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Arulraj T, Binder SC, Meyer-Hermann M. Rate of Immune Complex Cycling in Follicular Dendritic Cells Determines the Extent of Protecting Antigen Integrity and Availability to Germinal Center B Cells. THE JOURNAL OF IMMUNOLOGY 2021; 206:1436-1442. [PMID: 33608455 DOI: 10.4049/jimmunol.2001355] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 01/22/2021] [Indexed: 01/02/2023]
Abstract
Follicular dendritic cells (FDCs) retain immune complexes (ICs) for prolonged time periods and are important for germinal center (GC) reactions. ICs undergo periodic cycling in FDCs, a mechanism supporting an extended half-life of Ag. Based on experimental data, we estimated that the average residence time of PE-ICs on FDC surface and interior were 21 and 36 min, respectively. GC simulations show that Ag cycling might impact GC dynamics because of redistribution of Ag on the FDC surface and by protecting Ag from degradation. Ag protection and influence on GC dynamics varied with Ag cycling time and total Ag concentration. Simulations predict that blocking Ag cycling terminates the GC reaction and decreases plasma cell production. Considering that cycling of Ag could be a target for the modulation of GC reactions, our findings highlight the importance of understanding the mechanism and regulation of IC cycling in FDCs.
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Affiliation(s)
- Theinmozhi Arulraj
- Department of Systems Immunology, Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, 38106 Braunschweig, Germany
| | - Sebastian C Binder
- Department of Systems Immunology, Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, 38106 Braunschweig, Germany.,Centre for Individualized Infection Medicine, 30625 Hannover, Germany; and
| | - Michael Meyer-Hermann
- Department of Systems Immunology, Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, 38106 Braunschweig, Germany; .,Centre for Individualized Infection Medicine, 30625 Hannover, Germany; and.,Institute for Biochemistry, Biotechnology and Bioinformatics, Braunschweig University of Technology, 38106 Braunschweig, Germany
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Lambert L, Dubayle D, Fafouri A, Herzog E, Csaba Z, Dournaud P, El Mestikawy S, Bernard V. Endocytosis of Activated Muscarinic m2 Receptor (m2R) in Live Mouse Hippocampal Neurons Occurs via a Clathrin-Dependent Pathway. Front Cell Neurosci 2018; 12:450. [PMID: 30555302 PMCID: PMC6283979 DOI: 10.3389/fncel.2018.00450] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 11/07/2018] [Indexed: 02/02/2023] Open
Abstract
Our aim was to examine the dynamics of the muscarinic m2 receptor (m2R), a G-protein coupled receptor (GPCR), after agonist activation in living hippocampal neurons, and especially clathrin dependency endocytosis. We have previously shown that the m2R undergoes agonist-induced internalization in vivo. However, the nature of the endocytotic pathway used by m2R after activation is still unknown in living neurons. Using live cell imaging and quantitative analyses, we have monitored the effect of stimulation on the fate of the membrane-bound m2R and on its redistribution in intraneuronal compartments. Shortly (6 min) after activation, m2R is internalized into clathrin immunopositive structures. Furthermore, after clathrin-dependent endocytosis, m2R associates with early and late endosomes and with subcellular organelles involved in degradation. Together, these results provide, for the first time, a description of m2R trafficking in living neurons and prove that m2R undergoes clathrin-dependent endocytosis before being degraded.
