51
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Ke M, Chu B, Lin L, Tian R. SH2 Domains as Affinity Reagents for Phosphotyrosine Protein Enrichment and Proteomic Analysis. Methods Mol Biol 2017; 1555:395-406. [PMID: 28092045 DOI: 10.1007/978-1-4939-6762-9_22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Dynamic tyrosine phosphorylation is a key molecular modulation for many signal transduction events. Because of their low abundance and dynamic nature in cells, the detection and enrichment of phosphotyrosine proteins has long relied on specific antibodies, such as 4G10 and P-Tyr-100. Another well-established approach for phosphotyrosine proteins recognition and enrichment is by their specific binding domains, such as Src homology 2 (SH2) domains. In this chapter, we describe a typical analytical approach for purifying specific SH2 domains, enriching specific phosphotyrosine proteins from activated cells, mass spectrometry analysis, and related data analysis.
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Affiliation(s)
- Mi Ke
- Department of Chemistry, South University of Science and Technology of China, Shenzhen, 518055, People's Republic of China
| | - Bizhu Chu
- Department of Chemistry, South University of Science and Technology of China, Shenzhen, 518055, People's Republic of China
| | - Lin Lin
- Department of Chemistry, South University of Science and Technology of China, Shenzhen, 518055, People's Republic of China
- Materials Characterization and Preparation Center, South University of Science and Technology of China, Shenzhen, 518055, People's Republic of China
| | - Ruijun Tian
- Department of Chemistry, South University of Science and Technology of China, Shenzhen, 518055, People's Republic of China.
- Shenzhen Key Laboratory of Cell Microenvironment, South University of Science and Technology of China, Shenzhen, 518055, People's Republic of China.
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52
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Tape CJ, Jørgensen C. Cell-Specific Labeling for Analyzing Bidirectional Signaling by Mass Spectrometry. Methods Mol Biol 2017; 1636:219-234. [PMID: 28730482 DOI: 10.1007/978-1-4939-7154-1_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2024]
Abstract
Cell-specific proteome labeling enables global proteome-wide analysis of cell signaling in heterotypic co-cultures. Such approaches have provided unique insight in contact-initiated receptor tyrosine kinase signaling, transfer of proteomic material between heterotypic cells, and interactions between normal and oncogenic cells. Here we describe current methods for cell-specific labeling of heterotypic cells with isotopic labeled amino acids (e.g., SILAC and CTAP). We outline the advantages and disadvantages of individual approaches, describe typical experimental scenarios, and discuss where each experimental approach is optimally applied.
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Affiliation(s)
- Christopher J Tape
- The Institute of Cancer Research, London, SW3 6JB, UK
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Claus Jørgensen
- Systems Oncology, CRUK Manchester Institute, The University of Manchester, Wilmslow Road, Manchester, M20 4QL, UK.
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53
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O'Neill AK, Kindberg AA, Niethamer TK, Larson AR, Ho HYH, Greenberg ME, Bush JO. Unidirectional Eph/ephrin signaling creates a cortical actomyosin differential to drive cell segregation. J Cell Biol 2016; 215:217-229. [PMID: 27810913 PMCID: PMC5084648 DOI: 10.1083/jcb.201604097] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 09/13/2016] [Indexed: 01/01/2023] Open
Abstract
Cell segregation is the process by which cells self-organize to establish developmental boundaries, an essential step in tissue formation. Cell segregation is a common outcome of Eph/ephrin signaling, but the mechanisms remain unclear. In craniofrontonasal syndrome, X-linked mosaicism for ephrin-B1 expression has been hypothesized to lead to aberrant Eph/ephrin-mediated cell segregation. Here, we use mouse genetics to exploit mosaicism to study cell segregation in the mammalian embryo and integrate live-cell imaging to examine the underlying cellular and molecular mechanisms. Our data demonstrate that dramatic ephrin-B1-mediated cell segregation occurs in the early neuroepithelium. In contrast to the paradigm that repulsive bidirectional signaling drives cell segregation, unidirectional EphB kinase signaling leads to cell sorting by the Rho kinase-dependent generation of a cortical actin differential between ephrin-B1- and EphB-expressing cells. These results define mechanisms of Eph/ephrin-mediated cell segregation, implicating unidirectional regulation of cortical actomyosin contractility as a key effector of this fundamental process.
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Affiliation(s)
- Audrey K O'Neill
- Department of Cell and Tissue Biology, Program in Craniofacial Biology and Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143
| | - Abigail A Kindberg
- Department of Cell and Tissue Biology, Program in Craniofacial Biology and Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143
| | - Terren K Niethamer
- Department of Cell and Tissue Biology, Program in Craniofacial Biology and Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143
| | - Andrew R Larson
- Department of Cell and Tissue Biology, Program in Craniofacial Biology and Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143
| | - Hsin-Yi Henry Ho
- Department of Cell Biology and Human Anatomy, University of California Davis School of Medicine, Davis, CA 95817
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115
| | | | - Jeffrey O Bush
- Department of Cell and Tissue Biology, Program in Craniofacial Biology and Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143
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54
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Brown JAL, Ni Chonghaile T, Matchett KB, Lynam-Lennon N, Kiely PA. Big Data-Led Cancer Research, Application, and Insights. Cancer Res 2016; 76:6167-6170. [PMID: 27803103 DOI: 10.1158/0008-5472.can-16-0860] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 07/31/2016] [Indexed: 11/16/2022]
Abstract
Insights distilled from integrating multiple big-data or "omic" datasets have revealed functional hierarchies of molecular networks driving tumorigenesis and modifiers of treatment response. Identifying these novel key regulatory and dysregulated elements is now informing personalized medicine. Crucially, although there are many advantages to this approach, there are several key considerations to address. Here, we examine how this big data-led approach is impacting many diverse areas of cancer research, through review of the key presentations given at the Irish Association for Cancer Research Meeting and importantly how the results may be applied to positively affect patient outcomes. Cancer Res; 76(21); 6167-70. ©2016 AACR.
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Affiliation(s)
- James A L Brown
- Discipline of Surgery, School of Medicine, The Lambe Institute for Translational Research, National University of Ireland Galway, Galway, Ireland.
| | - Triona Ni Chonghaile
- Physiology & Medical Physics Department, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Kyle B Matchett
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, United Kingdom
| | - Niamh Lynam-Lennon
- Trinity Translational Medicine Institute, Department of Surgery, Trinity College Dublin, Dublin, Ireland
| | - Patrick A Kiely
- Graduate Entry Medical School, University of Limerick, Limerick, Ireland
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55
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Treindl F, Ruprecht B, Beiter Y, Schultz S, Döttinger A, Staebler A, Joos TO, Kling S, Poetz O, Fehm T, Neubauer H, Kuster B, Templin MF. A bead-based western for high-throughput cellular signal transduction analyses. Nat Commun 2016; 7:12852. [PMID: 27659302 PMCID: PMC5036152 DOI: 10.1038/ncomms12852] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 08/08/2016] [Indexed: 12/28/2022] Open
Abstract
Dissecting cellular signalling requires the analysis of large number of proteins. The DigiWest approach we describe here transfers the western blot to a bead-based microarray platform. By combining gel-based protein separation with immobilization on microspheres, hundreds of replicas of the initial blot are created, thus enabling the comprehensive analysis of limited material, such as cells collected by laser capture microdissection, and extending traditional western blotting to reach proteomic scales. The combination of molecular weight resolution, sensitivity and signal linearity on an automated platform enables the rapid quantification of hundreds of specific proteins and protein modifications in complex samples. This high-throughput western blot approach allowed us to identify and characterize alterations in cellular signal transduction that occur during the development of resistance to the kinase inhibitor Lapatinib, revealing major changes in the activation state of Ephrin-mediated signalling and a central role for p53-controlled processes. Dissecting cellular signalling requires the analysis of large numbers of proteins. Here the authors describe DigiWest, a high-throughput protein detection method that combines the concept of western and widely-used bead array systems that allows rapid quantification of hundreds of specific proteins.
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Affiliation(s)
- Fridolin Treindl
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany.,Pharmaceutical Biotechnology, Eberhard-Karls-Universität Tübingen, Tübingen, 72770 Reutlingen, Germany
| | - Benjamin Ruprecht
- Chair for Proteomics and Bioanalytics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, 85354 Freising, Germany.,Center for Integrated Protein Science Munich, 85354 Freising, Germany
| | - Yvonne Beiter
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany.,Pharmaceutical Biotechnology, Eberhard-Karls-Universität Tübingen, Tübingen, 72770 Reutlingen, Germany
| | - Silke Schultz
- Department of Obstetrics and Gynecology, Medical Faculty and University Hospital of the Heinrich-Heine University Duesseldorf, 40225 Düsseldorf, Germany
| | - Anette Döttinger
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany
| | - Annette Staebler
- Department of Pathology, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Thomas O Joos
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany
| | - Simon Kling
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany
| | - Oliver Poetz
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany
| | - Tanja Fehm
- Department of Obstetrics and Gynecology, Medical Faculty and University Hospital of the Heinrich-Heine University Duesseldorf, 40225 Düsseldorf, Germany
| | - Hans Neubauer
- Department of Obstetrics and Gynecology, Medical Faculty and University Hospital of the Heinrich-Heine University Duesseldorf, 40225 Düsseldorf, Germany
| | - Bernhard Kuster
- Chair for Proteomics and Bioanalytics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, 85354 Freising, Germany.,Center for Integrated Protein Science Munich, 85354 Freising, Germany.,Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), Technische Universität München, 85354 Freising, Germany
| | - Markus F Templin
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany.,Pharmaceutical Biotechnology, Eberhard-Karls-Universität Tübingen, Tübingen, 72770 Reutlingen, Germany
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56
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Gaitanos TN, Koerner J, Klein R. Tiam-Rac signaling mediates trans-endocytosis of ephrin receptor EphB2 and is important for cell repulsion. J Cell Biol 2016; 214:735-52. [PMID: 27597758 PMCID: PMC5021091 DOI: 10.1083/jcb.201512010] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 08/09/2016] [Indexed: 11/26/2022] Open
Abstract
Cell repulsion requires trans-endocytosis of ephrin receptors at cell–cell contact sites, but the mechanisms underlying this process are unclear. Here, Gaitanos et al. show that Tiam–Rac signaling mediates trans-endocytosis of EphB2 and is necessary for cell repulsion. Ephrin receptors interact with membrane-bound ephrin ligands to regulate contact-mediated attraction or repulsion between opposing cells, thereby influencing tissue morphogenesis. Cell repulsion requires bidirectional trans-endocytosis of clustered Eph–ephrin complexes at cell interfaces, but the mechanisms underlying this process are poorly understood. Here, we identified an actin-regulating pathway allowing ephrinB+ cells to trans-endocytose EphB receptors from opposing cells. Live imaging revealed Rac-dependent F-actin enrichment at sites of EphB2 internalization, but not during vesicle trafficking. Systematic depletion of Rho family GTPases and their regulatory proteins identified the Rac subfamily and the Rac-specific guanine nucleotide exchange factor Tiam2 as key components of EphB2 trans-endocytosis, a pathway previously implicated in Eph forward signaling, in which ephrins act as in trans ligands of Eph receptors. However, unlike in Eph signaling, this pathway is not required for uptake of soluble ligands in ephrinB+ cells. We also show that this pathway is required for EphB2-stimulated contact repulsion. These results support the existence of a conserved pathway for EphB trans-endocytosis that removes the physical tether between cells, thereby enabling cell repulsion.
