101
|
Lisabeth EM, Falivelli G, Pasquale EB. Eph receptor signaling and ephrins. Cold Spring Harb Perspect Biol 2013; 5:5/9/a009159. [PMID: 24003208 DOI: 10.1101/cshperspect.a009159] [Citation(s) in RCA: 292] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The Eph receptors are the largest of the RTK families. Like other RTKs, they transduce signals from the cell exterior to the interior through ligand-induced activation of their kinase domain. However, the Eph receptors also have distinctive features. Instead of binding soluble ligands, they generally mediate contact-dependent cell-cell communication by interacting with surface-associated ligands-the ephrins-on neighboring cells. Eph receptor-ephrin complexes emanate bidirectional signals that affect both receptor- and ephrin-expressing cells. Intriguingly, ephrins can also attenuate signaling by Eph receptors coexpressed in the same cell. Additionally, Eph receptors can modulate cell behavior independently of ephrin binding and kinase activity. The Eph/ephrin system regulates many developmental processes and adult tissue homeostasis. Its abnormal function has been implicated in various diseases, including cancer. Thus, Eph receptors represent promising therapeutic targets. However, more research is needed to better understand the many aspects of their complex biology that remain mysterious.
Collapse
Affiliation(s)
- Erika M Lisabeth
- Cancer Center, Sanford-Burnham Medical Research Institute, La Jolla, California 92037, USA
| | | | | |
Collapse
|
102
|
Blagovic K, Gong ES, Milano DF, Natividad RJ, Asthagiri AR. Engineering cell-cell signaling. Curr Opin Biotechnol 2013; 24:940-947. [PMID: 23856592 DOI: 10.1016/j.copbio.2013.05.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 05/25/2013] [Accepted: 05/28/2013] [Indexed: 10/26/2022]
Abstract
Juxtacrine cell-cell signaling mediated by the direct interaction of adjoining mammalian cells is arguably the mode of cell communication that is most recalcitrant to engineering. Overcoming this challenge is crucial for progress in biomedical applications, such as tissue engineering, regenerative medicine, immune system engineering and therapeutic design. Here, we describe the significant advances that have been made in developing synthetic platforms (materials and devices) and synthetic cells (cell surface engineering and synthetic gene circuits) to modulate juxtacrine cell-cell signaling. In addition, significant progress has been made in elucidating design rules and strategies to modulate juxtacrine signaling on the basis of quantitative, engineering analysis of the mechanical and regulatory role of juxtacrine signals in the context of other cues and physical constraints in the microenvironment. These advances in engineering juxtacrine signaling lay a strong foundation for an integrative approach to utilize synthetic cells, advanced 'chassis' and predictive modeling to engineer the form and function of living tissues.
Collapse
Affiliation(s)
- Katarina Blagovic
- Department of Chemical Engineering, Northeastern University, Boston, MA
| | - Emily S Gong
- Department of Chemical Engineering, Northeastern University, Boston, MA
| | - Daniel F Milano
- Department of Chemical Engineering, Northeastern University, Boston, MA
| | | | - Anand R Asthagiri
- Department of Chemical Engineering, Northeastern University, Boston, MA
| |
Collapse
|
103
|
Gauthier NP, Soufi B, Walkowicz WE, Pedicord VA, Mavrakis KJ, Macek B, Gin DY, Sander C, Miller ML. Cell-selective labeling using amino acid precursors for proteomic studies of multicellular environments. Nat Methods 2013; 10:768-73. [PMID: 23817070 PMCID: PMC4002004 DOI: 10.1038/nmeth.2529] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 05/08/2013] [Indexed: 11/23/2022]
Abstract
To address limitations of current high-throughput methods for studying cell-cell communication and determining the cell-of-origin of proteins in multicellular environments, we have developed a technique that selectively and continuously labels the proteome of individual cell types in co-culture. Through transgenic expression of exogenous amino acid biosynthesis enzymes, vertebrate cells overcome their dependence on essential amino acids and can be selectively labeled through metabolic incorporation of amino acids produced from heavy isotope-labeled precursors. We have named this method Type specific labeling with Amino acid Precursors (CTAP). Testing CTAP in several human and mouse cell lines, we were able to differentially label the proteome of distinct cell populations in co-culture and determine the relative expression of proteins by quantitative mass spectrometry. In addition, CTAP successfully identified the cell-of-origin of extracellular proteins in co-culture, highlighting its potential use in biomarker discovery for linking secreted factors to their cellular source.
Collapse
Affiliation(s)
- Nicholas P Gauthier
- Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, New York, USA.
| | | | | | | | | | | | | | | | | |
Collapse
|
104
|
Langenhan T, Aust G, Hamann J. Sticky Signaling--Adhesion Class G Protein-Coupled Receptors Take the Stage. Sci Signal 2013; 6:re3. [DOI: 10.1126/scisignal.2003825] [Citation(s) in RCA: 197] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
105
|
Vertebrate intersectin1 is repurposed to facilitate cortical midline connectivity and higher order cognition. J Neurosci 2013; 33:4055-65. [PMID: 23447614 DOI: 10.1523/jneurosci.4428-12.2013] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Invertebrate studies have highlighted a role for EH and SH3 domain Intersectin (Itsn) proteins in synaptic vesicle recycling and morphology. Mammals have two Itsn genes (Itsn1 and Itsn2), both of which can undergo alternative splicing to include DBL/PH and C2 domains not present in invertebrate Itsn proteins. To probe for specific and redundant functions of vertebrate Itsn genes, we generated Itsn1, Itsn2, and double mutant mice. While invertebrate mutants showed severe synaptic abnormalities, basal synaptic transmission and plasticity were unaffected at Schaffer CA1 synapses in mutant mice. Surprisingly, intercortical tracts-corpus callosum, ventral hippocampal, and anterior commissures-failed to cross the midline in mice lacking Itsn1, but not Itsn2. In contrast, tracts extending within hemispheres and those that decussate to more caudal brain segments appeared normal. Itsn1 mutant mice showed severe deficits in Morris water maze and contextual fear memory tasks, whereas mice lacking Itsn2 showed normal learning and memory. Thus, coincident with the acquisition of additional signaling domains, vertebrate Itsn1 has been functionally repurposed to also facilitate interhemispheric connectivity essential for high order cognitive functions.
Collapse
|
106
|
Multiplexed mass cytometry profiling of cellular states perturbed by small-molecule regulators. Nat Biotechnol 2013; 30:858-67. [PMID: 22902532 DOI: 10.1038/nbt.2317] [Citation(s) in RCA: 396] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 07/02/2012] [Indexed: 12/11/2022]
Abstract
Mass cytometry facilitates high-dimensional, quantitative analysis of the effects of bioactive molecules on human samples at single-cell resolution, but instruments process only one sample at a time. Here we describe mass-tag cellular barcoding (MCB), which increases mass cytometry throughput by using n metal ion tags to multiplex up to 2n samples. We used seven tags to multiplex an entire 96-well plate, and applied MCB to characterize human peripheral blood mononuclear cell (PBMC) signaling dynamics and cell-to-cell communication, signaling variability between PBMCs from eight human donors, and the effects of 27 inhibitors on this system. For each inhibitor, we measured 14 phosphorylation sites in 14 PBMC types at 96 conditions, resulting in 18,816 quantified phosphorylation levels from each multiplexed sample. This high-dimensional, systems-level inquiry allowed analysis across cell-type and signaling space, reclassified inhibitors and revealed off-target effects. High-content, high-throughput screening with MCB should be useful for drug discovery, preclinical testing and mechanistic investigation of human disease.
Collapse
|
107
|
Creixell P, Schoof EM, Erler JT, Linding R. Navigating cancer network attractors for tumor-specific therapy. Nat Biotechnol 2013; 30:842-8. [PMID: 22965061 DOI: 10.1038/nbt.2345] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cells employ highly dynamic signaling networks to drive biological decision processes. Perturbations to these signaling networks may attract cells to new malignant signaling and phenotypic states, termed cancer network attractors, that result in cancer development. As different cancer cells reach these malignant states by accumulating different molecular alterations, uncovering these mechanisms represents a grand challenge in cancer biology. Addressing this challenge will require new systems-based strategies that capture the intrinsic properties of cancer signaling networks and provide deeper understanding of the processes by which genetic lesions perturb these networks and lead to disease phenotypes. Network biology will help circumvent fundamental obstacles in cancer treatment, such as drug resistance and metastasis, empowering personalized and tumor-specific cancer therapies.
