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Girod M, Arquier D, Helms A, Juetten K, Brodbelt JS, Lemoine J, MacAleese L. Characterization of Phosphorylated Peptides by Electron-Activated and Ultraviolet Dissociation Mass Spectrometry: A Comparative Study with Collision-Induced Dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1040-1054. [PMID: 38626331 DOI: 10.1021/jasms.4c00048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2024]
Abstract
Mass-spectrometry-based methods have made significant progress in the characterization of post-translational modifications (PTMs) in peptides and proteins; however, room remains to improve fragmentation methods. Ideal MS/MS methods are expected to simultaneously provide extensive sequence information and localization of PTM sites and retain labile PTM groups. This collection of criteria is difficult to meet, and the various activation methods available today offer different capabilities. In order to examine the specific case of phosphorylation on peptides, we investigate electron transfer dissociation (ETD), electron-activated dissociation (EAD), and 193 nm ultraviolet photodissociation (UVPD) and compare all three methods with classical collision-induced dissociation (CID). EAD and UVPD show extensive backbone fragmentation, comparable in scope to that of CID. These methods provide diverse backbone fragmentation, producing a/x, b/y, and c/z ions with substantial sequence coverages. EAD displays a high retention efficiency of the phosphate modification, attributed to its electron-mediated fragmentation mechanisms, as observed in ETD. UVPD offers reasonable retention efficiency, also allowing localization of the PTM site. EAD experiments were also performed in an LC-MS/MS workflow by analyzing phosphopeptides spiked in human plasma, and spectra allow accurate identification of the modified sites and discrimination of isomers. Based on the overall performance, EAD and 193 nm UVPD offer alternative options to CID and ETD for phosphoproteomics.
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Affiliation(s)
- Marion Girod
- Universite Claude Bernard Lyon 1, CNRS, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France
| | - Delphine Arquier
- Universite Claude Bernard Lyon 1, CNRS, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France
| | - Amanda Helms
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Kyle Juetten
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jérôme Lemoine
- Universite Claude Bernard Lyon 1, CNRS, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France
| | - Luke MacAleese
- Universite Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, UMR5306, F-69100 Villeurbanne, France
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Gerritsen JS, White FM. Phosphoproteomics: a valuable tool for uncovering molecular signaling in cancer cells. Expert Rev Proteomics 2021; 18:661-674. [PMID: 34468274 PMCID: PMC8628306 DOI: 10.1080/14789450.2021.1976152] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 08/31/2021] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Many pathologies, including cancer, have been associated with aberrant phosphorylation-mediated signaling networks that drive altered cell proliferation, migration, metabolic regulation, and can lead to systemic inflammation. Phosphoproteomics, the large-scale analysis of protein phosphorylation sites, has emerged as a powerful tool to define signaling network regulation and dysregulation in normal and pathological conditions. AREAS COVERED We provide an overview of methodology for global phosphoproteomics as well as enrichment of specific subsets of the phosphoproteome, including phosphotyrosine and phospho-motif enrichment of kinase substrates. We review quantitative methods, advantages and limitations of different mass spectrometry acquisition formats, and computational approaches to extract biological insight from phosphoproteomics data. Throughout, we discuss various applications and their challenges in implementation. EXPERT OPINION Over the past 20 years the field of phosphoproteomics has advanced to enable deep biological and clinical insight through the quantitative analysis of signaling networks. Future areas of development include Clinical Laboratory Improvement Amendments (CLIA)-approved methods for analysis of clinical samples, continued improvements in sensitivity to enable analysis of small numbers of rare cells and tissue microarrays, and computational methods to integrate data resulting from multiple systems-level quantitative analytical methods.
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Affiliation(s)
- Jacqueline S Gerritsen
- Koch Institute for Integrative Cancer Research; Center for Precision Cancer Medicine; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, U.S.A
| | - Forest M White
- Koch Institute for Integrative Cancer Research; Center for Precision Cancer Medicine; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, U.S.A
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3
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Quantitative phosphoproteomics uncovers dysregulated kinase networks in Alzheimer’s disease. NATURE AGING 2021; 1:550-565. [PMID: 37117831 DOI: 10.1038/s43587-021-00071-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 04/30/2021] [Indexed: 12/31/2022]
Abstract
Alzheimer's disease (AD) is a form of dementia characterized by amyloid-β plaques and tau neurofibrillary tangles that progressively disrupt neural circuits in the brain. The signaling networks underlying AD pathological changes are poorly characterized at the phosphoproteome level. Using mass spectrometry, we analyzed the proteome and tyrosine, serine and threonine phosphoproteomes of temporal cortex tissue from patients with AD and aged-matched controls. We identified cocorrelated peptide clusters that were linked to varying levels of phospho-tau, oligodendrocyte, astrocyte, microglia and neuron pathologies. We found that neuronal synaptic protein abundances were strongly anti-correlated with markers of microglial reactivity. We also observed that phosphorylation sites on kinases targeting tau and other new signaling factors were correlated with these peptide modules. Finally, we used data-driven statistical modeling to identify individual peptides and peptide clusters that were predictive of AD histopathologies. Together, these results build a map of pathology-associated phosphorylation signaling events occurring in AD.
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The newly identified MEK1 tyrosine phosphorylation target MACC1 is druggable by approved MEK1 inhibitors to restrict colorectal cancer metastasis. Oncogene 2021; 40:5286-5301. [PMID: 34247190 PMCID: PMC8390371 DOI: 10.1038/s41388-021-01917-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 06/14/2021] [Accepted: 06/17/2021] [Indexed: 02/06/2023]
Abstract
Cancer metastasis causes >90% of cancer deaths and remains a major treatment challenge. Here we deciphered the impact of tyrosine phosphorylation of MACC1, a causative driver for cancer metastasis, for cancer cell signaling and novel interventions to restrict cancer metastasis. We identified MACC1 as new MEK1 substrate. MEK1 directly phosphorylates MACC1, leading to accelerated and increased ERK1 activation. Mutating in silico predicted hierarchical MACC1 tyrosine phosphorylation sites abrogates MACC1-induced migration, invasion, and MET expression, a transcriptional MACC1 target. Targeting MEK1 by RNAi or clinically applicable MEK1 inhibitors AZD6244 and GSK1120212 reduces MACC1 tyrosine phosphorylation and restricts MACC1-induced metastasis formation in mice. Although MEK1 levels, contrary to MACC1, are not of prognostic relevance for CRC patients, MEK1 expression was found indispensable for MACC1-induced metastasis. This study identifies MACC1 as new MEK1 substrate for tyrosine phosphorylation decisively impacting cell motility, tumor growth, and metastasis. Thus, MAP kinase signaling is not linear leading to ERK activation, but branches at the level of MEK1. This fundamental finding opens new therapeutic options for targeting the MEK1/MACC1 axis as novel vulnerability in patients at high risk for metastasis. This might be extended from CRC to further solid tumor entities.
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5
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EGFR vIII: An Oncogene with Ambiguous Role. JOURNAL OF ONCOLOGY 2019; 2019:1092587. [PMID: 32089685 PMCID: PMC7024087 DOI: 10.1155/2019/1092587] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 11/22/2019] [Indexed: 12/21/2022]
Abstract
Epidermal growth factor receptor variant III (EGFRvIII) seems to constitute the perfect therapeutic target for glioblastoma (GB), as it is specifically present on up to 28–30% of GB cells. In case of other tumor types, expression and possible role of this oncogene still remain controversial. In spite of EGFRvIII mechanism of action being crucial for the design of small active anticancer molecules and immunotherapies, i.e., CAR-T technology, it is yet to be precisely defined. EGFRvIII is known to be resistant to degradation, but it is still unclear whether it heterodimerizes with EGF-activated wild-type EGFR (EGFRWT) or homodimerizes (including covalent homodimerization). Constitutive kinase activity of this mutated receptor is relatively low, and some researchers even claim that a nuclear, but not a membrane function, is crucial for its activity. Based on the analyses of recurrent tumors that are often lacking EGFRvIII expression despite its initial presence in corresponding primary foci, this oncogene is suggested to play a marginal role during later stages of carcinogenesis, while even in primary tumors EGFRvIII expression is detected only in a small percentage of tumor cells, undermining the rationality of EGFRvIII-targeting therapies. On the other hand, EGFRvIII-positive cells are resistant to apoptosis, more invasive, and characterized with enhanced proliferation rate. Moreover, expression of this oncogenic receptor was also postulated to be a marker of cancer stem cells. Opinions regarding the role that EGFRvIII plays in tumorigenesis and for tumor aggressiveness are clearly contradictory and, therefore, it is crucial not only to determine its mechanism of action, but also to unambiguously define its role at early and advanced cancer stages.
