1
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Gerritsen JS, Faraguna JS, Bonavia R, Furnari FB, White FM. Predictive data-driven modeling of C-terminal tyrosine function in the EGFR signaling network. Life Sci Alliance 2023; 6:e202201466. [PMID: 37169593 PMCID: PMC10176108 DOI: 10.26508/lsa.202201466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/30/2023] [Accepted: 05/01/2023] [Indexed: 05/13/2023] Open
Abstract
The epidermal growth factor receptor (EGFR) has been studied extensively because of its critical role in cellular signaling and association with disease. Previous models have elucidated interactions between EGFR and downstream adaptor proteins or showed phenotypes affected by EGFR. However, the link between specific EGFR phosphorylation sites and phenotypic outcomes is still poorly understood. Here, we employed a suite of isogenic cell lines expressing site-specific mutations at each of the EGFR C-terminal phosphorylation sites to interrogate their role in the signaling network and cell biological response to stimulation. Our results demonstrate the resilience of the EGFR network, which was largely similar even in the context of multiple Y-to-F mutations in the EGFR C-terminal tail, while also revealing nodes in the network that have not previously been linked to EGFR signaling. Our data-driven model highlights the signaling network nodes associated with distinct EGF-driven cell responses, including migration, proliferation, and receptor trafficking. Application of this same approach to less-studied RTKs should provide a plethora of novel associations that should lead to an improved understanding of these signaling networks.
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Affiliation(s)
- Jacqueline S Gerritsen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Joseph S Faraguna
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Rudy Bonavia
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Frank B Furnari
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
- Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
- Department of Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Forest M White
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA
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2
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Abstract
Fodrin and its erythroid cell-specific isoform spectrin are actin-associated fibrous proteins that play crucial roles in the maintenance of structural integrity in mammalian cells, which is necessary for proper cell function. Normal cell morphology is altered in diseases such as various cancers and certain neuronal disorders. Fodrin and spectrin are two-chain (αβ) molecules that are encoded by paralogous genes and share many features but also demonstrate certain differences. Fodrin (in humans, typically a heterodimer of the products of the SPTAN1 and SPTBN1 genes) is expressed in nearly all cell types and is especially abundant in neuronal tissues, whereas spectrin (in humans, a heterodimer of the products of the SPTA1 and SPTB1 genes) is expressed almost exclusively in erythrocytes. To fulfill a role in such a variety of different cell types, it was anticipated that fodrin would need to be a more versatile scaffold than spectrin. Indeed, as summarized here, domains unique to fodrin and its regulation by Ca2+, calmodulin, and a variety of posttranslational modifications (PTMs) endow fodrin with additional specific functions. However, how fodrin structural variations and misregulated PTMs may contribute to the etiology of various cancers and neurodegenerative diseases needs to be further investigated.
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3
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Annunziata MC, Parisi M, Esposito G, Fabbrocini G, Ammendola R, Cattaneo F. Phosphorylation Sites in Protein Kinases and Phosphatases Regulated by Formyl Peptide Receptor 2 Signaling. Int J Mol Sci 2020; 21:ijms21113818. [PMID: 32471307 PMCID: PMC7312799 DOI: 10.3390/ijms21113818] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 05/22/2020] [Accepted: 05/25/2020] [Indexed: 12/19/2022] Open
Abstract
FPR1, FPR2, and FPR3 are members of Formyl Peptides Receptors (FPRs) family belonging to the GPCR superfamily. FPR2 is a low affinity receptor for formyl peptides and it is considered the most promiscuous member of this family. Intracellular signaling cascades triggered by FPRs include the activation of different protein kinases and phosphatase, as well as tyrosine kinase receptors transactivation. Protein kinases and phosphatases act coordinately and any impairment of their activation or regulation represents one of the most common causes of several human diseases. Several phospho-sites has been identified in protein kinases and phosphatases, whose role may be to expand the repertoire of molecular mechanisms of regulation or may be necessary for fine-tuning of switch properties. We previously performed a phospho-proteomic analysis in FPR2-stimulated cells that revealed, among other things, not yet identified phospho-sites on six protein kinases and one protein phosphatase. Herein, we discuss on the selective phosphorylation of Serine/Threonine-protein kinase N2, Serine/Threonine-protein kinase PRP4 homolog, Serine/Threonine-protein kinase MARK2, Serine/Threonine-protein kinase PAK4, Serine/Threonine-protein kinase 10, Dual specificity mitogen-activated protein kinase kinase 2, and Protein phosphatase 1 regulatory subunit 14A, triggered by FPR2 stimulation. We also describe the putative FPR2-dependent signaling cascades upstream to these specific phospho-sites.
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Affiliation(s)
- Maria Carmela Annunziata
- Department of Clinical Medicine and Surgery, School of Medicine, University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy; (M.C.A.); (M.P.); (G.F.)
| | - Melania Parisi
- Department of Clinical Medicine and Surgery, School of Medicine, University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy; (M.C.A.); (M.P.); (G.F.)
| | - Gabriella Esposito
- Department of Molecular Medicine and Medical Biotechnology, School of Medicine, University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy; (G.E.); (R.A.)
| | - Gabriella Fabbrocini
- Department of Clinical Medicine and Surgery, School of Medicine, University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy; (M.C.A.); (M.P.); (G.F.)
| | - Rosario Ammendola
- Department of Molecular Medicine and Medical Biotechnology, School of Medicine, University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy; (G.E.); (R.A.)
| | - Fabio Cattaneo
- Department of Molecular Medicine and Medical Biotechnology, School of Medicine, University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy; (G.E.); (R.A.)
