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Scheidt T, Alka O, Gonczarowska-Jorge H, Gruber W, Rathje F, Dell’Aica M, Rurik M, Kohlbacher O, Zahedi RP, Aberger F, Huber CG. Phosphoproteomics of short-term hedgehog signaling in human medulloblastoma cells. Cell Commun Signal 2020; 18:99. [PMID: 32576205 PMCID: PMC7310537 DOI: 10.1186/s12964-020-00591-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 05/05/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Aberrant hedgehog (HH) signaling is implicated in the development of various cancer entities such as medulloblastoma. Activation of GLI transcription factors was revealed as the driving force upon pathway activation. Increased phosphorylation of essential effectors such as Smoothened (SMO) and GLI proteins by kinases including Protein Kinase A, Casein Kinase 1, and Glycogen Synthase Kinase 3 β controls effector activity, stability and processing. However, a deeper and more comprehensive understanding of phosphorylation in the signal transduction remains unclear, particularly during early response processes involved in SMO activation and preceding GLI target gene regulation. METHODS We applied temporal quantitative phosphoproteomics to reveal phosphorylation dynamics underlying the short-term chemical activation and inhibition of early hedgehog signaling in HH responsive human medulloblastoma cells. Medulloblastoma cells were treated for 5.0 and 15 min with Smoothened Agonist (SAG) to induce and with vismodegib to inhibit the HH pathway. RESULTS Our phosphoproteomic profiling resulted in the quantification of 7700 and 10,000 phosphosites after 5.0 and 15 min treatment, respectively. The data suggest a central role of phosphorylation in the regulation of ciliary assembly, trafficking, and signal transduction already after 5.0 min treatment. ERK/MAPK signaling, besides Protein Kinase A signaling and mTOR signaling, were differentially regulated after short-term treatment. Activation of Polo-like Kinase 1 and inhibition of Casein Kinase 2A1 were characteristic for vismodegib treatment, while SAG treatment induced Aurora Kinase A activity. Distinctive phosphorylation of central players of HH signaling such as SMO, SUFU, GLI2 and GLI3 was observed only after 15 min treatment. CONCLUSIONS This study provides evidence that phosphorylation triggered in response to SMO modulation dictates the localization of hedgehog pathway components within the primary cilium and affects the regulation of the SMO-SUFU-GLI axis. The data are relevant for the development of targeted therapies of HH-associated cancers including sonic HH-type medulloblastoma. A deeper understanding of the mechanisms of action of SMO inhibitors such as vismodegib may lead to the development of compounds causing fewer adverse effects and lower frequencies of drug resistance. Video Abstract.
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Affiliation(s)
- Tamara Scheidt
- Department of Biosciences, Bioanalytical Research Laboratories and Molecular Cancer Research and Tumor Immunology, Cancer Cluster Salzburg, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria
| | - Oliver Alka
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076 Tübingen, Germany
| | - Humberto Gonczarowska-Jorge
- Leibniz-Institute of Analytical Sciences- ISAS - e.V, Dortmund, Germany
- Present address: CAPES Foundation, Ministry of Education of Brazil, Brasília, DF 70040-020 Brazil
| | - Wolfgang Gruber
- Department of Biosciences, Bioanalytical Research Laboratories and Molecular Cancer Research and Tumor Immunology, Cancer Cluster Salzburg, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria
- Present address: EVER Valinject GmbH, 4866 Unterach am Attersee, Austria
| | - Florian Rathje
- Department of Biosciences, Bioanalytical Research Laboratories and Molecular Cancer Research and Tumor Immunology, Cancer Cluster Salzburg, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria
| | | | - Marc Rurik
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076 Tübingen, Germany
| | - Oliver Kohlbacher
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076 Tübingen, Germany
- Biomolecular Interactions, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