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6
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Stec WJ, Rosiak K, Siejka P, Peciak J, Popeda M, Banaszczyk M, Pawlowska R, Treda C, Hulas-Bigoszewska K, Piaskowski S, Stoczynska-Fidelus E, Rieske P. Cell line with endogenous EGFRvIII expression is a suitable model for research and drug development purposes. Oncotarget 2017; 7:31907-25. [PMID: 27004406 PMCID: PMC5077985 DOI: 10.18632/oncotarget.8201] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 03/10/2016] [Indexed: 11/25/2022] Open
Abstract
Glioblastoma is the most common and malignant brain tumor, characterized by high cellular heterogeneity. About 50% of glioblastomas are positive for EGFR amplification, half of which express accompanying EGFR mutation, encoding truncated and constitutively active receptor termed EGFRvIII. Currently, no cell models suitable for development of EGFRvIII-targeting drugs exist, while the available ones lack the intratumoral heterogeneity or extrachromosomal nature of EGFRvIII. The reports regarding the biology of EGFRvIII expressed in the stable cell lines are often contradictory in observations and conclusions. In the present study, we use DK-MG cell line carrying endogenous non-modified EGFRvIII amplicons and derive a sub-line that is near depleted of amplicons, whilst remaining identical on the chromosomal level. By direct comparison of the two lines, we demonstrate positive effects of EGFRvIII on cell invasiveness and populational growth as a result of elevated cell survival but not proliferation rate. Investigation of the PI3K/Akt indicated no differences between the lines, whilst NFκB pathway was over-active in the line strongly expressing EGFRvIII, finding further supported by the effects of NFκB pathway specific inhibitors. Taken together, these results confirm the important role of EGFRvIII in intrinsic and extrinsic regulation of tumor behavior. Moreover, the proposed models are stable, making them suitable for research purposes as well as drug development process utilizing high throughput approach.
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Affiliation(s)
- Wojciech J Stec
- Research and Development Unit, Celther Polska Ltd., Lodz, Poland
| | - Kamila Rosiak
- Research and Development Unit, Celther Polska Ltd., Lodz, Poland.,Department of Tumor Biology, Medical University of Lodz, Lodz, Poland
| | - Paulina Siejka
- Research and Development Unit, Celther Polska Ltd., Lodz, Poland.,Department of Tumor Biology, Medical University of Lodz, Lodz, Poland
| | - Joanna Peciak
- Research and Development Unit, Celther Polska Ltd., Lodz, Poland.,Department of Tumor Biology, Medical University of Lodz, Lodz, Poland
| | - Marta Popeda
- Research and Development Unit, Celther Polska Ltd., Lodz, Poland
| | | | - Roza Pawlowska
- Research and Development Unit, Celther Polska Ltd., Lodz, Poland.,Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Lodz, Poland
| | - Cezary Treda
- Research and Development Unit, Celther Polska Ltd., Lodz, Poland
| | | | - Sylwester Piaskowski
- Research and Development Unit, Celther Polska Ltd., Lodz, Poland.,Department of Tumor Biology, Medical University of Lodz, Lodz, Poland
| | - Ewelina Stoczynska-Fidelus
- Research and Development Unit, Celther Polska Ltd., Lodz, Poland.,Department of Tumor Biology, Medical University of Lodz, Lodz, Poland
| | - Piotr Rieske
- Research and Development Unit, Celther Polska Ltd., Lodz, Poland.,Department of Tumor Biology, Medical University of Lodz, Lodz, Poland
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7
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Vyse S, Desmond H, Huang PH. Advances in mass spectrometry based strategies to study receptor tyrosine kinases. IUCRJ 2017; 4:119-130. [PMID: 28250950 PMCID: PMC5330522 DOI: 10.1107/s2052252516020546] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 12/27/2016] [Indexed: 06/06/2023]
Abstract
Receptor tyrosine kinases (RTKs) are key transmembrane environmental sensors that are capable of transmitting extracellular information into phenotypic responses, including cell proliferation, survival and metabolism. Advances in mass spectrometry (MS)-based phosphoproteomics have been instrumental in providing the foundations of much of our current understanding of RTK signalling networks and activation dynamics. Furthermore, new insights relating to the deregulation of RTKs in disease, for instance receptor co-activation and kinome reprogramming, have largely been identified using phosphoproteomic-based strategies. This review outlines the current approaches employed in phosphoproteomic workflows, including phosphopeptide enrichment and MS data-acquisition methods. Here, recent advances in the application of MS-based phosphoproteomics to bridge critical gaps in our knowledge of RTK signalling are focused on. The current limitations of the technology are discussed and emerging areas such as computational modelling, high-throughput phospho-proteomic workflows and next-generation single-cell approaches to further our understanding in new areas of RTK biology are highlighted.
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Affiliation(s)
- Simon Vyse
- Division of Cancer Biology, The Institute of Cancer Research, London SW3 6JB, England
| | - Howard Desmond
- Division of Cancer Biology, The Institute of Cancer Research, London SW3 6JB, England
| | - Paul H. Huang
- Division of Cancer Biology, The Institute of Cancer Research, London SW3 6JB, England
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8
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Xu AM, Kim SA, Wang DS, Aalipour A, Melosh NA. Temporally resolved direct delivery of second messengers into cells using nanostraws. LAB ON A CHIP 2016; 16:2434-2439. [PMID: 27292263 DOI: 10.1039/c6lc00463f] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Second messengers are biomolecules with the critical role of conveying information to intracellular targets. They are typically membrane-impermeable and only enter cells through tightly regulated transporters. Current methods for manipulating second messengers in cells require preparation of modified cell lines or significant disruptions in cell function, especially at the cell membrane. Here we demonstrate that 100 nm diameter 'nanostraws' penetrate the cell membrane to directly modulate second messenger concentrations within cells. Nanostraws are hollow vertical nanowires that provide a fluidic conduit into cells to allow time-resolved delivery of the signaling ion Ca(2+) without chemical permeabilization or genetic modification, minimizing cell perturbation. By integrating the nanostraw platform into a microfluidic device, we demonstrate coordinated delivery of Ca(2+) ions into hundreds of cells at the time scale of several seconds with the ability to deliver complex signal patterns, such as oscillations over time. The diffusive nature of nanostraw delivery gives the platform unique versatility, opening the possibility for time-resolved delivery of any freely diffusing molecules.
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Affiliation(s)
- Alexander M Xu
- Department of Materials Science and Engineering, Stanford University, Stanford, CA 94305, USA.
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9
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Tian Q, Sangar V, Price ND. Emerging Proteomic Technologies Provide Enormous and Underutilized Potential for Brain Cancer Research. Mol Cell Proteomics 2016; 15:362-7. [PMID: 26407994 PMCID: PMC4739660 DOI: 10.1074/mcp.r115.053884] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Revised: 09/22/2015] [Indexed: 01/11/2023] Open
Abstract
High-throughput technologies present immense opportunities to characterize brain cancer biology at a systems level. However, proteomic studies of brain cancers are still relatively scarce. Here we discuss the latest proteomic technologies, their application to profiling and quantitation of brain proteomes and how we expect these technologies will be applied to study brain cancer proteomes in the future. Mass spectrometry based proteomics with increased specificity, coverage and throughput will be pervasive in proteomics investigations of brain. Generated data needs to be captured by the curation of databases, and application of creative data analysis strategies is needed to provide meaningful insights into brain functions and associated pathologies. Overall, proteomics applications to brain cancers are in the earliest stages and the expanded use of these technologies holds enormous potential to improve our understanding of brain functions and pathologies.