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Affiliation(s)
- Thomas N Gaitanos
- Department of Molecules-Signaling-Development, Max Planck Institute of Neurobiology, 82152 Munich-Martinsried, Germany
| | - Jorg Koerner
- Department of Molecules-Signaling-Development, Max Planck Institute of Neurobiology, 82152 Munich-Martinsried, Germany
| | - Ruediger Klein
- Department of Molecules-Signaling-Development, Max Planck Institute of Neurobiology, 82152 Munich-Martinsried, Germany
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57
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KSR1 and EPHB4 Regulate Myc and PGC1β To Promote Survival of Human Colon Tumors. Mol Cell Biol 2016; 36:2246-61. [PMID: 27273865 DOI: 10.1128/mcb.00087-16] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 05/26/2016] [Indexed: 01/05/2023] Open
Abstract
Identification and characterization of survival pathways active in tumor cells but absent in normal tissues provide opportunities to develop effective anticancer therapies with reduced toxicity to the patient. We show here that, like kinase suppressor of Ras 1 (KSR1), EPH (erythropoietin-producing hepatocellular carcinoma) receptor B4 (EPHB4) is aberrantly overexpressed in human colon tumor cell lines and selectively required for their survival. KSR1 and EPHB4 support tumor cell survival by promoting the expression of downstream targets, Myc and the transcriptional coactivator peroxisome proliferator-activated receptor gamma coactivator 1β (PGC1β). While KSR1 promotes the aberrant expression of Myc and the PGC1β protein via a posttranscriptional mechanism, EPHB4 has a greater effect on Myc and PGC1β expression via its ability to elevate mRNA levels. Subsequent analysis of the posttranscriptional regulation demonstrated that KSR1 promotes the translation of Myc protein. These findings reveal novel KSR1- and EPHB4-dependent signaling pathways supporting the survival of colorectal cancer cells through regulation of Myc and PGC1β, suggesting that inhibition of KSR1 or EPHB4 effectors may lead to selective toxicity in colorectal tumors.
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58
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Tape CJ. Systems Biology Analysis of Heterocellular Signaling. Trends Biotechnol 2016; 34:627-637. [DOI: 10.1016/j.tibtech.2016.02.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 02/26/2016] [Accepted: 02/29/2016] [Indexed: 10/22/2022]
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59
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Gong J, Körner R, Gaitanos L, Klein R. Exosomes mediate cell contact-independent ephrin-Eph signaling during axon guidance. J Cell Biol 2016; 214:35-44. [PMID: 27354374 PMCID: PMC4932373 DOI: 10.1083/jcb.201601085] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 06/07/2016] [Indexed: 11/24/2022] Open
Abstract
Ephs interact with ESCRT complex components and are released via extracellular vesicles or exosomes. EphB2 released via exosomes mediates a novel cell contact–independent mode of ephrin-Eph signaling that contributes to axon guidance in cell–cell repulsion processes. The cellular release of membranous vesicles known as extracellular vesicles (EVs) or exosomes represents a novel mode of intercellular communication. Eph receptor tyrosine kinases and their membrane-tethered ephrin ligands have very important roles in such biologically diverse processes as neuronal development, plasticity, and pathological diseases. Until now, it was thought that ephrin-Eph signaling requires direct cell contact. Although the biological functions of ephrin-Eph signaling are well understood, our mechanistic understanding remains modest. Here we report the release of EVs containing Ephs and ephrins by different cell types, a process requiring endosomal sorting complex required for transport (ESCRT) activity and regulated by neuronal activity. Treatment of cells with purified EphB2+ EVs induces ephrinB1 reverse signaling and causes neuronal axon repulsion. These results indicate a novel mechanism of ephrin-Eph signaling independent of direct cell contact and proteolytic cleavage and suggest the participation of EphB2+ EVs in neural development and synapse physiology.
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Affiliation(s)
- Jingyi Gong
- Max Planck Institute of Neurobiology, 82152 Martinsried, Germany Munich Cluster for Systems Neurology (SyNergy), 80336 Munich, Germany
| | - Roman Körner
- Max Planck Institute of Biochemistry, 82152 Martinsried, Germany Munich Cluster for Systems Neurology (SyNergy), 80336 Munich, Germany
| | - Louise Gaitanos
- Max Planck Institute of Neurobiology, 82152 Martinsried, Germany
| | - Rüdiger Klein
- Max Planck Institute of Neurobiology, 82152 Martinsried, Germany Munich Cluster for Systems Neurology (SyNergy), 80336 Munich, Germany
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60
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Chitforoushzadeh Z, Ye Z, Sheng Z, LaRue S, Fry RC, Lauffenburger DA, Janes KA. TNF-insulin crosstalk at the transcription factor GATA6 is revealed by a model that links signaling and transcriptomic data tensors. Sci Signal 2016; 9:ra59. [PMID: 27273097 DOI: 10.1126/scisignal.aad3373] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Signal transduction networks coordinate transcriptional programs activated by diverse extracellular stimuli, such as growth factors and cytokines. Cells receive multiple stimuli simultaneously, and mapping how activation of the integrated signaling network affects gene expression is a challenge. We stimulated colon adenocarcinoma cells with various combinations of the cytokine tumor necrosis factor (TNF) and the growth factors insulin and epidermal growth factor (EGF) to investigate signal integration and transcriptional crosstalk. We quantitatively linked the proteomic and transcriptomic data sets by implementing a structured computational approach called tensor partial least squares regression. This statistical model accurately predicted transcriptional signatures from signaling arising from single and combined stimuli and also predicted time-dependent contributions of signaling events. Specifically, the model predicted that an early-phase, AKT-associated signal downstream of insulin repressed a set of transcripts induced by TNF. Through bioinformatics and cell-based experiments, we identified the AKT-repressed signal as glycogen synthase kinase 3 (GSK3)-catalyzed phosphorylation of Ser(37) on the long form of the transcription factor GATA6. Phosphorylation of GATA6 on Ser(37) promoted its degradation, thereby preventing GATA6 from repressing transcripts that are induced by TNF and attenuated by insulin. Our analysis showed that predictive tensor modeling of proteomic and transcriptomic data sets can uncover pathway crosstalk that produces specific patterns of gene expression in cells receiving multiple stimuli.
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Affiliation(s)
- Zeinab Chitforoushzadeh
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA. Department of Pharmacology, University of Virginia, Charlottesville, VA 22908, USA
| | - Zi Ye
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA
| | - Ziran Sheng
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA
| | - Silvia LaRue
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA
| | - Rebecca C Fry
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Douglas A Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kevin A Janes
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA.
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61
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Tape CJ, Ling S, Dimitriadi M, McMahon KM, Worboys JD, Leong HS, Norrie IC, Miller CJ, Poulogiannis G, Lauffenburger DA, Jørgensen C. Oncogenic KRAS Regulates Tumor Cell Signaling via Stromal Reciprocation. Cell 2016; 165:910-20. [PMID: 27087446 PMCID: PMC4868820 DOI: 10.1016/j.cell.2016.03.029] [Citation(s) in RCA: 213] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 02/05/2016] [Accepted: 03/17/2016] [Indexed: 12/12/2022]
Abstract
Oncogenic mutations regulate signaling within both tumor cells and adjacent stromal cells. Here, we show that oncogenic KRAS (KRAS(G12D)) also regulates tumor cell signaling via stromal cells. By combining cell-specific proteome labeling with multivariate phosphoproteomics, we analyzed heterocellular KRAS(G12D) signaling in pancreatic ductal adenocarcinoma (PDA) cells. Tumor cell KRAS(G12D) engages heterotypic fibroblasts, which subsequently instigate reciprocal signaling in the tumor cells. Reciprocal signaling employs additional kinases and doubles the number of regulated signaling nodes from cell-autonomous KRAS(G12D). Consequently, reciprocal KRAS(G12D) produces a tumor cell phosphoproteome and total proteome that is distinct from cell-autonomous KRAS(G12D) alone. Reciprocal signaling regulates tumor cell proliferation and apoptosis and increases mitochondrial capacity via an IGF1R/AXL-AKT axis. These results demonstrate that oncogene signaling should be viewed as a heterocellular process and that our existing cell-autonomous perspective underrepresents the extent of oncogene signaling in cancer. VIDEO ABSTRACT.
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Affiliation(s)
- Christopher J Tape
- The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Stephanie Ling
- The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Maria Dimitriadi
- The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Kelly M McMahon
- Cancer Research UK Manchester Institute, University of Manchester, Wilmslow Road, Manchester M20 4BX, UK
| | - Jonathan D Worboys
- The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK; Cancer Research UK Manchester Institute, University of Manchester, Wilmslow Road, Manchester M20 4BX, UK
| | - Hui Sun Leong
- Cancer Research UK Manchester Institute, University of Manchester, Wilmslow Road, Manchester M20 4BX, UK
| | - Ida C Norrie
- The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK; Cancer Research UK Manchester Institute, University of Manchester, Wilmslow Road, Manchester M20 4BX, UK
| | - Crispin J Miller
- Cancer Research UK Manchester Institute, University of Manchester, Wilmslow Road, Manchester M20 4BX, UK
| | | | - Douglas A Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Claus Jørgensen
- The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK; Cancer Research UK Manchester Institute, University of Manchester, Wilmslow Road, Manchester M20 4BX, UK.