- Institute for Translational Bioinformatics, University Hospital Tübingen, Hoppe-Seyler-Str. 9, 72076 Tübingen, Germany
- Applied Bioinformatics, Center for Bioinformatics, University of Tübingen, Sand 14, 72076 Tübingen, Germany
| | - René P. Zahedi
- Leibniz-Institute of Analytical Sciences- ISAS - e.V, Dortmund, Germany
- Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, Canada
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Canada
| | - Fritz Aberger
- Department of Biosciences, Bioanalytical Research Laboratories and Molecular Cancer Research and Tumor Immunology, Cancer Cluster Salzburg, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria
| | - Christian G. Huber
- Department of Biosciences, Bioanalytical Research Laboratories and Molecular Cancer Research and Tumor Immunology, Cancer Cluster Salzburg, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria
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Goel RK, Meyer M, Paczkowska M, Reimand J, Vizeacoumar F, Vizeacoumar F, Lam TT, Lukong KE. Global phosphoproteomic analysis identifies SRMS-regulated secondary signaling intermediates. Proteome Sci 2018; 16:16. [PMID: 30140170 PMCID: PMC6098843 DOI: 10.1186/s12953-018-0143-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 07/19/2018] [Indexed: 01/27/2023] Open
Abstract
Background The non-receptor tyrosine kinase, SRMS (Src-related kinase lacking C-terminal regulatory tyrosine and N-terminal myristoylation sites) is a member of the BRK family kinases (BFKs) which represents an evolutionarily conserved relative of the Src family kinases (SFKs). Tyrosine kinases are known to regulate a number of cellular processes and pathways via phosphorylating substrate proteins directly and/or by partaking in signaling cross-talks leading to the indirect modulation of various signaling intermediates. In a previous study, we profiled the tyrosine-phosphoproteome of SRMS and identified multiple candidate substrates of the kinase. The broader cellular signaling intermediates of SRMS are unknown. Methods In order to uncover the broader SRMS-regulated phosphoproteome and identify the SRMS-regulated indirect signaling intermediates, we performed label-free global phosphoproteomics analysis on cells expressing wild-type SRMS. Using computational database searching and bioinformatics analyses we characterized the dataset. Results Our analyses identified 60 hyperphosphorylated (phosphoserine/phosphothreonine) proteins mapped from 140 hyperphosphorylated peptides. Bioinfomatics analyses identified a number of significantly enriched biological and cellular processes among which DNA repair pathways were found to be upregulated while apoptotic pathways were found to be downregulated. Analyses of motifs derived from the upregulated phosphosites identified Casein kinase 2 alpha (CK2α) as one of the major potential kinases contributing to the SRMS-dependent indirect regulation of signaling intermediates. Conclusions Overall, our phosphoproteomics analyses identified serine/threonine phosphorylation dynamics as important secondary events of the SRMS-regulated phosphoproteome with implications in the regulation of cellular and biological processes. Electronic supplementary material The online version of this article (10.1186/s12953-018-0143-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Raghuveera Kumar Goel
- 1Department of Biochemistry, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5 Canada
| | - Mona Meyer
- 2Computational Biology Program, Ontario Institute for Cancer Research, 661 University Ave Suite 510, Toronto, ON M5G 0A3 Canada
| | - Marta Paczkowska
- 2Computational Biology Program, Ontario Institute for Cancer Research, 661 University Ave Suite 510, Toronto, ON M5G 0A3 Canada
| | - Jüri Reimand
- 2Computational Biology Program, Ontario Institute for Cancer Research, 661 University Ave Suite 510, Toronto, ON M5G 0A3 Canada.,3Department of Medical Biophysics, University of Toronto, 101 College Street Suite 15-701, Toronto, ON M5G 1L7 Canada
| | - Frederick Vizeacoumar
- 4Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5 Canada
| | - Franco Vizeacoumar
- 4Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5 Canada.,5Saskatchewan Cancer Agency, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5 Canada