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Affiliation(s)
- Qiang Tian
- From the ‡Institute for Systems Biology, Seattle, WA 98109
| | - Vineet Sangar
- From the ‡Institute for Systems Biology, Seattle, WA 98109
| | - Nathan D Price
- From the ‡Institute for Systems Biology, Seattle, WA 98109
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10
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Montermini L, Meehan B, Garnier D, Lee WJ, Lee TH, Guha A, Al-Nedawi K, Rak J. Inhibition of oncogenic epidermal growth factor receptor kinase triggers release of exosome-like extracellular vesicles and impacts their phosphoprotein and DNA content. J Biol Chem 2015; 290:24534-46. [PMID: 26272609 DOI: 10.1074/jbc.m115.679217] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Indexed: 01/07/2023] Open
Abstract
Cancer cells emit extracellular vesicles (EVs) containing unique molecular signatures. Here, we report that the oncogenic EGF receptor (EGFR) and its inhibitors reprogram phosphoproteomes and cargo of tumor cell-derived EVs. Thus, phosphorylated EGFR (P-EGFR) and several other receptor tyrosine kinases can be detected in EVs purified from plasma of tumor-bearing mice and from conditioned media of cultured cancer cells. Treatment of EGFR-driven tumor cells with second generation EGFR kinase inhibitors (EKIs), including CI-1033 and PF-00299804 but not with anti-EGFR antibody (Cetuximab) or etoposide, triggers a burst in emission of exosome-like EVs containing EGFR, P-EGFR, and genomic DNA (exo-gDNA). The EV release can be attenuated by treatment with inhibitors of exosome biogenesis (GW4869) and caspase pathways (ZVAD). The content of P-EGFR isoforms (Tyr-845, Tyr-1068, and Tyr-1173), ERK, and AKT varies between cells and their corresponding EVs and as a function of EKI treatment. Immunocapture experiments reveal the presence of EGFR and exo-gDNA within the same EV population following EKI treatment. These findings suggest that targeted agents may induce cancer cells to change the EV emission profiles reflective of drug-related therapeutic stress. We suggest that EV-based assays may serve as companion diagnostics for targeted anticancer agents.
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Affiliation(s)
- Laura Montermini
- From the Montreal Children's Hospital, Research Institute of the McGill University Health Centre, McGill University, Montreal, Quebec H4A 3J1
| | - Brian Meehan
- From the Montreal Children's Hospital, Research Institute of the McGill University Health Centre, McGill University, Montreal, Quebec H4A 3J1
| | - Delphine Garnier
- From the Montreal Children's Hospital, Research Institute of the McGill University Health Centre, McGill University, Montreal, Quebec H4A 3J1
| | - Wan Jin Lee
- From the Montreal Children's Hospital, Research Institute of the McGill University Health Centre, McGill University, Montreal, Quebec H4A 3J1
| | - Tae Hoon Lee
- From the Montreal Children's Hospital, Research Institute of the McGill University Health Centre, McGill University, Montreal, Quebec H4A 3J1
| | - Abhijit Guha
- the University of Toronto Health Network, Toronto, Ontario M5G 1L7, and
| | | | - Janusz Rak
- From the Montreal Children's Hospital, Research Institute of the McGill University Health Centre, McGill University, Montreal, Quebec H4A 3J1,
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Chantaravisoot N, Wongkongkathep P, Loo JA, Mischel PS, Tamanoi F. Significance of filamin A in mTORC2 function in glioblastoma. Mol Cancer 2015; 14:127. [PMID: 26134617 PMCID: PMC4489161 DOI: 10.1186/s12943-015-0396-z] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Accepted: 06/02/2015] [Indexed: 01/10/2023] Open
Abstract
Background Glioblastoma multiforme (GBM) is one of the most highly metastatic cancers. GBM has been associated with a high level of the mechanistic target of rapamycin complex 2 (mTORC2) activity. We aimed to observe roles of mTORC2 in GBM cells especially on actin cytoskeleton reorganization, cell migration and invasion, and further determine new important players involved in the regulation of these cellular processes. Methods To further investigate the significance of mTORC2 in GBM, we treated GBM cells with PP242, an ATP-competitive inhibitor of mTOR, and used RICTOR siRNA to knock down mTORC2 activity. Effects on actin cytoskeleton, focal adhesion, migration, and invasion of GBM cells were examined. To gain insight into molecular basis of the mTORC2 effects on cellular cytoskeletal arrangement and motility/invasion, we affinity purified mTORC2 from GBM cells and identified proteins of interest by mass spectrometry. Characterization of the protein of interest was performed. Results In addition to the inhibition of mTORC2 activity, we demonstrated significant alteration of actin distribution as revealed by the use of phalloidin staining. Furthermore, vinculin staining was altered which suggests changes in focal adhesion. Inhibition of cell migration and invasion was observed with PP242. Two major proteins that are associated with this mTORC2 multiprotein complex were found. Mass spectrometry identified one of them as Filamin A (FLNA). Association of FLNA with RICTOR but not mTOR was demonstrated. Moreover, in vitro, purified mTORC2 can phosphorylate FLNA likewise its known substrate, AKT. In GBM cells, colocalization of FLNA with RICTOR was observed, and the overall amounts of FLNA protein as well as phosphorylated FLNA are high. Upon treatments of RICTOR siRNA or PP242, phosphorylated FLNA levels at the regulatory residue (Ser2152) decreased. This treatment also disrupted colocalization of Actin filaments and FLNA. Conclusions Our results support FLNA as a new downstream effector of mTORC2 controlling GBM cell motility. This new mTORC2-FLNA signaling pathway plays important roles in motility and invasion of glioblastoma cells. Electronic supplementary material The online version of this article (doi:10.1186/s12943-015-0396-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Naphat Chantaravisoot
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, CA, 90095, USA
| | - Piriya Wongkongkathep
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
| | - Joseph A Loo
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA.,Department of Biological Chemistry, University of California, Los Angeles, CA, 90095, USA.,UCLA/DOE Institute of Genomics and Proteomics, University of California, Los Angeles, CA, 90095, USA
| | - Paul S Mischel
- Ludwig Institute for Cancer research, University of California, San Diego, CA, 92093, USA
| | - Fuyuhiko Tamanoi
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, CA, 90095, USA. .,Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, 90095, USA.
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12
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Alteration of major vault protein in human glioblastoma and its relation with EGFR and PTEN status. Neuroscience 2015; 297:243-51. [PMID: 25869624 DOI: 10.1016/j.neuroscience.2015.04.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 03/13/2015] [Accepted: 04/03/2015] [Indexed: 11/22/2022]
Abstract
Glioblastoma (GBM) is the most frequent and malignant primary brain tumor. Conventional therapy of surgical removal, radiation and chemotherapy is largely palliative. Major vault protein (MVP), the main component of the vault organelle has been associated with multidrug resistance by reducing cellular accumulation of chemotherapeutic agents. With regard to cancer, MVP has been shown to be overexpressed in drug resistance development and malignant progression. The aim of the present study was to evaluate the MVP gene dosage levels in 113 archival samples from GBM and its correlation with patients' survival and epidermal growth factor receptor (EGFR) and phosphatase and tensin homolog (PTEN) gene dosages. Fluorescent in situ hybridization revealed polysomy of chromosome 7 in 76.1% of the GBMs and EGFR amplification in a 64.6% of the tumors. Genetic status of EGFR, PTEN and MVP copies was determined by multiplex ligation-dependent probe amplification (MLPA) technique. 31% of the tumors showed the EGFR is variant III mutation (EGFRvIII) mutation and 74.3% of them presented amplification of MVP gene. Amplification of EGFR and MVP was found in a 63.7% and 56.6% of the GBM, respectively. An inverse correlation between MVP and PTEN dosage values was observed. Besides, an inverse relationship between the survival of the patients treated with chemotherapy and the levels of MVP copies was determined. In conclusion, our study reveals an important role of MVP, together with EGFRvIII and PTEN, in the progression of GBM and proposes it as a novel and interesting target for new treatment approaches.