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62
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Lyons J, Herring CA, Banerjee A, Simmons AJ, Lau KS. Multiscale analysis of the murine intestine for modeling human diseases. Integr Biol (Camb) 2016; 7:740-57. [PMID: 26040649 DOI: 10.1039/c5ib00030k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
When functioning properly, the intestine is one of the key interfaces between the human body and its environment. It is responsible for extracting nutrients from our food and excreting our waste products. It provides an environment for a host of healthful microbes and serves as a first defense against pathogenic ones. These processes require tight homeostatic controls, which are provided by the interactions of a complex mix of epithelial, stromal, neural and immune cells, as well as the resident microflora. This homeostasis can be disrupted by invasive microbes, genetic lesions, and carcinogens, resulting in diseases such Clostridium difficile infection, inflammatory bowel disease (IBD) and cancer. Enormous strides have been made in understanding how this important organ functions in health and disease using everything from cell culture systems to animal models to human tissue samples. This has resulted in better therapies for all of these diseases, but there is still significant room for improvement. In the United States alone, 14,000 people per year die of C. difficile, up to 1.6 million people suffer from IBD, and more than 50,000 people die every year from colon cancer. Because these and other intestinal diseases arise from complex interactions between the different components of the gut ecosystem, we propose that systems approaches that address this complexity in an integrative manner may eventually lead to improved therapeutics that deliver lasting cures. This review will discuss the use of systems biology for studying intestinal diseases in vivo with particular emphasis on mouse models. Additionally, it will focus on established experimental techniques that have been used to drive this systems-level analysis, and emerging techniques that will push this field forward in the future.
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Affiliation(s)
- Jesse Lyons
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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63
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Locard-Paulet M, Lim L, Veluscek G, McMahon K, Sinclair J, van Weverwijk A, Worboys JD, Yuan Y, Isacke CM, Jørgensen C. Phosphoproteomic analysis of interacting tumor and endothelial cells identifies regulatory mechanisms of transendothelial migration. Sci Signal 2016; 9:ra15. [PMID: 26861043 PMCID: PMC6485367 DOI: 10.1126/scisignal.aac5820] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The exit of metastasizing tumor cells from the vasculature, extravasation, is regulated by their dynamic interactions with the endothelial cells that line the internal surface of vessels. To elucidate signals controlling tumor cell adhesion to the endothelium and subsequent transendothelial migration, we performed phosphoproteomic analysis to map cell-specific changes in protein phosphorylation that were triggered by contact between metastatic MDA-MB-231 breast cancer cells and endothelial cells. From the 2669 unique phosphorylation sites identified, 77 and 43 were differentially phosphorylated in the tumor cells and endothelial cells, respectively. The receptor tyrosine kinase ephrin type A receptor 2 (EPHA2) exhibited decreased Tyr(772) phosphorylation in the cancer cells upon endothelial contact. Knockdown of EPHA2 increased adhesion of the breast cancer cells to human umbilical vein endothelial cells (HUVECs) and their transendothelial migration in coculture cell assays, as well as early-stage lung colonization in vivo. EPHA2-mediated inhibition of transendothelial migration of breast cancer cells depended on interaction with the ligand ephrinA1 on HUVECs and phosphorylation of EPHA2-Tyr(772). When EPHA2 phosphorylation dynamics were compared between cell lines of different metastatic ability, EPHA2-Tyr(772) was rapidly dephosphorylated after ephrinA1 stimulation specifically in cells targeting the lung. Knockdown of the phosphatase LMW-PTP reduced adhesion and transendothelial migration of the breast cancer cells. Overall, cell-specific phosphoproteomic analysis provides a bidirectional map of contact-initiated signaling between tumor and endothelial cells that can be further investigated to identify mechanisms controlling the transendothelial cell migration of cancer cells.
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Affiliation(s)
- Marie Locard-Paulet
- Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK. Cancer Research UK Manchester Institute, The University of Manchester, Wilmslow Road, Manchester M20 4BX, UK
| | - Lindsay Lim
- Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Giulia Veluscek
- Cancer Research UK Manchester Institute, The University of Manchester, Wilmslow Road, Manchester M20 4BX, UK
| | - Kelly McMahon
- Cancer Research UK Manchester Institute, The University of Manchester, Wilmslow Road, Manchester M20 4BX, UK
| | - John Sinclair
- Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Antoinette van Weverwijk
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
| | - Jonathan D Worboys
- Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK. Cancer Research UK Manchester Institute, The University of Manchester, Wilmslow Road, Manchester M20 4BX, UK
| | - Yinyin Yuan
- Centre for Evolution and Cancer and Centre for Molecular Pathology, Division of Molecular Pathology, The Institute of Cancer Research, 15 Cotswold Road, Sutton SM2 5NG, UK
| | - Clare M Isacke
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
| | - Claus Jørgensen
- Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK. Cancer Research UK Manchester Institute, The University of Manchester, Wilmslow Road, Manchester M20 4BX, UK.
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Mechanisms of ephrin-Eph signalling in development, physiology and disease. Nat Rev Mol Cell Biol 2016; 17:240-56. [PMID: 26790531 DOI: 10.1038/nrm.2015.16] [Citation(s) in RCA: 433] [Impact Index Per Article: 54.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Eph receptor Tyr kinases and their membrane-tethered ligands, the ephrins, elicit short-distance cell-cell signalling and thus regulate many developmental processes at the interface between pattern formation and morphogenesis, including cell sorting and positioning, and the formation of segmented structures and ordered neural maps. Their roles extend into adulthood, when ephrin-Eph signalling regulates neuronal plasticity, homeostatic events and disease processes. Recently, new insights have been gained into the mechanisms of ephrin-Eph signalling in different cell types, and into the physiological importance of ephrin-Eph in different organs and in disease, raising questions for future research directions.
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Locard-Paulet M, Pible O, Gonzalez de Peredo A, Alpha-Bazin B, Almunia C, Burlet-Schiltz O, Armengaud J. Clinical implications of recent advances in proteogenomics. Expert Rev Proteomics 2016; 13:185-99. [DOI: 10.1586/14789450.2016.1132169] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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66
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Welsh M, Jamalpour M, Zang G, Åkerblom B. The role of the Src Homology-2 domain containing protein B (SHB) in β cells. J Mol Endocrinol 2016; 56:R21-31. [PMID: 26489764 DOI: 10.1530/jme-15-0228] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/20/2015] [Indexed: 12/17/2022]
Abstract
This review will describe the SH2-domain signaling protein Src Homology-2 domain containing protein B (SHB) and its role in various physiological processes relating in particular to glucose homeostasis and β cell function. SHB operates downstream of several tyrosine kinase receptors and assembles signaling complexes in response to receptor activation by interacting with other signaling proteins via its other domains (proline-rich, phosphotyrosine-binding and tyrosine-phosphorylation sites). The subsequent responses are context-dependent. Absence of Shb in mice has been found to exert effects on hematopoiesis, angiogenesis and glucose metabolism. Specifically, first-phase insulin secretion in response to glucose was impaired and this effect was related to altered characteristics of focal adhesion kinase activation modulating signaling through Akt, ERK, β catenin and cAMP. It is believed that SHB plays a role in integrating adaptive responses to various stimuli by simultaneously modulating cellular responses in different cell-types, thus playing a role in maintaining physiological homeostasis.
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Affiliation(s)
- Michael Welsh
- Department of Medical Cell BiologyUppsala University, PO Box 571, Husargatan 3, SE-75123 Uppsala, Sweden
| | - Maria Jamalpour
- Department of Medical Cell BiologyUppsala University, PO Box 571, Husargatan 3, SE-75123 Uppsala, Sweden
| | - Guangxiang Zang
- Department of Medical Cell BiologyUppsala University, PO Box 571, Husargatan 3, SE-75123 Uppsala, Sweden
| | - Björn Åkerblom
- Department of Medical Cell BiologyUppsala University, PO Box 571, Husargatan 3, SE-75123 Uppsala, Sweden
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Li L, Xu N, Zhang JF, Xu LL, Zhou X, Huang BT, Li YL, Liu XL. EphB4/ephrinB2 Contributes to Imatinib Resistance in Chronic Myeloid Leukemia Involved in Cytoskeletal Proteins. Int J Med Sci 2016; 13:365-73. [PMID: 27226777 PMCID: PMC4879769 DOI: 10.7150/ijms.14989] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Accepted: 04/12/2016] [Indexed: 11/07/2022] Open
Abstract
INTRODUCTION The mechanism of EphB4/ephrinB2 in the resistance of chronic myelogenous leukemia to imatinib keeps unknown. METHODS The imatinib resistant chronic myelogenous leukemia cell line-K562-R, was established. EphB4 receptor expression was detected in patients and resistant cells. Cell migration and drug sensitivity were tested in the EphB4 knockdown cells and mouse models. RESULTS The EphB4 receptor was over-expressed in blast crisis patients compared to chronic phase patients. The level of EphB4 receptor expression was associated with a complete cytogenetic response within 12 months. Enhanced expression of the EphB4 receptor was detected in the K562-R cells. EphB4 knockdown inhibited cell migration ability and restored sensitivity to imatinib in vitro and in vivo. Restored sensitivity to imatinib was observed in K562-R cells, along with increased levels of phospho-EphB4 and decreased phosphorylation levels of RhoA, Rac1, and Cdc42. CONCLUSION Our study illustrates that aberrant activation of EphB4/ephrinB2 may mediate chronic myeloid leukemia resistance involved in cytoskeletal proteins.
