501
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502
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Baxt LA, Xavier RJ. Role of Autophagy in the Maintenance of Intestinal Homeostasis. Gastroenterology 2015; 149:553-62. [PMID: 26170139 PMCID: PMC4550567 DOI: 10.1053/j.gastro.2015.06.046] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 06/16/2015] [Accepted: 06/29/2015] [Indexed: 02/08/2023]
Abstract
Genome-wide association studies of inflammatory bowel disease have identified several risk loci in genes that regulate autophagy, and studies have provided insight into the functional effects of these polymorphisms. We review the mechanisms by which autophagy contributes to intestinal homeostasis, focusing on its cell type-specific roles in regulating gut ecology, restricting pathogenic bacteria, and controlling inflammation. Based on this information, we are beginning to understand how alterations in autophagy can contribute to intestinal inflammation.
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Affiliation(s)
- Leigh A. Baxt
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts
| | - Ramnik J. Xavier
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts,Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
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503
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Abstract
Ubiquitin (UB)-driven signaling systems permeate biology, and are often integrated with other types of post-translational modifications (PTMs), including phosphorylation. Flux through such pathways is dictated by the fractional stoichiometry of distinct modifications and protein assemblies as well as the spatial organization of pathway components. Yet, we rarely understand the dynamics and stoichiometry of rate-limiting intermediates along a reaction trajectory. Here, we review how quantitative proteomic tools and enrichment strategies are being used to quantify UB-dependent signaling systems, and to integrate UB signaling with regulatory phosphorylation events, illustrated with the PINK1/PARKIN pathway. A key feature of ubiquitylation is that the identity of UB chain linkage types can control downstream processes. We also describe how proteomic and enzymological tools can be used to identify and quantify UB chain synthesis and linkage preferences. The emergence of sophisticated quantitative proteomic approaches will set a new standard for elucidating biochemical mechanisms of UB-driven signaling systems.
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Affiliation(s)
- Alban Ordureau
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Christian Münch
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
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504
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Popelka H, Klionsky DJ. Post-translationally-modified structures in the autophagy machinery: an integrative perspective. FEBS J 2015; 282:3474-88. [PMID: 26108642 DOI: 10.1111/febs.13356] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 06/11/2015] [Accepted: 06/19/2015] [Indexed: 01/10/2023]
Abstract
Autophagy is a self-cleaning process that occurs at a constitutive basal level, and is upregulated in response to stress. Macroautophagy (hereafter autophagy) is the most robust type of autophagy, where cargo (specific or nonspecific) is engulfed within a double-membrane structure termed an autophagosome. This process needs to be tightly regulated to maintain normal cellular homeostasis and prevent dysfunction; therefore, a fuller knowledge of the mechanisms of autophagy regulation is crucial for understanding the entire pathway. The autophagy-related proteins are the primary components that carry out autophagy. Many of these proteins are conserved from yeast to humans. A number of significant discoveries with regard to protein functional domains, protein-protein interactions or post-translational modifications of proteins involved in autophagy have been reported in parallel with, or followed by, solving the NMR or crystal structures of autophagy proteins or their protein domains. In the present review, we summarize structural insights gathered to date on the proteins of the autophagy machinery that are modulated by a post-translational modification, specifically phosphorylation, acetylation, ubiquitination and/or SUMOylation. For each protein, we link the reported results with information on the propensity of the corresponding amino acid sequence toward order/disorder. This integrative approach yields a comprehensive overview for each post-translationally modified protein, and also reveals areas for further investigation.
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Affiliation(s)
- Hana Popelka
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
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505
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Abstract
Autophagy is a conserved catabolic process that degrades cytoplasmic constituents and organelles in the lysosome. Starvation-induced protein degradation is a salient feature of autophagy but recent progress has illuminated how autophagy, during both starvation and nutrient-replete conditions, can mobilize diverse cellular energy and nutrient stores such as lipids, carbohydrates and iron. Processes such as lipophagy, glycophagy and ferritinophagy enable cells to salvage key metabolites to sustain and facilitate core anabolic functions. Here, we discuss the established and emerging roles of autophagy in fuelling biosynthetic capacity and in promoting metabolic and nutrient homeostasis.
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506
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PI3K inhibitors in inflammation, autoimmunity and cancer. Curr Opin Pharmacol 2015; 23:82-91. [PMID: 26093105 PMCID: PMC4518027 DOI: 10.1016/j.coph.2015.05.017] [Citation(s) in RCA: 215] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 05/29/2015] [Indexed: 12/20/2022]
Abstract
The healthy immune system protects against infection and malignant transformation without causing significant damage to host tissues. Immune dysregulation results in diverse pathologies including autoimmune disease, chronic inflammatory disorders, allergies as well as immune deficiencies and cancer. Phosphoinositide 3-kinase (PI3K) signalling has been shown to be a key pathway in the regulation of the immune response and continues to be the focus of intense research. In recent years we have gained detailed understanding of PI3K signalling, and saw the development of potent and highly selective small molecule inhibitors, of which several are currently in clinical trials for the treatment of immune-related disorders and cancer. The role of PI3K signalling in the immune response has been the subject of detailed reviews; here we focus on relevant recent progress in pre-clinical and clinical development of PI3K inhibitors.
