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Podolsky MJ, Gupta D, Ha A, Ta R, Khalifeh-Soltani A, McKleroy W, Datta R, Sheppard D, Atabai K. Cell division cycle 7 kinase is a negative regulator of cell-mediated collagen degradation. Am J Physiol Lung Cell Mol Physiol 2018; 315:L360-L370. [PMID: 29792348 DOI: 10.1152/ajplung.00144.2018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Although extensive work has delineated many of the mechanisms of extracellular matrix (ECM) production, far less is known about pathways that regulate ECM degradation. This is particularly true of cellular internalization and degradation of matrix, which play an underappreciated role in ECM metabolism and lung fibrosis. For example, genetic perturbation of this pathway leads to exacerbated fibrosis in experimental animal models. In this work, we present the results of an unbiased screen of Drosophila phagocytes that yielded multiple genes that, when silenced, led to increased collagen uptake. We further describe the function of cell division cycle 7 kinase (CDC7) as a specific suppressor of collagen uptake. We show that the genetic or pharmacological inhibition of CDC7 results in increased expression of the collagen endocytic receptor Endo180. Chromobox 5 (CBX5) is a putative target of CDC7, and genetic silencing of CBX5 also results in increased Endo180 and collagen uptake. Finally, CRISPR-mediated activation of Endo180 expression results in increased collagen uptake, suggesting that CDC7 regulates collagen internalization through increased Endo180 expression. Targeting the regulatory elements of the collagen degradative machinery may be a useful therapeutic approach in diseases of fibrosis or malignancy.
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Affiliation(s)
- Michael J Podolsky
- Department of Medicine, Lung Biology Center, Cardiovascular Research Institute, University of California, San Francisco, California
| | - Deepti Gupta
- Department of Medicine, Lung Biology Center, Cardiovascular Research Institute, University of California, San Francisco, California
| | - Arnold Ha
- Department of Medicine, Lung Biology Center, Cardiovascular Research Institute, University of California, San Francisco, California
| | - Ryan Ta
- Department of Medicine, Lung Biology Center, Cardiovascular Research Institute, University of California, San Francisco, California
| | - Amin Khalifeh-Soltani
- Department of Medicine, Lung Biology Center, Cardiovascular Research Institute, University of California, San Francisco, California
| | - William McKleroy
- Department of Medicine, Lung Biology Center, Cardiovascular Research Institute, University of California, San Francisco, California
| | - Ritwik Datta
- Department of Medicine, Lung Biology Center, Cardiovascular Research Institute, University of California, San Francisco, California
| | - Dean Sheppard
- Department of Medicine, Lung Biology Center, Cardiovascular Research Institute, University of California, San Francisco, California
| | - Kamran Atabai
- Department of Medicine, Lung Biology Center, Cardiovascular Research Institute, University of California, San Francisco, California
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Radulovic M, Baqader NO, Stoeber K, Godovac-Zimmermann J. Spatial Cross-Talk between Oxidative Stress and DNA Replication in Human Fibroblasts. J Proteome Res 2016; 15:1907-38. [PMID: 27142241 DOI: 10.1021/acs.jproteome.6b00101] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
MS-based proteomics has been applied to a differential network analysis of the nuclear-cytoplasmic subcellular distribution of proteins between cell-cycle arrest: (a) at the origin activation checkpoint for DNA replication, or (b) in response to oxidative stress. Significant changes were identified for 401 proteins. Cellular response combines changes in trafficking and in total abundance to vary the local compartmental abundances that are the basis of cellular response. Appreciable changes for both perturbations were observed for 245 proteins, but cross-talk between oxidative stress and DNA replication is dominated by 49 proteins that show strong changes for both. Many nuclear processes are influenced by a spatial switch involving the proteins {KPNA2, KPNB1, PCNA, PTMA, SET} and heme/iron proteins HMOX1 and FTH1. Dynamic spatial distribution data are presented for proteins involved in caveolae, extracellular matrix remodelling, TGFβ signaling, IGF pathways, emerin complexes, mitochondrial protein import complexes, spliceosomes, proteasomes, and so on. The data indicate that for spatially heterogeneous cells cross-compartmental communication is integral to their system biology, that coordinated spatial redistribution for crucial protein networks underlies many functional changes, and that information on dynamic spatial redistribution of proteins is essential to obtain comprehensive pictures of cellular function. We describe how spatial data of the type presented here can provide priorities for further investigation of crucial features of high-level spatial coordination across cells. We suggest that the present data are related to increasing indications that much of subcellular protein transport is constitutive and that perturbation of these constitutive transport processes may be related to cancer and other diseases. A quantitative, spatially resolved nucleus-cytoplasm interaction network is provided for further investigations.