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Affiliation(s)
- Lin Li
- 1. Department of Hematology, Nanfang Hospital, Southern Medical University, 1838 North Guangzhou Ave, Guangzhou 510515, Guangdong, China
| | - Na Xu
- 1. Department of Hematology, Nanfang Hospital, Southern Medical University, 1838 North Guangzhou Ave, Guangzhou 510515, Guangdong, China
| | - Jin-Fang Zhang
- 2. Department of Paediatric Hematology and Oncology, Clinical Center of Tumor Therapy, Guangdong General Hospital, Guangdong Academy of Medical Sciences, 510000, China
| | - Lu-Lu Xu
- 1. Department of Hematology, Nanfang Hospital, Southern Medical University, 1838 North Guangzhou Ave, Guangzhou 510515, Guangdong, China
| | - Xuan Zhou
- 1. Department of Hematology, Nanfang Hospital, Southern Medical University, 1838 North Guangzhou Ave, Guangzhou 510515, Guangdong, China
| | - Bin-Tao Huang
- 3. Department of Hematology, The Affiliated Hospital of Inner Mongolia Medical University, 1 Tongdao Avenue North, Hohhot 010059, China
| | - Yu-Ling Li
- 1. Department of Hematology, Nanfang Hospital, Southern Medical University, 1838 North Guangzhou Ave, Guangzhou 510515, Guangdong, China
| | - Xiao-Li Liu
- 1. Department of Hematology, Nanfang Hospital, Southern Medical University, 1838 North Guangzhou Ave, Guangzhou 510515, Guangdong, China
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Lindoso RS, Sandim V, Collino F, Carvalho AB, Dias J, da Costa MR, Zingali RB, Vieyra A. Proteomics of cell-cell interactions in health and disease. Proteomics 2015; 16:328-44. [PMID: 26552723 DOI: 10.1002/pmic.201500341] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 09/29/2015] [Accepted: 11/02/2015] [Indexed: 12/11/2022]
Abstract
The mechanisms of cell-cell communications are now under intense study by proteomic approaches. Proteomics has unraveled changes in protein profiling as the result of cell interactions mediated by ligand/receptor, hormones, soluble factors, and the content of extracellular vesicles. Besides being a brief overview of the main and profitable methodologies now available (evaluating theory behind the methods, their usefulness, and pitfalls), this review focuses on-from a proteome perspective-some signaling pathways and post-translational modifications (PTMs), which are essential for understanding ischemic lesions and their recovery in two vital organs in mammals, the heart, and the kidney. Knowledge of misdirection of the proteome during tissue recovery, such as represented by the convergence between fibrosis and cancer, emerges as an important tool in prognosis. Proteomics of cell-cell interaction is also especially useful for understanding how stem cells interact in injured tissues, anticipating clues for rational therapeutic interventions. In the effervescent field of induced pluripotency and cell reprogramming, proteomic studies have shown what proteins from specialized cells contribute to the recovery of infarcted tissues. Overall, we conclude that proteomics is at the forefront in helping us to understand the mechanisms that underpin prevalent pathological processes.
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Affiliation(s)
- Rafael S Lindoso
- Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil.,National Institute of Science and Technology for Structural Biology and Bioimaging, Rio de Janeiro, RJ, Brazil
| | - Vanessa Sandim
- National Institute of Science and Technology for Structural Biology and Bioimaging, Rio de Janeiro, RJ, Brazil.,Leopoldo de Meis Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Federica Collino
- Department of Medical Sciences and Molecular Biotechnology Center, University of Turin, Turin, Italy.,Translational Center of Regenerative Medicine, University of Turin/Fresenius Medical Care, Turin, Italy
| | - Adriana B Carvalho
- Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil.,National Institute of Science and Technology for Structural Biology and Bioimaging, Rio de Janeiro, RJ, Brazil
| | - Juliana Dias
- National Institute of Cancer, Rio de Janeiro, RJ, Brazil
| | - Milene R da Costa
- Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Russolina B Zingali
- National Institute of Science and Technology for Structural Biology and Bioimaging, Rio de Janeiro, RJ, Brazil.,Leopoldo de Meis Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil.,Proteomic Network of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Adalberto Vieyra
- Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil.,National Institute of Science and Technology for Structural Biology and Bioimaging, Rio de Janeiro, RJ, Brazil.,Translational Biomedicine Graduate Program, Grand Rio University, Duque de Caxias, RJ, Brazil
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69
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Terriente J, Pujades C. Cell segregation in the vertebrate hindbrain: a matter of boundaries. Cell Mol Life Sci 2015; 72:3721-30. [PMID: 26089248 PMCID: PMC11113478 DOI: 10.1007/s00018-015-1953-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 05/06/2015] [Accepted: 06/08/2015] [Indexed: 02/07/2023]
Abstract
Segregating cells into compartments during embryonic development is essential for growth and pattern formation. In the developing hindbrain, boundaries separate molecularly, physically and neuroanatomically distinct segments called rhombomeres. After rhombomeric cells have acquired their identity, interhombomeric boundaries restrict cell intermingling between adjacent rhombomeres and act as signaling centers to pattern the surrounding tissue. Several works have stressed the relevance of Eph/ephrin signaling in rhombomeric cell sorting. Recent data have unveiled the role of this pathway in the assembly of actomyosin cables as an important mechanism for keeping cells from different rhombomeres segregated. In this Review, we will provide a short summary of recent evidences gathered in different systems suggesting that physical actomyosin barriers can be a general mechanism for tissue separation. We will discuss current evidences supporting a model where cell-cell signaling pathways, such as Eph/ephrin, govern compartmental cell sorting through modulation of the actomyosin cytoskeleton and cell adhesive properties to prevent cell intermingling.
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Affiliation(s)
- Javier Terriente
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, PRBB, Dr Aiguader 88, 08003, Barcelona, Spain.
| | - Cristina Pujades
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, PRBB, Dr Aiguader 88, 08003, Barcelona, Spain.
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70
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LIN L, LUO SS, WANG LJ, YANG J, SHEN HN, TIAN RJ. Progress and Application of LC-MS Technologies for Characterizing Protein Post Translational Modifications. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2015. [DOI: 10.1016/s1872-2040(15)60866-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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71
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Abstract
Cell signaling pathways control cells' responses to their environment through an intricate network of proteins and small molecules partitioned by intracellular structures, such as the cytoskeleton and nucleus. Our understanding of these pathways has been revised recently with the advent of more advanced experimental techniques; no longer are signaling pathways viewed as linear cascades of information flowing from membrane-bound receptors to the nucleus. Instead, such pathways must be understood in the context of networks, and studying such networks requires an integration of computational and experimental approaches. This understanding is becoming more important in designing novel therapies for diseases such as cancer. Using the MAPK (mitogen-activated protein kinase) and PI3K (class I phosphoinositide-3' kinase) pathways as case studies of cellular signaling, we give an overview of these pathways and their functions. We then describe, using a number of case studies, how computational modeling has aided in understanding these pathways' deregulation in cancer, and how such understanding can be used to optimally tailor current therapies or help design new therapies against cancer.
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Affiliation(s)
- Julio Saez-Rodriguez
- Current address: Joint Research Center for Computational Biomedicine, RWTH Aachen University Hospital, D-52074 Aachen, Germany;
- European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom;
| | - Aidan MacNamara
- European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom;
| | - Simon Cook
- Signalling Laboratory, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom;
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Abstract
There is increasing evidence that in addition to having major roles in morphogenesis, in some tissues Eph receptor and ephrin signaling regulates the differentiation of cells. In one mode of deployment, cell contact dependent Eph-ephrin activation induces a distinct fate of cells at the interface of their expression domains, for example in early ascidian embryos and in the vertebrate hindbrain. In another mode, overlapping Eph receptor and ephrin expression underlies activation within a cell population, which promotes or inhibits cell differentiation in bone remodelling, neural progenitors and keratinocytes. Eph-ephrin activation also contributes to formation of the appropriate number of progenitor cells by increasing or decreasing cell proliferation. These multiple roles of Eph receptor and ephrin signaling may enable a coupling between morphogenesis and the differentiation and proliferation of cells.
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Key Words
- Eph receptor
- Eph receptor, Erythropoietin-producing hepatocellular carcinoma cell receptor
- FGF, Fibroblast growth factor
- IGF-1, Insulin-like growth factor-1
- JNK, c-Jun N-terminal kinase
- MAPK, Mitogen activated protein kinase
- NFAT, Nuclear factor of activated T-cells
- RGS3, Regulator of G-protein signaling 3
- STAT3, Signal transducer and activator of transcription 3
- TAZ, Tafazzin
- TCR, T cell receptor
- TEC, Thymic epithelial cell
- TGF, Transforming growth factor
- ZHX2, Zinc fingers and homeoboxes 2
- ascidian development
- bone
- cell proliferation
- differentiation
- ephrin
- ephrin, Eph receptor interacting protein
- hindbrain
- keratinocytes
- neural progenitors
- p120GAP, GTPase activating protein
- thymocytes
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Affiliation(s)
- David G Wilkinson
- a Division of Developmental Neurobiology; MRC National Institute for Medical Research ; London , UK
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McIntyre RE, Buczacki SJ, Arends MJ, Adams DJ. Mouse models of colorectal cancer as preclinical models. Bioessays 2015; 37:909-20. [PMID: 26115037 PMCID: PMC4755199 DOI: 10.1002/bies.201500032] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 06/04/2015] [Accepted: 06/05/2015] [Indexed: 12/15/2022]
Abstract
In this review, we discuss the application of mouse models to the identification and pre-clinical validation of novel therapeutic targets in colorectal cancer, and to the search for early disease biomarkers. Large-scale genomic, transcriptomic and epigenomic profiling of colorectal carcinomas has led to the identification of many candidate genes whose direct contribution to tumourigenesis is yet to be defined; we discuss the utility of cross-species comparative 'omics-based approaches to this problem. We highlight recent progress in modelling late-stage disease using mice, and discuss ways in which mouse models could better recapitulate the complexity of human cancers to tackle the problem of therapeutic resistance and recurrence after surgical resection.