- Correspondence: ; Fax: +39-081-7464-359
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4
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Misra P, Singh S. Role of cytokines in combinatorial immunotherapeutics of non-small cell lung cancer through systems perspective. Cancer Med 2019; 8:1976-1995. [PMID: 30997737 PMCID: PMC6536974 DOI: 10.1002/cam4.2112] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 02/22/2019] [Accepted: 03/07/2019] [Indexed: 12/21/2022] Open
Abstract
Lung cancer is the leading cause of deaths related to cancer and accounts for more than a million deaths per year. Various new strategies have been developed and adapted for treatment; still the survival for 5 years is just 16% in patients with non‐small cell lung cancer (NSCLC). Most of these strategies to combat NSCLC whether it is a drug molecule or immunotherapy/vaccine candidate require a big cost and time. Integration of computational modeling with systems biology has opened new avenues for understanding complex cancer biology. Resolving the complex interactions of various pathways and their crosstalk leading to oncogenic changes could identify new therapeutic targets with lesser cost and time. Herein, this review provides an overview of various aspects of NSCLC along with available strategies for its cure concluding with our insight into how systems approach could serve as a therapeutic intervention dissecting the immunologic parameters and cross talk between various pathways involved.
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Affiliation(s)
- Pragya Misra
- National Centre for Cell ScienceSP Pune University CampusPuneIndia
| | - Shailza Singh
- National Centre for Cell ScienceSP Pune University CampusPuneIndia
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Awasthi S, Maity T, Oyler BL, Qi Y, Zhang X, Goodlett DR, Guha U. Quantitative targeted proteomic analysis of potential markers of tyrosine kinase inhibitor (TKI) sensitivity in EGFR mutated lung adenocarcinoma. J Proteomics 2018; 189:48-59. [PMID: 29660496 DOI: 10.1016/j.jprot.2018.04.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 03/25/2018] [Accepted: 04/03/2018] [Indexed: 01/03/2023]
Abstract
Lung cancer causes the highest mortality among all cancers. Patients harboring kinase domain mutations in the epidermal growth factor receptor (EGFR) respond to EGFR tyrosine kinase inhibitors (TKIs), however, acquired resistance always develops. Moreover, 30-40% of patients with EGFR mutations exhibit primary resistance. Hence, there is an unmet need for additional biomarkers of TKI sensitivity that complement EGFR mutation testing and predict treatment response. We previously identified phosphopeptides whose phosphorylation is inhibited upon treatment with EGFR TKIs, erlotinib and afatinib in TKI sensitive cells, but not in resistant cells. These phosphosites are potential biomarkers of TKI sensitivity. Here, we sought to develop modified immuno-multiple reaction monitoring (immuno-MRM)-based quantitation assays for select phosphosites including EGFR-pY1197, pY1172, pY998, AHNAK-pY160, pY715, DAPP1-pY139, CAV1-pY14, INPPL1-pY1135, NEDD9-pY164, NF1-pY2579, and STAT5A-pY694. These sites were significantly hypophosphorylated by erlotinib and a 3rd generation EGFR TKI, osimertinib, in TKI-sensitive H3255 cells, which harbor the TKI-sensitizing EGFRL858R mutation. However, in H1975 cells, which harbor the TKI-resistant EGFRL858R/T790M mutant, osimertinib, but not erlotinib, could significantly inhibit phosphorylation of EGFR-pY-1197, STAT5A-pY694 and CAV1-pY14, suggesting these sites also predict response in TKI-resistant cells. We could further validate EGFR-pY-1197 as a biomarker of TKI sensitivity by developing a calibration curve-based modified immuno-MRM assay. SIGNIFICANCE: In this report, we have shown the development and optimization of MRM assays coupled with global phosphotyrosine enrichment (modified immuno-MRM) for a list of 11 phosphotyrosine peptides. Our optimized assays identified the targets reproducibly in biological samples with good selectivity. We also developed and characterized quantitation methods to determine endogenous abundance of these targets and correlated the results of the relative quantification with amounts estimated from the calibration curves. This approach represents a way to validate and verify biomarker candidates discovered from large-scale global phospho-proteomics analysis. The application of these modified immuno-MRM assays in lung adenocarcinoma cells provides proof-of concept for the feasibility of clinical applications. These assays may be used in prospective clinical studies of EGFR TKI treatment of EGFR mutant lung cancer to correlate treatment response and other clinical endpoints.
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Affiliation(s)
- Shivangi Awasthi
- Thoracic & Gastrointestinal Oncology Branch, Center for Cancer Research, NCI, Bethesda, MD, United States; School of Pharmacy, University of Maryland, Baltimore, MD, United States
| | - Tapan Maity
- Thoracic & Gastrointestinal Oncology Branch, Center for Cancer Research, NCI, Bethesda, MD, United States
| | - Benjamin L Oyler
- School of Medicine, University of Maryland, Baltimore, MD, United States
| | - Yue Qi
- Thoracic & Gastrointestinal Oncology Branch, Center for Cancer Research, NCI, Bethesda, MD, United States
| | - Xu Zhang
- Thoracic & Gastrointestinal Oncology Branch, Center for Cancer Research, NCI, Bethesda, MD, United States
| | - David R Goodlett
- School of Pharmacy, University of Maryland, Baltimore, MD, United States
| | - Udayan Guha
- Thoracic & Gastrointestinal Oncology Branch, Center for Cancer Research, NCI, Bethesda, MD, United States.