Collapse
Affiliation(s)
- Pau Creixell
- Cellular Signal Integration Group (C-SIG), Center for Biological Sequence Analysis (CBS), Department of Systems Biology, Technical University of Denmark (DTU), Lyngby, Denmark
| | | | | | | |
Collapse
|
108
|
Zanivan S, Meves A, Behrendt K, Schoof EM, Neilson LJ, Cox J, Tang HR, Kalna G, van Ree JH, van Deursen JM, Trempus CS, Machesky LM, Linding R, Wickström SA, Fässler R, Mann M. In vivo SILAC-based proteomics reveals phosphoproteome changes during mouse skin carcinogenesis. Cell Rep 2013; 3:552-66. [PMID: 23375375 DOI: 10.1016/j.celrep.2013.01.003] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 11/27/2012] [Accepted: 01/03/2013] [Indexed: 12/16/2022] Open
Abstract
Cancer progresses through distinct stages, and mouse models recapitulating traits of this progression are frequently used to explore genetic, morphological, and pharmacological aspects of tumor development. To complement genomic investigations of this process, we here quantify phosphoproteomic changes in skin cancer development using the SILAC mouse technology coupled to high-resolution mass spectrometry. We distill protein expression signatures from our data that distinguish between skin cancer stages. A distinct phosphoproteome of the two stages of cancer progression is identified that correlates with perturbed cell growth and implicates cell adhesion as a major driver of malignancy. Importantly, integrated analysis of phosphoproteomic data and prediction of kinase activity revealed PAK4-PKC/SRC network to be highly deregulated in SCC but not in papilloma. This detailed molecular picture, both at the proteome and phosphoproteome level, will prove useful for the study of mechanisms of tumor progression.
Collapse
Affiliation(s)
- Sara Zanivan
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
109
|
Xu Q, Wilkinson DG. Boundary formation in the development of the vertebrate hindbrain. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2013; 2:735-45. [PMID: 24014457 DOI: 10.1002/wdev.106] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The formation of a sharp interface of adjacent subdivisions is important for establishing the precision of tissue organization, and at specific borders it serves to organize key signaling centers. We discuss studies of vertebrate hindbrain development that have given important insights into mechanisms that underlie the formation and maintenance of sharp borders. The hindbrain is subdivided into a series of segments with distinct anteroposterior identity that underlies the specification of distinct neuronal cell types. During early stages of segmentation, cell identity switching contributes to the refinement of borders and enables homogenous territories to be maintained despite intermingling of cells between segments. At later stages, there is a specific restriction to cell intermingling between segments that is mediated by Eph receptor and ephrin signaling. Eph-ephrin signaling can restrict cell intermingling and sharpen borders through multiple mechanisms, including the regulation of cell adhesion and contact inhibition of cell migration.
Collapse
Affiliation(s)
- Qiling Xu
- Division of Developmental Neurobiology, MRC National Institute for Medical Research, London, UK
| | | |
Collapse
|
110
|
Abstract
Eph receptors and their membrane-tethered ligands have important functions in development. Trans interactions of Eph receptors with ephrins at cell-cell interfaces promote a variety of cellular responses, including repulsion, attraction and migration. Eph-ephrin signalling can be bi-directional and controls actin cytoskeleton dynamics, thereby leading to changes in cellular shape. This article provides an overview of the general structures and signalling mechanisms, and of typical developmental functions along with cell biological principles.
Collapse
Affiliation(s)
- Rüdiger Klein
- Max-Planck Institute of Neurobiology, Department of Molecular Neurobiology, Am Klopferspitz 18, Munich-Martinsried, Germany.
| |
Collapse
|
111
|
Proteomics analysis of contact-initiated eph receptor-ephrin signaling. Methods Mol Biol 2013; 1066:1-16. [PMID: 23955729 DOI: 10.1007/978-1-62703-604-7_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Large-scale biochemical analysis of cell-specific signaling can be interrogated in cocultures of Eph receptor- and ephrin-expressing cells by combining proteomics analysis with cell-specific metabolic labeling. In this chapter, we describe how to perform such large-scale analysis, including the generation of cells stably expressing the receptors and ligands of interest, optimization steps for Eph-ephrin coculture, and the proteomics analysis. As the experimental details may vary depending on the specific system that is being interrogated, the goal of the chapter is mainly to provide sufficient experimental context for experienced researchers to set up and conduct these experiments.
Collapse
|
112
|
Zhang A, Sun H, Sun W, Ye Y, Wang X. Proteomic identification network analysis of haptoglobin as a key regulator associated with liver fibrosis. Appl Biochem Biotechnol 2012; 169:832-46. [PMID: 23274719 DOI: 10.1007/s12010-012-0001-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Accepted: 11/29/2012] [Indexed: 02/03/2023]
Abstract
Liver fibrosis (LF) is the final stage of liver dysfunction, characterized by diffuse fibrosis which is the main response to the liver injury. Haptoglobin (HP) protein, produced as an acute phase reactant during LF, preventing liver damage, may be potential molecular targets for early LF diagnostics and therapeutic applications. However, protein networks associated with the HP are largely unknown. To address this issue, we used a pathological mouse model of LF that was induced by treatment with carbon tetrachloride for 8 days. HP protein was separated and identified by two-dimensional gel electrophoresis and matrix-assisted laser desorption/ionization time-of-flight/time-of-flight mass spectrometry. HP protein was subjected to functional pathway analysis using STRING and Cytoscape software for better understanding of the protein-protein interaction (PPI) networks in biological context. Bioinformatics analyses revealed that HP expression associated with fibrosis was upregulated, and suggested that HP responsible for fibrosis may precede the onset and progression of LF. Using the web-based database, functional pathway analysis suggested the modulation of multiple vital physiological pathways, including antioxidation immunity, signal transduction, metabolic process, energy production, cell apoptosis, oxidation reduction, DNA repair process, cell communication, and regulation of cellular process. The generation of protein interaction networks clearly enhances the interpretation and understanding of the molecular mechanisms of HP. HP protein represents targets for further experimental investigation that will provide biological insight and potentially could be exploited for novel therapeutic approaches to combat LF.
Collapse
Affiliation(s)
- Aihua Zhang
- National TCM Key Lab of Serum Pharmacochemistry, Heilongjiang University of Chinese Medicine, and Key Pharmacometabolomics Platform of Chinese Medicines, Heping Road 24, Harbin 150040, China
| | | | | | | | | |
Collapse
|
113
|
Atapattu L, Saha N, Llerena C, Vail ME, Scott AM, Nikolov DB, Lackmann M, Janes PW. Antibodies binding the ADAM10 substrate recognition domain inhibit Eph function. J Cell Sci 2012; 125:6084-93. [PMID: 23108669 DOI: 10.1242/jcs.112631] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The ADAM10 transmembrane metalloprotease cleaves a variety of cell surface proteins that are important in disease, including ligands for receptor tyrosine kinases of the erbB and Eph families. ADAM10-mediated cleavage of ephrins, the ligands for Eph receptors, is suggested to control Eph/ephrin-mediated cell-cell adhesion and segregation, important during normal developmental processes, and implicated in tumour neo-angiogenesis and metastasis. We previously identified a substrate-binding pocket in the ADAM10 C domain that binds the EphA/ephrin-A complex thereby regulating ephrin cleavage. We have now generated monoclonal antibodies specifically recognising this region of ADAM10, which inhibit ephrin cleavage and Eph/ephrin-mediated cell function, including ephrin-induced Eph receptor internalisation, phosphorylation and Eph-mediated cell segregation. Our studies confirm the important role of ADAM10 in cell-cell interactions mediated by both A- and B-type Eph receptors, and suggest antibodies against the ADAM10 substrate-recognition pocket as promising therapeutic agents, acting by inhibiting cleavage of ephrins and potentially other ADAM10 substrates.
Collapse
Affiliation(s)
- Lakmali Atapattu
- Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
| | | | | | | | | | | | | | | |
Collapse
|
114
|
Boyer AP, Collier TS, Vidavsky I, Bose R. Quantitative proteomics with siRNA screening identifies novel mechanisms of trastuzumab resistance in HER2 amplified breast cancers. Mol Cell Proteomics 2012; 12:180-93. [PMID: 23105007 DOI: 10.1074/mcp.m112.020115] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
HER2 is a receptor tyrosine kinase that is overexpressed in 20% to 30% of human breast cancers and which affects patient prognosis and survival. Treatment of HER2-positive breast cancer with the monoclonal antibody trastuzumab (Herceptin) has improved patient survival, but the development of trastuzumab resistance is a major medical problem. Many of the known mechanisms of trastuzumab resistance cause changes in protein phosphorylation patterns, and therefore quantitative proteomics was used to examine phosphotyrosine signaling networks in trastuzumab-resistant cells. The model system used in this study was two pairs of trastuzumab-sensitive and -resistant breast cancer cell lines. Using stable isotope labeling, phosphotyrosine immunoprecipitations, and online TiO(2) chromatography utilizing a dual trap configuration, ~1700 proteins were quantified. Comparing quantified proteins between the two cell line pairs showed only a small number of common protein ratio changes, demonstrating heterogeneity in phosphotyrosine signaling networks across different trastuzumab-resistant cancers. Proteins showing significant increases in resistant versus sensitive cells were subjected to a focused siRNA screen to evaluate their functional relevance to trastuzumab resistance. The screen revealed proteins related to the Src kinase pathway, such as CDCP1/Trask, embryonal Fyn substrate, and Paxillin. We also identify several novel proteins that increased trastuzumab sensitivity in resistant cells when targeted by siRNAs, including FAM83A and MAPK1. These proteins may present targets for the development of clinical diagnostics or therapeutic strategies to guide the treatment of HER2+ breast cancer patients who develop trastuzumab resistance.
