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Bongartz H, Mehwald N, Seiß EA, Schumertl T, Naß N, Dittrich A. Dysregulated Gab1 signalling in triple negative breast cancer. Cell Commun Signal 2024; 22:161. [PMID: 38448989 PMCID: PMC10916281 DOI: 10.1186/s12964-024-01542-9] [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] [Received: 04/28/2023] [Accepted: 02/24/2024] [Indexed: 03/08/2024] Open
Abstract
BACKGROUND Breast cancer is the most common cancer in women worldwide. Triple-negative breast cancer (TNBC) is especially aggressive and associated with high metastasis. The aetiology of TNBC is heterogeneous and characterised by multiple different mutations that amongst others cause constitutive and dysregulated MAPK and PI3K signalling. Additionally, in more than 50% of TNBC patients, the epidermal growth factor receptor (EGFR) is overexpressed and constitutively active. The multi-site docking protein Grb2-associated binder 1 (Gab1) is a central signalling hub that connects MAPK and PI3K signalling. METHODS Expression and activation of members of the Gab1/PI3K/MAPK signalling network were assessed in cells from different breast cancer subtypes. Influence of short- and long-term inhibition of EGFR, MAPK and PI3K on the activation of the Gab1/PI3K/MAPK signalling network as well as on cell viability, proliferation and migration was determined. Additionally, cellular localisation of Gab1 and Gab1 variants in naive cells and cells treated with the above-mentioned inhibitors was investigated. RESULTS We show that, activation of the Gab1/PI3K/MAPK signalling network is heterogeneous between different breast cancer subtypes. Gab1 phosphorylation and plasma membrane recruitment of Gab1 are dysregulated in the EGFRhigh TNBC cell line MDA-MB-468. While the Gab1/MAPK/PI3K signalling network follows canonical Gab1 signalling in naive MDA-MB-468 cells, Gab1 signalling is changed in cells that acquired resistance towards MAPK and PI3K inhibition. In resistant cells, Gab1 is not located at the plasma membrane despite strong activation of PI3K and MAPK. Furthermore, Gab1 tyrosine phosphorylation is uncoupled from plasma membrane recruitment. CONCLUSION Our study indicates that Gab1 signalling changes fundamentally during the acquisition of resistance to pharmacological inhibitors. Given the molecular heterogeneity between breast cancer subtypes, the detailed understanding of dysregulated and aberrant signalling is an absolute necessity in order to develop personalised therapies for patients with TNBC.
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Affiliation(s)
- Hannes Bongartz
- Institute of Biology, Department of Systems Biology, Otto-von-Guericke University, Universitätsplatz 2, Magdeburg, 39106, Germany
- Present address: Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD, 20892, USA
| | - Nora Mehwald
- Institute of Biology, Department of Systems Biology, Otto-von-Guericke University, Universitätsplatz 2, Magdeburg, 39106, Germany
| | - Elena A Seiß
- Institute of Biology, Department of Systems Biology, Otto-von-Guericke University, Universitätsplatz 2, Magdeburg, 39106, Germany
| | - Tim Schumertl
- Institute of Biology, Department of Systems Biology, Otto-von-Guericke University, Universitätsplatz 2, Magdeburg, 39106, Germany
- Present address: Institute of Clinical Biochemistry, Hannover Medical School, Carl-Neuberg-Straße 1, Hannover, 30625, Germany
| | - Norbert Naß
- Department of Pathology, Brandenburg Medical School Theodor Fontane, University Hospital Brandenburg / Havel, Hochstraße 29, Brandenburg, 14770, Germany
| | - Anna Dittrich
- Institute of Biology, Department of Systems Biology, Otto-von-Guericke University, Universitätsplatz 2, Magdeburg, 39106, Germany.
- Center for Dynamic Systems: Systems Engineering (CDS), Otto-von-Guericke University, Universitätsplatz 2, Magdeburg, 39106, Germany.
- Magdeburg Center for Systems Biology (MACS), Otto-von-Guericke University, Universitätsplatz 2, Magdeburg, 39106, Germany.