| | - TuKiet T Lam
- 6Department of Molecular Biophysics and Biochemistry and MS & Proteomics Resource, WM Keck Foundation Biotechnology Resource Laboratory, Yale University, New Haven, CT USA
| | - Kiven Erique Lukong
- 1Department of Biochemistry, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5 Canada
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Moniz LS, Surinova S, Ghazaly E, Velasco LG, Haider S, Rodríguez-Prados JC, Berenjeno IM, Chelala C, Vanhaesebroeck B. Phosphoproteomic comparison of Pik3ca and Pten signalling identifies the nucleotidase NT5C as a novel AKT substrate. Sci Rep 2017; 7:39985. [PMID: 28059163 PMCID: PMC5216349 DOI: 10.1038/srep39985] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 11/30/2016] [Indexed: 12/16/2022] Open
Abstract
To identify novel effectors and processes regulated by PI3K pathway activation, we performed an unbiased phosphoproteomic screen comparing two common events of PI3K deregulation in cancer: oncogenic Pik3ca mutation (Pik3caH1047R) and deletion of Pten. Using mouse embryonic fibroblast (MEF) models that generate inducible, low-level pathway activation as observed in cancer, we quantified 7566 unique phosphopeptides from 3279 proteins. A number of proteins were found to be differentially-regulated by Pik3caH1047R and Pten loss, suggesting unique roles for these two events in processes such as vesicular trafficking, DNA damage repair and RNA splicing. We also identified novel PI3K effectors that were commonly-regulated, including putative AKT substrates. Validation of one of these hits, confirmed NT5C (5',3'-Nucleotidase, Cytosolic) as a novel AKT substrate, with an unexpected role in actin cytoskeleton regulation via an interaction with the ARP2/3 complex. This study has produced a comprehensive data resource and identified a new link between PI3K pathway activation and actin regulation.
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Affiliation(s)
- Larissa S. Moniz
- UCL Cancer Institute, Paul O’Gorman Building, University College London, 72 Huntley Street London WC1E 6DD, UK
| | - Silvia Surinova
- UCL Cancer Institute, Paul O’Gorman Building, University College London, 72 Huntley Street London WC1E 6DD, UK
| | - Essam Ghazaly
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Lorena Gonzalez Velasco
- UCL Cancer Institute, Paul O’Gorman Building, University College London, 72 Huntley Street London WC1E 6DD, UK
| | - Syed Haider
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | | | - Inma M. Berenjeno
- UCL Cancer Institute, Paul O’Gorman Building, University College London, 72 Huntley Street London WC1E 6DD, UK
| | - Claude Chelala
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Bart Vanhaesebroeck
- UCL Cancer Institute, Paul O’Gorman Building, University College London, 72 Huntley Street London WC1E 6DD, UK
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Gnad F, Doll S, Song K, Stokes MP, Moffat J, Liu B, Arnott D, Wallin J, Friedman LS, Hatzivassiliou G, Belvin M. Phosphoproteome analysis of the MAPK pathway reveals previously undetected feedback mechanisms. Proteomics 2016; 16:1998-2004. [DOI: 10.1002/pmic.201600119] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 05/09/2016] [Accepted: 06/05/2016] [Indexed: 12/13/2022]
Affiliation(s)
- Florian Gnad
- Department of Bioinformatics and Computational Biology; Genentech Inc; South San Francisco CA USA
| | - Sophia Doll
- Department of Protein Chemistry; Genentech Inc; South San Francisco CA USA
| | - Kyung Song
- Department of Translational Oncology; Genentech Inc; South San Francisco CA USA
| | | | - John Moffat
- Department of Biochemical Pharmacology; Genentech Inc; South San Francisco CA USA
| | - Bonnie Liu
- Department of Translational Oncology; Genentech Inc; South San Francisco CA USA
| | - David Arnott
- Department of Protein Chemistry; Genentech Inc; South San Francisco CA USA
| | - Jeffrey Wallin
- Department of Translational Oncology; Genentech Inc; South San Francisco CA USA
| | - Lori S. Friedman
- Department of Translational Oncology; Genentech Inc; South San Francisco CA USA
| | | | - Marcia Belvin
- Department of Translational Oncology; Genentech Inc; South San Francisco CA USA
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