Collapse
Affiliation(s)
- Alaina P Boyer
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | | | | |
Collapse
|
115
|
Lau KS, Cortez-Retamozo V, Philips SR, Pittet MJ, Lauffenburger DA, Haigis KM. Multi-scale in vivo systems analysis reveals the influence of immune cells on TNF-α-induced apoptosis in the intestinal epithelium. PLoS Biol 2012; 10:e1001393. [PMID: 23055830 PMCID: PMC3463506 DOI: 10.1371/journal.pbio.1001393] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 08/07/2012] [Indexed: 12/19/2022] Open
Abstract
Intestinal epithelial cells exist within a complex environment that affects how they interpret and respond to stimuli. We have applied a multi-scale in vivo systems approach to understand how intestinal immune cells communicate with epithelial cells to regulate responses to inflammatory signals. Multivariate modeling analysis of a large dataset composed of phospho-signals, cytokines, and immune cell populations within the intestine revealed an intimate relationship between immune cells and the epithelial response to TNF-α. Ablation of lymphocytes in the intestine prompted a decrease in the expression of MCP-1, which in turn increased the steady state number of intestinal plasmacytoid dendritic cells (pDCs). This change in the immune compartment affected the intestinal cytokine milieu and subsequent epithelial cell signaling network, with cells becoming hypersensitive to TNF-α-induced apoptosis in a way that could be predicted by mathematical modeling. In summary, we have uncovered a novel cellular network that regulates the response of intestinal epithelial cells to inflammatory stimuli in an in vivo setting.
Collapse
Affiliation(s)
- Ken S. Lau
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts, United States of America
- Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, United States of America
- Center for Systems Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Pathology, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Virna Cortez-Retamozo
- Center for Systems Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Sarah R. Philips
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts, United States of America
- Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, United States of America
- Center for Systems Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Mikael J. Pittet
- Center for Systems Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Douglas A. Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Kevin M. Haigis
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts, United States of America
- Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, United States of America
- Center for Systems Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Pathology, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail:
| |
Collapse
|
116
|
Imami K, Sugiyama N, Imamura H, Wakabayashi M, Tomita M, Taniguchi M, Ueno T, Toi M, Ishihama Y. Temporal profiling of lapatinib-suppressed phosphorylation signals in EGFR/HER2 pathways. Mol Cell Proteomics 2012; 11:1741-57. [PMID: 22964224 DOI: 10.1074/mcp.m112.019919] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Lapatinib is a clinically potent kinase inhibitor for breast cancer patients because of its outstanding selectivity for epidermal growth factor receptor (EGFR) and EGFR2 (also known as HER2). However, there is only limited information about the in vivo effects of lapatinib on EGFR/HER2 and downstream signaling targets. Here, we profiled the lapatinib-induced time- and dose-dependent phosphorylation dynamics in SKBR3 breast cancer cells by means of quantitative phosphoproteomics. Among 4953 identified phosphopeptides from 1548 proteins, a small proportion (5-7%) was regulated at least twofold by 1-10 μm lapatinib. We obtained a comprehensive phosphorylation map of 21 sites on EGFR/HER2, including nine novel sites on HER2. Among them, serine/threonine phosphosites located in a small region of HER2 (amino acid residues 1049-1083) were up-regulated by the drug, whereas all other sites were down-regulated. We show that cAMP-dependent protein kinase is involved in phosphorylation of this particular region of HER2 and regulates HER2 tyrosine kinase activity. Computational analyses of quantitative phosphoproteome data indicated for the first time that protein-protein networks related to cytoskeletal organization and transcriptional/translational regulation, such as RNP complexes (i.e. hnRNP, snRNP, telomerase, ribosome), are linked to EGFR/HER2 signaling networks. To our knowledge, this is the first report to profile the temporal response of phosphorylation dynamics to a kinase inhibitor. The results provide new insights into EGFR/HER2 regulation through region-specific phosphorylation, as well as a global view of the cellular signaling networks associated with the anti-breast cancer action of lapatinib.
Collapse
Affiliation(s)
- Koshi Imami
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | | | | | | | | | | | | | | | | |
Collapse
|
117
|
Abstract
In the life sciences, a new paradigm is emerging that places networks of interacting molecules between genotype and phenotype. These networks are dynamically modulated by a multitude of factors, and the properties emerging from the network as a whole determine observable phenotypes. This paradigm is usually referred to as systems biology, network biology, or integrative biology. Mass spectrometry (MS)-based proteomics is a central life science technology that has realized great progress toward the identification, quantification, and characterization of the proteins that constitute a proteome. Here, we review how MS-based proteomics has been applied to network biology to identify the nodes and edges of biological networks, to detect and quantify perturbation-induced network changes, and to correlate dynamic network rewiring with the cellular phenotype. We discuss future directions for MS-based proteomics within the network biology paradigm.
Collapse
Affiliation(s)
- Ariel Bensimon
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, CH 8093, Switzerland.
| | | | | |
Collapse
|
118
|
Kulkarni YM, Chambers E, McGray AJR, Ware JS, Bramson JL, Klinke DJ. A quantitative systems approach to identify paracrine mechanisms that locally suppress immune response to Interleukin-12 in the B16 melanoma model. Integr Biol (Camb) 2012; 4:925-36. [PMID: 22777646 PMCID: PMC3428131 DOI: 10.1039/c2ib20053h] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Interleukin-12 (IL12) enhances anti-tumor immunity when delivered to the tumor microenvironment. However, local immunoregulatory elements dampen the efficacy of IL12. The identity of these local mechanisms used by tumors to suppress immunosurveillance represents a key knowledge gap for improving tumor immunotherapy. From a systems perspective, local suppression of anti-tumor immunity is a closed-loop system - where system response is determined by an unknown combination of external inputs and local cellular cross-talk. Here, we recreated this closed-loop system in vitro and combined quantitative high content assays, in silico model-based inference, and a proteomic workflow to identify the biochemical cues responsible for immunosuppression. Following an induction period, the B16 melanoma cell model, a transplantable model for spontaneous malignant melanoma, inhibited the response of a T helper cell model to IL12. This paracrine effect was not explained by induction of apoptosis or creation of a cytokine sink, despite both mechanisms present within the co-culture assay. Tumor-derived Wnt-inducible signaling protein-1 (WISP-1) was identified to exert paracrine action on immune cells by inhibiting their response to IL12. Moreover, WISP-1 was expressed in vivo following intradermal challenge with B16F10 cells and was inferred to be expressed at the tumor periphery. Collectively, the data suggest that (1) biochemical cues associated with epithelial-to-mesenchymal transition can shape anti-tumor immunity through paracrine action and (2) remnants of the immunoselective pressure associated with evolution in cancer include both sculpting of tumor antigens and expression of proteins that proactively shape anti-tumor immunity.
Collapse
Affiliation(s)
- Yogesh M Kulkarni
- Department of Chemical Engineering and Mary Babb Randolph Cancer Center, West Virginia University, P.O. Box 6102, Morgantown, WV 26506, USA
| | | | | | | | | | | |
Collapse
|
119
|
Palmisano G, Parker BL, Engholm-Keller K, Lendal SE, Kulej K, Schulz M, Schwämmle V, Graham ME, Saxtorph H, Cordwell SJ, Larsen MR. A novel method for the simultaneous enrichment, identification, and quantification of phosphopeptides and sialylated glycopeptides applied to a temporal profile of mouse brain development. Mol Cell Proteomics 2012; 11:1191-202. [PMID: 22843994 DOI: 10.1074/mcp.m112.017509] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We describe a method that combines an optimized titanium dioxide protocol and hydrophilic interaction liquid chromatography to simultaneously enrich, identify and quantify phosphopeptides and formerly N-linked sialylated glycopeptides to monitor changes associated with cell signaling during mouse brain development. We initially applied the method to enriched membrane fractions from HeLa cells, which allowed the identification of 4468 unique phosphopeptides and 1809 formerly N-linked sialylated glycopeptides. We subsequently combined the method with isobaric tagging for relative quantification to compare changes in phosphopeptide and formerly N-linked sialylated glycopeptide abundance in the developing mouse brain. A total of 7682 unique phosphopeptide sequences and 3246 unique formerly sialylated glycopeptides were identified. Moreover 669 phosphopeptides and 300 formerly N-sialylated glycopeptides differentially regulated during mouse brain development were detected. This strategy allowed us to reveal extensive changes in post-translational modifications from postnatal mice from day 0 until maturity at day 80. The results of this study confirm the role of sialylation in organ development and provide the first extensive global view of dynamic changes between N-linked sialylation and phosphorylation.