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Affiliation(s)
- Rebecca E. McIntyre
- Experimental Cancer GeneticsWellcome Trust Sanger InstituteHinxtonCambridgeUK
| | | | - Mark J. Arends
- Edinburgh Cancer Research UK CentreUniversity of EdinburghEdinburghUK
| | - David J. Adams
- Experimental Cancer GeneticsWellcome Trust Sanger InstituteHinxtonCambridgeUK
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74
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Takeuchi S, Katoh H, Negishi M. Eph/ephrin reverse signalling induces axonal retraction through RhoA/ROCK pathway. J Biochem 2015; 158:245-52. [PMID: 25922200 DOI: 10.1093/jb/mvv042] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 03/26/2015] [Indexed: 01/09/2023] Open
Abstract
Eph/ephrin signalling plays essential roles in various tissue developments, such as axon guidance, angiogenesis and tissue separation. Interaction between Ephs and ephrins upon cell-cell contact results in forward (towards Eph-expressing cells) and reverse (towards ephrin-expressing cells) signalling. Although the molecular mechanisms downstream of Eph/ephrin forward signalling have been extensively studied, the functions and intracellular molecular mechanisms of Eph/ephrin reverse signalling are not fully understood. Rho GTPases are key regulators of the actin cytoskeleton to regulate cell morphology. In this study, we revealed that stimulation with the extracellular domain of EphB2 to activate Eph/ephrin reverse signalling induced axonal retraction in hippocampal neurons. The reduction of axonal length and branching by Eph/ephrin reverse signalling was blocked by inhibition of RhoA or Rho-associated coiled-coil-containing protein kinase (ROCK). These results suggest that Eph/ephrin reverse signalling negatively regulates axonal outgrowth and branching through RhoA/ROCK pathway in hippocampal neurons.
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Affiliation(s)
- Shingo Takeuchi
- Laboratory of Molecular Neurobiology, Graduate School of Biostudies, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hironori Katoh
- Laboratory of Molecular Neurobiology, Graduate School of Biostudies, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Manabu Negishi
- Laboratory of Molecular Neurobiology, Graduate School of Biostudies, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
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75
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EphB4 forward signalling regulates lymphatic valve development. Nat Commun 2015; 6:6625. [PMID: 25865237 PMCID: PMC4403310 DOI: 10.1038/ncomms7625] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 02/12/2015] [Indexed: 01/08/2023] Open
Abstract
Bidirectional signalling is regarded as a notable hallmark of the Eph-ephrin signalling system: Eph-dependent forward signalling in Eph-expressing cells and ephrin-dependent reverse signalling in Ephrin-expressing cells. The notion of ephrin-dependent reverse signalling derives from genetic experiments utilizing mice carrying mutations in the intracellular region of ephrinBs. Here we show that EphB4-dependent forward signalling regulates lymphatic valve development, a process previously thought to be regulated by ephrinB2-dependent reverse signalling. We develop antibodies that selectively target EphB4 and ephrinB2. We find that mice bearing genetically altered cytoplasmic region of ephrinB2 have significantly altered EphB4-dependent forward signalling. Selective inhibition of EphB4 using a functional blocking antibody results in defective lymphatic valve development. Furthermore, a chemical genetic approach is used to unequivocally show that the kinase activity of EphB4 is essential for lymphatic valve development.
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76
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So J, Pasculescu A, Dai AY, Williton K, James A, Nguyen V, Creixell P, Schoof EM, Sinclair J, Barrios-Rodiles M, Gu J, Krizus A, Williams R, Olhovsky M, Dennis JW, Wrana JL, Linding R, Jorgensen C, Pawson T, Colwill K. Integrative analysis of kinase networks in TRAIL-induced apoptosis provides a source of potential targets for combination therapy. Sci Signal 2015; 8:rs3. [PMID: 25852190 DOI: 10.1126/scisignal.2005700] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2024]
Abstract
Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) is an endogenous secreted peptide and, in preclinical studies, preferentially induces apoptosis in tumor cells rather than in normal cells. The acquisition of resistance in cells exposed to TRAIL or its mimics limits their clinical efficacy. Because kinases are intimately involved in the regulation of apoptosis, we systematically characterized kinases involved in TRAIL signaling. Using RNA interference (RNAi) loss-of-function and cDNA overexpression screens, we identified 169 protein kinases that influenced the dynamics of TRAIL-induced apoptosis in the colon adenocarcinoma cell line DLD-1. We classified the kinases as sensitizers or resistors or modulators, depending on the effect that knockdown and overexpression had on TRAIL-induced apoptosis. Two of these kinases that were classified as resistors were PX domain-containing serine/threonine kinase (PXK) and AP2-associated kinase 1 (AAK1), which promote receptor endocytosis and may enable cells to resist TRAIL-induced apoptosis by enhancing endocytosis of the TRAIL receptors. We assembled protein interaction maps using mass spectrometry-based protein interaction analysis and quantitative phosphoproteomics. With these protein interaction maps, we modeled information flow through the networks and identified apoptosis-modifying kinases that are highly connected to regulated substrates downstream of TRAIL. The results of this analysis provide a resource of potential targets for the development of TRAIL combination therapies to selectively kill cancer cells.
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Affiliation(s)
- Jonathan So
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada. Institute of Medical Science, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Adrian Pasculescu
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Anna Y Dai
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Kelly Williton
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Andrew James
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Vivian Nguyen
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Pau Creixell
- Cellular Signal Integration Group (C-SIG), Technical University of Denmark (DTU), DK-2800 Lyngby, Denmark
| | - Erwin M Schoof
- Cellular Signal Integration Group (C-SIG), Technical University of Denmark (DTU), DK-2800 Lyngby, Denmark
| | - John Sinclair
- Cell Communication Team, The Institute of Cancer Research, London SW3 6JB, UK
| | - Miriam Barrios-Rodiles
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Jun Gu
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Aldis Krizus
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Ryan Williams
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Marina Olhovsky
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - James W Dennis
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada. Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Jeffrey L Wrana
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada. Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Rune Linding
- Cellular Signal Integration Group (C-SIG), Technical University of Denmark (DTU), DK-2800 Lyngby, Denmark. Biotech Research and Innovation Centre (BRIC), University of Copenhagen (UCPH), DK-2200 Copenhagen, Denmark.
| | - Claus Jorgensen
- Cell Communication Team, The Institute of Cancer Research, London SW3 6JB, UK.
| | - Tony Pawson
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada. Institute of Medical Science, University of Toronto, Toronto, Ontario M5S 1A8, Canada. Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Karen Colwill
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada.
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77
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EphrinB2 controls vessel pruning through STAT1-JNK3 signalling. Nat Commun 2015; 6:6576. [PMID: 25807892 PMCID: PMC4377839 DOI: 10.1038/ncomms7576] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 02/09/2015] [Indexed: 12/25/2022] Open
Abstract
Angiogenesis produces primitive vascular networks that need pruning to yield hierarchically organized and functional vessels. Despite the critical importance of vessel pruning to vessel patterning and function, the mechanisms regulating this process are not clear. Here we show that EphrinB2, a well-known player in angiogenesis, is an essential regulator of endothelial cell death and vessel pruning. This regulation depends upon phosphotyrosine-EphrinB2 signaling repressing JNK3 activity via STAT1. JNK3 activation causes endothelial cell death. In the absence of JNK3, hyaloid vessel physiological pruning is impaired, associated with abnormal persistence of hyaloid vessels, defective retinal vasculature and microphthalmia. This syndrome closely resembles human persistent hyperplastic primary vitreus (PHPV), attributed to failed involution of hyaloid vessels. Our results provide evidence that EphrinB2/STAT1/JNK3 signaling is essential for vessel pruning, and that defects in this pathway may contribute to PHPV.
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78
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Combinatorial proteomic analysis of intercellular signaling applied to the CD28 T-cell costimulatory receptor. Proc Natl Acad Sci U S A 2015; 112:E1594-603. [PMID: 25829543 DOI: 10.1073/pnas.1503286112] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Systematic characterization of intercellular signaling approximating the physiological conditions of stimulation that involve direct cell-cell contact is challenging. We describe a proteomic strategy to analyze physiological signaling mediated by the T-cell costimulatory receptor CD28. We identified signaling pathways activated by CD28 during direct cell-cell contact by global analysis of protein phosphorylation. To define immediate CD28 targets, we used phosphorylated forms of the CD28 cytoplasmic region to obtain the CD28 interactome. The interaction profiles of selected CD28-interacting proteins were further characterized in vivo for amplifying the CD28 interactome. The combination of the global phosphorylation and interactome analyses revealed broad regulation of CD28 and its interactome by phosphorylation. Among the cellular phosphoproteins influenced by CD28 signaling, CapZ-interacting protein (CapZIP), a regulator of the actin cytoskeleton, was implicated by functional studies. The combinatorial approach applied herein is widely applicable for characterizing signaling networks associated with membrane receptors with short cytoplasmic tails.
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79
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Park I, Lee HS. EphB/ephrinB signaling in cell adhesion and migration. Mol Cells 2015; 38:14-9. [PMID: 25475547 PMCID: PMC4314128 DOI: 10.14348/molcells.2015.2116] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 10/14/2014] [Accepted: 10/17/2014] [Indexed: 11/27/2022] Open
Abstract
Eph receptors and their ligands, ephrins, represent the largest group of the receptor tyrosine kinase (RTK) family, and they mediate numerous developmental processes in a variety of organisms. Ephrins are membrane-bound proteins that are mainly divided into two classes: A class ephrins, which are linked to the membrane by a glycosylphosphatidylinositol (GPI) linkage, and B class ephrins, which are transmembrane ligands. Based on their domain structures and affinities for ligand binding, the Eph receptors are also divided into two groups. Trans-dimerization of Eph receptors with their membrane-tethered ligands regulates cell-cell interactions and initiates bidirectional signaling pathways. These pathways are intimately involved in regulating cytoskeleton dynamics, cell migration, and alterations in cellular dynamics and shapes. The EphBs and ephrinBs are specifically localized and modified to promote higher-order clustering and initiate of bidirectional signaling. In this review, we present an in-depth overview of the structure, mechanisms, cell signaling, and functions of EphB/ephrinB in cell adhesion and migration.