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Affiliation(s)
- Lisa Lambert
- Sorbonne Université, Université Pierre et Marie Curie UM 119 - CNRS UMR 8246 - INSERM U1130, Neurosciences Paris Seine - Institut de Biologie Paris Seine (NPS - IBPS), Paris, France
| | - David Dubayle
- Sorbonne Université, Université Pierre et Marie Curie UM 119 - CNRS UMR 8246 - INSERM U1130, Neurosciences Paris Seine - Institut de Biologie Paris Seine (NPS - IBPS), Paris, France.,Université Paris Descartes - CNRS UMR 8119, Centre de Neurophysique, Physiologie et Pathologie, Paris, France
| | - Assia Fafouri
- PROTECT, INSERM U1141, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Etienne Herzog
- Sorbonne Université, Université Pierre et Marie Curie UM 119 - CNRS UMR 8246 - INSERM U1130, Neurosciences Paris Seine - Institut de Biologie Paris Seine (NPS - IBPS), Paris, France.,Interdisciplinary Institute for Neuroscience, University Bordeaux, UMR 5297, Bordeaux, France.,Interdisciplinary Institute for Neuroscience, CNRS, UMR 5297, Bordeaux, France
| | - Zsolt Csaba
- PROTECT, INSERM U1141, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Pascal Dournaud
- PROTECT, INSERM U1141, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Salah El Mestikawy
- Sorbonne Université, Université Pierre et Marie Curie UM 119 - CNRS UMR 8246 - INSERM U1130, Neurosciences Paris Seine - Institut de Biologie Paris Seine (NPS - IBPS), Paris, France.,Department of Psychiatry, Douglas Hospital Research Center, McGill University, Montréal, QC, Canada
| | - Véronique Bernard
- Sorbonne Université, Université Pierre et Marie Curie UM 119 - CNRS UMR 8246 - INSERM U1130, Neurosciences Paris Seine - Institut de Biologie Paris Seine (NPS - IBPS), Paris, France
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3
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Becker AK, Erfle H, Gunkel M, Beil N, Kaderali L, Starkuviene V. Comparison of Cell Arrays and Multi-Well Plates in Microscopy-Based Screening. High Throughput 2018; 7:ht7020013. [PMID: 29762489 PMCID: PMC6023461 DOI: 10.3390/ht7020013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 05/08/2018] [Accepted: 05/09/2018] [Indexed: 01/30/2023] Open
Abstract
Multi-well plates and cell arrays enable microscopy-based screening assays in which many samples can be analysed in parallel. Each of the formats possesses its own strengths and weaknesses, but reference comparisons between these platforms and their application rationale is lacking. We aim to fill this gap by comparing two RNA interference (RNAi)-mediated fluorescence microscopy-based assays, namely epidermal growth factor (EGF) internalization and cell cycle progression, on both platforms. Quantitative analysis revealed that both platforms enabled the generation of data with the appearance of the expected phenotypes significantly distinct from the negative controls. The measurements of cell cycle progression were less variable in multi-well plates. The result can largely be attributed to higher cell numbers resulting in less data variability when dealing with the assay generating phenotypic cell subpopulations. The EGF internalization assay with a uniform phenotype over nearly the whole cell population performed better on cell arrays than in multi-well plates. The result was achieved by scoring five times less cells on cell arrays than in multi-well plates, indicating the efficiency of the cell array format. Our data indicate that the choice of the screening platform primarily depends on the type of the cellular assay to achieve a maximum data quality and screen efficiency.
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Affiliation(s)
- Ann-Kristin Becker
- Institute of Bioinformatics, University Medicine Greifswald, 17475 Greifswald, Germany.
| | - Holger Erfle
- BioQuant, Heidelberg University, 69120 Heidelberg, Germany.
| | - Manuel Gunkel
- BioQuant, Heidelberg University, 69120 Heidelberg, Germany.
| | - Nina Beil
- BioQuant, Heidelberg University, 69120 Heidelberg, Germany.
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, 17475 Greifswald, Germany.
| | - Vytaute Starkuviene
- BioQuant, Heidelberg University, 69120 Heidelberg, Germany.
- Institute of Biosciences, Vilnius University Life Sciences Center, LT-10257 Vilnius, Lithuania.
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4
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Quantitative analysis reveals how EGFR activation and downregulation are coupled in normal but not in cancer cells. Nat Commun 2015; 6:7999. [PMID: 26264748 PMCID: PMC4538861 DOI: 10.1038/ncomms8999] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2014] [Accepted: 07/03/2015] [Indexed: 12/31/2022] Open
Abstract
Ubiquitination of the epidermal growth factor receptor (EGFR) that occurs when Cbl and Grb2 bind to three phosphotyrosine residues (pY1045, pY1068 and pY1086) on the receptor displays a sharp threshold effect as a function of EGF concentration. Here we use a simple modelling approach together with experiments to show that the establishment of the threshold requires both the multiplicity of binding sites and cooperative binding of Cbl and Grb2 to the EGFR. While the threshold is remarkably robust, a more sophisticated model predicted that it could be modulated as a function of EGFR levels on the cell surface. We confirmed experimentally that the system has evolved to perform optimally at physiological levels of EGFR. As a consequence, this system displays an intrinsic weakness that causes--at the supraphysiological levels of receptor and/or ligand associated with cancer--uncoupling of the mechanisms leading to signalling through phosphorylation and attenuation through ubiquitination.