Collapse
Affiliation(s)
- Giuseppe Palmisano
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, and Biomedical Laboratory, Odense University Hospital, Campusvej 55, 5230 Odense M, Denmark
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
120
|
George CH, Parthimos D, Silvester NC. A network-oriented perspective on cardiac calcium signaling. Am J Physiol Cell Physiol 2012; 303:C897-910. [PMID: 22843795 DOI: 10.1152/ajpcell.00388.2011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The normal contractile, electrical, and energetic function of the heart depends on the synchronization of biological oscillators and signal integrators that make up cellular signaling networks. In this review we interpret experimental data from molecular, cellular, and transgenic models of cardiac signaling behavior in the context of established concepts in cell network architecture and organization. Focusing on the cellular Ca(2+) handling machinery, we describe how the plasticity and adaptability of normal Ca(2+) signaling is dependent on dynamic network configurations that operate across a wide range of functional states. We consider how (mal)adaptive changes in signaling pathways restrict the dynamic range of the network such that it cannot respond appropriately to physiologic stimuli or perturbation. Based on these concepts, a model is proposed in which pathologic abnormalities in cardiac rhythm and contractility (e.g., arrhythmias and heart failure) arise as a consequence of progressive desynchronization and reduction in the dynamic range of the Ca(2+) signaling network. We discuss how a systems-level understanding of the network organization, cellular noise, and chaotic behavior may inform the design of new therapeutic modalities that prevent or reverse the disease-linked unraveling of the Ca(2+) signaling network.
Collapse
Affiliation(s)
- Christopher H George
- Wales Heart Research Institute and Institute of Molecular and Experimental Medicine, School of Medicine, Cardiff Univ., Heath Park, Cardiff, Wales, UK CF14 4XN.
| | | | | |
Collapse
|
121
|
Key issues in the acquisition and analysis of qualitative and quantitative mass spectrometry data for peptide-centric proteomic experiments. Amino Acids 2012; 43:1075-85. [PMID: 22821266 DOI: 10.1007/s00726-012-1287-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Accepted: 04/03/2012] [Indexed: 01/05/2023]
Abstract
Proteomic technologies have matured to a level enabling accurate and reproducible quantitation of peptides and proteins from complex biological matrices. Analysis of samples as diverse as assembled protein complexes, whole cell lysates or sub-cellular proteomes from cell cultures, and direct analysis of animal and human tissues and fluids demonstrate the incredible versatility of the fundamental nature of the technique that forms the basis of most proteomic applications today (mass spectrometry). Determining the mass of biomolecules and their fragments or related products with high accuracy can convey a highly specific assay for detection and identification. Importantly, ion currents representative of these specifically identified analytes can be accurately quantified with the correct application of smart isobaric tagging chemistries, heavy and light isotopically derivatised samples or standards, or by careful application of workflows to compare unlabelled samples in so-called 'label-free' and targeted selected reaction monitoring experiments. In terms of exploring biology, a myriad of protein changes and modifications are being increasingly probed and quantified, including diverse chemical changes from relatively decisive modifications such as protein splicing and truncation, to more transient dynamic modifications such as phosphorylation, acetylation and ubiquitination. Proteomic workflows can be complex beasts and several key considerations to ensure effective applications have been outlined in the recent literature. The past year has witnessed the publication of several excellent reviews that thoroughly describe the fundamental principles underlying the state of the art. This review further elaborates on specific critical issues introduced by these publications and raises other important unaddressed considerations and new developments that directly impact on the effectiveness of proteomic technologies, in particular for, but not necessarily exclusive to peptide-centric experiments. These factors are discussed both in terms of qualitative analyses, including dynamic range and sampling issues, and developments to improve the translation of peptide fragmentation data into peptide and protein identities, as well as quantitative analyses, including data normalisation and the utility of ontology or functional annotation, the effects of modified peptides, and considered experimental design to facilitate the use of robust statistical methods.
Collapse
|
122
|
Analysing signalling networks by mass spectrometry. Amino Acids 2012; 43:1061-74. [PMID: 22821269 DOI: 10.1007/s00726-012-1293-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2011] [Accepted: 04/03/2012] [Indexed: 12/31/2022]
Abstract
Sequence analysis of the human genome and the association of genetic aberrations with diseases have provided a rough framework whereby the impact of individual genotypes can be assessed. To fully understand the effect of individual and co-occurring genetic aberrations, as well as their individual and collected contribution to the development of diseases, it is critical to analyse the matching proteome and to determine how the organisation, expression level and function of protein networks are affected. Sensitive mass spectrometric platforms in combination with innovative workflows allow qualitative and quantitative analyses of the cellular as well as the extracellular proteome. Importantly, in addition to specifically identifying the content of the proteome, several aspects of the proteomic organisation can be analysed including protein complexes, protein modifications, enzymatic activities and subcellular/organelle localisation. Together, these measurements will provide novel insight into the biological effect of disease-causing mutations ultimately coupling genotype and phenotype.
Collapse
|
123
|
Tiedemann HB, Schneltzer E, Zeiser S, Hoesel B, Beckers J, Przemeck GKH, de Angelis MH. From dynamic expression patterns to boundary formation in the presomitic mesoderm. PLoS Comput Biol 2012; 8:e1002586. [PMID: 22761566 PMCID: PMC3386180 DOI: 10.1371/journal.pcbi.1002586] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Accepted: 04/24/2012] [Indexed: 11/19/2022] Open
Abstract
The segmentation of the vertebrate body is laid down during early embryogenesis. The formation of signaling gradients, the periodic expression of genes of the Notch-, Fgf- and Wnt-pathways and their interplay in the unsegmented presomitic mesoderm (PSM) precedes the rhythmic budding of nascent somites at its anterior end, which later develops into epithelialized structures, the somites. Although many in silico models describing partial aspects of somitogenesis already exist, simulations of a complete causal chain from gene expression in the growth zone via the interaction of multiple cells to segmentation are rare. Here, we present an enhanced gene regulatory network (GRN) for mice in a simulation program that models the growing PSM by many virtual cells and integrates WNT3A and FGF8 gradient formation, periodic gene expression and Delta/Notch signaling. Assuming Hes7 as core of the somitogenesis clock and LFNG as modulator, we postulate a negative feedback of HES7 on Dll1 leading to an oscillating Dll1 expression as seen in vivo. Furthermore, we are able to simulate the experimentally observed wave of activated NOTCH (NICD) as a result of the interactions in the GRN. We esteem our model as robust for a wide range of parameter values with the Hes7 mRNA and protein decays exerting a strong influence on the core oscillator. Moreover, our model predicts interference between Hes1 and HES7 oscillators when their intrinsic frequencies differ. In conclusion, we have built a comprehensive model of somitogenesis with HES7 as core oscillator that is able to reproduce many experimentally observed data in mice.
Collapse
Affiliation(s)
- Hendrik B. Tiedemann
- Institute of Experimental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Elida Schneltzer
- Institute of Experimental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | | | - Bastian Hoesel
- Institute of Experimental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Johannes Beckers
- Institute of Experimental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Technische Universitaet Muenchen, Center of Life and Food Sciences Weihenstephan, Chair of Experimental Genetics, Freising, Germany
| | - Gerhard K. H. Przemeck
- Institute of Experimental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Martin Hrabě de Angelis
- Institute of Experimental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Technische Universitaet Muenchen, Center of Life and Food Sciences Weihenstephan, Chair of Experimental Genetics, Freising, Germany
- * E-mail:
| |
Collapse
|
124
|
Kozlov IA, Thomsen ER, Munchel SE, Villegas P, Capek P, Gower AJ, Pond SJK, Chudin E, Chee MS. A highly scalable peptide-based assay system for proteomics. PLoS One 2012; 7:e37441. [PMID: 22701568 PMCID: PMC3373263 DOI: 10.1371/journal.pone.0037441] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Accepted: 04/19/2012] [Indexed: 11/18/2022] Open
Abstract
We report a scalable and cost-effective technology for generating and screening high-complexity customizable peptide sets. The peptides are made as peptide-cDNA fusions by in vitro transcription/translation from pools of DNA templates generated by microarray-based synthesis. This approach enables large custom sets of peptides to be designed in silico, manufactured cost-effectively in parallel, and assayed efficiently in a multiplexed fashion. The utility of our peptide-cDNA fusion pools was demonstrated in two activity-based assays designed to discover protease and kinase substrates. In the protease assay, cleaved peptide substrates were separated from uncleaved and identified by digital sequencing of their cognate cDNAs. We screened the 3,011 amino acid HCV proteome for susceptibility to cleavage by the HCV NS3/4A protease and identified all 3 known trans cleavage sites with high specificity. In the kinase assay, peptide substrates phosphorylated by tyrosine kinases were captured and identified by sequencing of their cDNAs. We screened a pool of 3,243 peptides against Abl kinase and showed that phosphorylation events detected were specific and consistent with the known substrate preferences of Abl kinase. Our approach is scalable and adaptable to other protein-based assays.