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Bongartz H, Gille K, Hessenkemper W, Mandel K, Lewitzky M, Feller SM, Schaper F. The multi-site docking protein Grb2-associated binder 1 (Gab1) enhances interleukin-6-induced MAPK-pathway activation in an SHP2-, Grb2-, and time-dependent manner. Cell Commun Signal 2019; 17:135. [PMID: 31651330 PMCID: PMC6814103 DOI: 10.1186/s12964-019-0451-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 10/04/2019] [Indexed: 12/13/2022] Open
Abstract
Background Cytokine-dependent activation of signalling pathways is tightly orchestrated. The spatiotemporal activation of signalling pathways dictates the specific physiological responses to cytokines. Dysregulated signalling accounts for neoplastic, developmental, and inflammatory diseases. Grb2-associated binder (Gab) family proteins are multi-site docking proteins, which expand cytokine-induced signal transduction in a spatial- and time-dependent manner by coordinating the recruitment of proteins involved in mitogen activated protein kinase (MAPK)/extracellular-signal regulated kinase (ERK) and phosphatidyl-inositol-3-kinase (PI3K) signalling. Interaction of Gab family proteins with these signalling proteins determines strength, duration and localization of active signalling cascades. However, the underlying molecular mechanisms of signal orchestration by Gab family proteins in IL-6-induced signalling are only scarcely understood. Methods We performed kinetic analyses of interleukin-6 (IL-6)-induced MAPK activation and analysed downstream responses. We compared signalling in wild-type cells, Gab1 knock-out cells, those reconstituted to express Gab1 mutants, and cells expressing gp130 receptors or receptor mutants. Results Interleukin-6-induced MAPK pathway activation can be sub-divided into an early Gab1-independent and a subsequent Gab1-dependent phase. Early Gab1-independent MAPK activation is critical for the subsequent initiation of Gab1-dependent amplification of MAPK pathway activation and requires binding of SH2 domain-containing phosphatase 2 (SHP2) to the interleukin-6 receptor complex. Subsequent and coordinated recruitment of Grb2 and SHP2 to Gab1 is essential for Gab1-dependent amplification of IL-6-induced late MAPK pathway activation and subsequent gene expression. Conclusions Overall, we elaborated the molecular requirements for Gab1-dependent, spatiotemporal orchestration of interleukin-6-dependent MAPK signalling. We discriminated IL-6-induced Gab1-independent, early activation of MAPK signalling and Gab1-dependent, sustained activation of MAPK signalling.
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Affiliation(s)
- Hannes Bongartz
- Institute of Biology, Department of Systems Biology, Otto-von-Guericke University, Universitätsplatz 2, Gebäude 28/Pfälzer Platz, 39106, Magdeburg, Germany
| | - Karen Gille
- Institute of Biology, Department of Systems Biology, Otto-von-Guericke University, Universitätsplatz 2, Gebäude 28/Pfälzer Platz, 39106, Magdeburg, Germany
| | - Wiebke Hessenkemper
- Institute of Biology, Department of Systems Biology, Otto-von-Guericke University, Universitätsplatz 2, Gebäude 28/Pfälzer Platz, 39106, Magdeburg, Germany
| | - Katharina Mandel
- Institute of Molecular Medicine, Charles Tanford Protein Research Center, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Straße 3a, 06120, Halle (Saale), Germany
| | - Marc Lewitzky
- Institute of Molecular Medicine, Charles Tanford Protein Research Center, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Straße 3a, 06120, Halle (Saale), Germany
| | - Stephan M Feller
- Institute of Molecular Medicine, Charles Tanford Protein Research Center, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Straße 3a, 06120, Halle (Saale), Germany
| | - Fred Schaper
- Institute of Biology, Department of Systems Biology, Otto-von-Guericke University, Universitätsplatz 2, Gebäude 28/Pfälzer Platz, 39106, Magdeburg, Germany.