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Sangrar W, Shi C, Mullins G, LeBrun D, Ingalls B, Greer PA. Amplified Ras-MAPK signal states correlate with accelerated EGFR internalization, cytostasis and delayed HER2 tumor onset in Fer-deficient model systems. Oncogene 2014; 34:4109-17. [DOI: 10.1038/onc.2014.340] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 08/29/2014] [Accepted: 09/16/2014] [Indexed: 12/20/2022]
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Kozyulina PY, Loskutov YV, Kozyreva VK, Rajulapati A, Ice RJ, Jones BC, Pugacheva EN. Prometastatic NEDD9 Regulates Individual Cell Migration via Caveolin-1-Dependent Trafficking of Integrins. Mol Cancer Res 2014; 13:423-38. [PMID: 25319010 DOI: 10.1158/1541-7786.mcr-14-0353] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
UNLABELLED The dissemination of tumor cells relies on efficient cell adhesion and migration, which in turn depends upon endocytic trafficking of integrins. In the current work, it was found that depletion of the prometastatic protein, NEDD9, in breast cancer cells results in a significant decrease in individual cell migration due to impaired trafficking of ligand-bound integrins. NEDD9 deficiency does not affect the expression or internalization of integrins but heightens caveolae-dependent trafficking of ligand-bound integrins to early endosomes. Increase in mobility of ligand-bound integrins is concomitant with an increase in tyrosine phosphorylation of caveolin-1 (CAV1) and volume of CAV1-vesicles. NEDD9 directly binds to CAV1 and colocalizes within CAV1 vesicles. In the absence of NEDD9, the trafficking of ligand-bound integrins from early to late endosomes is impaired, resulting in a significant decrease in degradation of ligand-integrin complexes and an increase in recycling of ligand-bound integrins from early endosomes back to the plasma membrane without ligand disengagement, thus leading to low adhesion and migration. Reexpression of NEDD9 or decrease in the amount of active, tyrosine 14 phosphorylated (Tyr14) CAV1 in NEDD9-depleted cells rescues the integrin trafficking deficiency and restores cellular adhesion and migration capacity. Collectively, these findings indicate that NEDD9 orchestrates trafficking of ligand-bound integrins through the attenuation of CAV1 activity. IMPLICATIONS This study provides valuable new insight into the potential therapeutic benefit of NEDD9 depletion to reduce dissemination of tumor cells and discovers a new regulatory role of NEDD9 in promoting migration through modulation of CAV1-dependent trafficking of integrins.
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Affiliation(s)
- Polina Y Kozyulina
- Department of Biochemistry, School of Medicine, West Virginia University, Morgantown, West Virginia. Institute of Cytology Russian Academy of Sciences, St. Petersburg, Russia
| | - Yuriy V Loskutov
- Mary Babb Randolph Cancer Center, School of Medicine, West Virginia University, Morgantown, West Virginia
| | - Varvara K Kozyreva
- Mary Babb Randolph Cancer Center, School of Medicine, West Virginia University, Morgantown, West Virginia
| | - Anuradha Rajulapati
- Mary Babb Randolph Cancer Center, School of Medicine, West Virginia University, Morgantown, West Virginia
| | - Ryan J Ice
- Mary Babb Randolph Cancer Center, School of Medicine, West Virginia University, Morgantown, West Virginia
| | - Brandon C Jones
- Department of Biochemistry, School of Medicine, West Virginia University, Morgantown, West Virginia
| | - Elena N Pugacheva
- Department of Biochemistry, School of Medicine, West Virginia University, Morgantown, West Virginia. Mary Babb Randolph Cancer Center, School of Medicine, West Virginia University, Morgantown, West Virginia.
