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Alkhanjaf AAM, Raggiaschi R, Crawford M, Pinto G, Godovac‐Zimmermann J. Moonlighting Proteins and Cardiopathy in the Spatial Response of MCF-7 Breast Cancer Cells to Tamoxifen. Proteomics Clin Appl 2019; 13:e1900029. [PMID: 31282103 PMCID: PMC6771495 DOI: 10.1002/prca.201900029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 07/03/2019] [Indexed: 01/18/2023]
Abstract
BACKGROUND The purpose of this study is to apply quantitative high-throughput proteomics methods to investigate dynamic aspects of protein changes in nucleocytoplasmic distribution of proteins and of total protein abundance for MCF-7 cells exposed to tamoxifen (Tam) in order to reveal the agonistic and antagonistic roles of the drug. EXPERIMENTAL DESIGN The MS-based global quantitative proteomics with the analysis of fractions enriched in target subcellular locations is applied to measure the changes in total abundance and in the compartmental abundance/distribution between the nucleus and cytoplasm for several thousand proteins differentially expressed in MCF-7 cells in response to Tam stimulation. RESULTS The response of MCF-7 cells to the Tam treatment shows significant changes in subcellular abundance rather than in their total abundance. The bioinformatics study reveals the relevance of moonlighting proteins and numerous pathways involved in Tam response of MCF-7 including some of which may explain the agonistic and antagonistic roles of the drug. CONCLUSIONS The results indicate possible protective role of Tam against cardiovascular diseases as well as its involvement in G-protein coupled receptors pathways that enhance breast tissue proliferation.
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Affiliation(s)
- Abdulrab Ahmed M. Alkhanjaf
- Proteomics and Molecular Cell DynamicsDivision of MedicineSchool of Life and Medical SciencesUniversity College LondonNW3 2PFLondonUK
- Molecular Biotechnology, Department of Clinical Laboratory SciencesCollege of Applied Medical sciencesNajran UniversityNajran61441Saudi Arabia
| | - Roberto Raggiaschi
- Proteomics and Molecular Cell DynamicsDivision of MedicineSchool of Life and Medical SciencesUniversity College LondonNW3 2PFLondonUK
| | - Mark Crawford
- Proteomics and Molecular Cell DynamicsDivision of MedicineSchool of Life and Medical SciencesUniversity College LondonNW3 2PFLondonUK
| | - Gabriella Pinto
- Proteomics and Molecular Cell DynamicsDivision of MedicineSchool of Life and Medical SciencesUniversity College LondonNW3 2PFLondonUK
- Department of Chemical SciencesUniversity of Naples Federico II80126NaplesItaly
| | - Jasminka Godovac‐Zimmermann
- Proteomics and Molecular Cell DynamicsDivision of MedicineSchool of Life and Medical SciencesUniversity College LondonNW3 2PFLondonUK
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Alkhanjaf AAM, Raggiaschi R, Crawford M, Pinto G, Godovac-Zimmermann J. Moonlighting Proteins and Cardiopathy in the Spatial Response of MCF-7 Breast Cancer Cells to Tamoxifen. PROTEOMICS. CLINICAL APPLICATIONS 2019. [PMID: 31282103 DOI: 10.1002/prca.201900029,] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
BACKGROUND The purpose of this study is to apply quantitative high-throughput proteomics methods to investigate dynamic aspects of protein changes in nucleocytoplasmic distribution of proteins and of total protein abundance for MCF-7 cells exposed to tamoxifen (Tam) in order to reveal the agonistic and antagonistic roles of the drug. EXPERIMENTAL DESIGN The MS-based global quantitative proteomics with the analysis of fractions enriched in target subcellular locations is applied to measure the changes in total abundance and in the compartmental abundance/distribution between the nucleus and cytoplasm for several thousand proteins differentially expressed in MCF-7 cells in response to Tam stimulation. RESULTS The response of MCF-7 cells to the Tam treatment shows significant changes in subcellular abundance rather than in their total abundance. The bioinformatics study reveals the relevance of moonlighting proteins and numerous pathways involved in Tam response of MCF-7 including some of which may explain the agonistic and antagonistic roles of the drug. CONCLUSIONS The results indicate possible protective role of Tam against cardiovascular diseases as well as its involvement in G-protein coupled receptors pathways that enhance breast tissue proliferation.