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6
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Kenney RM, Lloyd CC, Whitman NA, Lockett MR. 3D cellular invasion platforms: how do paper-based cultures stack up? Chem Commun (Camb) 2018. [PMID: 28621775 DOI: 10.1039/c7cc02357j] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Cellular invasion is the gateway to metastasis, which is the leading cause of cancer-related deaths. Invasion is driven by a number of chemical and mechanical stresses that arise in the tumor microenvironment. In vitro assays are needed for the systematic study of cancer progress. To be truly predictive, these assays must generate tissue-like environments that can be experimentally controlled and manipulated. While two-dimensional (2D) monolayer cultures are easily assembled and evaluated, they lack the extracellular components needed to assess invasion. Three-dimensional (3D) cultures are better suited for invasion studies because they generate cellular phenotypes that are more representative of those found in vivo. This feature article provides an overview of four invasion platforms. We focus on paper-based cultures, an emerging 3D culture platform capable of generating tissue-like structures and quantifying cellular invasion. Paper-based cultures are as easily assembled and analyzed as monolayers, but provide an experimentally powerful platform capable of supporting: co-cultures and representative extracellular environments; experimentally controlled gradients; readouts capable of quantifying, discerning, and separating cells based on their invasiveness. With a series of examples we highlight the potential of paper-based cultures, and discuss how they stack up against other invasion platforms.
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Affiliation(s)
- Rachael M Kenney
- Department of Chemistry, University of North Carolina at Chapel Hill, Kenan and Caudill Laboratories, 125 South Road, Chapel Hill, NC 27599-3290, USA.
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Dou H, Yan Z, Zhang M, Xu X. APRIL promotes non-small cell lung cancer growth and metastasis by targeting ERK1/2 signaling. Oncotarget 2017; 8:109289-109300. [PMID: 29312608 PMCID: PMC5752521 DOI: 10.18632/oncotarget.22672] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 11/09/2017] [Indexed: 12/12/2022] Open
Abstract
Non-small-cell lung cancer (NSCLC) is the major subtype of lung cancer, which is the most common cause of cancer-related mortality in the world. It is a complex disease involving multiple genetic alterations. As a cytokine belonging to the Tumor Necrosis Factor-α (TNF- α) family, the - a proliferation-inducing ligand (APRIL) expression and its signaling have been studied in many human solid tumor types, but the data on APRIL signaling in NSCLC are lacking. The aim of this study was to evaluate the APRIL expression and investigate its signaling in NSCLC. The expression of APRIL and its receptors, B cell maturation antigen (BCMA) and transmembrane activator and calcium-modulatorand cyclophilin ligand interactor (TACI), was analyzed by using immunohistochemistry in NSCLC samples. Quantitative RT-PCR was performed to evaluate mRNA expression of APRIL, BCMA and TACI in human lung adenocarcinoma cell lines A549, H1299, and H1650. Cell proliferation was measured by using the cell proliferation and cytotoxicity assay kit 8 (CCK8) assay, cell migration by using wound healing assay, and cell invasion by using transwall assay. The protein level of APRIL, BCMA and TAC, and the activation of extracellular regulated protein kinases 1/2 (ERK1/2) signaling, were determined by western blot. Our results indicated, APRIL and its receptors BCMA and TACI, were overexpressed in most of human NSCLC samples and cell lines; APRIL promoted tumor proliferation, migration and metastasis in A549 and H1299 cells via BCMA and TACI. Furthermore, ERK1/2 activation was involved in APRIL signaling through TACI but not BCMA in A549 and H1299 cells. APRIL might serve as a potential prognostic biomarker for NSCLC, and APRIL related signaling pathway could be a therapeutic target for NSCLC.
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Affiliation(s)
- Hengli Dou
- Department of Neurosurgery, The Fourth Hospital of Jinan, Jinan 250013, Shandong, China
| | - Zhaohua Yan
- Department of Neurosurgery, The Fourth Hospital of Jinan, Jinan 250013, Shandong, China
| | - Meng Zhang
- Department of Neurosurgery, The Fourth Hospital of Jinan, Jinan 250013, Shandong, China
| | - Xiaoxin Xu
- Department of Neurosurgery, The Fourth Hospital of Jinan, Jinan 250013, Shandong, China
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8
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Oweida A, Sharifi Z, Halabi H, Xu Y, Sabri S, Abdulkarim B. Differential response to ablative ionizing radiation in genetically distinct non-small cell lung cancer cells. Cancer Biol Ther 2017; 17:390-9. [PMID: 27096542 DOI: 10.1080/15384047.2016.1139241] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Stereotactic ablative radiotherapy (SABR) has emerged as a highly promising treatment for medically inoperable early-stage non-small cell lung cancer patients. Treatment outcomes after SABR have been excellent compared to conventional fractionated radiotherapy (CFRT). However, the biological determinants of the response to ablative doses of radiation remain poorly characterized. Furthermore, there's little data on the cellular and molecular response of genetically distinct NSCLC subtypes to radiation. We assessed the response of 3 genetically distinct lung adenocarcinoma cell lines to ablative and fractionated ionizing radiation (AIR and FIR). We studied clonogenic survival, cell proliferation, migration, invasion, apoptosis and senescence. We also investigated the effect of AIR and FIR on the expression of pro-invasive proteins, epithelial-to-mesenchymal transition (EMT), extracellular signal-regulated kinases (ERK1/2) and the transmembrane receptor cMET. Our findings reveal that AIR significantly reduced cell proliferation and clonogenic survival compared to FIR in A549 cells only. This differential response was not observed in HCC827 or H1975 cells. AIR significantly enhanced the invasiveness of A549 cells, but not HCC827 or H1975 cells compared to FIR. Molecular analysis of pathways involved in cell proliferation and invasion revealed that AIR significantly reduced phosphorylation of ERK1/2 and upregulated cMET expression in A549 cells. Our results show a differential proliferative and invasive response to AIR that is dependent on genetic subtype and independent of intrinsic radioresistance. Further examination of these findings in a larger panel of NSCLC cell lines and in pre-clinical models is warranted for identification of biomarkers of tumor response to AIR.