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Koch Y, Wolf T, Sorger PK, Eils R, Brors B. Decision-tree based model analysis for efficient identification of parameter relations leading to different signaling states. PLoS One 2013; 8:e82593. [PMID: 24367526 PMCID: PMC3867358 DOI: 10.1371/journal.pone.0082593] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 11/03/2013] [Indexed: 11/18/2022] Open
Abstract
In systems biology, a mathematical description of signal transduction processes is used to gain a more detailed mechanistic understanding of cellular signaling networks. Such models typically depend on a number of parameters that have different influence on the model behavior. Local sensitivity analysis is able to identify parameters that have the largest effect on signaling strength. Bifurcation analysis shows on which parameters a qualitative model response depends. Most methods for model analysis are intrinsically univariate. They typically cannot consider combinations of parameters since the search space for such analysis would be too large. This limitation is important since activation of a signaling pathway often relies on multiple rather than on single factors. Here, we present a novel method for model analysis that overcomes this limitation. As input to a model defined by a system of ordinary differential equations, we consider parameters for initial chemical species concentrations. The model is used to simulate the system response, which is then classified into pre-defined classes (e.g., active or not active). This is combined with a scan of the parameter space. Parameter sets leading to a certain system response are subjected to a decision tree algorithm, which learns conditions that lead to this response. We compare our method to two alternative multivariate approaches to model analysis: analytical solution for steady states combined with a parameter scan, and direct Lyapunov exponent (DLE) analysis. We use three previously published models including a model for EGF receptor internalization and two apoptosis models to demonstrate the power of our approach. Our method reproduces critical parameter relations previously obtained by both steady-state and DLE analysis while being more generally applicable and substantially less computationally expensive. The method can be used as a general tool to predict multivariate control strategies for pathway activation and to suggest strategies for drug intervention.
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Affiliation(s)
- Yvonne Koch
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, Heidelberg, Germany
| | - Thomas Wolf
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, Heidelberg, Germany
- Institute of General Pathology, Heidelberg University Medical School, University of Heidelberg, Im Neuenheimer Feld 224, Heidelberg, Germany
| | - Peter K. Sorger
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, Massachusetts, United States of America
| | - Roland Eils
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, Heidelberg, Germany
- Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology, and Bioquant Center, University of Heidelberg, Im Neuenheimer Feld 267, Heidelberg, Germany
| | - Benedikt Brors
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, Heidelberg, Germany
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Threshold-controlled ubiquitination of the EGFR directs receptor fate. EMBO J 2013; 32:2140-57. [PMID: 23799367 PMCID: PMC3730230 DOI: 10.1038/emboj.2013.149] [Citation(s) in RCA: 142] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Accepted: 06/03/2013] [Indexed: 11/30/2022] Open
Abstract
How the cell converts graded signals into threshold-activated responses is a question of great biological relevance. Here, we uncover a nonlinear modality of epidermal growth factor receptor (EGFR)-activated signal transduction, by demonstrating that the ubiquitination of the EGFR at the PM is threshold controlled. The ubiquitination threshold is mechanistically determined by the cooperative recruitment of the E3 ligase Cbl, in complex with Grb2, to the EGFR. This, in turn, is dependent on the simultaneous presence of two phosphotyrosines, pY1045 and either one of pY1068 or pY1086, on the same EGFR moiety. The dose–response curve of EGFR ubiquitination correlate precisely with the non-clathrin endocytosis (NCE) mode of EGFR internalization. Finally, EGFR-NCE mechanistically depends on EGFR ubiquitination, as the two events can be simultaneously re-engineered on a phosphorylation/ubiquitination-incompetent EGFR backbone. Since NCE controls the degradation of the EGFR, our findings have implications for how the cell responds to increasing levels of EGFR signalling, by varying the balance of receptor signalling and degradation/attenuation. The amount of EGF present for binding to its receptor governs an on–off switch of EGFR ubiquitination and hence ligand-controlled non-clathrin-mediated endocytosis and EGFR degradation.
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Birtwistle MR, Kholodenko BN. Endocytosis and signalling: a meeting with mathematics. Mol Oncol 2009; 3:308-20. [PMID: 19596615 DOI: 10.1016/j.molonc.2009.05.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2009] [Accepted: 05/27/2009] [Indexed: 10/20/2022] Open
Abstract
Although endocytosis has traditionally been understood as a signal attenuation mechanism, an emerging view considers endocytosis as an integral part of signal propagation and processing. On the short time scale, trafficking of endocytic vesicles contributes to signal propagation from the surface to distant targets, with bi-directional communication between signalling and trafficking. Mathematical modelling helps combine the mechanistic, molecular knowledge with rigorous analysis of the complex output dynamics of endocytosis in time and space. Simulations reveal novel roles for endocytosis, including the control of cell polarity, enhancing the spatial signal propagation, and controlling the signal magnitudes, kinetics, and synchronization with stimulus dynamics.