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13
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Lombardi B, Rendell N, Edwards M, Katan M, Zimmermann JG. Evaluation of phosphopeptide enrichment strategies for quantitative TMT analysis of complex network dynamics in cancer-associated cell signalling. EUPA OPEN PROTEOMICS 2015; 6:10-15. [PMID: 25893165 PMCID: PMC4398868 DOI: 10.1016/j.euprot.2015.01.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Defining alterations in signalling pathways in normal and malignant cells is becoming a major field in proteomics. A number of different approaches have been established to isolate, identify and quantify phosphorylated proteins and peptides. In the current report, a comparison between SCX prefractionation versus an antibody based approach, both coupled to TiO2 enrichment and applied to TMT labelled cellular lysates, is described. The antibody strategy was more complete for enriching phosphopeptides and allowed the identification of a large set of proteins known to be phosphorylated (715 protein groups) with a minimum number of not previously known phosphorylated proteins (2).
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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, Royal Free Campus, Rowland Hill Street, London NW3 2PF, United Kingdom
| | - Nigel Rendell
- Wolfson Drug Discovery Unit, Centre for Amyloidosis and Acute Phase Proteins, Division of Medicine, University College London, London NW3 2PF, United Kingdom
| | - Mina Edwards
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Matilda Katan
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, 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, Royal Free Campus, Rowland Hill Street, London NW3 2PF, United Kingdom
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14
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Gajadhar AS, Johnson H, Slebos RJC, Shaddox K, Wiles K, Washington MK, Herline AJ, Levine DA, Liebler DC, White FM. Phosphotyrosine signaling analysis in human tumors is confounded by systemic ischemia-driven artifacts and intra-specimen heterogeneity. Cancer Res 2015; 75:1495-503. [PMID: 25670172 DOI: 10.1158/0008-5472.can-14-2309] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 01/05/2015] [Indexed: 01/25/2023]
Abstract
Tumor protein phosphorylation analysis may provide insight into intracellular signaling networks underlying tumor behavior, revealing diagnostic, prognostic or therapeutic information. Human tumors collected by The Cancer Genome Atlas program potentially offer the opportunity to characterize activated networks driving tumor progression, in parallel with the genetic and transcriptional landscape already documented for these tumors. However, a critical question is whether cellular signaling networks can be reliably analyzed in surgical specimens, where freezing delays and spatial sampling disparities may potentially obscure physiologic signaling. To quantify the extent of these effects, we analyzed the stability of phosphotyrosine (pTyr) sites in ovarian and colon tumors collected under conditions of controlled ischemia and in the context of defined intratumoral sampling. Cold-ischemia produced a rapid, unpredictable, and widespread impact on tumor pTyr networks within 5 minutes of resection, altering up to 50% of pTyr sites by more than 2-fold. Effects on adhesion and migration, inflammatory response, proliferation, and stress response pathways were recapitulated in both ovarian and colon tumors. In addition, sampling of spatially distinct colon tumor biopsies revealed pTyr differences as dramatic as those associated with ischemic times, despite uniform protein expression profiles. Moreover, intratumoral spatial heterogeneity and pTyr dynamic response to ischemia varied dramatically between tumors collected from different patients. Overall, these findings reveal unforeseen phosphorylation complexity, thereby increasing the difficulty of extracting physiologically relevant pTyr signaling networks from archived tissue specimens. In light of this data, prospective tumor pTyr analysis will require appropriate sampling and collection protocols to preserve in vivo signaling features.
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Affiliation(s)
- Aaron S Gajadhar
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts. David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Hannah Johnson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts. David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Robbert J C Slebos
- Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee. The Jim Ayers Institute for Precancer Detection and Diagnosis, Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
| | - Kent Shaddox
- The Jim Ayers Institute for Precancer Detection and Diagnosis, Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
| | - Kerry Wiles
- Cooperative Human Tissue Network Western Division, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Mary Kay Washington
- Department of Pathology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Alan J Herline
- Department of Surgery, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Douglas A Levine
- Gynecology Service, Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Daniel C Liebler
- The Jim Ayers Institute for Precancer Detection and Diagnosis, Vanderbilt-Ingram Cancer Center, Nashville, Tennessee. Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Forest M White
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts. David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts.
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15
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Li G, Liu X, Liu Z, Su Z. Interactions of connexin 43 and aquaporin-4 in the formation of glioma-induced brain edema. Mol Med Rep 2014; 11:1188-94. [PMID: 25373717 DOI: 10.3892/mmr.2014.2867] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 09/18/2014] [Indexed: 11/05/2022] Open
Abstract
Connexin 43 (Cx43) and aquaporin-4 (AQP4) have important roles in the formation of glioma-induced brain edema; however, the association between these two factors in the development of edema has remained to be elucidated. In the present study, immunofluorescence and western blot analysis revealed that in a rat model of intracranial C6 glioma, Cx43 expression levels were low to undetectable and AQP4 expression levels were low in glioma cells. Significantly higher Cx43 and AQP4 levels were detected in the tissue surrounding the glioma. To further investigate the potential interaction between Cx43 and AQP4, normal glial cells and C6 glioma cells were cultured in hypotonic medium. Reverse transcription quantitative polymerase chain reaction indicated that AQP4 and Cx43 mRNA expression levels increased as a function of time in normal glial cells and C6 glioma cells in a hypotonic environment. However, the increase observed in normal glial cells was significantly lower than that observed in C6 glioma cells. Furthermore, AQP4 expression levels changed prior to alterations in Cx43 expression. Following AQP4 silencing in C6 cells, the increase in Cx43 expression was significantly attenuated (P<0.05). In normal cells, Cx43 silencing did not influence AQP4 expression (P>0.05). Therefore, it was hypothesized that AQP4 and Cx43 had two distinct mechanisms underlying brain edema formation within and surrounding the glioma. Cx43 may be a downstream effector of AQP4. The elucidation of this pathway may aid in the development of drugs targeting the interaction between AQP4 and Cx43, providing novel therapeutic possibilities for glioma-induced brain edema.
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Affiliation(s)
- Gang Li
- Department of Neurosurgery, Tianjin 5th Center Hospital, Tianjin 300450, P.R. China
| | - Xiaozhi Liu
- Department of Neurosurgery, Tianjin 5th Center Hospital, Tianjin 300450, P.R. China
| | - Zhenlin Liu
- Department of Neurosurgery, Tianjin 5th Center Hospital, Tianjin 300450, P.R. China
| | - Zhiguo Su
- Department of Neurosurgery, Tianjin 5th Center Hospital, Tianjin 300450, P.R. China
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16
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Sangar V, Funk CC, Kusebauch U, Campbell DS, Moritz RL, Price ND. Quantitative proteomic analysis reveals effects of epidermal growth factor receptor (EGFR) on invasion-promoting proteins secreted by glioblastoma cells. Mol Cell Proteomics 2014; 13:2618-31. [PMID: 24997998 DOI: 10.1074/mcp.m114.040428] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Glioblastoma multiforme is a highly invasive and aggressive brain tumor with an invariably poor prognosis. The overexpression of epidermal growth factor receptor (EGFR) is a primary influencer of invasion and proliferation in tumor cells and the constitutively active EGFRvIII mutant, found in 30-65% of Glioblastoma multiforme, confers more aggressive invasion. To better understand how EGFR contributes to tumor aggressiveness, we investigated the effect of EGFR on the secreted levels of 65 rationally selected proteins involved in invasion. We employed selected reaction monitoring targeted mass spectrometry using stable isotope labeled internal peptide standards to quantity proteins in the secretome from five GBM (U87) isogenic cell lines in which EGFR, EGFRvIII, and/or PTEN were expressed. Our results show that cell lines with EGFR overexpression and constitutive EGFRvIII expression differ remarkably in the expression profiles for both secreted and intracellular signaling proteins, and alterations in EGFR signaling result in reproducible changes in concentrations of secreted proteins. Furthermore, the EGFRvIII-expressing mutant cell line secretes the majority of the selected invasion-promoting proteins at higher levels than other cell lines tested. Additionally, the intracellular and extracellular protein measurements indicate elevated oxidative stress in the EGFRvIII-expressing cell line. In conclusion, the results of our study demonstrate that EGFR signaling has a significant effect on the levels of secreted invasion-promoting proteins, likely contributing to the aggressiveness of Glioblastoma multiforme. Further characterization of these proteins may provide candidates for new therapeutic strategies and targets as well as biomarkers for this aggressive disease.