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Affiliation(s)
- Inji Park
- ABRC, CMRI, School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu 702-701,
Korea
| | - Hyun-Shik Lee
- ABRC, CMRI, School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu 702-701,
Korea
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80
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Abstract
The succession of protein activation and deactivation mediated by phosphorylation and dephosphorylation events constitutes a key mechanism of molecular information transfer in cellular systems. To deduce the details of those molecular information cascades and networks has been a central goal pursued by both experimental and computational approaches. Many computational network reconstruction methods employing an array of different statistical learning methods have been developed to infer phosphorylation networks based on different types of molecular data sets such as protein sequence, protein structure, or phosphoproteomics data. In this chapter, different computational network inference methods and resources for biological network reconstruction with a particular focus on phosphorylation networks are surveyed.
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81
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Aharon R, Janes PW, Burgess AW, Hamza K, Klebaner F, Lackmann M. A mathematical model for eph/ephrin-directed segregation of intermingled cells. PLoS One 2014; 9:e111803. [PMID: 25436892 PMCID: PMC4249859 DOI: 10.1371/journal.pone.0111803] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 10/04/2014] [Indexed: 11/19/2022] Open
Abstract
Eph receptors, the largest family of receptor tyrosine kinases, control cell-cell adhesion/de-adhesion, cell morphology and cell positioning through interaction with cell surface ephrin ligands. Bi-directional signalling from the Eph and ephrin complexes on interacting cells have a significant role in controlling normal tissue development and oncogenic tissue patterning. Eph-mediated tissue patterning is based on the fine-tuned balance of adhesion and de-adhesion reactions between distinct Eph- and ephrin-expressing cell populations, and adhesion within like populations (expressing either Eph or ephrin). Here we develop a stochastic, Lagrangian model that is based on Eph/ephrin biology: incorporating independent Brownian motion to describe cell movement and a deterministic term (the drift term) to represent repulsive and adhesive interactions between neighbouring cells. Comparison between the experimental and computer simulated Eph/ephrin cell patterning events shows that the model recapitulates the dynamics of cell-cell segregation and cell cluster formation. Moreover, by modulating the term for Eph/ephrin-mediated repulsion, the model can be tuned to match the actual behaviour of cells with different levels of Eph expression or activity. Together the results of our experiments and modelling suggest that the complexity of Eph/ephrin signalling mechanisms that control cell-cell interactions can be described well by a mathematical model with a single term balancing adhesion and de-adhesion between interacting cells. This model allows reliable prediction of Eph/ephrin-dependent control of cell patterning behaviour.
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Affiliation(s)
- Rotem Aharon
- School of Mathematical Sciences, Monash University, Clayton, Victoria, Australia
- * E-mail: (RA); (PWJ)
| | - Peter W. Janes
- Department of Biochemistry & Molecular Biology, Monash University, Clayton, Victoria, Australia
- * E-mail: (RA); (PWJ)
| | - Anthony W. Burgess
- Structural Biology Division, The Walter and Eliza Hall Institute, Parkville, Victoria, Australia
| | - Kais Hamza
- School of Mathematical Sciences, Monash University, Clayton, Victoria, Australia
| | - Fima Klebaner
- School of Mathematical Sciences, Monash University, Clayton, Victoria, Australia
| | - Martin Lackmann
- Department of Biochemistry & Molecular Biology, Monash University, Clayton, Victoria, Australia
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82
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Ma B, Kolb S, Diprima M, Karna M, Tosato G, Yang Q, Huang Q, Nussinov R. Investigation of the interactions between the EphB2 receptor and SNEW peptide variants. Growth Factors 2014; 32:236-46. [PMID: 25410963 PMCID: PMC4627370 DOI: 10.3109/08977194.2014.985786] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
EphB2 interacts with cell surface-bound ephrin ligands to relay bidirectional signals. Overexpression of the EphB2 receptor protein has been linked to different types of cancer. The SNEW (SNEWIQPRLPQH) peptide binds with high selectivity and moderate affinity to EphB2, inhibiting Eph-ephrin interactions by competing with ephrin ligands for the EphB2 high-affinity pocket. We used rigorous free energy perturbation (FEP) calculations to re-evaluate the binding interactions of SNEW peptide with the EphB2 receptor, followed by experimental testing of the computational results. Our results provide insight into dynamic interactions of EphB2 with SNEW peptide. While the first four residues of the SNEW peptide are already highly optimized, change of the C-terminal end of the peptide has the potential to improve SNEW-binding affinity. We identified a PXSPY motif that can be similarly aligned with several other EphB2-binding peptides.
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Affiliation(s)
- Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, USA
| | - Stephanie Kolb
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, USA
| | - Michael Diprima
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Molleshree Karna
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Giovanna Tosato
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Qiqi Yang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Qiang Huang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, USA
- Sackler Inst. of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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83
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Abstract
Eph receptor tyrosine kinases control cell-cell interactions during normal and oncogenic development, and are implicated in a range of processes including angiogenesis, stem cell maintenance and metastasis. They are thus of great interest as targets for cancer therapy. EphA3, originally isolated from leukemic and melanoma cells, is presently one of the most promising therapeutic targets, with multiple tumor-promoting roles in a variety of cancer types. This review focuses on EphA3, its functions in controlling cellular behavior, both in normal and pathological development, and most particularly in cancer.
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Affiliation(s)
- Peter W Janes
- Department of Biochemistry and Molecular Biology, Monash University , Victoria , Australia and
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84
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Cayuso J, Xu Q, Wilkinson DG. Mechanisms of boundary formation by Eph receptor and ephrin signaling. Dev Biol 2014; 401:122-31. [PMID: 25448699 DOI: 10.1016/j.ydbio.2014.11.013] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 11/11/2014] [Accepted: 11/12/2014] [Indexed: 12/21/2022]
Abstract
The formation of sharp borders, across which cell intermingling is restricted, has a crucial role in the establishment and maintenance of organized tissues. Signaling of Eph receptors and ephrins underlies formation of a number of boundaries between and within tissues during vertebrate development. Eph-ephrin signaling can regulate several types of cell response-adhesion, repulsion and tension-that can in principle underlie the segregation of cells and formation of sharp borders. Recent studies have implicated each of these cell responses as having important roles at different boundaries: repulsion at the mesoderm-ectoderm border, decreased adhesion at the notochord-presomitic mesoderm border, and tension at boundaries within the hindbrain and forebrain. These distinct responses to Eph receptor and ephrin activation may in part be due to the adhesive properties of the tissue.
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Affiliation(s)
- Jordi Cayuso
- Division of Developmental Neurobiology, MRC National Institute for Medical Research, London NW7 1AA, United Kingdom
| | - Qiling Xu
- Division of Developmental Neurobiology, MRC National Institute for Medical Research, London NW7 1AA, United Kingdom
| | - David G Wilkinson
- Division of Developmental Neurobiology, MRC National Institute for Medical Research, London NW7 1AA, United Kingdom.
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85
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Gucciardo E, Sugiyama N, Lehti K. Eph- and ephrin-dependent mechanisms in tumor and stem cell dynamics. Cell Mol Life Sci 2014; 71:3685-710. [PMID: 24794629 PMCID: PMC11113620 DOI: 10.1007/s00018-014-1633-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Revised: 03/31/2014] [Accepted: 04/17/2014] [Indexed: 01/17/2023]
Abstract
The erythropoietin-producing hepatocellular (Eph) receptors comprise the largest family of receptor tyrosine kinases (RTKs). Initially regarded as axon-guidance and tissue-patterning molecules, Eph receptors have now been attributed with various functions during development, tissue homeostasis, and disease pathogenesis. Their ligands, ephrins, are synthesized as membrane-associated molecules. At least two properties make this signaling system unique: (1) the signal can be simultaneously transduced in the receptor- and the ligand-expressing cell, (2) the signaling outcome through the same molecules can be opposite depending on cellular context. Moreover, shedding of Eph and ephrin ectodomains as well as ligand-dependent and -independent receptor crosstalk with other RTKs, proteases, and adhesion molecules broadens the repertoire of Eph/ephrin functions. These integrated pathways provide plasticity to cell-microenvironment communication in varying tissue contexts. The complex molecular networks and dynamic cellular outcomes connected to the Eph/ephrin signaling in tumor-host communication and stem cell niche are the main focus of this review.
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Affiliation(s)
- Erika Gucciardo
- Research Programs Unit, Genome-Scale Biology, Biomedicum Helsinki, University of Helsinki, P.O.B. 63, 00014 Helsinki, Finland
| | - Nami Sugiyama
- Research Programs Unit, Genome-Scale Biology, Biomedicum Helsinki, University of Helsinki, P.O.B. 63, 00014 Helsinki, Finland
- Department of Biosystems Science and Bioengineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Kaisa Lehti
- Research Programs Unit, Genome-Scale Biology, Biomedicum Helsinki, University of Helsinki, P.O.B. 63, 00014 Helsinki, Finland
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86
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Yugi K, Kubota H, Toyoshima Y, Noguchi R, Kawata K, Komori Y, Uda S, Kunida K, Tomizawa Y, Funato Y, Miki H, Matsumoto M, Nakayama KI, Kashikura K, Endo K, Ikeda K, Soga T, Kuroda S. Reconstruction of insulin signal flow from phosphoproteome and metabolome data. Cell Rep 2014; 8:1171-83. [PMID: 25131207 DOI: 10.1016/j.celrep.2014.07.021] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 06/13/2014] [Accepted: 07/15/2014] [Indexed: 12/20/2022] Open
Abstract
Cellular homeostasis is regulated by signals through multiple molecular networks that include protein phosphorylation and metabolites. However, where and when the signal flows through a network and regulates homeostasis has not been explored. We have developed a reconstruction method for the signal flow based on time-course phosphoproteome and metabolome data, using multiple databases, and have applied it to acute action of insulin, an important hormone for metabolic homeostasis. An insulin signal flows through a network, through signaling pathways that involve 13 protein kinases, 26 phosphorylated metabolic enzymes, and 35 allosteric effectors, resulting in quantitative changes in 44 metabolites. Analysis of the network reveals that insulin induces phosphorylation and activation of liver-type phosphofructokinase 1, thereby controlling a key reaction in glycolysis. We thus provide a versatile method of reconstruction of signal flow through the network using phosphoproteome and metabolome data.