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Affiliation(s)
- Ayman Oweida
- a Department of Oncology , McGill University , Montreal , Quebec , Canada
| | - Zeinab Sharifi
- a Department of Oncology , McGill University , Montreal , Quebec , Canada
| | - Hani Halabi
- a Department of Oncology , McGill University , Montreal , Quebec , Canada
| | - Yaoxian Xu
- a Department of Oncology , McGill University , Montreal , Quebec , Canada
| | - Siham Sabri
- a Department of Oncology , McGill University , Montreal , Quebec , Canada
| | - Bassam Abdulkarim
- a Department of Oncology , McGill University , Montreal , Quebec , Canada
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9
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Diaz JE, Morgan CW, Minogue CE, Hebert AS, Coon JJ, Wells JA. A Split-Abl Kinase for Direct Activation in Cells. Cell Chem Biol 2017; 24:1250-1258.e4. [PMID: 28919041 DOI: 10.1016/j.chembiol.2017.08.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 06/15/2017] [Accepted: 08/02/2017] [Indexed: 12/18/2022]
Abstract
To dissect the cellular roles of individual kinases, it is useful to design tools for their selective activation. We describe the engineering of a split-cAbl kinase (sKin-Abl) that is rapidly activated in cells with rapamycin and allows temporal, dose, and compartmentalization control. Our design strategy involves an empirical screen in mammalian cells and identification of split site in the N lobe. This split site leads to complete loss of activity, which can be restored upon small-molecule-induced dimerization in cells. Remarkably, the split site is transportable to the related Src Tyr kinase and the distantly related Ser/Thr kinase, AKT, suggesting broader applications to kinases. To quantify the fold induction of phosphotyrosine (pTyr) modification, we employed quantitative proteomics, NeuCode SILAC. We identified a number of known Abl substrates, including autophosphorylation sites and novel pTyr targets, 432 pTyr sites in total. We believe that this split-kinase technology will be useful for direct activation of protein kinases in cells.
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Affiliation(s)
- Juan E Diaz
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Charles W Morgan
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | | | | | - Joshua J Coon
- Department of Chemistry, University of Wisconsin, Madison, WI 53706, USA; Genome Center of Wisconsin, Madison, WI 53706, USA; Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53706, USA; Morgridge Institute for Research, Madison, WI 53706, USA
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA; Department of Cellular & Molecular Pharmacology, University of California, San Francisco, CA 94158, USA.
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10
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Dong M, Bian Y, Wang Y, Dong J, Yao Y, Deng Z, Qin H, Zou H, Ye M. Sensitive, Robust, and Cost-Effective Approach for Tyrosine Phosphoproteome Analysis. Anal Chem 2017; 89:9307-9314. [DOI: 10.1021/acs.analchem.7b02078] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Mingming Dong
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yangyang Bian
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
- Medical Research Center, The First Affiliated
Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Yan Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Dong
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
| | - Yating Yao
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhenzhen Deng
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongqiang Qin
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
| | - Hanfa Zou
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
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11
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Stichel D, Middleton AM, Müller BF, Depner S, Klingmüller U, Breuhahn K, Matthäus F. An individual-based model for collective cancer cell migration explains speed dynamics and phenotype variability in response to growth factors. NPJ Syst Biol Appl 2017. [PMID: 28649432 PMCID: PMC5460121 DOI: 10.1038/s41540-017-0006-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Collective cell migration is a common phenotype in epithelial cancers, which is associated with tumor cell metastasis and poor patient survival. However, the interplay between physiologically relevant pro-migratory stimuli and the underlying mechanical cell–cell interactions are poorly understood. We investigated the migratory behavior of different collectively migrating non-small cell lung cancer cell lines in response to motogenic growth factors (e.g. epidermal growth factor) or clinically relevant small compound inhibitors. Depending on the treatment, we observed distinct behaviors in a classical lateral migration assay involving traveling fronts, finger-shapes or the development of cellular bridges. Particle image velocimetry analysis revealed characteristic speed dynamics (evolution of the average speed of all cells in a frame) in all experiments exhibiting initial acceleration and subsequent deceleration of the cell populations. To better understand the mechanical properties of individual cells leading to the observed speed dynamics and the phenotypic differences we developed a mathematical model based on a Langevin approach. This model describes intercellular forces, random motility, and stimulation of active migration by mechanical interaction between cells. Simulations show that the model is able to reproduce the characteristic spatio-temporal speed distributions as well as most migratory phenotypes of the studied cell lines. A specific strength of the proposed model is that it identifies a small set of mechanical features necessary to explain all phenotypic and dynamical features of the migratory response of non-small cell lung cancer cells to chemical stimulation/inhibition. Furthermore, all processes included in the model can be associated with potential molecular components, and are therefore amenable to experimental validation. Thus, the presented mathematical model may help to predict which mechanical aspects involved in non-small cell lung cancer cell migration are affected by the respective therapeutic treatment. In many cancers, spreading and the formation of metastasis involve the coordinated migration of many cells. An interdisciplinary team of researchers from Heidelberg and Frankfurt studied the collective movement of cultured lung cancer cells subject to chemical stimulation. Based on extensive data analysis a mathematical model was developed to explain the variety of migration behaviors observed under different treatments. The model describes the mechanics of compression, stretch, cell elasticity and force-regulated active motion—which in sum lead to coordination within large cell groups. Simulations demonstrate how these mechanical features affect cell coordination and collective behavior. In tests of potential medical treatment strategies, the model can be used to predict the effects of the drug on specific mechanical properties of single cells.