Collapse
Affiliation(s)
- Igor A Kozlov
- Prognosys Biosciences Inc., La Jolla, California, United States of America.
| | | | | | | | | | | | | | | | | |
Collapse
|
125
|
Nievergall E, Lackmann M, Janes PW. Eph-dependent cell-cell adhesion and segregation in development and cancer. Cell Mol Life Sci 2012; 69:1813-42. [PMID: 22204021 PMCID: PMC11114713 DOI: 10.1007/s00018-011-0900-6] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Revised: 11/06/2011] [Accepted: 11/28/2011] [Indexed: 01/23/2023]
Abstract
Numerous studies attest to essential roles for Eph receptors and their ephrin ligands in controlling cell positioning and tissue patterning during normal and oncogenic development. These studies suggest multiple, sometimes contradictory, functions of Eph-ephrin signalling, which under different conditions can promote either spreading and cell-cell adhesion or cytoskeletal collapse, cell rounding, de-adhesion and cell-cell segregation. A principle determinant of the balance between these two opposing responses is the degree of receptor/ligand clustering and activation. This equilibrium is likely altered in cancers and modulated by somatic mutations of key Eph family members that have emerged as candidate cancer markers in recent profiling studies. In addition, cross-talk amongst Ephs and with other signalling pathways significantly modulates cell-cell adhesion, both between and within Eph- and ephrin-expressing cell populations. This review summarises our current understanding of how Eph receptors control cell adhesion and morphology, and presents examples demonstrating the importance of these events in normal development and cancer.
Collapse
Affiliation(s)
- Eva Nievergall
- Department of Biochemistry and Molecular Biology, Monash University, Wellington Road, Clayton, VIC 3800 Australia
- Present Address: Haematology Department, SA Pathology, Frome Road, Adelaide, SA 5000 Australia
| | - Martin Lackmann
- Department of Biochemistry and Molecular Biology, Monash University, Wellington Road, Clayton, VIC 3800 Australia
| | - Peter W. Janes
- Department of Biochemistry and Molecular Biology, Monash University, Wellington Road, Clayton, VIC 3800 Australia
| |
Collapse
|
126
|
Bennetzen MV, Cox J, Mann M, Andersen JS. PhosphoSiteAnalyzer: a bioinformatic platform for deciphering phospho proteomes using kinase predictions retrieved from NetworKIN. J Proteome Res 2012; 11:3480-6. [PMID: 22471441 DOI: 10.1021/pr300016e] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Phosphoproteomic experiments are routinely conducted in laboratories worldwide, and because of the fast development of mass spectrometric techniques and efficient phosphopeptide enrichment methods, researchers frequently end up having lists with tens of thousands of phosphorylation sites for further interrogation. To answer biologically relevant questions from these complex data sets, it becomes essential to apply computational, statistical, and predictive analytical methods. Here we provide an advanced bioinformatic platform termed "PhosphoSiteAnalyzer" to explore large phosphoproteomic data sets that have been subjected to kinase prediction using the previously published NetworKIN algorithm. NetworKIN applies sophisticated linear motif analysis and contextual network modeling to obtain kinase-substrate associations with high accuracy and sensitivity. PhosphoSiteAnalyzer provides an algorithm to retrieve kinase predictions from the public NetworKIN webpage in a semiautomated way and applies hereafter advanced statistics to facilitate a user-tailored in-depth analysis of the phosphoproteomic data sets. The interface of the software provides a high degree of analytical flexibility and is designed to be intuitive for most users. PhosphoSiteAnalyzer is a freeware program available at http://phosphosite.sourceforge.net .
Collapse
Affiliation(s)
- Martin V Bennetzen
- Center for Experimental BioInformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark , Odense, Campusvej 55, DK-5230 Odense M, Denmark
| | | | | | | |
Collapse
|
127
|
van Eekelen M, Runtuwene V, Masselink W, den Hertog J. Pair-wise regulation of convergence and extension cell movements by four phosphatases via RhoA. PLoS One 2012; 7:e35913. [PMID: 22545146 PMCID: PMC3335823 DOI: 10.1371/journal.pone.0035913] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Accepted: 03/26/2012] [Indexed: 11/18/2022] Open
Abstract
Various signaling pathways regulate shaping of the main body axis during early vertebrate development. Here, we focused on the role of protein-tyrosine phosphatase signaling in convergence and extension cell movements. We identified Ptpn20 as a structural paralogue of PTP-BL and both phosphatases were required for normal gastrulation cell movements. Interestingly, knockdowns of PTP-BL and Ptpn20 evoked similar developmental defects as knockdown of RPTPα and PTPε. Co-knockdown of RPTPα and PTP-BL, but not Ptpn20, had synergistic effects and conversely, PTPε and Ptpn20, but not PTP-BL, cooperated, demonstrating the specificity of our approach. RPTPα and PTPε knockdowns were rescued by constitutively active RhoA, whereas PTP-BL and Ptpn20 knockdowns were rescued by dominant negative RhoA. Consistently, RPTPα and PTP-BL had opposite effects on RhoA activation, both in a PTP-dependent manner. Downstream of the PTPs, we identified NGEF and Arhgap29, regulating RhoA activation and inactivation, respectively, in convergence and extension cell movements. We propose a model in which two phosphatases activate RhoA and two phosphatases inhibit RhoA, resulting in proper cell polarization and normal convergence and extension cell movements.
Collapse
Affiliation(s)
- Mark van Eekelen
- Hubrecht Institute and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Vincent Runtuwene
- Hubrecht Institute and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Wouter Masselink
- Hubrecht Institute and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jeroen den Hertog
- Hubrecht Institute and University Medical Center Utrecht, Utrecht, the Netherlands
- Institute of Biology, Leiden, the Netherlands
- * E-mail:
| |
Collapse
|
128
|
Reactive oxygen species and epidermal growth factor are antagonistic cues controlling SHP-2 dimerization. Mol Cell Biol 2012; 32:1998-2009. [PMID: 22411627 DOI: 10.1128/mcb.06674-11] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The SHP-2 tyrosine phosphatase plays key regulatory roles in the modulation of the cell response to growth factors and cytokines. Over the past decade, the integration of genetic, biochemical, and structural data has helped in interpreting the pathological consequences of altered SHP-2 function. Using complementary approaches, we provide evidence here that endogenous SHP-2 can dimerize through the formation of disulfide bonds that may also involve the catalytic cysteine. We show that the fraction of dimeric SHP-2 is modulated by growth factor stimulation and by the cell redox state. Comparison of the phosphatase activities of the monomeric self-inhibited and dimeric forms indicated that the latter is 3-fold less active, thus pointing to the dimerization process as an additional mechanism for controlling SHP-2 activity. Remarkably, dimers formed by different SHP-2 mutants displaying diverse biochemical properties were found to respond differently to epidermal growth factor (EGF) stimulation. Although this differential behavior cannot be rationalized mechanistically yet, these findings suggest a possible regulatory role of dimerization in SHP-2 function.
Collapse
|
129
|
Mollapour M, Neckers L. Post-translational modifications of Hsp90 and their contributions to chaperone regulation. BIOCHIMICA ET BIOPHYSICA ACTA 2012; 1823:648-55. [PMID: 21856339 PMCID: PMC3226900 DOI: 10.1016/j.bbamcr.2011.07.018] [Citation(s) in RCA: 213] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Revised: 07/21/2011] [Accepted: 07/27/2011] [Indexed: 12/20/2022]
Abstract
Molecular chaperones, as the name suggests, are involved in folding, maintenance, intracellular transport, and degradation of proteins as well as in facilitating cell signaling. Heat shock protein 90 (Hsp90) is an essential eukaryotic molecular chaperone that carries out these processes in normal and cancer cells. Hsp90 function in vivo is coupled to its ability to hydrolyze ATP and this can be regulated by co-chaperones and post-translational modifications. In this review, we explore the varied roles of known post-translational modifications of cytosolic and nuclear Hsp90 (phosphorylation, acetylation, S-nitrosylation, oxidation and ubiquitination) in fine-tuning chaperone function in eukaryotes. This article is part of a Special Issue entitled: Heat Shock Protein 90 (HSP90).
Collapse
Affiliation(s)
- Mehdi Mollapour
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Len Neckers
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, 9000 Rockville Pike, Bethesda, MD 20892, USA
| |
Collapse
|
130
|
Lind SB, Artemenko KA, Pettersson U. A strategy for identification of protein tyrosine phosphorylation. Methods 2012; 56:275-83. [DOI: 10.1016/j.ymeth.2011.09.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Revised: 09/23/2011] [Accepted: 09/26/2011] [Indexed: 01/14/2023] Open
|
131
|
Abstract
Great strides have been made regarding our understanding of the processes and signaling events influenced by Eph/ephrin signaling that play a role in cell adhesion and cell movement. However, the precise mechanisms by which these signaling events regulate cell and tissue architecture still need further resolution. The Eph/ephrin signaling pathways and the ability to regulate cell-cell adhesion and motility constitutes an impressive system for regulating tissue separation and morphogenesis (Pasquale, 2005, 2008 [1,2]). Moreover, the de-regulation of this signaling system is linked to the promotion of aggressive and metastatic tumors in humans [2]. In the following section, we discuss some of the interesting mechanisms by which ephrins can signal through their own intracellular domains (reverse signaling) either independent of forward signaling or in addition to forward signaling through a cognate receptor. In this review we discuss how ephrins (Eph ligands) "reverse signal" through their intracellular domains to affect cell adhesion and movement, but the focus is on modes of action that are independent of SH2 and PDZ interactions.