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Affiliation(s)
- Abdulrab Ahmed M Alkhanjaf
- Proteomics and Molecular Cell Dynamics, Division of Medicine, School of Life and Medical Sciences, University College London, NW3 2PF, London, UK.,Molecular Biotechnology, Department of Clinical Laboratory Sciences, College of Applied Medical sciences, Najran University, Najran, 61441, Saudi Arabia
| | - Roberto Raggiaschi
- Proteomics and Molecular Cell Dynamics, Division of Medicine, School of Life and Medical Sciences, University College London, NW3 2PF, London, UK
| | - Mark Crawford
- Proteomics and Molecular Cell Dynamics, Division of Medicine, School of Life and Medical Sciences, University College London, NW3 2PF, London, UK
| | - Gabriella Pinto
- Proteomics and Molecular Cell Dynamics, Division of Medicine, School of Life and Medical Sciences, University College London, NW3 2PF, London, UK.,Department of Chemical Sciences, University of Naples Federico II, 80126, Naples, Italy
| | - Jasminka Godovac-Zimmermann
- Proteomics and Molecular Cell Dynamics, Division of Medicine, School of Life and Medical Sciences, University College London, NW3 2PF, London, UK
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Pinto G, Radulovic M, Godovac-Zimmermann J. Spatial perspectives in the redox code-Mass spectrometric proteomics studies of moonlighting proteins. MASS SPECTROMETRY REVIEWS 2018; 37:81-100. [PMID: 27186965 DOI: 10.1002/mas.21508] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 05/03/2016] [Indexed: 06/05/2023]
Abstract
The Redox Code involves specific, reversible oxidative changes in proteins that modulate protein tertiary structure, interactions, trafficking, and activity, and hence couple the proteome to the metabolic/oxidative state of cells. It is currently a major focus of study in cell biology. Recent studies of dynamic cellular spatial reorganization with MS-based subcellular-spatial-razor proteomics reveal that protein constituents of many subcellular structures, including mitochondria, the endoplasmic reticulum, the plasma membrane, and the extracellular matrix, undergo changes in their subcellular abundance/distribution in response to oxidative stress. These proteins are components of a diverse variety of functional processes spatially distributed across cells. Many of the same proteins are involved in response to suppression of DNA replication indicate that oxidative stress is strongly intertwined with DNA replication/proliferation. Both are replete with networks of moonlighting proteins that show coordinated changes in subcellular location and that include primary protein actuators of the redox code involved in the processing of NAD+ /NADH, NADP+ /NADPH, Cys/CySS, and GSH/GSSG redox couples. Small groups of key proteins such as {KPNA2, KPNB1, PCNA, PTMA, SET} constitute "spatial switches" that modulate many nuclear processes. Much of the functional response involves subcellular protein trafficking, including nuclear import/export processes, vesicle-mediated trafficking, the endoplasmic reticulum/Golgi pathway, chaperone-assisted processes, and other transport systems. This is not visible to measurements of total protein abundance by transcriptomics or proteomics. Comprehensive pictures of cellular function will require collection of data on the subcellular transport and local functions of many moonlighting proteins, especially of those with critical roles in spatial coordination across cells. The proteome-wide analysis of coordinated changes in abundance and trafficking of proteins offered by MS-based proteomics has a unique, crucial role to play in deciphering the complex adaptive systems that underlie cellular function. © 2016 Wiley Periodicals, Inc. Mass Spec Rev.