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Affiliation(s)
- Damian Stichel
- BIOMS/IWR, University of Heidelberg, Im Neuenheimer Feld 267, Heidelberg, 69120 Germany.,DKFZ Heidelberg, KKE Neuropathologie, Im Neuenheimer Feld 221, Heidelberg, 69120 Germany
| | - Alistair M Middleton
- BIOMS/IWR, University of Heidelberg, Im Neuenheimer Feld 267, Heidelberg, 69120 Germany
| | - Benedikt F Müller
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 221, Heidelberg, Germany
| | - Sofia Depner
- DKFZ Heidelberg, KKE Neuropathologie, Im Neuenheimer Feld 221, Heidelberg, 69120 Germany.,Translational Lung Research Center (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - Ursula Klingmüller
- DKFZ Heidelberg, KKE Neuropathologie, Im Neuenheimer Feld 221, Heidelberg, 69120 Germany.,Translational Lung Research Center (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - Kai Breuhahn
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 221, Heidelberg, Germany
| | - Franziska Matthäus
- BIOMS/IWR, University of Heidelberg, Im Neuenheimer Feld 267, Heidelberg, 69120 Germany.,CCTB, University of Würzburg, Campus Hubland Nord 32, Würzburg, 97074 Germany.,FIAS, University of Frankfurt, Ruth-Moufang-Str. 1, Frankfurt am Main, 60438 Germany
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12
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Bourgeois DL, Kreeger PK. Partial Least Squares Regression Models for the Analysis of Kinase Signaling. Methods Mol Biol 2017; 1636:523-533. [PMID: 28730500 DOI: 10.1007/978-1-4939-7154-1_32] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Partial least squares regression (PLSR) is a data-driven modeling approach that can be used to analyze multivariate relationships between kinase networks and cellular decisions or patient outcomes. In PLSR, a linear model relating an X matrix of dependent variables and a Y matrix of independent variables is generated by extracting the factors with the strongest covariation. While the identified relationship is correlative, PLSR models can be used to generate quantitative predictions for new conditions or perturbations to the network, allowing for mechanisms to be identified. This chapter will provide a brief explanation of PLSR and provide an instructive example to demonstrate the use of PLSR to analyze kinase signaling.
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Affiliation(s)
- Danielle L Bourgeois
- Department of Biomedical Engineering, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, WI, 53705, USA
| | - Pamela K Kreeger
- Department of Biomedical Engineering, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, WI, 53705, USA.
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Radhakrishnan A, Nanjappa V, Raja R, Sathe G, Puttamallesh VN, Jain AP, Pinto SM, Balaji SA, Chavan S, Sahasrabuddhe NA, Mathur PP, Kumar MM, Prasad TSK, Santosh V, Sukumar G, Califano JA, Rangarajan A, Sidransky D, Pandey A, Gowda H, Chatterjee A. A dual specificity kinase, DYRK1A, as a potential therapeutic target for head and neck squamous cell carcinoma. Sci Rep 2016; 6:36132. [PMID: 27796319 PMCID: PMC5086852 DOI: 10.1038/srep36132] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 10/10/2016] [Indexed: 12/18/2022] Open
Abstract
Despite advances in clinical management, 5-year survival rate in patients with late-stage head and neck squamous cell carcinoma (HNSCC) has not improved significantly over the past decade. Targeted therapies have emerged as one of the most promising approaches to treat several malignancies. Though tyrosine phosphorylation accounts for a minority of total phosphorylation, it is critical for activation of signaling pathways and plays a significant role in driving cancers. To identify activated tyrosine kinase signaling pathways in HNSCC, we compared the phosphotyrosine profiles of a panel of HNSCC cell lines to a normal oral keratinocyte cell line. Dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A (DYRK1A) was one of the kinases hyperphosphorylated at Tyr-321 in all HNSCC cell lines. Inhibition of DYRK1A resulted in an increased apoptosis and decrease in invasion and colony formation ability of HNSCC cell lines. Further, administration of the small molecular inhibitor against DYRK1A in mice bearing HNSCC xenograft tumors induced regression of tumor growth. Immunohistochemical labeling of DYRK1A in primary tumor tissues using tissue microarrays revealed strong to moderate staining of DYRK1A in 97.5% (39/40) of HNSCC tissues analyzed. Taken together our results suggest that DYRK1A could be a novel therapeutic target in HNSCC.