Collapse
Affiliation(s)
- Ira O Daar
- Laboratory of Cell & Developmental Signaling, National Cancer Institute-Frederick, Frederick, MD 21702, USA.
| |
Collapse
|
132
|
Liu Y, Wang Y, Zhang Y, Fu J, Zhang G. Knockdown of HMGA1 expression by short/small hairpin RNA inhibits growth of ovarian carcinoma cells. Biotechnol Appl Biochem 2012; 59:1-5. [PMID: 22332738 DOI: 10.1002/bab.56] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Accepted: 09/01/2011] [Indexed: 01/04/2023]
Abstract
The aim of the current study was to investigate the influence of downregulating high-mobility group protein A1 (HMGA1) on the tumor gene and the mechanisms underlying the antitumor of HMGA1. The efficient short/small hairpin RNAs (shRNAs) of HMGA1 were constructed and transfected into human ovarian carcinoma OVCAR cells. The changes were identified by reverse transcription PCR (RT-PCR), Western blotting, methyl thiazolyl tetrazolium, and invasion assay. The knockdown of HMGA1 expression in OVCAR cells could obviously change cell morphology, decrease cell proliferation, and reduce invasion in vitro. BALB/C nude mice injected with OVCAR cells transfected HMGA1 shRNA showed a significantly lower tumor weight and volume than those in the control group. Taken together, HMGA1 knockdown could reduce the growth and metastasis potentials of OVCAR cells.
Collapse
Affiliation(s)
- Yinglan Liu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Harbin University, Harbin, People's Republic of China
| | | | | | | | | |
Collapse
|
133
|
Huyck L, Van Troys M, Ampe C. Phosphosite conservation in single domain orthologs versus paralogs: a way to combine differential regulation with redundant core functions. FEBS Lett 2012; 586:296-302. [PMID: 22265693 DOI: 10.1016/j.febslet.2012.01.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Revised: 01/04/2012] [Accepted: 01/09/2012] [Indexed: 11/19/2022]
Abstract
Evolutionary conservation for structure function relations is commonly accepted. Here we hypothesize that closely related single domain paralogous proteins, having similar expression profiles and redundant biochemical core functions, additionally evolved to allow and maintain isoform specific differential regulation by single conserved amino acid substitutions. To substantiate this, we considered two families of closely related actin binding proteins combined with data mining of phosphorylated residues in human and mouse proteins. We show that such residues are identical in other orthologs whereas paralogs have a different, but also conserved, non-phosphorylatable residue at the equivalent positions.
Collapse
Affiliation(s)
- Lynn Huyck
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | | | | |
Collapse
|
134
|
Abstract
Protein and genetic interaction maps can reveal the overall physical and functional landscape of a biological system. To date, these interaction maps have typically been generated under a single condition, even though biological systems undergo differential change that is dependent on environment, tissue type, disease state, development or speciation. Several recent interaction mapping studies have demonstrated the power of differential analysis for elucidating fundamental biological responses, revealing that the architecture of an interactome can be massively re-wired during a cellular or adaptive response. Here, we review the technological developments and experimental designs that have enabled differential network mapping at very large scales and highlight biological insight that has been derived from this type of analysis. We argue that differential network mapping, which allows for the interrogation of previously unexplored interaction spaces, will become a standard mode of network analysis in the future, just as differential gene expression and protein phosphorylation studies are already pervasive in genomic and proteomic analysis.
Collapse
Affiliation(s)
- Trey Ideker
- Departments of Medicine and Bioengineering, University of California San Diego, La Jolla, CA, USA
- The Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- California Institute for Quantitative Biosciences, QB3, San Francisco, CA, USA
- J David Gladstone Institutes, San Francisco, CA, USA
| |
Collapse
|
135
|
Concepts and consequences of Eph receptor clustering. Semin Cell Dev Biol 2012; 23:43-50. [PMID: 22261642 DOI: 10.1016/j.semcdb.2012.01.001] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2012] [Accepted: 01/04/2012] [Indexed: 12/31/2022]
Abstract
Polymeric receptor-ligand complexes between interacting Eph and ephrin-expressing cells are regarded as dynamic intercellular signalling scaffolds that control cell-to-cell contact: the resulting Eph-ephrin signalling clusters function as positional cues that facilitate cell navigation and tissue patterning during normal and oncogenic development. The considerable complexity of this task, coordinating a multitude of cell movements and cellular interactions, is achieved by accurate translation of spatial information from Eph and ephrin expression gradients into fine-tuned changes in cell-cell adhesion and position. Here we review emerging evidence suggesting that the required combinatorial diversity is not only achieved by the large number of possible Eph-ephrin interactions and selective use of Eph forward and ephrin reverse signals, but in particular through the composition and signal capacity of Eph-ephrin clusters, which is adjusted dynamically to reflect overall Eph and ephrin surface densities on interacting cells. Fine-tuning is provided through multi-layered cluster assembly, where homo- and heterotypic Eph and ephrin interactions define the composition - whilst intracellular signalling feedbacks determine the size and lifetime - of signalling clusters.
Collapse
|
136
|
Lin C, Ear J, Pavlova Y, Mittal Y, Kufareva I, Ghassemian M, Abagyan R, Garcia-Marcos M, Ghosh P. Tyrosine phosphorylation of the Gα-interacting protein GIV promotes activation of phosphoinositide 3-kinase during cell migration. Sci Signal 2012; 4:ra64. [PMID: 21954290 DOI: 10.1126/scisignal.2002049] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
GIV (Gα-interacting vesicle-associated protein; also known as Girdin) enhances Akt activation downstream of multiple growth factor- and G protein (heterotrimeric guanosine 5'-triphosphate-binding protein)-coupled receptors to trigger cell migration and cancer invasion. We demonstrate that GIV is a tyrosine phosphoprotein that directly binds to and activates phosphoinositide 3-kinase (PI3K). Upon ligand stimulation of various receptors, GIV was phosphorylated at tyrosine-1764 and tyrosine-1798 by both receptor and non-receptor tyrosine kinases. These phosphorylation events enabled direct binding of GIV to the amino- and carboxyl-terminal Src homology 2 domains of p85α, a regulatory subunit of PI3K; stabilized receptor association with PI3K; and enhanced PI3K activity at the plasma membrane to trigger cell migration. Tyrosine phosphorylation of GIV and its association with p85α increased during metastatic progression of a breast carcinoma. These results suggest a mechanism by which multiple receptors activate PI3K through tyrosine phosphorylation of GIV, thereby making the GIV-PI3K interaction a potential therapeutic target within the PI3K-Akt pathway.
Collapse
Affiliation(s)
- Changsheng Lin
- Department of Medicine, University of California, San Diego, School of Medicine, La Jolla, CA 92093, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
137
|
da Silva VCH, Ramos CHI. The network interaction of the human cytosolic 90 kDa heat shock protein Hsp90: A target for cancer therapeutics. J Proteomics 2012; 75:2790-802. [PMID: 22236519 DOI: 10.1016/j.jprot.2011.12.028] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Revised: 12/18/2011] [Accepted: 12/19/2011] [Indexed: 10/14/2022]
Abstract
In the cell, proteins interact within a network in which a small number of proteins are highly connected nodes or hubs. A disturbance in the hub proteins usually has a higher impact on the cell physiology than a disturbance in poorly connected nodes. In eukaryotes, the cytosolic Hsp90 is considered to be a hub protein as it interacts with molecular chaperones and co-chaperones, and has key regulatory proteins as clients, such as transcriptional factors, protein kinases and hormone receptors. The large number of Hsp90 partners suggests that Hsp90 is involved in very important functions, such as signaling, proteostasis and epigenetics. Some of these functions are dysregulated in cancer, making Hsp90 a potential target for therapeutics. The number of Hsp90 interactors appears to be so large that a precise answer to the question of how many proteins interact with this chaperone has no definitive answer yet, not even if the question refers to specific Hsp90s as one of the human cytosolic forms. Here we review the major chaperones and co-chaperones that interact with cytosolic Hsp90s, highlighting the latest findings regarding client proteins and the role that posttranslational modifications have on the function and interactions of these molecular chaperones. This article is part of a Special Issue entitled: Proteomics: The clinical link.