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Affiliation(s)
- Gabriella Pinto
- Division of Medicine, Center for Nephrology, Royal Free Campus, University College London, Rowland Hill Street, London, NW3 2PF, United Kingdom
| | - Marko Radulovic
- Insitute of Oncology and Radiology, Pasterova 14, Belgrade, 11000, Serbia
| | - Jasminka Godovac-Zimmermann
- Division of Medicine, Center for Nephrology, Royal Free Campus, University College London, Rowland Hill Street, London, NW3 2PF, United Kingdom
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Lombardi B, Ashford P, Moya-Garcia AA, Rust A, Crawford M, Williams SV, Knowles MA, Katan M, Orengo C, Godovac-Zimmermann J. Unique signalling connectivity of FGFR3-TACC3 oncoprotein revealed by quantitative phosphoproteomics and differential network analysis. Oncotarget 2017; 8:102898-102911. [PMID: 29262532 PMCID: PMC5732698 DOI: 10.18632/oncotarget.22048] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 10/03/2017] [Indexed: 12/14/2022] Open
Abstract
The FGFR3-TACC3 fusion is an oncogenic driver in diverse malignancies, including bladder cancer, characterized by upregulated tyrosine kinase activity. To gain insights into distinct properties of FGFR3-TACC3 down-stream signalling, we utilised telomerase-immortalised normal human urothelial cell lines expressing either the fusion or wild-type FGFR3 (isoform IIIb) for subsequent quantitative proteomics and network analysis. Cellular lysates were chemically labelled with isobaric tandem mass tag reagents and, after phosphopeptide enrichment, liquid chromatography-high mass accuracy tandem mass spectrometry (LC-MS/MS) was used for peptide identification and quantification. Comparison of data from the two cell lines under non-stimulated and FGF1 stimulated conditions and of data representing physiological stimulation of FGFR3 identified about 200 regulated phosphosites. The identified phosphoproteins and quantified phosphosites were further analysed in the context of functional biological networks by inferring kinase-substrate interactions, mapping these to a comprehensive human signalling interaction network, filtering based on tissue-expression profiles and applying disease module detection and pathway enrichment methods. Analysis of our phosphoproteomics data using these bioinformatics methods combined into a new protocol-Disease Relevant Analysis of Genes On Networks (DRAGON)-allowed us to tease apart pathways differentially involved in FGFR3-TACC3 signalling in comparison to wild-type FGFR3 and to investigate their local phospho-signalling context. We highlight 9 pathways significantly regulated only in the cell line expressing FGFR3-TACC3 fusion and 5 pathways regulated only by stimulation of the wild-type FGFR3. Pathways differentially linked to FGFR3-TACC3 fusion include those related to chaperone activation and stress response and to regulation of TP53 expression and degradation that could contribute to development and maintenance of the cancer phenotype.
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Affiliation(s)
- Benedetta Lombardi
- Proteomics and Molecular Cell Dynamics, Center for Nephrology, School of Life and Medical Sciences, University College London, London NW3 2PF, United Kingdom
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom
| | - Paul Ashford
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom
| | - Aurelio A. Moya-Garcia
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom
| | - Aleksander Rust
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom
| | - Mark Crawford
- Proteomics and Molecular Cell Dynamics, Center for Nephrology, School of Life and Medical Sciences, University College London, London NW3 2PF, United Kingdom
| | - Sarah V. Williams
- Section of Molecular Oncology, Leeds Institute of Molecular Medicine, St James’s University Hospital, Leeds LS9 7TF, United Kingdom
| | - Margaret A. Knowles
- Section of Molecular Oncology, Leeds Institute of Molecular Medicine, St James’s University Hospital, Leeds LS9 7TF, United Kingdom
| | - Matilda Katan
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom
| | - Christine Orengo