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Affiliation(s)
- Aneesha Radhakrishnan
- Institute of Bioinformatics, International Technology Park, Bangalore, 560 066, India
- Department of Biochemistry and Molecular Biology, Pondicherry University, Puducherry 605014, India
| | - Vishalakshi Nanjappa
- Institute of Bioinformatics, International Technology Park, Bangalore, 560 066, India
- Amrita School of Biotechnology, Amrita University, Kollam 690 525, India
| | - Remya Raja
- Institute of Bioinformatics, International Technology Park, Bangalore, 560 066, India
| | - Gajanan Sathe
- Institute of Bioinformatics, International Technology Park, Bangalore, 560 066, India
- Manipal University, Madhav Nagar, Manipal 576104, India
| | - Vinuth N. Puttamallesh
- Institute of Bioinformatics, International Technology Park, Bangalore, 560 066, India
- Amrita School of Biotechnology, Amrita University, Kollam 690 525, India
| | - Ankit P. Jain
- Institute of Bioinformatics, International Technology Park, Bangalore, 560 066, India
- School of Biotechnology, KIIT University, Bhubaneswar 751024, India
| | - Sneha M. Pinto
- Institute of Bioinformatics, International Technology Park, Bangalore, 560 066, India
| | - Sai A. Balaji
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, 560012, India
| | - Sandip Chavan
- Institute of Bioinformatics, International Technology Park, Bangalore, 560 066, India
- Manipal University, Madhav Nagar, Manipal 576104, India
| | | | - Premendu P. Mathur
- Department of Biochemistry and Molecular Biology, Pondicherry University, Puducherry 605014, India
- School of Biotechnology, KIIT University, Bhubaneswar 751024, India
| | - Mahesh M. Kumar
- Department of Neuro-Virology, National Institute of Mental Health and Neurosciences, Bangalore 560029, India
| | - T. S. Keshava Prasad
- Institute of Bioinformatics, International Technology Park, Bangalore, 560 066, India
- Amrita School of Biotechnology, Amrita University, Kollam 690 525, India
- YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore 575018, India
| | - Vani Santosh
- Department of Pathology, National Institute of Mental Health and Neurosciences, Bangalore 560029, India
| | - Geethanjali Sukumar
- Institute of Bioinformatics, International Technology Park, Bangalore, 560 066, India
| | - Joseph A. Califano
- Milton J. Dance Head and Neck Center, Greater Baltimore Medical Center, Baltimore, MD 21204, USA
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Annapoorni Rangarajan
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, 560012, India
| | - David Sidransky
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine,Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, Bangalore, 560 066, India
- YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore 575018, India
| | - Aditi Chatterjee
- Institute of Bioinformatics, International Technology Park, Bangalore, 560 066, India
- YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore 575018, India
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14
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Rajadurai CV, Havrylov S, Coelho PP, Ratcliffe CDH, Zaoui K, Huang BH, Monast A, Chughtai N, Sangwan V, Gertler FB, Siegel PM, Park M. 5'-Inositol phosphatase SHIP2 recruits Mena to stabilize invadopodia for cancer cell invasion. J Cell Biol 2016; 214:719-34. [PMID: 27597754 PMCID: PMC5021089 DOI: 10.1083/jcb.201501003] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2015] [Accepted: 08/05/2016] [Indexed: 12/11/2022] Open
Abstract
Invadopodia are membrane protrusions used by cancer cells to remodel and invade the extracellular matrix. Here, Rajadurai et al. show that the lipid phosphatase SHIP2 recruits the Ena/VASP-family actin regulatory protein Mena to stabilize invadopodia membrane protrusions and promote cell invasion. Invadopodia are specialized membrane protrusions that support degradation of extracellular matrix (ECM) by cancer cells, allowing invasion and metastatic spread. Although early stages of invadopodia assembly have been elucidated, little is known about maturation of invadopodia into structures competent for ECM proteolysis. The localized conversion of phosphatidylinositol(3,4,5)-triphosphate and accumulation of phosphatidylinositol(3,4)-bisphosphate at invadopodia is a key determinant for invadopodia maturation. Here we investigate the role of the 5′-inositol phosphatase, SHIP2, and reveal an unexpected scaffold function of SHIP2 as a prerequisite for invadopodia-mediated ECM degradation. Through biochemical and structure-function analyses, we identify specific interactions between SHIP2 and Mena, an Ena/VASP-family actin regulatory protein. We demonstrate that SHIP2 recruits Mena, but not VASP, to invadopodia and that disruption of SHIP2–Mena interaction in cancer cells leads to attenuated capacity for ECM degradation and invasion in vitro, as well as reduced metastasis in vivo. Together, these findings identify SHIP2 as a key modulator of carcinoma invasiveness and a target for metastatic disease.