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Affiliation(s)
- Vineet Sangar
- From the ‡Institute for Systems Biology, 401 Terry Ave N, Seattle, Washington, 98109
| | - Cory C Funk
- From the ‡Institute for Systems Biology, 401 Terry Ave N, Seattle, Washington, 98109
| | - Ulrike Kusebauch
- From the ‡Institute for Systems Biology, 401 Terry Ave N, Seattle, Washington, 98109
| | - David S Campbell
- From the ‡Institute for Systems Biology, 401 Terry Ave N, Seattle, Washington, 98109
| | - Robert L Moritz
- From the ‡Institute for Systems Biology, 401 Terry Ave N, Seattle, Washington, 98109
| | - Nathan D Price
- From the ‡Institute for Systems Biology, 401 Terry Ave N, Seattle, Washington, 98109
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17
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Liu Z, Jiang Z, Huang J, Huang S, Li Y, Yu S, Yu S, Liu X. miR-7 inhibits glioblastoma growth by simultaneously interfering with the PI3K/ATK and Raf/MEK/ERK pathways. Int J Oncol 2014; 44:1571-80. [PMID: 24603851 DOI: 10.3892/ijo.2014.2322] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2013] [Accepted: 02/14/2014] [Indexed: 01/08/2023] Open
Abstract
Epidermal growth factor receptor (EGFR) signaling regulates glioblastoma cell proliferation, survival, migration and invasion and plays a key role in tumor progression. We show that microRNA-7 (miR-7) is a common regulator of the phosphoinositide-3-kinase (PI3K)/ATK and Raf/mitogen-activated protein kinase kinase (MEK)/extracellular signal-regulated kinase (ERK) pathways, both of which are launched by EGFR through its two direct targets, the transcription factors PI3K and Raf-1, respectively. Enforced expression of miR-7 markedly decreased expression of PI3K, phosphorylated Akt, Raf-1, phosphorylated MEK 1/2, and cyclin D1, as well as slightly reduced expression of EGFR. Forced expression of PI3K or Raf-1 transcripts lacking the 3'-untranslated region (3'-UTR) partially reversed the effects of miR-7 on cell growth inhibition and cell cycle arrest in glioma cells. Additionally, transient expression of miR-7 in glioblastoma cells strongly inhibited in vivo glioblastoma xenograft growth. We conclude that miR-7 is a potential tumor suppressor in glioblastoma that acts by targeting multiple oncogenes related to the downstream pathway of EGFR and may serve as a novel therapeutic target for malignant gliomas.
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Affiliation(s)
- Zhenlin Liu
- Department of Neurosurgery, The Fifth Central Hospital of Tianjin, Tianjin, P.R. China
| | - Zhongmin Jiang
- Department of Pathology, The Fifth Central Hospital of Tianjin, Tianjin, P.R. China
| | - Jianyong Huang
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Shuqiang Huang
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Yanxia Li
- The Central Laboratory, The Fifth Central Hospital of Tianjin, Tianjin, P.R. China
| | - Simiao Yu
- Department of Neurosurgery, The Fifth Central Hospital of Tianjin, Tianjin, P.R. China
| | - Shizhu Yu
- Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, P.R. China
| | - Xiaozhi Liu
- Department of Neurosurgery, The Fifth Central Hospital of Tianjin, Tianjin, P.R. China
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18
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Gomez GG, Volinia S, Croce CM, Zanca C, Li M, Emnett R, Gutmann DH, Brennan CW, Furnari FB, Cavenee WK. Suppression of microRNA-9 by mutant EGFR signaling upregulates FOXP1 to enhance glioblastoma tumorigenicity. Cancer Res 2014; 74:1429-39. [PMID: 24436148 DOI: 10.1158/0008-5472.can-13-2117] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The EGF receptor (EGFR) is amplified and mutated in glioblastoma, in which its common mutation (ΔEGFR, also called EGFRvIII) has a variety of activities that promote growth and inhibit death, thereby conferring a strong tumor-enhancing effect. This range of activities suggested to us that ΔEGFR might exert its influence through pleiotropic effectors, and we hypothesized that microRNAs might serve such a function. Here, we report that ΔEGFR specifically suppresses one such microRNA, namely miR-9, through the Ras/PI3K/AKT axis that it is known to activate. Correspondingly, expression of miR-9 antagonizes the tumor growth advantage conferred by ΔEGFR. Silencing of FOXP1, a miR-9 target, inhibits ΔEGFR-dependent tumor growth and, conversely, de-repression of FOXP1, as a consequence of miR-9 inhibition, increases tumorigenicity. FOXP1 was sufficient to increase tumor growth in the absence of oncogenic ΔEGFR signaling. The significance of these findings is underscored by our finding that high FOXP1 expression predicts poor survival in a cohort of 131 patients with glioblastoma. Collectively, these data suggest a novel regulatory mechanism by which ΔEGFR suppression of miR-9 upregulates FOXP1 to increase tumorigenicity.
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Affiliation(s)
- German G Gomez
- Authors' Affiliations: Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, California; Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio; Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, Virginia; Department of Neurology, Washington University School of Medicine, St. Louis, Missouri; and Department of Neurosurgery, Memorial Sloan-Kettering Cancer Center, New York, New York
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19
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Gajadhar AS, White FM. System level dynamics of post-translational modifications. Curr Opin Biotechnol 2014; 28:83-7. [PMID: 24441143 DOI: 10.1016/j.copbio.2013.12.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 12/24/2013] [Indexed: 11/20/2022]
Abstract
Attempts to characterize cellular behaviors with static, univariate measurements cannot fully capture biological complexity and lead to an inadequate interpretation of cellular processes. Significant biological insight can be gleaned by considering the contribution of dynamic protein post-translational modifications (PTMs) utilizing systems-level quantitative analysis. High-resolution mass spectrometry coupled with computational modeling of dynamic signal-response relationships is a powerful tool to reveal PTM-mediated regulatory networks. Recent advances using this approach have defined network kinetics of growth factor signaling pathways, identified systems level responses to cytotoxic perturbations, elucidated kinase-substrate relationships, and unraveled the dynamics of PTM cross-talk. Innovations in multiplex measurement capacity, PTM annotation accuracy, and computational integration of datasets promise enhanced resolution of dynamic PTM networks and further insight into biological intricacies.