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom
| | - Jasminka Godovac-Zimmermann
- Proteomics and Molecular Cell Dynamics, Center for Nephrology, School of Life and Medical Sciences, University College London, London NW3 2PF, United Kingdom
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Guarino MPL, Altomare A, Barera S, Locato V, Cocca S, Franchin C, Arrigoni G, Vannini C, Grossi S, Campomenosi P, Pasqualetti V, Bracale M, Alloni R, De Gara L, Cicala M. Effect of Inulin on Proteome Changes Induced by Pathogenic Lipopolysaccharide in Human Colon. PLoS One 2017; 12:e0169481. [PMID: 28068390 PMCID: PMC5222518 DOI: 10.1371/journal.pone.0169481] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 12/16/2016] [Indexed: 12/27/2022] Open
Abstract
In the present study, the protective role of inulin against lipopolysaccharide (LPS)-induced oxidative stress was evaluated on human colonic mucosa using a proteomic approach. Human colonic mucosa and submucosa were sealed between two chambers, with the luminal side facing upwards and overlaid with Krebs (control), LPS or LPS+ inulin IQ solution. The solutions on the submucosal side (undernatants) were collected following 30 min of mucosal exposure. iTRAQ based analysis was used to analyze the total soluble proteomes from human colonic mucosa and submucosa treated with different undernatants. Human colonic muscle strips were exposed to the undernatants to evaluate the response to acetylcholine. Inulin exposure was able to counteract, in human colonic mucosa, the LPS-dependent alteration of some proteins involved in the intestinal contraction (myosin light chain kinase (MLCK), myosin regulatory subunit (MYL)), to reduce the up-regulation of two proteins involved in the radical-mediated oxidative stress (the DNA-apurinic or apyrimidinic site) lyase) APEX1 and the T-complex protein 1 subunit eta (CCT7) and to entail a higher level of some detoxification enzymes (the metallothionein-2 MT2A, the glutathione–S-transferase K GSTk, and two UDP- glucuronosyltransferases UGT2B4, UGT2B17). Inulin exposure was also able to prevent the LPS-dependent intestinal muscle strips contraction impairment and the mucosa glutathione level alterations. Exposure of colonic mucosa to inulin seems to prevent LPS-induced alteration in expression of some key proteins, which promote intestinal motility and inflammation, reducing the radical-mediated oxidative stress.
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Affiliation(s)
| | - Annamaria Altomare
- Gastroenterology Unit, University Campus Bio-Medico di Roma, Rome, Italy
- * E-mail:
| | - Simone Barera
- Department of Biotechnology and Life Science, University of Insubria, Varese, Italy
| | - Vittoria Locato
- Food Sciences and Human Nutrition Unit, University Campus Bio-Medico di Roma, Rome, Italy
| | - Silvia Cocca
- Gastroenterology Unit, University Campus Bio-Medico di Roma, Rome, Italy
| | - Cinzia Franchin
- Department of Biomedical Sciences, University of Padova, Padova, Italy
- Proteomics Center, University of Padova and Azienda Ospedaliera di Padova, Padova, Italy
| | - Giorgio Arrigoni
- Department of Biomedical Sciences, University of Padova, Padova, Italy
- Proteomics Center, University of Padova and Azienda Ospedaliera di Padova, Padova, Italy
| | - Candida Vannini
- Department of Biotechnology and Life Science, University of Insubria, Varese, Italy
| | - Sarah Grossi
- Department of Biotechnology and Life Science, University of Insubria, Varese, Italy
| | - Paola Campomenosi
- Department of Biotechnology and Life Science, University of Insubria, Varese, Italy
| | - Valentina Pasqualetti
- Food Sciences and Human Nutrition Unit, University Campus Bio-Medico di Roma, Rome, Italy
| | - Marcella Bracale
- Department of Biotechnology and Life Science, University of Insubria, Varese, Italy
| | - Rossana Alloni
- Surgery Unit, University Campus Bio-Medico di Roma, Roma, Italy
| | - Laura De Gara
- Food Sciences and Human Nutrition Unit, University Campus Bio-Medico di Roma, Rome, Italy
| | - Michele Cicala
- Gastroenterology Unit, University Campus Bio-Medico di Roma, Rome, Italy
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