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Al-Husseinawi E, Bui MM, Ahmed AA. Grb2-associated binding protein-1 as a biomarker in bone and soft tissue sarcomas. Pathology 2019; 51:610-614. [DOI: 10.1016/j.pathol.2019.05.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 05/09/2019] [Accepted: 05/16/2019] [Indexed: 12/31/2022]
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Sutherland L, Ruhe M, Gattegno-Ho D, Mann K, Greaves J, Koscielniak M, Meek S, Lu Z, Waterfall M, Taylor R, Tsakiridis A, Brown H, Maciver SK, Joshi A, Clinton M, Chamberlain LH, Smith A, Burdon T. LIF-dependent survival of embryonic stem cells is regulated by a novel palmitoylated Gab1 signalling protein. J Cell Sci 2018; 131:jcs.222257. [PMID: 30154213 PMCID: PMC6176924 DOI: 10.1242/jcs.222257] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 08/17/2018] [Indexed: 01/25/2023] Open
Abstract
The cytokine leukaemia inhibitory factor (LIF) promotes self-renewal of mouse embryonic stem cells (ESCs) through activation of the transcription factor Stat3. However, the contribution of other ancillary pathways stimulated by LIF in ESCs, such as the MAPK and PI3K pathways, is less well understood. We show here that naive-type mouse ESCs express high levels of a novel effector of the MAPK and PI3K pathways. This effector is an isoform of the Gab1 (Grb2-associated binder protein 1) adaptor protein that lacks the N-terminal pleckstrin homology (PH) membrane-binding domain. Although not essential for rapid unrestricted growth of ESCs under optimal conditions, the novel Gab1 variant (Gab1β) is required for LIF-mediated cell survival under conditions of limited nutrient availability. This enhanced survival is absolutely dependent upon a latent palmitoylation site that targets Gab1β directly to ESC membranes. These results show that constitutive association of Gab1 with membranes through a novel mechanism promotes LIF-dependent survival of murine ESCs in nutrient-poor conditions.
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Affiliation(s)
- Linda Sutherland
- Division of Developmental Biology, The Roslin Institute and R(D)VS, University of Edinburgh, Midlothian, EH25 9RG, UK
| | - Madeleine Ruhe
- Division of Developmental Biology, The Roslin Institute and R(D)VS, University of Edinburgh, Midlothian, EH25 9RG, UK
| | - Daniela Gattegno-Ho
- Division of Developmental Biology, The Roslin Institute and R(D)VS, University of Edinburgh, Midlothian, EH25 9RG, UK
| | - Karanjit Mann
- Division of Developmental Biology, The Roslin Institute and R(D)VS, University of Edinburgh, Midlothian, EH25 9RG, UK,Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, UK
| | - Jennifer Greaves
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, UK
| | - Magdalena Koscielniak
- Division of Developmental Biology, The Roslin Institute and R(D)VS, University of Edinburgh, Midlothian, EH25 9RG, UK
| | - Stephen Meek
- Division of Developmental Biology, The Roslin Institute and R(D)VS, University of Edinburgh, Midlothian, EH25 9RG, UK
| | - Zen Lu
- Division of Genetics and Genomics, The Roslin Institute and R(D)SVS, University of Edinburgh, Midlothian, EH25 9RG, UK
| | - Martin Waterfall
- Division of Developmental Biology, The Roslin Institute and R(D)VS, University of Edinburgh, Midlothian, EH25 9RG, UK
| | - Ryan Taylor
- Division of Developmental Biology, The Roslin Institute and R(D)VS, University of Edinburgh, Midlothian, EH25 9RG, UK
| | - Anestis Tsakiridis
- Department of Biomedical Science, The University of Sheffield, Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK
| | - Helen Brown
- Division of Genetics and Genomics, The Roslin Institute and R(D)SVS, University of Edinburgh, Midlothian, EH25 9RG, UK
| | | | - Anagha Joshi
- Division of Developmental Biology, The Roslin Institute and R(D)VS, University of Edinburgh, Midlothian, EH25 9RG, UK
| | - Michael Clinton
- Division of Developmental Biology, The Roslin Institute and R(D)VS, University of Edinburgh, Midlothian, EH25 9RG, UK
| | - Luke H. Chamberlain
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, UK
| | - Austin Smith
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge CB2 1QT, UK
| | - Tom Burdon
- Division of Developmental Biology, The Roslin Institute and R(D)VS, University of Edinburgh, Midlothian, EH25 9RG, UK
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Identification of a Novel Invasion-Promoting Region in Insulin Receptor Substrate 2. Mol Cell Biol 2018; 38:MCB.00590-17. [PMID: 29685905 DOI: 10.1128/mcb.00590-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 04/15/2018] [Indexed: 12/13/2022] Open
Abstract
Although the insulin receptor substrate (IRS) proteins IRS1 and IRS2 share considerable homology and activate common signaling pathways, their contributions to breast cancer are distinct. IRS1 has been implicated in the proliferation and survival of breast tumor cells. In contrast, IRS2 facilitates glycolysis, invasion, and metastasis. To determine the mechanistic basis for IRS2-dependent functions, we investigated unique structural features of IRS2 that are required for invasion. Our studies revealed that the ability of IRS2 to promote invasion is dependent upon upstream insulin-like growth factor 1 receptor (IGF-1R)/insulin receptor (IR) activation and the recruitment and activation of phosphatidylinositol 3-kinase (PI3K), functions shared with IRS1. In addition, a 174-amino-acid region in the IRS2 C-terminal tail, which is not conserved in IRS1, is also required for IRS2-mediated invasion. Importantly, this "invasion (INV) region" is sufficient to confer invasion-promoting ability when swapped into IRS1. However, the INV region is not required for the IRS2-dependent regulation of glucose uptake. Bone morphogenetic protein 2-inducible kinase (BMP2K) binds to the INV region and contributes to IRS2-dependent invasion. Taken together, our data advance the mechanistic understanding of how IRS2 regulates invasion and reveal that IRS2 functions important for cancer can be independently targeted without interfering with the metabolic activities of this adaptor protein.