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Affiliation(s)
- Aaron S Gajadhar
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Forest M White
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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20
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Epithelial wounds induce differential phosphorylation changes in response to purinergic and EGF receptor activation. THE AMERICAN JOURNAL OF PATHOLOGY 2013; 183:1841-1852. [PMID: 24095926 DOI: 10.1016/j.ajpath.2013.08.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 08/06/2013] [Accepted: 08/12/2013] [Indexed: 11/22/2022]
Abstract
Protein phosphorylation is a dynamic post-translational modification. Mass spectrometry-based quantitation was performed to determine the phosphoproteome profile of epithelial cells in response to injury, nucleotide, or epidermal growth factor. Phosphotyrosine enrichment used immunoprecipitation and immobilized metal affinity chromatography. Nucleotides released after scratch wounding activate purinergic receptors, leading to a distinct phosphorylation profile on epidermal growth factor receptor (EGFR) compared with its natural ligand. ATP induced a 2- to 15-fold phosphorylation increase over control on EGFR Y974, Y1086, and Y1148, with minimal phosphorylation intensity on EGFR Y1173 compared with the level measured in response to epidermal growth factor. Differential phosphorylation induced by epidermal growth factor or ATP was site specific on Src, Shc, phospholipase Cγ, protein kinase C, focal adhesion kinase, paxillin, and mitogen-activated protein kinases 1, 12, and 13. After wounding, the P2Y2 receptor mRNA expression increased, and after knockdown, migration and Ca(2+) mobilization were impaired. To examine phosphorylation mediated by P2Y2, cells were cultured in media containing stable isotope-labeled amino acids, the receptor was knocked down, and the cells were stimulated. Mass spectrometry-based comparison of the phosphorylation profiles of control versus transfected cells revealed a 50-fold decrease in phosphorylation of EGFR Y974 and 1086, with no decrease in Y1173 phosphorylation. A similarfold decrease in Src Y421 and Y446 and paxillin Y118 was detected, indicating the far-reaching importance of the P2Y2 receptor in mediating migration.
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21
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Zhang P, Zhang P, Zhou M, Jiang H, Zhang H, Shi B, Pan X, Gao H, Sun H, Li Z. Exon 4 deletion variant of epidermal growth factor receptor enhances invasiveness and cisplatin resistance in epithelial ovarian cancer. Carcinogenesis 2013; 34:2639-46. [DOI: 10.1093/carcin/bgt216] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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22
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Cellular functions regulated by phosphorylation of EGFR on Tyr845. Int J Mol Sci 2013; 14:10761-90. [PMID: 23702846 PMCID: PMC3709701 DOI: 10.3390/ijms140610761] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 05/06/2013] [Accepted: 05/13/2013] [Indexed: 11/17/2022] Open
Abstract
The Src gene product (Src) and the epidermal growth factor receptor (EGFR) are prototypes of oncogene products and function primarily as a cytoplasmic non-receptor tyrosine kinase and a transmembrane receptor tyrosine kinase, respectively. The identification of Src and EGFR, and the subsequent extensive investigations of these proteins have long provided cutting edge research in cancer and other molecular and cellular biological studies. In 1995, we reported that the human epidermoid carcinoma cells, A431, contain a small fraction of Src and EGFR in which these two kinase were in physical association with each other, and that Src phosphorylates EGFR on tyrosine 845 (Y845) in the Src-EGFR complex. Y845 of EGFR is located in the activation segment of the kinase domain, where many protein kinases contain kinase-activating autophosphorylation sites (e.g., cAMP-dependent protein kinase, Src family kinases, transmembrane receptor type tyrosine kinases) or trans-phosphorylation sites (e.g., cyclin-dependent protein kinase, mitogen-activated protein kinase, Akt protein kinase). A number of studies have demonstrated that Y845 phosphorylation serves an important role in cancer as well as normal cells. Here we compile the experimental facts involving Src phosphorylation of EGFR on Y845, by which cell proliferation, cell cycle control, mitochondrial regulation of cell metabolism, gamete activation and other cellular functions are regulated. We also discuss the physiological relevance, as well as structural insights of the Y845 phosphorylation.
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23
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Miraldi ER, Sharfi H, Friedline RH, Johnson H, Zhang T, Lau KS, Ko HJ, Curran TG, Haigis KM, Yaffe MB, Bonneau R, Lauffenburger DA, Kahn BB, Kim JK, Neel BG, Saghatelian A, White FM. Molecular network analysis of phosphotyrosine and lipid metabolism in hepatic PTP1b deletion mice. Integr Biol (Camb) 2013; 5:940-63. [PMID: 23685806 DOI: 10.1039/c3ib40013a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Metabolic syndrome describes a set of obesity-related disorders that increase diabetes, cardiovascular, and mortality risk. Studies of liver-specific protein-tyrosine phosphatase 1b (PTP1b) deletion mice (L-PTP1b(-/-)) suggest that hepatic PTP1b inhibition would mitigate metabolic-syndrome through amelioration of hepatic insulin resistance, endoplasmic-reticulum stress, and whole-body lipid metabolism. However, the altered molecular-network states underlying these phenotypes are poorly understood. We used mass spectrometry to quantify protein-phosphotyrosine network changes in L-PTP1b(-/-) mouse livers relative to control mice on normal and high-fat diets. We applied a phosphosite-set-enrichment analysis to identify known and novel pathways exhibiting PTP1b- and diet-dependent phosphotyrosine regulation. Detection of a PTP1b-dependent, but functionally uncharacterized, set of phosphosites on lipid-metabolic proteins motivated global lipidomic analyses that revealed altered polyunsaturated-fatty-acid (PUFA) and triglyceride metabolism in L-PTP1b(-/-) mice. To connect phosphosites and lipid measurements in a unified model, we developed a multivariate-regression framework, which accounts for measurement noise and systematically missing proteomics data. This analysis resulted in quantitative models that predict roles for phosphoproteins involved in oxidation-reduction in altered PUFA and triglyceride metabolism.
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Affiliation(s)
- Emily R Miraldi
- Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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24
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Johnson H, Lescarbeau RS, Gutierrez JA, White FM. Phosphotyrosine profiling of NSCLC cells in response to EGF and HGF reveals network specific mediators of invasion. J Proteome Res 2013; 12:1856-67. [PMID: 23438512 DOI: 10.1021/pr301192t] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Growth factor signaling is deregulated in cancer and often leads to invasion, yet receptor tyrosine kinase signaling pathways driving invasion under different growth factor conditions are not well understood. To identify specific signaling molecules regulating invasion of A549 non-small cell lung carcinoma (NSCLC) cells downstream of the epidermal growth factor receptor (EGFR) and Met, quantitative site-specific mass spectrometric analysis of tyrosine phosphorylation was performed following epidermal growth factor (EGF) or hepatocyte growth factor (HGF) stimulation, at three different growth factor concentrations and at two time points. Through this analysis, the temporal and concentration dependent phosphorylation profiles were obtained for 131 and 139 sites downstream of EGF and HGF stimulation, respectively. To characterize the effect of these signaling network alterations, we quantified 3D cell migration/invasion through Matrigel. Partial least-squares regression (PLSR) analysis was performed to identify the tyrosine phosphorylation sites most strongly correlated with EGF and/or HGF mediated invasion. Potential common and specific signaling events required for driving invasion downstream of EGFR and Met were identified using either a combined or two independent PLSR models, based on the quantitative EGF or HGF data. Our data highlight the integration and compartmentalization of signaling required for invasion in cancer.
