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Lloyd-Lewis B, Krueger CC, Sargeant TJ, D'Angelo ME, Deery MJ, Feret R, Howard JA, Lilley KS, Watson CJ. Stat3-mediated alterations in lysosomal membrane protein composition. J Biol Chem 2018; 293:4244-4261. [PMID: 29343516 PMCID: PMC5868265 DOI: 10.1074/jbc.ra118.001777] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Indexed: 12/19/2022] Open
Abstract
Lysosome function is essential in cellular homeostasis. In addition to its recycling role, the lysosome has recently been recognized as a cellular signaling hub. We have shown in mammary epithelial cells, both in vivo and in vitro, that signal transducer and activator of transcription 3 (Stat3) modulates lysosome biogenesis and can promote the release of lysosomal proteases that culminates in cell death. To further investigate the impact of Stat3 on lysosomal function, we conducted a proteomic screen of changes in lysosomal membrane protein components induced by Stat3 using an iron nanoparticle enrichment strategy. Our results show that Stat3 activation not only elevates the levels of known membrane proteins but results in the appearance of unexpected factors, including cell surface proteins such as annexins and flotillins. These data suggest that Stat3 may coordinately regulate endocytosis, intracellular trafficking, and lysosome biogenesis to drive lysosome-mediated cell death in mammary epithelial cells. The methodologies described in this study also provide significant improvements to current techniques used for the purification and analysis of the lysosomal proteome.
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Affiliation(s)
- Bethan Lloyd-Lewis
- From the Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom,
| | - Caroline C Krueger
- From the Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - Timothy J Sargeant
- the Lysosomal Diseases Research Unit, South Australian Health and Medical Research Institute, Adelaide, South Australia 5000, Australia, and
| | - Michael E D'Angelo
- From the Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - Michael J Deery
- the Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, United Kingdom
| | - Renata Feret
- the Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, United Kingdom
| | - Julie A Howard
- the Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, United Kingdom
| | - Kathryn S Lilley
- the Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, United Kingdom
| | - Christine J Watson
- From the Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom,
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Chapel A, Kieffer-Jaquinod S, Sagné C, Verdon Q, Ivaldi C, Mellal M, Thirion J, Jadot M, Bruley C, Garin J, Gasnier B, Journet A. An extended proteome map of the lysosomal membrane reveals novel potential transporters. Mol Cell Proteomics 2013; 12:1572-88. [PMID: 23436907 PMCID: PMC3675815 DOI: 10.1074/mcp.m112.021980] [Citation(s) in RCA: 143] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2012] [Revised: 02/01/2013] [Indexed: 12/22/2022] Open
Abstract
Lysosomes are membrane-bound endocytic organelles that play a major role in degrading cell macromolecules and recycling their building blocks. A comprehensive knowledge of the lysosome function requires an extensive description of its content, an issue partially addressed by previous proteomic analyses. However, the proteins underlying many lysosomal membrane functions, including numerous membrane transporters, remain unidentified. We performed a comparative, semi-quantitative proteomic analysis of rat liver lysosome-enriched and lysosome-nonenriched membranes and used spectral counts to evaluate the relative abundance of proteins. Among a total of 2,385 identified proteins, 734 proteins were significantly enriched in the lysosomal fraction, including 207 proteins already known or predicted as endo-lysosomal and 94 proteins without any known or predicted subcellular localization. The remaining 433 proteins had been previously assigned to other subcellular compartments but may in fact reside on lysosomes either predominantly or as a secondary location. Many membrane-associated complexes implicated in diverse processes such as degradation, membrane trafficking, lysosome biogenesis, lysosome acidification, signaling, and nutrient sensing were enriched in the lysosomal fraction. They were identified to an unprecedented extent as most, if not all, of their subunits were found and retained by our screen. Numerous transporters were also identified, including 46 novel potentially lysosomal proteins. We expressed 12 candidates in HeLa cells and observed that most of them colocalized with the lysosomal marker LAMP1, thus confirming their lysosomal residency. This list of candidate lysosomal proteins substantially increases our knowledge of the lysosomal membrane and provides a basis for further characterization of lysosomal functions.