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Thiele S, Heise S, Hessenkemper W, Bongartz H, Fensky M, Schaper F, Klamt S. Designing optimal experiments to discriminate interaction graph models. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018; 16:925-935. [PMID: 29993657 DOI: 10.1109/tcbb.2018.2812184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Modern methods for the inference of cellular networks from experimental data often express nondeterminism through an ensemble of candidate models. To discriminate among these candidates new experiments need to be carried out. Theoretically, the number of possible experiments is exponential in the number of possible perturbations. In praxis, experiments are expensive and there exist several limiting constraints. Limiting factors exist on the combinations of perturbations that are technically possible, which components can be measured, and on the number of affordable experiments. Further, not all experiments are equally well suited to discriminate model candidates. The goal of optimal experiment design is to determine those experiments that discriminate most of the candidates while minimizing the costs. We present an approach for experiment planning with interaction graph models and sign consistency methods. This new approach can be used in combination with methods for network inference and consistency checking. We applied our method to study the Erythropoietin signal transduction in human kidney cells HEK293. We first used simulated experiment data from an ODE model to demonstrate in silico that our experimental design results in the inference of the gold standard model. Finally, we used the approach to plan in vivo experiments that discriminate model candidates for the Erythropoietin signal transduction in this cell line.
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Bongartz H, Hessenkemper W, Müller C, Fensky M, Fritsch J, Mandel K, Behrmann I, Haan C, Fischer T, Feller SM, Schaper F. The multi-site docking protein Gab1 is constitutively phosphorylated independent from its recruitment to the plasma membrane in Jak2-V617F-positive cells and mediates proliferation of human erythroleukaemia cells. Cell Signal 2017; 35:37-47. [PMID: 28365441 DOI: 10.1016/j.cellsig.2017.03.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 02/28/2017] [Accepted: 03/26/2017] [Indexed: 10/19/2022]
Abstract
The constitutively active Janus kinase 2 mutant Jak2-V617F is responsible for cytokine-independent growth of hematopoietic cells and the development of myeloproliferative neoplasms, such as polycythaemia vera and essential thrombocythaemia. Cells expressing Jak2-V617F exhibit constitutive STAT, MAPK, and PI3K signalling, and constitutive association of the multi-site docking protein Gab1 to PIP3 at the plasma membrane. Here, we demonstrate the crucial role of Gab1 for the proliferation of Jak2-V617F-positive human erythroleukaemia (HEL) cells. In Jak2-V617F-expressing cells Gab1 is constitutively phosphorylated by Erk1/2 on serine residue 552, which regulates binding to PIP3. Additionally, Gab1 is constitutively phosphorylated on tyrosine residue 627. Tyrosine 627 is a SHP2 binding site and required for Gab1-dependent Erk1/2 activation. As previously shown, Jak2-V617F-dependent Erk1/2 and PI3K activation act synergistically on the proliferation of Jak2-V617F-positive cells. Here, we examined whether constitutive membrane association of Gab1 explains cytokine-independent Gab1 phosphorylation in Jak2-V617F-expressing cells. Although we could demonstrate Jak2-V617F-dependent constitutive serine 552 and tyrosine 627 phosphorylation of Gab1, interestingly, both phosphorylations do not require binding of Gab1 to PIP3 at the plasma membrane. Instead, we observed a constitutive interaction of Gab1 with the erythropoietin receptor in Jak2-V617F-expressing cells, which depends on Janus kinase activity. Thus, constitutive Gab1-dependent signalling in Jak2-V617F-expressing cells does not occur due to the constitutive association of Gab1 with PIP3 at the plasma membrane.