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Affiliation(s)
- Marko Radulovic
- Division of Medicine, University College London, Center for Nephrology , Royal Free Campus, Rowland Hill Street, London NW3 2PF, United Kingdom.,Insitute of Oncology and Radiology , Pasterova 14, 11000 Belgrade, Serbia
| | - Noor O Baqader
- Division of Medicine, University College London, Center for Nephrology , Royal Free Campus, Rowland Hill Street, London NW3 2PF, United Kingdom
| | - Kai Stoeber
- Research Department of Pathology and UCL Cancer Institute, Rockefeller Building, University College London , University Street, London WC1E 6JJ, United Kingdom
| | - Jasminka Godovac-Zimmermann
- Division of Medicine, University College London, Center for Nephrology , Royal Free Campus, Rowland Hill Street, London NW3 2PF, United Kingdom
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Baqader NO, Radulovic M, Crawford M, Stoeber K, Godovac-Zimmermann J. Nuclear cytoplasmic trafficking of proteins is a major response of human fibroblasts to oxidative stress. J Proteome Res 2014; 13:4398-423. [PMID: 25133973 PMCID: PMC4259009 DOI: 10.1021/pr500638h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We have used a subcellular spatial razor approach based on LC-MS/MS-based proteomics with SILAC isotope labeling to determine changes in protein abundances in the nuclear and cytoplasmic compartments of human IMR90 fibroblasts subjected to mild oxidative stress. We show that response to mild tert-butyl hydrogen peroxide treatment includes redistribution between the nucleus and cytoplasm of numerous proteins not previously associated with oxidative stress. The 121 proteins with the most significant changes encompass proteins with known functions in a wide variety of subcellular locations and of cellular functional processes (transcription, signal transduction, autophagy, iron metabolism, TCA cycle, ATP synthesis) and are consistent with functional networks that are spatially dispersed across the cell. Both nuclear respiratory factor 2 and the proline regulatory axis appear to contribute to the cellular metabolic response. Proteins involved in iron metabolism or with iron/heme as a cofactor as well as mitochondrial proteins are prominent in the response. Evidence suggesting that nuclear import/export and vesicle-mediated protein transport contribute to the cellular response was obtained. We suggest that measurements of global changes in total cellular protein abundances need to be complemented with measurements of the dynamic subcellular spatial redistribution of proteins to obtain comprehensive pictures of cellular function.
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Affiliation(s)
- Noor O. Baqader
- Division of Medicine, Center for Nephrology, University College London, Royal Free Campus, Rowland Hill Street, London NW3 2PF, United Kingdom
| | - Marko Radulovic
- Division of Medicine, Center for Nephrology, University College London, Royal Free Campus, Rowland Hill Street, London NW3 2PF, United Kingdom
- Insitute of Oncology and Radiology, Pasterova 14, 11000 Belgrade, Serbia
| | - Mark Crawford
- Division of Medicine, Center for Nephrology, University College London, Royal Free Campus, Rowland Hill Street, London NW3 2PF, United Kingdom
| | - Kai Stoeber
- Research Department of Pathology and UCL Cancer Institute, Rockefeller Building, University College London, University Street, London WC1E 6JJ, United Kingdom
| | - Jasminka Godovac-Zimmermann
- Division of Medicine, Center for Nephrology, University College London, Royal Free Campus, Rowland Hill Street, London NW3 2PF, United Kingdom
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Mulvey CM, Tudzarova S, Crawford M, Williams GH, Stoeber K, Godovac-Zimmermann J. Subcellular proteomics reveals a role for nucleo-cytoplasmic trafficking at the DNA replication origin activation checkpoint. J Proteome Res 2013; 12:1436-53. [PMID: 23320540 PMCID: PMC4261602 DOI: 10.1021/pr3010919] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Depletion of DNA replication initiation factors such as CDC7 kinase triggers the origin activation checkpoint in healthy cells and leads to a protective cell cycle arrest at the G1 phase of the mitotic cell division cycle. This protective mechanism is thought to be defective in cancer cells. To investigate how this checkpoint is activated and maintained in healthy cells, we conducted a quantitative SILAC analysis of the nuclear- and cytoplasmic-enriched compartments of CDC7-depleted fibroblasts and compared them to a total cell lysate preparation. Substantial changes in total abundance and/or subcellular location were detected for 124 proteins, including many essential proteins associated with DNA replication/cell cycle. Similar changes in protein abundance and subcellular distribution were observed for various metabolic processes, including oxidative stress, iron metabolism, protein translation and the tricarboxylic acid cycle. This is accompanied by reduced abundance of two karyopherin proteins, suggestive of reduced nuclear import. We propose that altered nucleo-cytoplasmic trafficking plays a key role in the regulation of cell cycle arrest. The results increase understanding of the mechanisms underlying maintenance of the DNA replication origin activation checkpoint and are consistent with our proposal that cell cycle arrest is an actively maintained process that appears to be distributed over various subcellular locations.