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Affiliation(s)
- Agnès Chapel
- From the ‡Commissariat à l'Energie Atomique, Institut de Recherches en Technologies et Sciences du Vivant, Laboratoire Biologie à Grande Echelle, F-38054 Grenoble, France
- §INSERM, U1038, F-38054 Grenoble, France
- the ¶Université Joseph Fourier, Grenoble 1, F-38000, France
| | - Sylvie Kieffer-Jaquinod
- From the ‡Commissariat à l'Energie Atomique, Institut de Recherches en Technologies et Sciences du Vivant, Laboratoire Biologie à Grande Echelle, F-38054 Grenoble, France
- §INSERM, U1038, F-38054 Grenoble, France
- the ¶Université Joseph Fourier, Grenoble 1, F-38000, France
| | - Corinne Sagné
- the ‖Université Paris Descartes, Sorbonne Paris Cité, CNRS, UMR 8192, Centre Universitaire des Saints-Pères, 45 Rue des Saints-Pères, F-75006 Paris, France
| | - Quentin Verdon
- the ‖Université Paris Descartes, Sorbonne Paris Cité, CNRS, UMR 8192, Centre Universitaire des Saints-Pères, 45 Rue des Saints-Pères, F-75006 Paris, France
- §§Graduate School ED 419, Université Paris-Sud 11, Hôpital Bicêtre, F-94276 Le Kremlin Bicêtre France, and
| | - Corinne Ivaldi
- From the ‡Commissariat à l'Energie Atomique, Institut de Recherches en Technologies et Sciences du Vivant, Laboratoire Biologie à Grande Echelle, F-38054 Grenoble, France
- §INSERM, U1038, F-38054 Grenoble, France
- the ¶Université Joseph Fourier, Grenoble 1, F-38000, France
| | - Mourad Mellal
- From the ‡Commissariat à l'Energie Atomique, Institut de Recherches en Technologies et Sciences du Vivant, Laboratoire Biologie à Grande Echelle, F-38054 Grenoble, France
- §INSERM, U1038, F-38054 Grenoble, France
- the ¶Université Joseph Fourier, Grenoble 1, F-38000, France
| | - Jaqueline Thirion
- the **Unité de Recherche en Physiologie Moléculaire, Namur Research Institute for Life Sciences, University of Namur (FUNDP), 61, Rue de Bruxelles B,-5000, Namur, Belgium
| | - Michel Jadot
- the **Unité de Recherche en Physiologie Moléculaire, Namur Research Institute for Life Sciences, University of Namur (FUNDP), 61, Rue de Bruxelles B,-5000, Namur, Belgium
| | - Christophe Bruley
- From the ‡Commissariat à l'Energie Atomique, Institut de Recherches en Technologies et Sciences du Vivant, Laboratoire Biologie à Grande Echelle, F-38054 Grenoble, France
- §INSERM, U1038, F-38054 Grenoble, France
- the ¶Université Joseph Fourier, Grenoble 1, F-38000, France
| | - Jérôme Garin
- From the ‡Commissariat à l'Energie Atomique, Institut de Recherches en Technologies et Sciences du Vivant, Laboratoire Biologie à Grande Echelle, F-38054 Grenoble, France
- §INSERM, U1038, F-38054 Grenoble, France
- the ¶Université Joseph Fourier, Grenoble 1, F-38000, France
| | - Bruno Gasnier
- the ‖Université Paris Descartes, Sorbonne Paris Cité, CNRS, UMR 8192, Centre Universitaire des Saints-Pères, 45 Rue des Saints-Pères, F-75006 Paris, France
| | - Agnès Journet
- From the ‡Commissariat à l'Energie Atomique, Institut de Recherches en Technologies et Sciences du Vivant, Laboratoire Biologie à Grande Echelle, F-38054 Grenoble, France
- §INSERM, U1038, F-38054 Grenoble, France
- the ¶Université Joseph Fourier, Grenoble 1, F-38000, France
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Simpson RJ, Lim JW, Moritz RL, Mathivanan S. Exosomes: proteomic insights and diagnostic potential. Expert Rev Proteomics 2009; 6:267-83. [PMID: 19489699 DOI: 10.1586/epr.09.17] [Citation(s) in RCA: 799] [Impact Index Per Article: 53.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Exosomes are 40-100-nm diameter membrane vesicles of endocytic origin that are released by most cell types upon fusion of multivesicular bodies with the plasma membrane, presumably as a vehicle for cell-free intercellular communication. While early studies focused on their secretion from diverse cell types in vitro, exosomes have now been identified in body fluids such as urine, amniotic fluid, malignant ascites, bronchoalveolar lavage fluid, synovial fluid, breast milk, saliva and blood. Exosomes have pleiotropic biological functions, including immune response, antigen presentation, intracellular communication and the transfer of RNA and proteins. While they have also been implicated in the transport and propagation of infectious cargo, such as prions, and retroviruses, including HIV, suggesting a role in pathological situations, recent studies suggest that the presence of such infectious cargo may be artefacts of exosome-purification strategies. Improvements in mass spectrometry-based proteomic tools, both hardware and software, coupled with improved purification schemes for exosomes, has allowed more in-depth proteome analyses, contributing immensely to our understanding of the molecular composition of exosomes. Proteomic cataloguing of exosomes from diverse cell types has revealed a common set of membrane and cytosolic proteins, suggesting the evolutionary importance of these membrane particles. Additionally, exosomes express an array of proteins that reflect the originating host cell. Recent findings that exosomes contain inactive forms of both mRNA and microRNA that can be transferred to another cell and be functional in that new environment, have initiated many microRNA profiling studies of exosomes circulating in blood. These studies highlight the potential of exosomal microRNA profiles for use as diagnostic biomarkers of disease through a noninvasive blood test. The exacerbated release of exosomes in tumor cells, as evidenced by their increased levels in blood during the late stage of a disease and their overexpression of certain tumor cell biomarkers, suggests an important role of exosomes in diagnosis and biomarker studies. The aim of this article is to provide a brief overview of exosomes, including methods used to isolate and characterize exosomes. New advances in proteomic methods, and both mass spectrometry hardware and informatics tools will be covered briefly.
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Affiliation(s)
- Richard J Simpson
- Ludwig Institute for Cancer Research, PO Box 2008, Royal Melbourne Hospital, Parkville, Victoria 3050, Australia.
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