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Affiliation(s)
- Hannah Johnson
- Department of Biological Engineering, Massachusetts Institute of Technology , Cambridge, Massachusetts, United States
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25
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Johnson H, Del Rosario AM, Bryson BD, Schroeder MA, Sarkaria JN, White FM. Molecular characterization of EGFR and EGFRvIII signaling networks in human glioblastoma tumor xenografts. Mol Cell Proteomics 2012; 11:1724-40. [PMID: 22964225 DOI: 10.1074/mcp.m112.019984] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Glioblastoma multiforme (GBM) is a malignant primary brain tumor with a mean survival of 15 months with the current standard of care. Genetic profiling efforts have identified the amplification, overexpression, and mutation of the wild-type (wt) epidermal growth factor receptor tyrosine kinase (EGFR) in ≈ 50% of GBM patients. The genetic aberration of wtEGFR is frequently accompanied by the overexpression of a mutant EGFR known as EGFR variant III (EGFRvIII, de2-7EGFR, ΔEGFR), which is expressed in 30% of GBM tumors. The molecular mechanisms of tumorigenesis driven by EGFRvIII overexpression in human tumors have not been fully elucidated. To identify specific therapeutic targets for EGFRvIII driven tumors, it is important to gather a broad understanding of EGFRvIII specific signaling. Here, we have characterized signaling through the quantitative analysis of protein expression and tyrosine phosphorylation across a panel of glioblastoma tumor xenografts established from patient surgical specimens expressing wtEGFR or overexpressing wtEGFR (wtEGFR+) or EGFRvIII (EGFRvIII+). S100A10 (p11), major vault protein, guanylate-binding protein 1(GBP1), and carbonic anhydrase III (CAIII) were identified to have significantly increased expression in EGFRvIII expressing xenograft tumors relative to wtEGFR xenograft tumors. Increased expression of these four individual proteins was found to be correlated with poor survival in patients with GBM; the combination of these four proteins represents a prognostic signature for poor survival in gliomas. Integration of protein expression and phosphorylation data has uncovered significant heterogeneity among the various tumors and has highlighted several novel pathways, related to EGFR trafficking, activated in glioblastoma. The pathways and proteins identified in these tumor xenografts represent potential therapeutic targets for this disease.
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Affiliation(s)
- Hannah Johnson
- Department of Bioengineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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26
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Abstract
AS (alternative splicing) and its role in disease, especially cancer, has come to forefront in research over the last few years. Alterations in the ratio of splice variants have been widely observed in cancer. Splice variants of cancer-associated genes have functions that can alter cellular phenotype, ultimately altering metastatic potential. As metastases are the cause of approximately 90% of all human cancer deaths, it is crucial to understand how AS is dysregulated in metastatic disease. We highlight some recent studies into the relationship between altered AS of key genes and the initiation of prostate cancer metastasis.
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27
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Liotta LA, Petricoin EF. -Omics and cancer biomarkers: link to the biological truth or bear the consequences. Cancer Epidemiol Biomarkers Prev 2012; 21:1229-35. [PMID: 22810955 DOI: 10.1158/1055-9965.epi-12-0635] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
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29
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At the crossroads: EGFR and PTHrP signaling in cancer-mediated diseases of bone. Odontology 2012; 100:109-29. [PMID: 22684584 DOI: 10.1007/s10266-012-0070-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Accepted: 05/21/2012] [Indexed: 01/01/2023]
Abstract
The epidermal growth factor receptor is a well-established cancer therapeutic target due to its stimulation of proliferation, motility, and resistance to apoptosis. Recently, additional roles for the receptor have been identified in growth of metastases. Similar to development, metastatic spread requires signaling interactions between epithelial-derived tumor cells and mesenchymal derivatives of the microenvironment. This necessitates reactivation of developmental signaling molecules, including the hypercalcemia factor parathyroid hormone-related protein. This review covers the variations of epidermal growth factor receptor signaling in cancers that produce bone metastases, regulation of parathyroid hormone-related protein, and evidence that the two molecules drive cancer-mediated diseases of bone.
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30
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Johnson H, White FM. Toward quantitative phosphotyrosine profiling in vivo. Semin Cell Dev Biol 2012; 23:854-62. [PMID: 22677333 DOI: 10.1016/j.semcdb.2012.05.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Accepted: 05/29/2012] [Indexed: 11/25/2022]
Abstract
Tyrosine phosphorylation is a dynamic reversible post-translational modification that regulates many aspects of cell biology. To understand how this modification controls biological function, it is necessary to not only identify the specific sites of phosphorylation, but also to quantify how phosphorylation levels on these sites may be altered under specific physiological conditions. Due to its sensitivity and accuracy, mass spectrometry (MS) has widely been applied to the identification and characterization of phosphotyrosine signaling across biological systems. In this review we highlight the advances in both MS and phosphotyrosine enrichment methods that have been developed to enable the identification of low level tyrosine phosphorylation events. Computational and manual approaches to ensure confident identification of phosphopeptide sequence and determination of phosphorylation site localization are discussed along with methods that have been applied to the relative quantification of large numbers of phosphorylation sites. Finally, we provide an overview of the challenges ahead as we extend these technologies to the characterization of tyrosine phosphorylation signaling in vivo. With these latest developments in analytical and computational techniques, it is now possible to derive biological insight from quantitative MS-based analysis of signaling networks in vitro and in vivo. Application of these approaches to a wide variety of biological systems will define how signal transduction regulates cellular physiology in health and disease.
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Affiliation(s)
- Hannah Johnson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
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31
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Negrutskii B, Vlasenko D, El'skaya A. From global phosphoproteomics to individual proteins: the case of translation elongation factor eEF1A. Expert Rev Proteomics 2012; 9:71-83. [PMID: 22292825 DOI: 10.1586/epr.11.71] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Phosphoproteomics is often aimed at deciphering the modified components of signaling pathways in certain organisms, tissues and pathologies. Phosphorylation of housekeeping proteins, albeit important, usually attracts less attention. Here, we provide targeted analysis of eukaryotic translation elongation factor 1A (eEF1A), which is the main element of peptide elongation machinery. There are 97% homologous A1 and A2 isoforms of eEF1A; their expression in mammalian tissues is mutually exclusive and differentially regulated in development. The A2 isoform reveals proto-oncogenic properties and specifically interacts with some cellular proteins. Several tyrosine residues shown experimentally to be phosphorylated in eEF1A1 are hardly solution accessible, so their phosphorylation could be linked with structural rearrangement of the protein molecule. The possible role of tyrosine phosphorylation in providing the background for structural differences between the 'extended' A1 isoform and the compact oncogenic A2 isoform is discussed. The 'road map' for targeted analysis of any protein of interest using phosphoproteomics data is presented.
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Affiliation(s)
- Boris Negrutskii
- Institute of Molecular Biology & Genetics, National Academy of Sciences of Ukraine, Kiev, 03680, Ukraine.
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Shan Y, Eastwood M, Zhang X, Kim E, Arkhipov A, Dror R, Jumper J, Kuriyan J, Shaw D. Oncogenic Mutations Counteract Intrinsic Disorder in the EGFR Kinase and Promote Receptor Dimerization. Cell 2012; 149:860-70. [DOI: 10.1016/j.cell.2012.02.063] [Citation(s) in RCA: 219] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Revised: 01/20/2012] [Accepted: 02/23/2012] [Indexed: 10/28/2022]
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Gajadhar AS, Bogdanovic E, Muñoz DM, Guha A. In Situ Analysis of Mutant EGFRs Prevalent in Glioblastoma Multiforme Reveals Aberrant Dimerization, Activation, and Differential Response to Anti-EGFR Targeted Therapy. Mol Cancer Res 2012; 10:428-40. [DOI: 10.1158/1541-7786.mcr-11-0531] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Single-cell proteomic chip for profiling intracellular signaling pathways in single tumor cells. Proc Natl Acad Sci U S A 2011; 109:419-24. [PMID: 22203961 DOI: 10.1073/pnas.1110865109] [Citation(s) in RCA: 252] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
We describe a microchip designed to quantify the levels of a dozen cytoplasmic and membrane proteins from single cells. We use the platform to assess protein-protein interactions associated with the EGF-receptor-mediated PI3K signaling pathway. Single-cell sensitivity is achieved by isolating a defined number of cells (n = 0-5) in 2 nL volume chambers, each of which is patterned with two copies of a miniature antibody array. The cells are lysed on-chip, and the levels of released proteins are assayed using the antibody arrays. We investigate three isogenic cell lines representing the cancer glioblastoma multiforme, at the basal level, under EGF stimulation, and under erlotinib inhibition plus EGF stimulation. The measured protein abundances are consistent with previous work, and single-cell analysis uniquely reveals single-cell heterogeneity, and different types and strengths of protein-protein interactions. This platform helps provide a comprehensive picture of altered signal transduction networks in tumor cells and provides insight into the effect of targeted therapies on protein signaling networks.