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Affiliation(s)
- Katsuyuki Yugi
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroyuki Kubota
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan; Division of integrated Omics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan; PRESTO, Japan Science and Technology Corporation, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
| | - Yu Toyoshima
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Rei Noguchi
- Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kentaro Kawata
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yasunori Komori
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shinsuke Uda
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan; Division of integrated Omics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
| | - Katsuyuki Kunida
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yoko Tomizawa
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yosuke Funato
- Department of Cellular Regulation, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Hiroaki Miki
- Department of Cellular Regulation, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Masaki Matsumoto
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
| | - Keiichi I Nakayama
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
| | - Kasumi Kashikura
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan
| | - Keiko Endo
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan
| | - Kazutaka Ikeda
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan
| | - Shinya Kuroda
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan; Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan; CREST, Japan Science and Technology Corporation, Bunkyo-ku, Tokyo 113-0033, Japan.
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87
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Anton KA, Sinclair J, Ohoka A, Kajita M, Ishikawa S, Benz PM, Renne T, Balda M, Jorgensen C, Matter K, Fujita Y. PKA-regulated VASP phosphorylation promotes extrusion of transformed cells from the epithelium. J Cell Sci 2014; 127:3425-33. [PMID: 24963131 DOI: 10.1242/jcs.149674] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
At the early stages of carcinogenesis, transformation occurs in single cells within tissues. In an epithelial monolayer, such mutated cells are recognized by their normal neighbors and are often apically extruded. The apical extrusion requires cytoskeletal reorganization and changes in cell shape, but the molecular switches involved in the regulation of these processes are poorly understood. Here, using stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative mass spectrometry, we have identified proteins that are modulated in transformed cells upon their interaction with normal cells. Phosphorylation of VASP at serine 239 is specifically upregulated in Ras(V12)-transformed cells when they are surrounded by normal cells. VASP phosphorylation is required for the cell shape changes and apical extrusion of Ras-transformed cells. Furthermore, PKA is activated in Ras-transformed cells that are surrounded by normal cells, leading to VASP phosphorylation. These results indicate that the PKA-VASP pathway is a crucial regulator of tumor cell extrusion from the epithelium, and they shed light on the events occurring at the early stage of carcinogenesis.
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Affiliation(s)
- Katarzyna A Anton
- Department of Cell Biology, UCL Institute of Ophthalmology, University College London, London EC1V 9EL, UK MRC Laboratory for Molecular Cell Biology and Cell Biology Unit, University College London, London WC1E 6BT, UK
| | - John Sinclair
- Division of Cancer Biology, Cell Communication Team, The Institute of Cancer Research, London SW3 6JB, UK
| | - Atsuko Ohoka
- Division of Molecular Oncology, Institute for Genetic Medicine, Hokkaido University, Sapporo 060-0815, Japan
| | - Mihoko Kajita
- Division of Molecular Oncology, Institute for Genetic Medicine, Hokkaido University, Sapporo 060-0815, Japan
| | - Susumu Ishikawa
- Division of Molecular Oncology, Institute for Genetic Medicine, Hokkaido University, Sapporo 060-0815, Japan
| | - Peter M Benz
- Institute for Vascular Signaling, University of Frankfurt, Frankfurt D-60590, Germany
| | - Thomas Renne
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institute, Stockholm SE-171 77, Sweden Institute for Clinical Chemistry, University Hospital Hamburg-Eppendorf, Hamburg 20246, Germany
| | - Maria Balda
- Department of Cell Biology, UCL Institute of Ophthalmology, University College London, London EC1V 9EL, UK
| | - Claus Jorgensen
- Division of Cancer Biology, Cell Communication Team, The Institute of Cancer Research, London SW3 6JB, UK
| | - Karl Matter
- Department of Cell Biology, UCL Institute of Ophthalmology, University College London, London EC1V 9EL, UK
| | - Yasuyuki Fujita
- MRC Laboratory for Molecular Cell Biology and Cell Biology Unit, University College London, London WC1E 6BT, UK Division of Molecular Oncology, Institute for Genetic Medicine, Hokkaido University, Sapporo 060-0815, Japan
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88
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Tape CJ, Norrie IC, Worboys JD, Lim L, Lauffenburger DA, Jørgensen C. Cell-specific labeling enzymes for analysis of cell-cell communication in continuous co-culture. Mol Cell Proteomics 2014; 13:1866-76. [PMID: 24820872 DOI: 10.1074/mcp.o113.037119] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We report the orthologous screening, engineering, and optimization of amino acid conversion enzymes for cell-specific proteomic labeling. Intracellular endoplasmic-reticulum-anchored Mycobacterium tuberculosis diaminopimelate decarboxylase (DDC(M.tub-KDEL)) confers cell-specific meso-2,6-diaminopimelate-dependent proliferation to multiple eukaryotic cell types. Optimized lysine racemase (Lyr(M37-KDEL)) supports D-lysine specific proliferation and efficient cell-specific isotopic labeling. When ectopically expressed in discrete cell types, these enzymes confer 90% cell-specific isotopic labeling efficiency after 10 days of co-culture. Moreover, DDC(M.tub-KDEL) and Lyr(M37-KDEL) facilitate equally high cell-specific labeling fidelity without daily media exchange. Consequently, the reported novel enzyme pairing can be used to study cell-specific signaling in uninterrupted, continuous co-cultures. Demonstrating the importance of increased labeling stability for addressing novel biological questions, we compare the cell-specific phosphoproteome of fibroblasts in direct co-culture with epithelial tumor cells in both interrupted (daily media exchange) and continuous (no media exchange) co-cultures. This analysis identified multiple cell-specific phosphorylation sites specifically regulated in the continuous co-culture. Given their applicability to multiple cell types, continuous co-culture labeling fidelity, and suitability for long-term cell-cell phospho-signaling experiments, we propose DDC(M.tub-KDEL) and Lyr(M37-KDEL) as excellent enzymes for cell-specific labeling with amino acid precursors.
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Affiliation(s)
- Christopher J Tape
- From the ‡Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK; §Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Ida C Norrie
- From the ‡Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Jonathan D Worboys
- From the ‡Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Lindsay Lim
- From the ‡Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Douglas A Lauffenburger
- §Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Claus Jørgensen
- From the ‡Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK;
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89
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Djidja MC, Chang J, Hadjiprocopis A, Schmich F, Sinclair J, Mršnik M, Schoof EM, Barker HE, Linding R, Jørgensen C, Erler JT. Identification of hypoxia-regulated proteins using MALDI-mass spectrometry imaging combined with quantitative proteomics. J Proteome Res 2014; 13:2297-313. [PMID: 24702160 DOI: 10.1021/pr401056c] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Hypoxia is present in most solid tumors and is clinically correlated with increased metastasis and poor patient survival. While studies have demonstrated the role of hypoxia and hypoxia-regulated proteins in cancer progression, no attempts have been made to identify hypoxia-regulated proteins using quantitative proteomics combined with MALDI-mass spectrometry imaging (MALDI-MSI). Here we present a comprehensive hypoxic proteome study and are the first to investigate changes in situ using tumor samples. In vitro quantitative mass spectrometry analysis of the hypoxic proteome was performed on breast cancer cells using stable isotope labeling with amino acids in cell culture (SILAC). MS analyses were performed on laser-capture microdissected samples isolated from normoxic and hypoxic regions from tumors derived from the same cells used in vitro. MALDI-MSI was used in combination to investigate hypoxia-regulated protein localization within tumor sections. Here we identified more than 100 proteins, both novel and previously reported, that were associated with hypoxia. Several proteins were localized in hypoxic regions, as identified by MALDI-MSI. Visualization and data extrapolation methods for the in vitro SILAC data were also developed, and computational mapping of MALDI-MSI data to IHC results was applied for data validation. The results and limitations of the methodologies described are discussed.
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Affiliation(s)
- Marie-Claude Djidja
- Hypoxia and Metastasis Team and ‡Cell Communications Team, Cancer Research U.K. Tumour Cell Signalling Unit, Division of Cancer Biology, The Institute of Cancer Research , London, United Kingdom
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90
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Abstract
Conventional methods for studying paracrine signaling in vitro may not be sensitive to short-range effects resulting from signal dilution or decay. We employ a microfabricated culture substrate to maintain two cell populations in microscale proximity. Individual populations can be quickly retrieved for cell-specific readouts by standard high-throughput assays. We show that this platform is sensitive to short-range interactions that are not detectable by common methods such as conditioned media transfer or porous cell culture inserts, as revealed by gene expression changes in a tumor-stromal crosstalk model. In addition, we are able to detect population-specific gene expression changes that would have been masked in mixed co-cultures. We thus demonstrate a tool for investigating an important class of intercellular communication that may be overlooked in conventional biological studies.
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Affiliation(s)
- K H Spencer
- Department of Biomedical Engineering, University of California, Irvine, CA 92697-2715, USA.
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91
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Pastrello C, Pasini E, Kotlyar M, Otasek D, Wong S, Sangrar W, Rahmati S, Jurisica I. Integration, visualization and analysis of human interactome. Biochem Biophys Res Commun 2014; 445:757-73. [DOI: 10.1016/j.bbrc.2014.01.151] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Accepted: 01/24/2014] [Indexed: 02/06/2023]
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92
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Schoof EM, Linding R. Experimental and computational tools for analysis of signaling networks in primary cells. ACTA ACUST UNITED AC 2014; 104:11.11.1-11.11.23. [PMID: 24510617 DOI: 10.1002/0471142735.im1111s104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Cellular information processing in signaling networks forms the basis of responses to environmental stimuli. At any given time, cells receive multiple simultaneous input cues, which are processed and integrated to determine cellular responses such as migration, proliferation, apoptosis, or differentiation. Protein phosphorylation events play a major role in this process and are often involved in fundamental biological and cellular processes such as protein-protein interactions, enzyme activity, and immune responses. Determining which kinases phosphorylate specific phospho sites poses a challenge; this information is critical when trying to elucidate key proteins involved in specific cellular responses. Here, methods to generate high-quality quantitative phosphorylation data from cell lysates originating from primary cells, and how to analyze the generated data to construct quantitative signaling network models, are presented. These models can subsequently be used to guide follow-up in vitro/in vivo validation studies.