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Affiliation(s)
- Hannes Bongartz
- Institute of Biology, Department of Systems Biology, Otto-von-Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany.
| | - Wiebke Hessenkemper
- Institute of Biology, Department of Systems Biology, Otto-von-Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany.
| | - Christian Müller
- Department of Hematology and Oncology, Medical Center, Otto-von-Guericke University, Leipziger Straße 44, 39120 Magdeburg, Germany.
| | - Melissa Fensky
- Institute of Biology, Department of Systems Biology, Otto-von-Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany.
| | - Johannes Fritsch
- Institute of Biology, Department of Systems Biology, Otto-von-Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany.
| | - Katharina Mandel
- Institute of Molecular Medicine, Martin-Luther-University Halle-Wittenberg, ZAMED, Heinrich-Damerow-Straße 1, 06120 Halle, Germany.
| | - Iris Behrmann
- University of Luxembourg, Signal Transduction Laboratory, Life Sciences Research Unit, 6, avenue du Swing, L-4367 Belvaux, Luxembourg.
| | - Claude Haan
- University of Luxembourg, Signal Transduction Laboratory, Life Sciences Research Unit, 6, avenue du Swing, L-4367 Belvaux, Luxembourg.
| | - Thomas Fischer
- Department of Hematology and Oncology, Medical Center, Otto-von-Guericke University, Leipziger Straße 44, 39120 Magdeburg, Germany; Health Campus Immunology, Infectiology and Inflammation, Otto-von-Guericke-University, Leipziger Straße 44, 39120 Magdeburg, Germany.
| | - Stephan M Feller
- Institute of Molecular Medicine, Martin-Luther-University Halle-Wittenberg, ZAMED, Heinrich-Damerow-Straße 1, 06120 Halle, Germany.
| | - Fred Schaper
- Institute of Biology, Department of Systems Biology, Otto-von-Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany.
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Goto S, Cao F, Kono T, Ogawa H. Microarray Analysis of Differentially Expressed Genes in Inner Cell Mass and Trophectoderm of Parthenogenetic Embryos. ACTA ACUST UNITED AC 2016. [DOI: 10.1274/032.033.0107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Golkowski M, Shimizu-Albergine M, Suh HW, Beavo JA, Ong SE. Studying mechanisms of cAMP and cyclic nucleotide phosphodiesterase signaling in Leydig cell function with phosphoproteomics. Cell Signal 2015; 28:764-78. [PMID: 26643407 DOI: 10.1016/j.cellsig.2015.11.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Accepted: 11/26/2015] [Indexed: 12/21/2022]
Abstract
Many cellular processes are modulated by cyclic AMP and nucleotide phosphodiesterases (PDEs) regulate this second messenger by catalyzing its breakdown. The major unique function of testicular Leydig cells is to produce testosterone in response to luteinizing hormone (LH). Treatment of Leydig cells with PDE inhibitors increases cAMP levels and the activity of its downstream effector, cAMP-dependent protein kinase (PKA), leading to a series of kinase-dependent signaling and transcription events that ultimately increase testosterone release. We have recently shown that PDE4B and PDE4C as well as PDE8A and PDE8B are expressed in rodent Leydig cells and that combined inhibition of PDE4 and PDE8 leads to dramatically increased steroid biosynthesis. Here we investigated the effect of PDE4 and PDE8 inhibition on the molecular mechanisms of cAMP actions in a mouse MA10 Leydig cell line model with SILAC mass spectrometry-based phosphoproteomics. We treated MA10 cells either with PDE4 family specific inhibitor (Rolipram) and PDE8 family specific inhibitor (PF-04957325) alone or in combination and quantified the resulting phosphorylation changes at five different time points between 0 and 180min. We identified 28,336 phosphosites from 4837 proteins and observed significant regulation of 749 sites in response to PDE4 and PDE8 inhibitor treatment. Of these, 132 phosphosites were consensus PKA sites. Our data strongly suggest that PDE4 and PDE8 inhibitors synergistically regulate phosphorylation of proteins required for many different cellular processes, including cell cycle progression, lipid and glucose metabolism, transcription, endocytosis and vesicle transport. Our data suggests that cAMP, PDE4 and PDE8 coordinate steroidogenesis by acting on not one rate-limiting step but rather multiple pathways. Moreover, the pools of cAMP controlled by these PDEs also coordinate many other metabolic processes that may be regulated to assure timely and sufficient testosterone secretion in response to LH.