Collapse
Affiliation(s)
- Viviane C H da Silva
- Institute of Chemistry, University of Campinas-UNICAMP. P.O. Box 6154, 13083-970, Campinas, SP, Brazil
| | | |
Collapse
|
138
|
Batlle E, Wilkinson DG. Molecular mechanisms of cell segregation and boundary formation in development and tumorigenesis. Cold Spring Harb Perspect Biol 2012; 4:a008227. [PMID: 22214769 PMCID: PMC3249626 DOI: 10.1101/cshperspect.a008227] [Citation(s) in RCA: 137] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The establishment and maintenance of precisely organized tissues requires the formation of sharp borders between distinct cell populations. The maintenance of segregated cell populations is also required for tissue homeostasis in the adult, and deficiencies in segregation underlie the metastatic spreading of tumor cells. Three classes of mechanisms that underlie cell segregation and border formation have been uncovered. The first involves differences in cadherin-mediated cell-cell adhesion that establishes interfacial tension at the border between distinct cell populations. A second mechanism involves the induction of actomyosin-mediated contraction by intercellular signaling, such that cortical tension is generated at the border. Third, activation of Eph receptors and ephrins can lead to both decreased adhesion by triggering cleavage of E-cadherin, and to repulsion of cells by regulation of the actin cytoskeleton, thus preventing intermingling between cell populations. These mechanisms play crucial roles at distinct boundaries during development, and alterations in cadherin or Eph/ephrin expression have been implicated in tumor metastasis.
Collapse
Affiliation(s)
- Eduard Batlle
- Oncology Program and ICREA, Institute for Research in Biomedicine, Josep Samitier 1-5, 08028 Barcelona, Spain
| | | |
Collapse
|
139
|
Wang CC, Jamal L, Janes KA. Normal morphogenesis of epithelial tissues and progression of epithelial tumors. WILEY INTERDISCIPLINARY REVIEWS. SYSTEMS BIOLOGY AND MEDICINE 2012; 4:51-78. [PMID: 21898857 PMCID: PMC3242861 DOI: 10.1002/wsbm.159] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Epithelial cells organize into various tissue architectures that largely maintain their structure throughout the life of an organism. For decades, the morphogenesis of epithelial tissues has fascinated scientists at the interface of cell, developmental, and molecular biology. Systems biology offers ways to combine knowledge from these disciplines by building integrative models that are quantitative and predictive. Can such models be useful for gaining a deeper understanding of epithelial morphogenesis? Here, we take inventory of some recurring themes in epithelial morphogenesis that systems approaches could strive to capture. Predictive understanding of morphogenesis at the systems level would prove especially valuable for diseases such as cancer, where epithelial tissue architecture is profoundly disrupted.
Collapse
Affiliation(s)
- Chun-Chao Wang
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
| | - Leen Jamal
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
| | - Kevin A. Janes
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
| |
Collapse
|
140
|
Mass Spectrometric Tools for Systematic Analysis of Protein Phosphorylation. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2012; 106:3-32. [DOI: 10.1016/b978-0-12-396456-4.00014-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
|
141
|
Wang X, Zhang A, Sun H, Wu G, Sun W, Yan G. Network generation enhances interpretation of proteomics data sets by a combination of two-dimensional polyacrylamide gel electrophoresis and matrix-assisted laser desorption/ionization-time of flight mass spectrometry. Analyst 2012; 137:4703-11. [DOI: 10.1039/c2an35891c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|
142
|
Sacco F, Gherardini PF, Paoluzi S, Saez-Rodriguez J, Helmer-Citterich M, Ragnini-Wilson A, Castagnoli L, Cesareni G. Mapping the human phosphatome on growth pathways. Mol Syst Biol 2012; 8:603. [PMID: 22893001 PMCID: PMC3435503 DOI: 10.1038/msb.2012.36] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Accepted: 07/10/2012] [Indexed: 01/13/2023] Open
Abstract
Large-scale siRNA screenings allow linking the function of poorly characterized genes to phenotypic readouts. According to this strategy, genes are associated with a function of interest if the alteration of their expression perturbs the phenotypic readouts. However, given the intricacy of the cell regulatory network, the mapping procedure is low resolution and the resulting models provide little mechanistic insights. We have developed a new strategy that combines multiparametric analysis of cell perturbation with logic modeling to achieve a more detailed functional mapping of human genes onto complex pathways. A literature-derived optimized model is used to infer the cell activation state following upregulation or downregulation of the model entities. By matching this signature with the experimental profile obtained in the high-throughput siRNA screening it is possible to infer the target of each protein, thus defining its 'entry point' in the network. By this novel approach, 41 phosphatases that affect key growth pathways were identified and mapped onto a human epithelial cell-specific growth model, thus providing insights into the mechanisms underlying their function.
Collapse
Affiliation(s)
- Francesca Sacco
- Department of Biology, University of Rome ‘Tor Vergata’, Rome, Italy
| | | | - Serena Paoluzi
- Department of Biology, University of Rome ‘Tor Vergata’, Rome, Italy
| | | | | | - Antonella Ragnini-Wilson
- Department of Biology, University of Rome ‘Tor Vergata’, Rome, Italy
- High-throughput Microscopy Facility, Department of Translational and Cellular Pharmacology, Consorzio Mario Negri Sud, SM Imbaro, Italy
| | - Luisa Castagnoli
- Department of Biology, University of Rome ‘Tor Vergata’, Rome, Italy
| | - Gianni Cesareni
- Department of Biology, University of Rome ‘Tor Vergata’, Rome, Italy
- IRCCS Fondazione Santa Lucia, Rome, Italy
| |
Collapse
|
143
|
Sabidó E, Selevsek N, Aebersold R. Mass spectrometry-based proteomics for systems biology. Curr Opin Biotechnol 2011; 23:591-7. [PMID: 22169889 DOI: 10.1016/j.copbio.2011.11.014] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Accepted: 11/11/2011] [Indexed: 11/29/2022]
Abstract
Mass spectrometry (MS)-based proteomics has significantly contributed to the development of systems biology, a new paradigm for the life sciences in which biological processes are addressed in terms of dynamic networks of interacting molecules. Because of its advanced analytical capabilities, MS-based proteomics has been used extensively to identify the components of biological systems, and it is the method of choice to consistently quantify the effects of network perturbation in time and space. Herein, we review recent contributions of MS to systems biology and discuss several examples that illustrate the importance of mass spectrometry to elucidate the components and interactions of molecular networks.
Collapse
Affiliation(s)
- Eduard Sabidó
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Wolfgang-Pauli-Strasse 16, 8093 Zurich, Switzerland
| | | | | |
Collapse
|
144
|
Janes PW, Griesshaber B, Atapattu L, Nievergall E, Hii LL, Mensinga A, Chheang C, Day BW, Boyd AW, Bastiaens PI, Jørgensen C, Pawson T, Lackmann M. Eph receptor function is modulated by heterooligomerization of A and B type Eph receptors. ACTA ACUST UNITED AC 2011; 195:1033-45. [PMID: 22144690 PMCID: PMC3241718 DOI: 10.1083/jcb.201104037] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Beyond homotypic receptor interactions that are required for Eph signaling, ligand-independent association and crosstalk between members of the EphA and -B subclasses determine cell signaling outcomes. Eph receptors interact with ephrin ligands on adjacent cells to facilitate tissue patterning during normal and oncogenic development, in which unscheduled expression and somatic mutations contribute to tumor progression. EphA and B subtypes preferentially bind A- and B-type ephrins, respectively, resulting in receptor complexes that propagate via homotypic Eph–Eph interactions. We now show that EphA and B receptors cocluster, such that specific ligation of one receptor promotes recruitment and cross-activation of the other. Remarkably, coexpression of a kinase-inactive mutant EphA3 with wild-type EphB2 can cause either cross-activation or cross-inhibition, depending on relative expression. Our findings indicate that cellular responses to ephrin contact are determined by the EphA/EphB receptor profile on a given cell rather than the individual Eph subclass. Importantly, they imply that in tumor cells coexpressing different Ephs, functional mutations in one subtype may cause phenotypes that are a result of altered signaling from heterotypic rather from homotypic Eph clusters.
Collapse
Affiliation(s)
- Peter W Janes
- Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
145
|
Zhang G, Neubert TA. Comparison of three quantitative phosphoproteomic strategies to study receptor tyrosine kinase signaling. J Proteome Res 2011; 10:5454-62. [PMID: 22013880 PMCID: PMC3229182 DOI: 10.1021/pr200697x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
![]()
There are three quantitative phosphoproteomic strategies most commonly used to study receptor tyrosine kinase (RTK) signaling. These strategies quantify changes in: (1) all three forms of phosphosites (phosphoserine, phosphothreonine and phosphotyrosine) following enrichment of phosphopeptides by titanium dioxide or immobilized metal affinity chromatography; (2) phosphotyrosine sites following anti- phosphotyrosine antibody enrichment of phosphotyrosine peptides; or (3) phosphotyrosine proteins and their binding partners following anti-phosphotyrosine protein immunoprecipitation. However, it is not clear from literature which strategy is more effective. In this study, we assessed the utility of these three phosphoproteomic strategies in RTK signaling studies by using EphB receptor signaling as an example. We used all three strategies with stable isotope labeling with amino acids in cell culture (SILAC) to compare changes in phosphoproteomes upon EphB receptor activation. We used bioinformatic analysis to compare results from the three analyses. Our results show that the three strategies provide complementary information about RTK pathways. Quantitative phosphoproteomic strategies are most commonly used to study receptor tyrosine kinase (RTK) signaling by quantifying changes in: (1) phosphopeptides containing pS, pT, or pY; (2) phosphotyrosine-containing peptides; (3) phosphotyrosine-containing proteins. In this study, we assessed the utility of the three strategies for RTK signaling studies by using EphB receptor signaling as an example. Our results show that the three strategies are very complementary in providing information about RTK pathways.