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Affiliation(s)
- Charles V Rajadurai
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montréal, Québec H3A 1A1, Canada Department of Biochemistry, McGill University, Montréal, Québec H3A 1A1, Canada
| | - Serhiy Havrylov
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montréal, Québec H3A 1A1, Canada
| | - Paula P Coelho
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montréal, Québec H3A 1A1, Canada Department of Biochemistry, McGill University, Montréal, Québec H3A 1A1, Canada
| | - Colin D H Ratcliffe
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montréal, Québec H3A 1A1, Canada Department of Biochemistry, McGill University, Montréal, Québec H3A 1A1, Canada
| | - Kossay Zaoui
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montréal, Québec H3A 1A1, Canada
| | - Bruce H Huang
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montréal, Québec H3A 1A1, Canada Department of Biochemistry, McGill University, Montréal, Québec H3A 1A1, Canada
| | - Anie Monast
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montréal, Québec H3A 1A1, Canada
| | - Naila Chughtai
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montréal, Québec H3A 1A1, Canada
| | - Veena Sangwan
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montréal, Québec H3A 1A1, Canada Department of Oncology, McGill University, Montréal, Québec H3A 1A1, Canada
| | - Frank B Gertler
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139 Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Peter M Siegel
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montréal, Québec H3A 1A1, Canada Department of Biochemistry, McGill University, Montréal, Québec H3A 1A1, Canada Department of Medicine, McGill University, Montréal, Québec H3A 1A1, Canada
| | - Morag Park
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montréal, Québec H3A 1A1, Canada Department of Biochemistry, McGill University, Montréal, Québec H3A 1A1, Canada Department of Medicine, McGill University, Montréal, Québec H3A 1A1, Canada Department of Oncology, McGill University, Montréal, Québec H3A 1A1, Canada
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15
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Lescarbeau RS, Lei L, Bakken KK, Sims PA, Sarkaria JN, Canoll P, White FM. Quantitative Phosphoproteomics Reveals Wee1 Kinase as a Therapeutic Target in a Model of Proneural Glioblastoma. Mol Cancer Ther 2016; 15:1332-43. [PMID: 27196784 PMCID: PMC4893926 DOI: 10.1158/1535-7163.mct-15-0692] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 02/24/2016] [Indexed: 01/09/2023]
Abstract
Glioblastoma (GBM) is the most common malignant primary brain cancer. With a median survival of about a year, new approaches to treating this disease are necessary. To identify signaling molecules regulating GBM progression in a genetically engineered murine model of proneural GBM, we quantified phosphotyrosine-mediated signaling using mass spectrometry. Oncogenic signals, including phosphorylated ERK MAPK, PI3K, and PDGFR, were found to be increased in the murine tumors relative to brain. Phosphorylation of CDK1 pY15, associated with the G2 arrest checkpoint, was identified as the most differentially phosphorylated site, with a 14-fold increase in phosphorylation in the tumors. To assess the role of this checkpoint as a potential therapeutic target, syngeneic primary cell lines derived from these tumors were treated with MK-1775, an inhibitor of Wee1, the kinase responsible for CDK1 Y15 phosphorylation. MK-1775 treatment led to mitotic catastrophe, as defined by increased DNA damage and cell death by apoptosis. To assess the extensibility of targeting Wee1/CDK1 in GBM, patient-derived xenograft (PDX) cell lines were also treated with MK-1775. Although the response was more heterogeneous, on-target Wee1 inhibition led to decreased CDK1 Y15 phosphorylation and increased DNA damage and apoptosis in each line. These results were also validated in vivo, where single-agent MK-1775 demonstrated an antitumor effect on a flank PDX tumor model, increasing mouse survival by 1.74-fold. This study highlights the ability of unbiased quantitative phosphoproteomics to reveal therapeutic targets in tumor models, and the potential for Wee1 inhibition as a treatment approach in preclinical models of GBM. Mol Cancer Ther; 15(6); 1332-43. ©2016 AACR.
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Affiliation(s)
- Rebecca S Lescarbeau
- Department of Biological Engineering and David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Liang Lei
- Department of Pathology and Cell Biology and Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York
| | - Katrina K Bakken
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | - Peter A Sims
- Department of Systems Biology and Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York
| | - Jann N Sarkaria
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | - Peter Canoll
- Department of Pathology and Cell Biology and Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York
| | - Forest M White
- Department of Biological Engineering and David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts.
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16
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Lescarbeau RS, Lei L, Bakken KK, Sims PA, Sarkaria JN, Canoll P, White FM. Quantitative Phosphoproteomics Reveals Wee1 Kinase as a Therapeutic Target in a Model of Proneural Glioblastoma. Mol Cancer Ther 2016. [PMID: 27196784 DOI: 10.1158/1535-7163.mct-15-0692-t] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Glioblastoma (GBM) is the most common malignant primary brain cancer. With a median survival of about a year, new approaches to treating this disease are necessary. To identify signaling molecules regulating GBM progression in a genetically engineered murine model of proneural GBM, we quantified phosphotyrosine-mediated signaling using mass spectrometry. Oncogenic signals, including phosphorylated ERK MAPK, PI3K, and PDGFR, were found to be increased in the murine tumors relative to brain. Phosphorylation of CDK1 pY15, associated with the G2 arrest checkpoint, was identified as the most differentially phosphorylated site, with a 14-fold increase in phosphorylation in the tumors. To assess the role of this checkpoint as a potential therapeutic target, syngeneic primary cell lines derived from these tumors were treated with MK-1775, an inhibitor of Wee1, the kinase responsible for CDK1 Y15 phosphorylation. MK-1775 treatment led to mitotic catastrophe, as defined by increased DNA damage and cell death by apoptosis. To assess the extensibility of targeting Wee1/CDK1 in GBM, patient-derived xenograft (PDX) cell lines were also treated with MK-1775. Although the response was more heterogeneous, on-target Wee1 inhibition led to decreased CDK1 Y15 phosphorylation and increased DNA damage and apoptosis in each line. These results were also validated in vivo, where single-agent MK-1775 demonstrated an antitumor effect on a flank PDX tumor model, increasing mouse survival by 1.74-fold. This study highlights the ability of unbiased quantitative phosphoproteomics to reveal therapeutic targets in tumor models, and the potential for Wee1 inhibition as a treatment approach in preclinical models of GBM. Mol Cancer Ther; 15(6); 1332-43. ©2016 AACR.