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Affiliation(s)
- Carol L Nilsson
- Department of Pharmacology & Toxicology, University of Texas Medical Branch, 301 University Blvd., Galveston, Texas 77555-0617, United States.
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36
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Identification of an exon 4-deletion variant of epidermal growth factor receptor with increased metastasis-promoting capacity. Neoplasia 2011; 13:461-71. [PMID: 21532887 DOI: 10.1593/neo.101744] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Revised: 01/27/2011] [Accepted: 02/01/2011] [Indexed: 12/28/2022] Open
Abstract
Several types of epidermal growth factor receptor (EGFR) gene alternations have been observed in human tumors. Here we present a novel EGFR variant with aberrant splicing of exon 4 (named as de4 EGFR). Variant-specific polymerase chain reaction showed that de4 EGFR was expressed in some glioma (4/40), prostate cancer (3/11), and ovarian cancer (3/9) tissues but not in tissues adjacent to tumors or normal tissues. de4 EGFR displayed an enhanced transformation and a higher metastasis-promoting capacity in comparison to wild-type EGFR. With minimal EGF-binding activity, de4 EGFR underwent ligand-independent autophosphorylation and self-dimerization. Moreover, in serum-starved condition, de4 EGFR expression in U87 MG cells significantly upregulated the extracellular signal-regulated kinase and AKT phosphorylation and expression of JUN and Src. Importantly, E-cadherin expression was barely detectable in the U87 MG cells expressing de4 EGFR and restored expression of E-cadherin in these cells inhibited their metastatic behaviors. Taken together, we identified a novel EGFR variant with increased metastasis-promoting activity that may become a promising new target for cancer therapy.
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Zoumaro-Djayoon AD, Heck AJR, Muñoz J. Targeted analysis of tyrosine phosphorylation by immuno-affinity enrichment of tyrosine phosphorylated peptides prior to mass spectrometric analysis. Methods 2011; 56:268-74. [PMID: 21945579 DOI: 10.1016/j.ymeth.2011.09.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Revised: 09/08/2011] [Accepted: 09/09/2011] [Indexed: 01/18/2023] Open
Abstract
Tyrosine phosphorylation is a key process that regulates seminal biological functions, hence, deregulation of this mechanism is an underlying cause of several diseases including cancer and immunological disorders. Due to its low abundance, tyrosine phosphorylation is typically under-represented in most of the global MS-based phosphoproteomic studies. Here, we describe a selective approach based on immuno-affinity purification using specific antibodies to enrich tyrosine phosphorylated peptides from a complex proteolytic digest. LC-MS/MS analysis is subsequently used for peptide identification allowing the exact localization of the phosphorylated residue within the sequence. Using this approach more than 1000 non-redundant phosphotyrosine peptides can be identified in less than 6h of MS analysis, reflecting the high sensitivity and specificity of the technique. The identified tyrosine phosphorylated peptides can be used to study different biological aspects of tyrosine signaling and disease.
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Affiliation(s)
- Adja D Zoumaro-Djayoon
- Biomolecular Mass and Spectrometry and Proteomics Group, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands
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38
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Ymer SI, Greenall SA, Cvrljevic A, Cao DX, Donoghue JF, Epa VC, Scott AM, Adams TE, Johns TG. Glioma Specific Extracellular Missense Mutations in the First Cysteine Rich Region of Epidermal Growth Factor Receptor (EGFR) Initiate Ligand Independent Activation. Cancers (Basel) 2011; 3:2032-49. [PMID: 24212795 PMCID: PMC3757403 DOI: 10.3390/cancers3022032] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Revised: 03/29/2011] [Accepted: 04/07/2011] [Indexed: 02/04/2023] Open
Abstract
The epidermal growth factor receptor (EGFR) is overexpressed or mutated in glioma. Recently, a series of missense mutations in the extracellular domain (ECD) of EGFR were reported in glioma patients. Some of these mutations clustered within a cysteine-rich region of the EGFR targeted by the therapeutic antibody mAb806. This region is only exposed when EGFR activates and appears to locally misfold during activation. We expressed two of these mutations (R324L and E330K) in NR6 mouse fibroblasts, as they do not express any EGFR-related receptors. Both mutants were autophosphorylated in the absence of ligand and enhanced cell survival and anchorage-independent and xenograft growth. The ECD truncation that produces the de2-7EGFR (or EGFRvIII), the most common EGFR mutation in glioma, generates a free cysteine in this same region. Using a technique optimized for detecting disulfide-bonded dimers, we definitively demonstrated that the de2-7EGFR is robustly dimerized and that ablation of the free cysteine prevents dimerization and activation. Modeling of the R324L mutation suggests it may cause transient breaking of disulfide bonds, leading to similar disulfide-bonded dimers as seen for the de2-7EGFR. These ECD mutations confirm that the cysteine-rich region of EGFR around the mAb806 epitope has a significant role in receptor activation.
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Affiliation(s)
- Susie I. Ymer
- Oncogenic Signaling Laboratory, Monash Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; E-Mails: (S.I.Y.), (S.A.G.), (A.G.)
| | - Sameer A. Greenall
- Oncogenic Signaling Laboratory, Monash Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; E-Mails: (S.I.Y.), (S.A.G.), (A.G.)
| | - Anna Cvrljevic
- Oncogenic Signaling Laboratory, Monash Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; E-Mails: (S.I.Y.), (S.A.G.), (A.G.)
| | - Diana X. Cao
- Tumor Targeting Laboratory, Ludwig Institute for Cancer Research, Heidelberg, VIC 3084, Australia; E-Mails: (D.X.C.), (A.M.S.)
| | - Jacqui F. Donoghue
- Oncogenic Signaling Laboratory, Monash Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; E-Mails: (S.I.Y.), (S.A.G.), (A.G.)
| | - V. Chandana Epa
- CSIRO Division of Materials Science and Engineering, Parkville, VIC 3052, Australia; E-Mails: (V.C.E.); (T.E.A.)
| | - Andrew M. Scott
- Tumor Targeting Laboratory, Ludwig Institute for Cancer Research, Heidelberg, VIC 3084, Australia; E-Mails: (D.X.C.), (A.M.S.)
| | - Timothy E. Adams
- CSIRO Division of Materials Science and Engineering, Parkville, VIC 3052, Australia; E-Mails: (V.C.E.); (T.E.A.)
| | - Terrance G. Johns
- Oncogenic Signaling Laboratory, Monash Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; E-Mails: (S.I.Y.), (S.A.G.), (A.G.)
- Author to whom correspondence should be addressed; E-Mail: Tel: +613-9594-7247; Fax: +613-9594-7114
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Washburn MP. Driving biochemical discovery with quantitative proteomics. Trends Biochem Sci 2010; 36:170-7. [PMID: 20880711 DOI: 10.1016/j.tibs.2010.09.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2010] [Revised: 08/31/2010] [Accepted: 09/01/2010] [Indexed: 11/26/2022]
Abstract
Proteomic analysis of biological samples plays an increasing role in modern research. Although the application of proteomics technologies varies across many disciplines, proteomics largely is a tool for discovery that then leads to novel hypotheses. In recent years, new methods and technologies have been developed and applied in many areas of proteomics, and there is a strong push towards using proteomics in a quantitative manner. Indeed, mass spectrometry-based, quantitative proteomics approaches have been applied to great success in a variety of biochemical studies. In particular, the use of quantitative proteomics provides new insights into protein complexes and post-translational modifications and leads to the generation of novel insights into these important biochemical systems.
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Affiliation(s)
- Michael P Washburn
- Stowers Institute for Medical Research, Kansas City, 1000 E. 50(th) St., MO 64110, USA.
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