Collapse
Affiliation(s)
- Guoan Zhang
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, New York 10016, United States
| | | |
Collapse
|
146
|
Maddigan A, Truitt L, Arsenault R, Freywald T, Allonby O, Dean J, Narendran A, Xiang J, Weng A, Napper S, Freywald A. EphB receptors trigger Akt activation and suppress Fas receptor-induced apoptosis in malignant T lymphocytes. THE JOURNAL OF IMMUNOLOGY 2011; 187:5983-94. [PMID: 22039307 DOI: 10.4049/jimmunol.1003482] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Treatment of hematopoietic malignancies often requires allogeneic bone marrow transplantation, and the subsequent graft-versus-leukemia response is crucial for the elimination of malignant cells. Cytotoxic T lymphocytes and NK cells responsible for the immunoelimination express Fas ligand and strongly rely on the induction of Fas receptor-mediated apoptosis for their action. Although cancer cells are removed successfully by graft-versus-leukemia reactions in myeloid malignancies, their efficiency is low in T cell leukemias. This may be partially because of the ability of malignant T cells to escape apoptosis. Our work shows that Eph family receptor EphB3 is consistently expressed by malignant T lymphocytes, most frequently in combination with EphB6, and that stimulation with their common ligands, ephrin-B1 and ephrin-B2, strongly suppresses Fas-induced apoptosis in these cells. This effect is associated with Akt activation and with the inhibition of the Fas receptor-initiated caspase proteolytic cascade. Akt proved to be crucial for the prosurvival response, because inhibition of Akt, but not of other molecules central to T cell biology, including Src kinases, MEK1 and MEK2, blocked the antiapoptotic effect. Overall, this demonstrates a new role for EphB receptors in the protection of malignant T cells from Fas-induced apoptosis through Akt engagement and prevention of caspase activation. Because Fas-triggered apoptosis is actively involved in the graft-versus-leukemia response and cytotoxic T cells express ephrin-Bs, our observations suggest that EphB receptors are likely to support immunoevasivenes of T cell malignancies and may represent promising targets for therapies, aiming to enhance immunoelimination of cancerous T cells.
Collapse
Affiliation(s)
- Alison Maddigan
- Department of Chemistry and Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
147
|
Biarc J, Chalkley RJ, Burlingame AL, Bradshaw RA. The induction of serine/threonine protein phosphorylations by a PDGFR/TrkA chimera in stably transfected PC12 cells. Mol Cell Proteomics 2011; 11:15-30. [PMID: 22027198 DOI: 10.1074/mcp.m111.013375] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Stably transfected PC12 cells expressing a chimeric receptor composed of the extracellular domain of the platelet-derived growth factor receptor BB and the transmembrane and intracellular domains of TrkA, the nerve growth factor receptor, were stimulated for 20 min with platelet-derived growth factor and the resulting phosphoproteome was determined from affinity purified tryptic peptides identified by tandem MS (MS/MS) analyses. The changes in the levels of individual phosphorylation sites in stimulated cells versus control were ascertained by the stable isotope labeling of amino acids in cell culture technique. A total of 2035 peptides (806 proteins) were indentified and quantified in both data sets. Of these, 424 phosphopeptides on 259 proteins were found to be up-regulated and 392 sites on 206 proteins were down-regulated (1.8-fold or more). Protein kinases and phosphatases, as well as sites in many proteins involved in G-protein signaling, were prominently represented in the up-regulated group and more than half of the kinase up-regulated phosphosites could be clustered into three sequence motifs; a similar distribution was also found for the down-regulated sites. A comparison of the up-regulated motif profile observed to that calculated from a previous study of the EGFR-induced phosphoproteome in human HeLa cells at the same time point showed a considerable amount of similarity, supporting the view that RTK signal transduction pathways and downstream modifications are likely to be extensively overlapping.
Collapse
Affiliation(s)
- Jordane Biarc
- Department of Pharmaceutical Chemistry, University of California, San Francisco CA 94158, USA
| | | | | | | |
Collapse
|
148
|
Bush JO, Soriano P. Eph/ephrin signaling: genetic, phosphoproteomic, and transcriptomic approaches. Semin Cell Dev Biol 2011; 23:26-34. [PMID: 22040918 DOI: 10.1016/j.semcdb.2011.10.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Accepted: 10/17/2011] [Indexed: 10/16/2022]
Abstract
The Eph receptor tyrosine kinases and their ephrin partners compose a large and complex family of signaling molecules involved in a wide variety of processes in development, homeostasis, and disease. The complexity inherent to Eph/ephrin signaling derives from several characteristics of the family. First, the large size and functional redundancy/compensation by family members presents a challenge in defining their in vivo roles. Second, the capacity for bidirectional signaling doubles the potential complexity, since every member has the ability to act both as a ligand and a receptor. Third, Ephs and ephrins can utilize a wide array of signal transduction pathways with a tremendous diversity of cell biological effect. The daunting complexity of Eph/ephrin signaling has increasingly prompted investigators to resort to multiple technological approaches to gain mechanistic insight. Here we review recent progress in the use of advanced mouse genetics in combination with proteomic and transcriptomic approaches to gain a more complete understanding of signaling mechanism in vivo. Integrating insights from such disparate approaches provides advantages in continuing to advance our understanding of how this multifarious group of signaling molecules functions in a diverse array of biological contexts.
Collapse
Affiliation(s)
- Jeffrey O Bush
- Department of Cell and Tissue Biology and Program in Craniofacial and Mesenchymal Biology, University of California at San Francisco, San Francisco, CA 94143, USA.
| | | |
Collapse
|
149
|
Eph/ephrin signaling in epidermal differentiation and disease. Semin Cell Dev Biol 2011; 23:92-101. [PMID: 22040910 DOI: 10.1016/j.semcdb.2011.10.017] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Accepted: 10/17/2011] [Indexed: 01/09/2023]
Abstract
Eph receptor tyrosine kinases mediate cell-cell communication by interacting with ephrin ligands residing on adjacent cell surfaces. In doing so, these juxtamembrane signaling complexes provide important contextual information about the cellular microenvironment that helps orchestrate tissue morphogenesis and maintain homeostasis. Eph/ephrin signaling has been implicated in various aspects of mammalian skin physiology, with several members of this large family of receptor tyrosine kinases and their ligands present in the epidermis, hair follicles, sebaceous glands, and underlying dermis. This review focuses on the emerging role of Eph receptors and ephrins in epidermal keratinocytes where they can modulate proliferation, migration, differentiation, and death. The activation of Eph receptors by ephrins at sites of cell-cell contact also appears to play a key role in the maturation of intercellular junctional complexes as keratinocytes move out of the basal layer and differentiate in the suprabasal layers of this stratified, squamous epithelium. Furthermore, alterations in the epidermal Eph/ephrin axis have been associated with cutaneous malignancy, wound healing defects and inflammatory skin conditions. These collective observations suggest that the Eph/ephrin cell-cell communication pathway may be amenable to therapeutic intervention for the purpose of restoring epidermal tissue homeostasis and integrity in dermatological disorders.
Collapse
|
150
|
Mollapour M, Tsutsumi S, Kim YS, Trepel J, Neckers L. Casein kinase 2 phosphorylation of Hsp90 threonine 22 modulates chaperone function and drug sensitivity. Oncotarget 2011; 2:407-17. [PMID: 21576760 PMCID: PMC3248188 DOI: 10.18632/oncotarget.272] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The molecular chaperone Heat Shock Protein 90 (Hsp90) is essential for the function of various oncoproteins that are vital components of multiple signaling networks regulating cancer cell proliferation, survival, and metastasis. Hsp90 chaperone function is coupled to its ATPase activity, which can be inhibited by natural products such as the ansamycin geldanamycin (GA) and the resorcinol radicicol (RD). These compounds have served as templates for development of numerous natural product Hsp90 inhibitors. More recently, second generation, fully synthetic Hsp90 inhibitors, based on a variety of chemical scaffolds, have also been synthesized. Together, 18 natural product and synthetic Hsp90 inhibitors have entered clinical trial in cancer patients. To successfully develop Hsp90 inhibitors for oncology indications it is important to understand the factors that influence the susceptibility of Hsp90 to these drugs in vivo. We recently reported that Casein Kinase 2 phosphorylates a conserved threonine residue (T22) in helix-1 of the yeast Hsp90 N-domain both in vitro and in vivo. Phosphorylation of this residue reduces ATPase activity and affects Hsp90 chaperone function. Here, we present additional data demonstrating that ATP binding but not N-domain dimerization is a prerequisite for T22 phosphorylation. We also provide evidence that T22 is an important determinant of Hsp90 inhibitor sensitivity in yeast and we show that T22 phosphorylation status contributes to drug sensitivity in vivo.
Collapse
Affiliation(s)
- Mehdi Mollapour
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA.
| | | | | | | | | |
Collapse
|