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Affiliation(s)
- Claire M. Mulvey
- Division of Medicine, University College London, Royal Free Campus, Rowland Hill Street, London NW3 2PF, United Kingdom
| | - Slavica Tudzarova
- Wolfson Institute for Biomedical Research, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Mark Crawford
- Division of Medicine, University College London, Royal Free Campus, Rowland Hill Street, London NW3 2PF, United Kingdom
| | - Gareth H. Williams
- Research Department of Pathology and UCL Cancer Institute, Rockefeller Building, University College London, University Street, London WC1E 6JJ, United Kingdom
| | - Kai Stoeber
- Research Department of Pathology and UCL Cancer Institute, Rockefeller Building, University College London, University Street, London WC1E 6JJ, United Kingdom
| | - Jasminka Godovac-Zimmermann
- Division of Medicine, University College London, Royal Free Campus, Rowland Hill Street, London NW3 2PF, United Kingdom
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Pérez de Diego R, Mulvey C, Crawford M, Trotter MWB, Lorenzo L, Sancho-Shimizu V, Abel L, Zhang SY, Casanova JL, Godovac-Zimmermann J. The proteome of Toll-like receptor 3-stimulated human immortalized fibroblasts: implications for susceptibility to herpes simplex virus encephalitis. J Allergy Clin Immunol 2013; 131:1157-66. [PMID: 23434283 DOI: 10.1016/j.jaci.2013.01.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2012] [Revised: 12/13/2012] [Accepted: 01/10/2013] [Indexed: 01/09/2023]
Abstract
BACKGROUND Inborn errors in Toll-like receptor 3 (TLR3)-IFN type I and III pathways have been implicated in susceptibility to herpes simplex virus encephalitis (HSE) in children, but most patients studied do not carry mutations in any of the genes presently associated with HSE susceptibility. Moreover, many patients do not display any TLR3-IFN-related fibroblastic phenotype. OBJECTIVE To study other signaling pathways downstream of TLR3 and/or other independent pathways that may contribute to HSE susceptibility. METHODS We used the stable isotope labeling of amino acids in cell culture proteomics methodology to measure changes in the human immortalized fibroblast proteome after TLR3 activation. RESULTS Cells from healthy controls were compared with cells from a patient with a known genetic etiology of HSE (UNC-93B-/-) and also to cells from an HSE patient with an unknown gene defect. Consistent with known variation in susceptibility of individuals to viral infections, substantial variation in the response level of different healthy controls was observed, but common functional networks could be identified, including upregulation of superoxide dismutase 2. The 2 patients with HSE studied show clear differences in functional response networks when compared with healthy controls and also when compared with each other. CONCLUSIONS The present study delineates a number of novel proteins, TLR3-related pathways, and cellular phenotypes that may help elucidate the genetic basis of childhood HSE. Furthermore, our results reveal superoxide dismutase 2 as a potential therapeutic target for amelioration of the neurologic sequelae caused by HSE.
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Affiliation(s)
- Rebeca Pérez de Diego
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Necker Medical School, and Pediatric Hematology-Immunology Unit, Necker Hospital, Paris, France.
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Qattan AT, Radulovic M, Crawford M, Godovac-Zimmermann J. Spatial distribution of cellular function: the partitioning of proteins between mitochondria and the nucleus in MCF7 breast cancer cells. J Proteome Res 2012; 11:6080-101. [PMID: 23051583 PMCID: PMC4261608 DOI: 10.1021/pr300736v] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Concurrent proteomics analysis of the nuclei and mitochondria of MCF7 breast cancer cells identified 985 proteins (40% of all detected proteins) present in both organelles. Numerous proteins from all five complexes involved in oxidative phosphorylation (e.g., NDUFA5, NDUFB10, NDUFS1, NDUF2, SDHA, UQRB, UQRC2, UQCRH, COX5A, COX5B, MT-CO2, ATP5A1, ATP5B, ATP5H, etc.), from the TCA-cycle (DLST, IDH2, IDH3A, OGDH, SUCLAG2, etc.), and from glycolysis (ALDOA, ENO1, FBP1, GPI, PGK1, TALDO1, etc.) were distributed to both the nucleus and mitochondria. In contrast, proteins involved in nuclear/mitochondrial RNA processing/translation and Ras/Rab signaling showed different partitioning patterns. The identity of the OxPhos, TCA-cycle, and glycolysis proteins distributed to both the nucleus and mitochondria provides evidence for spatio-functional integration of these processes over the two different subcellular organelles. We suggest that there are unrecognized aspects of functional coordination between the nucleus and mitochondria, that integration of core functional processes via wide subcellular distribution of constituent proteins is a common characteristic of cells, and that subcellular spatial integration of function may be a vital aspect of cancer.
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Affiliation(s)
- Amal T. Qattan
- Proteomics and Molecular Cell Dynamics, Division of Medicine, School of Life and Medical Sciences, University College London, Royal Free Campus, Rowland Hill Street NW3 2PF, United Kingdom
| | - Marko Radulovic
- Proteomics and Molecular Cell Dynamics, Division of Medicine, School of Life and Medical Sciences, University College London, Royal Free Campus, Rowland Hill Street NW3 2PF, United Kingdom
| | - Mark Crawford
- Proteomics and Molecular Cell Dynamics, Division of Medicine, School of Life and Medical Sciences, University College London, Royal Free Campus, Rowland Hill Street NW3 2PF, United Kingdom
| | - Jasminka Godovac-Zimmermann
- Proteomics and Molecular Cell Dynamics, Division of Medicine, School of Life and Medical Sciences, University College London, Royal Free Campus, Rowland Hill Street NW3 2PF, United Kingdom
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