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Affiliation(s)
- Rebecca S Lescarbeau
- Department of Biological Engineering and David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Liang Lei
- Department of Pathology and Cell Biology and Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York
| | - Katrina K Bakken
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | - Peter A Sims
- Department of Systems Biology and Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York
| | - Jann N Sarkaria
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | - Peter Canoll
- Department of Pathology and Cell Biology and Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York
| | - Forest M White
- Department of Biological Engineering and David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts.
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17
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Kim HJ, Lin D, Lee HJ, Li M, Liebler DC. Quantitative Profiling of Protein Tyrosine Kinases in Human Cancer Cell Lines by Multiplexed Parallel Reaction Monitoring Assays. Mol Cell Proteomics 2015; 15:682-91. [PMID: 26631510 DOI: 10.1074/mcp.o115.056713] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Indexed: 12/12/2022] Open
Abstract
Protein tyrosine kinases (PTKs) play key roles in cellular signal transduction, cell cycle regulation, cell division, and cell differentiation. Dysregulation of PTK-activated pathways, often by receptor overexpression, gene amplification, or genetic mutation, is a causal factor underlying numerous cancers. In this study, we have developed a parallel reaction monitoring-based assay for quantitative profiling of 83 PTKs. The assay detects 308 proteotypic peptides from 54 receptor tyrosine kinases and 29 nonreceptor tyrosine kinases in a single run. Quantitative comparisons were based on the labeled reference peptide method. We implemented the assay in four cell models: 1) a comparison of proliferating versus epidermal growth factor-stimulated A431 cells, 2) a comparison of SW480Null (mutant APC) and SW480APC (APC restored) colon tumor cell lines, and 3) a comparison of 10 colorectal cancer cell lines with different genomic abnormalities, and 4) lung cancer cell lines with either susceptibility (11-18) or acquired resistance (11-18R) to the epidermal growth factor receptor tyrosine kinase inhibitor erlotinib. We observed distinct PTK expression changes that were induced by stimuli, genomic features or drug resistance, which were consistent with previous reports. However, most of the measured expression differences were novel observations. For example, acquired resistance to erlotinib in the 11-18 cell model was associated not only with previously reported up-regulation of MET, but also with up-regulation of FLK2 and down-regulation of LYN and PTK7. Immunoblot analyses and shotgun proteomics data were highly consistent with parallel reaction monitoring data. Multiplexed parallel reaction monitoring assays provide a targeted, systems-level profiling approach to evaluate cancer-related proteotypes and adaptations. Data are available through Proteome eXchange Accession PXD002706.
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Affiliation(s)
- Hye-Jung Kim
- From the ‡Jim Ayers Institute for Precancer Detection and Diagnosis and Departments of §Biochemistry and
| | - De Lin
- From the ‡Jim Ayers Institute for Precancer Detection and Diagnosis and Departments of §Biochemistry and
| | - Hyoung-Joo Lee
- From the ‡Jim Ayers Institute for Precancer Detection and Diagnosis and Departments of §Biochemistry and
| | - Ming Li
- ¶Biostatistics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Daniel C Liebler
- From the ‡Jim Ayers Institute for Precancer Detection and Diagnosis and Departments of §Biochemistry and
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18
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Chen L, Li C, Zhu Y. The HGF inhibitory peptide HGP-1 displays promising in vitro and in vivo efficacy for targeted cancer therapy. Oncotarget 2015; 6:30088-101. [PMID: 26254225 PMCID: PMC4745783 DOI: 10.18632/oncotarget.3937] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 04/28/2015] [Indexed: 12/15/2022] Open
Abstract
HGF/MET pathway mediates cancer initiation and development. Thus, inhibition on HGF-initiated MET signaling pathway would provide a new approach to cancer targeted therapeutics. In our study, we identified a targeting peptide candidate binding to HGF which was named HGF binding peptide-1 (HGP-1) via bacterial surface display methods coupled with fluorescence-activated cell sorting (FACS). HGP-1 showed the moderate affinity when determined with surface plasmon resonance (SPR) technique and high specificity in binding to HGF while assessed by fluorescence-based ELISA assay. The results from MTT and in vitro migration assay indicated that HGF-dependent cell proliferation and migration could be inhibited by HGP-1. In vivo administration of HGP-1 led to an effective inhibitory effect on tumor growth in A549 tumor xenograft models. Moreover, findings from Western Blots revealed that HGP-1 could down-regulated the phosphorylation levels of MET and ERK1/2 initiated by HGF, which suggested that HGP-1 could disrupt the activation of HGF/MET signaling to influence the cell activity. All the data highlighted the potential of HGP-1 to be a potent inhibitor for HGF/MET signaling.
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Affiliation(s)
- Lisha Chen
- Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China.,Suzhou Institute of Nano-Tech and Nano-Bionics, CAS, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunlin Li
- Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China.,Suzhou Institute of Nano-Tech and Nano-Bionics, CAS, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yimin Zhu
- Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
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19
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Adaptive protein and phosphoprotein networks which promote therapeutic sensitivity or acquired resistance. Biochem Soc Trans 2015; 42:758-64. [PMID: 25109954 DOI: 10.1042/bst20140038] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Despite the emergence of dozens of oncogenic targets and corresponding molecularly targeted therapies, in most cases tumours continue to progress or recur due to therapeutic resistance. In the present review, we highlight the ability of MS-based phosphoproteomics to quantify oncogenic signalling networks driving tumour growth and invasion, as well as those networks enabling tumour cell survival in the presence of chemotherapeutics. Quantitative protein phosphorylation profiling will facilitate the design and development of optimal therapeutic strategies targeting the initial tumour while simultaneously blocking the predominant resistance mechanisms.
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20
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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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