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Affiliation(s)
- Martin Golkowski
- Department of Pharmacology, School of Medicine, University of Washington, USA
| | | | - Hyong Won Suh
- Department of Pharmacology, School of Medicine, University of Washington, USA
| | - Joseph A Beavo
- Department of Pharmacology, School of Medicine, University of Washington, USA.
| | - Shao-En Ong
- Department of Pharmacology, School of Medicine, University of Washington, USA.
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Zeke A, Bastys T, Alexa A, Garai Á, Mészáros B, Kirsch K, Dosztányi Z, Kalinina OV, Reményi A. Systematic discovery of linear binding motifs targeting an ancient protein interaction surface on MAP kinases. Mol Syst Biol 2015; 11:837. [PMID: 26538579 PMCID: PMC4670726 DOI: 10.15252/msb.20156269] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Mitogen‐activated protein kinases (MAPK) are broadly used regulators of cellular signaling. However, how these enzymes can be involved in such a broad spectrum of physiological functions is not understood. Systematic discovery of MAPK networks both experimentally and in silico has been hindered because MAPKs bind to other proteins with low affinity and mostly in less‐characterized disordered regions. We used a structurally consistent model on kinase‐docking motif interactions to facilitate the discovery of short functional sites in the structurally flexible and functionally under‐explored part of the human proteome and applied experimental tools specifically tailored to detect low‐affinity protein–protein interactions for their validation in vitro and in cell‐based assays. The combined computational and experimental approach enabled the identification of many novel MAPK‐docking motifs that were elusive for other large‐scale protein–protein interaction screens. The analysis produced an extensive list of independently evolved linear binding motifs from a functionally diverse set of proteins. These all target, with characteristic binding specificity, an ancient protein interaction surface on evolutionarily related but physiologically clearly distinct three MAPKs (JNK, ERK, and p38). This inventory of human protein kinase binding sites was compared with that of other organisms to examine how kinase‐mediated partnerships evolved over time. The analysis suggests that most human MAPK‐binding motifs are surprisingly new evolutionarily inventions and newly found links highlight (previously hidden) roles of MAPKs. We propose that short MAPK‐binding stretches are created in disordered protein segments through a variety of ways and they represent a major resource for ancient signaling enzymes to acquire new regulatory roles.
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Affiliation(s)
- András Zeke
- Lendület Protein Interaction Group, Institute of Enzymology Research Center for Natural Sciences Hungarian Academy of Sciences, Budapest, Hungary
| | - Tomas Bastys
- Max Planck Institute for Informatics, Saarbrücken, Germany Graduate School of Computer Science, Saarland University, Saarbrücken, Germany
| | - Anita Alexa
- Lendület Protein Interaction Group, Institute of Enzymology Research Center for Natural Sciences Hungarian Academy of Sciences, Budapest, Hungary
| | - Ágnes Garai
- Lendület Protein Interaction Group, Institute of Enzymology Research Center for Natural Sciences Hungarian Academy of Sciences, Budapest, Hungary
| | - Bálint Mészáros
- Institute of Enzymology Research Center for Natural Sciences Hungarian Academy of Sciences, Budapest, Hungary
| | - Klára Kirsch
- Lendület Protein Interaction Group, Institute of Enzymology Research Center for Natural Sciences Hungarian Academy of Sciences, Budapest, Hungary
| | - Zsuzsanna Dosztányi
- MTA-ELTE Lendület Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
| | | | - Attila Reményi
- Lendület Protein Interaction Group, Institute of Enzymology Research Center for Natural Sciences Hungarian Academy of Sciences, Budapest, Hungary
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Schaper F, Rose-John S. Interleukin-6: Biology, signaling and strategies of blockade. Cytokine Growth Factor Rev 2015; 26:475-87. [DOI: 10.1016/j.cytogfr.2015.07.004] [Citation(s) in RCA: 287] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 07/01/2015] [Indexed: 02/07/2023]
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