID: PMC3837576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The past few years have seen significant advances in the use of modern proteomics approaches for biological discoveries. Among the fields impacted by proteomics is that of epigenetics, as mass spectrometry-based approaches have allowed the identification and characterization of transcriptional regulators, epigenetic marks, and the constantly evolving epigenetic landscape of a cell in health and disease states. These studies have substantially expanded our understanding of critical genes that mediate cell processes, such as differentiation, cell cycle regulation, and apoptosis. Not surprisingly, a great emphasis has been placed on defining factors that are de-regulated in cancers, in an attempt to define new and specific targets for therapeutic design. Differential gene expression observed during carcinogenesis can be induced by aberrant activities of transcription factors and chromatin remodeling enzymes. Through a series of recent mass spectrometry studies of histone deacetylases and nuclear receptors, Deleted in Breast Cancer 1 (DBC1) has emerged as a master regulator of transcriptional processes. DBC1 acts as a modulator of cellular epigenetic mechanisms and is frequently associated with human metastasis. Through its negative regulation of SIRT1 and HDAC3 deacetylation activities, DBC1 has a broad impact on gene expression, downstream cellular pathways, and associated human diseases. Here, we review the identified roles of DBC1, highlighting the critical contribution of mass spectrometry to these findings. Additionally, we provide a perspective of integrative proteomics approaches that can continue to shed light on the interplay between DBC1 and its protein targets, helping to further define its role in epigenetic modifications and to identify novel targets for cancer therapy.
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Affiliation(s)
- P Joshi
- Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA
| | - O L Quach
- Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA
| | - S S B Giguere
- Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA
| | - I M Cristea
- Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA
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Byron A, Humphries JD, Humphries MJ. Defining the extracellular matrix using proteomics. Int J Exp Pathol 2013; 94:75-92. [PMID: 23419153 DOI: 10.1111/iep.12011] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Revised: 09/13/2012] [Accepted: 11/16/2012] [Indexed: 12/11/2022] Open
Abstract
The cell microenvironment has a profound influence on the behaviour, growth and survival of cells. The extracellular matrix (ECM) provides not only mechanical and structural support to cells and tissues but also binds soluble ligands and transmembrane receptors to provide spatial coordination of signalling processes. The ability of cells to sense the chemical, mechanical and topographical features of the ECM enables them to integrate complex, multiparametric information into a coherent response to the surrounding microenvironment. Consequently, dysregulation or mutation of ECM components results in a broad range of pathological conditions. Characterization of the composition of ECM derived from various cells has begun to reveal insights into ECM structure and function, and mechanisms of disease. Proteomic methodologies permit the global analysis of subcellular systems, but extracellular and transmembrane proteins present analytical difficulties to proteomic strategies owing to the particular biochemical properties of these molecules. Here, we review advances in proteomic approaches that have been applied to furthering our understanding of the ECM microenvironment. We survey recent studies that have addressed challenges in the analysis of ECM and discuss major outcomes in the context of health and disease. In addition, we summarize efforts to progress towards a systems-level understanding of ECM biology.
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Affiliation(s)
- Adam Byron
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester, UK
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50
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Byron A, Humphries JD, Humphries MJ. Alternative cellular roles for proteins identified using proteomics. J Proteomics 2012; 75:4184-5. [PMID: 22579753 PMCID: PMC4234028 DOI: 10.1016/j.jprot.2012.04.049] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Accepted: 04/30/2012] [Indexed: 10/28/2022]
Affiliation(s)
- Adam Byron
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Jonathan D. Humphries
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Martin J. Humphries
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
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