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Affiliation(s)
- Erwin M Schoof
- Cellular Signal Integration Group (C-SIG), Center for Biological Sequence Analysis (CBS), Department of Systems Biology, Technical University of Denmark (DTU), Lyngby, Denmark
| | - Rune Linding
- Cellular Signal Integration Group (C-SIG), Center for Biological Sequence Analysis (CBS), Department of Systems Biology, Technical University of Denmark (DTU), Lyngby, Denmark
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93
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Pasculescu A, Schoof EM, Creixell P, Zheng Y, Olhovsky M, Tian R, So J, Vanderlaan RD, Pawson T, Linding R, Colwill K. CoreFlow: a computational platform for integration, analysis and modeling of complex biological data. J Proteomics 2014; 100:167-73. [PMID: 24503186 DOI: 10.1016/j.jprot.2014.01.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 01/20/2014] [Accepted: 01/24/2014] [Indexed: 11/16/2022]
Abstract
UNLABELLED A major challenge in mass spectrometry and other large-scale applications is how to handle, integrate, and model the data that is produced. Given the speed at which technology advances and the need to keep pace with biological experiments, we designed a computational platform, CoreFlow, which provides programmers with a framework to manage data in real-time. It allows users to upload data into a relational database (MySQL), and to create custom scripts in high-level languages such as R, Python, or Perl for processing, correcting and modeling this data. CoreFlow organizes these scripts into project-specific pipelines, tracks interdependencies between related tasks, and enables the generation of summary reports as well as publication-quality images. As a result, the gap between experimental and computational components of a typical large-scale biology project is reduced, decreasing the time between data generation, analysis and manuscript writing. CoreFlow is being released to the scientific community as an open-sourced software package complete with proteomics-specific examples, which include corrections for incomplete isotopic labeling of peptides (SILAC) or arginine-to-proline conversion, and modeling of multiple/selected reaction monitoring (MRM/SRM) results. BIOLOGICAL SIGNIFICANCE CoreFlow was purposely designed as an environment for programmers to rapidly perform data analysis. These analyses are assembled into project-specific workflows that are readily shared with biologists to guide the next stages of experimentation. Its simple yet powerful interface provides a structure where scripts can be written and tested virtually simultaneously to shorten the life cycle of code development for a particular task. The scripts are exposed at every step so that a user can quickly see the relationships between the data, the assumptions that have been made, and the manipulations that have been performed. Since the scripts use commonly available programming languages, they can easily be transferred to and from other computational environments for debugging or faster processing. This focus on 'on the fly' analysis sets CoreFlow apart from other workflow applications that require wrapping of scripts into particular formats and development of specific user interfaces. Importantly, current and future releases of data analysis scripts in CoreFlow format will be of widespread benefit to the proteomics community, not only for uptake and use in individual labs, but to enable full scrutiny of all analysis steps, thus increasing experimental reproducibility and decreasing errors. This article is part of a Special Issue entitled: Can Proteomics Fill the Gap Between Genomics and Phenotypes?
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Affiliation(s)
- Adrian Pasculescu
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Erwin M Schoof
- Cellular Signal Integration Group (C-SIG), Center for Biological Sequence Analysis (CBS), Department of Systems Biology, Technical University of Denmark (DTU), Building 301, DK-2800, Lyngby, Denmark
| | - Pau Creixell
- Cellular Signal Integration Group (C-SIG), Center for Biological Sequence Analysis (CBS), Department of Systems Biology, Technical University of Denmark (DTU), Building 301, DK-2800, Lyngby, Denmark
| | - Yong Zheng
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Marina Olhovsky
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Ruijun Tian
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Jonathan So
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada; Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - Rachel D Vanderlaan
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada; Department of Cardiac Surgery, University of Toronto, Ontario, Canada
| | - Tony Pawson
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Rune Linding
- Cellular Signal Integration Group (C-SIG), Center for Biological Sequence Analysis (CBS), Department of Systems Biology, Technical University of Denmark (DTU), Building 301, DK-2800, Lyngby, Denmark.
| | - Karen Colwill
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
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Mann M. Fifteen years of Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC). Methods Mol Biol 2014; 1188:1-7. [PMID: 25059600 DOI: 10.1007/978-1-4939-1142-4_1] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Here I describe the history of the Stable Isotope Labeling by Amino Acids in Cell culture (SILAC) technology. Although published in 2002, it had already been developed and used in my laboratory for a number of years. From the beginning, it was applied to challenging problems in cell signaling that were considered out of reach for proteomics at the time. It was also used to pioneer proteomic interactomics, time series and dynamic posttranslational modification studies. While initially developed for metabolically accessible systems, such as cell lines, it was subsequently extended to whole animal labeling as well as to clinical applications-in the form or spike-in or super-SILAC. New formats and applications for SILAC labeling continue to be developed, for instance for protein-turnover studies.
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Affiliation(s)
- Matthias Mann
- Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, 82152, Germany,
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96
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Duan G, Walther D, Schulze WX. Reconstruction and analysis of nutrient-induced phosphorylation networks in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2013; 4:540. [PMID: 24400017 PMCID: PMC3872036 DOI: 10.3389/fpls.2013.00540] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 12/12/2013] [Indexed: 05/23/2023]
Abstract
Elucidating the dynamics of molecular processes in living organisms in response to external perturbations is a central goal in modern systems biology. We investigated the dynamics of protein phosphorylation events in Arabidopsis thaliana exposed to changing nutrient conditions. Phosphopeptide expression levels were detected at five consecutive time points over a time interval of 30 min after nutrient resupply following prior starvation. The three tested inorganic, ionic nutrients NH(+) 4, NO(-) 3, PO(3-) 4 elicited similar phosphosignaling responses that were distinguishable from those invoked by the sugars mannitol, sucrose. When embedded in the protein-protein interaction network of Arabidopsis thaliana, phosphoproteins were found to exhibit a higher degree compared to average proteins. Based on the time-series data, we reconstructed a network of regulatory interactions mediated by phosphorylation. The performance of different network inference methods was evaluated by the observed likelihood of physical interactions within and across different subcellular compartments and based on gene ontology semantic similarity. The dynamic phosphorylation network was then reconstructed using a Pearson correlation method with added directionality based on partial variance differences. The topology of the inferred integrated network corresponds to an information dissemination architecture, in which the phosphorylation signal is passed on to an increasing number of phosphoproteins stratified into an initiation, processing, and effector layer. Specific phosphorylation peptide motifs associated with the distinct layers were identified indicating the action of layer-specific kinases. Despite the limited temporal resolution, combined with information on subcellular location, the available time-series data proved useful for reconstructing the dynamics of the molecular signaling cascade in response to nutrient stress conditions in the plant Arabidopsis thaliana.
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Affiliation(s)
- Guangyou Duan
- Max Planck Institute of Molecular Plant PhysiologyPotsdam, Germany
| | - Dirk Walther
- Max Planck Institute of Molecular Plant PhysiologyPotsdam, Germany
| | - Waltraud X. Schulze
- Max Planck Institute of Molecular Plant PhysiologyPotsdam, Germany
- Department of Plant Systems Biology, Universität HohenheimStuttgart, Germany
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97
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Tian R. Exploring intercellular signaling by proteomic approaches. Proteomics 2013; 14:498-512. [DOI: 10.1002/pmic.201300259] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Revised: 08/15/2013] [Accepted: 08/28/2013] [Indexed: 11/07/2022]
Affiliation(s)
- Ruijun Tian
- Lunenfeld-Tanenbaum Research Institute; Mount Sinai Hospital; Toronto ON Canada
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98
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Janes KA, Lauffenburger DA. Models of signalling networks - what cell biologists can gain from them and give to them. J Cell Sci 2013; 126:1913-21. [PMID: 23720376 DOI: 10.1242/jcs.112045] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Computational models of cell signalling are perceived by many biologists to be prohibitively complicated. Why do math when you can simply do another experiment? Here, we explain how conceptual models, which have been formulated mathematically, have provided insights that directly advance experimental cell biology. In the past several years, models have influenced the way we talk about signalling networks, how we monitor them, and what we conclude when we perturb them. These insights required wet-lab experiments but would not have arisen without explicit computational modelling and quantitative analysis. Today, the best modellers are cross-trained investigators in experimental biology who work closely with collaborators but also undertake experimental work in their own laboratories. Biologists would benefit by becoming conversant in core principles of modelling in order to identify when a computational model could be a useful complement to their experiments. Although the mathematical foundations of a model are useful to appreciate its strengths and weaknesses, they are not required to test or generate a worthwhile biological hypothesis computationally.
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Affiliation(s)
- Kevin A Janes
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA
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99
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Roux PP, Thibault P. The coming of age of phosphoproteomics--from large data sets to inference of protein functions. Mol Cell Proteomics 2013; 12:3453-64. [PMID: 24037665 DOI: 10.1074/mcp.r113.032862] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Protein phosphorylation is one of the most common post-translational modifications used in signal transduction to control cell growth, proliferation, and survival in response to both intracellular and extracellular stimuli. This modification is finely coordinated by a network of kinases and phosphatases that recognize unique sequence motifs and/or mediate their functions through scaffold and adaptor proteins. Detailed information on the nature of kinase substrates and site-specific phosphoregulation is required in order for one to better understand their pathophysiological roles. Recent advances in affinity chromatography and mass spectrometry (MS) sensitivity have enabled the large-scale identification and profiling of protein phosphorylation, but appropriate follow-up experiments are required in order to ascertain the functional significance of identified phosphorylation sites. In this review, we present meaningful technical details for MS-based phosphoproteomic analyses and describe important considerations for the selection of model systems and the functional characterization of identified phosphorylation sites.
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Affiliation(s)
- Philippe P Roux
- Institute for Research in Immunology and Cancer, Université de Montréal, P.O. Box 6128, Station. Centre-ville, Montréal, Québec H3C 3J7, Canada
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Dimidschstein J, Passante L, Dufour A, van den Ameele J, Tiberi L, Hrechdakian T, Adams R, Klein R, Lie D, Jossin Y, Vanderhaeghen P. Ephrin-B1 Controls the Columnar Distribution of Cortical Pyramidal Neurons by Restricting Their Tangential Migration. Neuron 2013; 79:1123-35. [DOI: 10.1016/j.neuron.2013.07.015] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/12/2013] [Indexed: 10/26/2022]
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