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Affiliation(s)
- Marc R Birtwistle
- Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland
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Schmidt-Glenewinkel H, Reinz E, Eils R, Brady NR. Systems biological analysis of epidermal growth factor receptor internalization dynamics for altered receptor levels. J Biol Chem 2009; 284:17243-17252. [PMID: 19297331 DOI: 10.1074/jbc.m809586200] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Epidermal growth factor (EGF) receptor (EGFR) overexpression is a hallmark of many cancers. EGFR endocytosis is a critical step in signal attenuation, raising the question of how receptor expression levels affect the internalization process. Here we combined quantitative experimental and mathematical modeling approaches to investigate the role of the EGFR expression level on the rate of receptor internalization. Using tetramethylrhodamine-labeled EGF, we established assays for quantifying EGF-triggered EGFR internalization by both high resolution confocal microscopy and flow cytometry. We determined that the flow cytometry approach was more sensitive for examining large populations of cells. Mathematical modeling was used to investigate the relationship between EGF internalization kinetics, EGFR expression, and internalization machinery. We predicted that the standard parameter used to assess internalization kinetics, the temporal evolution r(t) of the ratio of internalized versus surface-located ligand.receptor complexes, does not describe a straight line, as proposed previously. Instead, a convex or concave curve occurs depending on whether initial receptor numbers or internalization adaptors are limiting the uptake reaction, respectively. To test model predictions, we measured EGF-EGFR binding and internalization in cells expressing different levels of green fluorescent protein-EGFR. As expected, surface binding of rhodamine-labeled EGF increased with green fluorescent protein-EGFR expression level. Unexpectedly, internalization of ligand. receptor complexes increased linearly with increasing receptor expression level, suggesting that receptors and not internalization adaptors were limiting the uptake in our experimental model. Finally, determining the ratio of internalized versus surface-located ligand.receptor complexes for this cell line confirmed that it follows a convex curve, supporting our model predictions.
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Affiliation(s)
| | - Eileen Reinz
- Infection and Cancer Research Program, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Roland Eils
- From the Division of Theoretical Bioinformatics, 69120 Heidelberg, Germany; Institute for Pharmacy and Molecular Biotechnology and Bioquant, University of Heidelberg, 69120 Heidelberg, Germany.
| | - Nathan R Brady
- From the Division of Theoretical Bioinformatics, 69120 Heidelberg, Germany
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Sadowski L, Pilecka I, Miaczynska M. Signaling from endosomes: location makes a difference. Exp Cell Res 2008; 315:1601-9. [PMID: 18930045 DOI: 10.1016/j.yexcr.2008.09.021] [Citation(s) in RCA: 138] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2008] [Accepted: 09/23/2008] [Indexed: 01/14/2023]
Abstract
In all transmembrane receptor systems the kinetics of receptor trafficking upon ligand stimulation is maintained in a balance between degradative and recycling pathways in order to keep homeostasis and to strictly control receptor-mediated signaling. Endocytosis is commonly considered as an efficient mechanism of uptake and transport of membrane-associated signaling molecules leading to attenuation of ligand-induced responses. Accumulating evidence, however, shows that signaling from internalized receptors not only continues in endosomal compartments, but that there are also distinct signaling events that require endocytosis. Endocytic organelles form a dynamic network of subcellular compartments, which actively control the timing, amplitude, and specificity of signaling. In this review we provide examples in which signal transduction either requires an active endocytic machinery, or directly originates from various types of endosomes. Based on recent discoveries, we emphasize the close interdependence between signaling and endocytosis, and the physiological relevance of endocytic transport in health and disease.
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Affiliation(s)
- Lukasz Sadowski
- International Institute of Molecular and Cell Biology, Laboratory of Cell Biology, 4 Ks. Trojdena Street, 02-109 Warsaw, Poland
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