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507
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Emerging strategies to effectively target autophagy in cancer. Oncogene 2015; 35:1-11. [PMID: 25893285 DOI: 10.1038/onc.2015.99] [Citation(s) in RCA: 196] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 02/18/2015] [Accepted: 02/18/2015] [Indexed: 02/07/2023]
Abstract
Autophagy serves a dichotomous role in cancer and recent advances have helped delineate the appropriate settings where inhibiting or promoting autophagy may confer therapeutic efficacy in patients. Our evolving understanding of the molecular machinery responsible for the tightly controlled regulation of this homeostatic mechanism has begun to bear fruit in the way of autophagy-oriented clinical trials and promising lead compounds to modulate autophagy for therapeutic benefit. In this manuscript we review the recent preclinical and clinical therapeutic strategies that involve autophagy modulation in cancer.
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508
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Yu K, Phu L, Varfolomeev E, Bustos D, Vucic D, Kirkpatrick DS. Immunoaffinity enrichment coupled to quantitative mass spectrometry reveals ubiquitin-mediated signaling events. J Mol Biol 2015; 427:2121-34. [PMID: 25861760 DOI: 10.1016/j.jmb.2015.03.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Revised: 03/25/2015] [Accepted: 03/30/2015] [Indexed: 12/30/2022]
Abstract
Ubiquitination is one of the most prevalent posttranslational modifications in eukaryotic cells, with functional importance in protein degradation, subcellular localization and signal transduction pathways. Immunoaffinity enrichment coupled with quantitative mass spectrometry enables the in-depth characterization of protein ubiquitination events at the site-specific level. We have applied this strategy to investigate cellular response triggered by two distinct type agents: small molecule inhibitors of the tumor-associated kinases MEK and PI3K or the pro-inflammatory cytokine IL-17. Temporal profiling of protein ubiquitination events across a series of time points covering the biological response permits interrogation of signaling through thousands of quantified proteins, of which only a subset display significant and physiologically meaningful regulation. Distinctive clusters of residues within proteins can display distinct temporal patterns attributable to diverse molecular functions, although the majority of differential ubiquitination appears as a coordinated response across the modifiable residues present within an individual substrate. In cells treated with a combination of MEK and PI3K inhibitors, we found differential ubiquitination of MEK within the first hour after treatment and a series of mitochondria proteins at later time points. In the IL-17 signaling pathway, ubiquitination events on several signaling proteins including HOIL-1 and Tollip were observed. The functional relevance of these putative IL-17 mediators was subsequently validated by knockdown of HOIL-1, HOIP and TOLIP, each of which decreased IL-17-stimulated cytokine production. Together, these data validate proteomic profiling of protein ubiquitination as a viable approach for identifying dynamic signaling components in response to intracellular and extracellular perturbations.
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Affiliation(s)
- Kebing Yu
- Department of Protein Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Lilian Phu
- Department of Protein Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Eugene Varfolomeev
- Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Daisy Bustos
- Department of Protein Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Domagoj Vucic
- Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
| | - Donald S Kirkpatrick
- Department of Protein Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
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509
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Silva B, Faustino P. An overview of molecular basis of iron metabolism regulation and the associated pathologies. Biochim Biophys Acta Mol Basis Dis 2015; 1852:1347-59. [PMID: 25843914 DOI: 10.1016/j.bbadis.2015.03.011] [Citation(s) in RCA: 182] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 03/05/2015] [Accepted: 03/27/2015] [Indexed: 12/18/2022]
Abstract
Iron is essential for several vital biological processes. Its deficiency or overload drives to the development of several pathologies. To maintain iron homeostasis, the organism controls the dietary iron absorption by enterocytes, its recycling by macrophages and storage in hepatocytes. These processes are mainly controlled by hepcidin, a liver-derived hormone which synthesis is regulated by iron levels, inflammation, infection, anemia and erythropoiesis. Besides the systemic regulation of iron metabolism mediated by hepcidin, cellular regulatory processes also occur. Cells are able to regulate themselves the expression of the iron metabolism-related genes through different post-transcriptional mechanisms, such as the alternative splicing, microRNAs, the IRP/IRE system and the proteolytic cleavage. Whenever those mechanisms are disturbed, due to genetic or environmental factors, iron homeostasis is disrupted and iron related pathologies may arise.
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Affiliation(s)
- Bruno Silva
- Departamento de Genética Humana, Instituto Nacional de Saúde Dr. Ricardo Jorge, Lisboa, Portugal
| | - Paula Faustino
- Departamento de Genética Humana, Instituto Nacional de Saúde Dr. Ricardo Jorge, Lisboa, Portugal.
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510
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Petherick KJ, Conway OJL, Mpamhanga C, Osborne SA, Kamal A, Saxty B, Ganley IG. Pharmacological inhibition of ULK1 kinase blocks mammalian target of rapamycin (mTOR)-dependent autophagy. J Biol Chem 2015; 290:11376-83. [PMID: 25833948 PMCID: PMC4416842 DOI: 10.1074/jbc.c114.627778] [Citation(s) in RCA: 210] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Indexed: 12/31/2022] Open
Abstract
Autophagy is a cell-protective and degradative process that recycles damaged and long-lived cellular components. Cancer cells are thought to take advantage of autophagy to help them to cope with the stress of tumorigenesis; thus targeting autophagy is an attractive therapeutic approach. However, there are currently no specific inhibitors of autophagy. ULK1, a serine/threonine protein kinase, is essential for the initial stages of autophagy, and here we report that two compounds, MRT67307 and MRT68921, potently inhibit ULK1 and ULK2 in vitro and block autophagy in cells. Using a drug-resistant ULK1 mutant, we show that the autophagy-inhibiting capacity of the compounds is specifically through ULK1. ULK1 inhibition results in accumulation of stalled early autophagosomal structures, indicating a role for ULK1 in the maturation of autophagosomes as well as initiation.
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Affiliation(s)
- Katy J Petherick
- From the Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland and
| | - Owen J L Conway
- From the Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland and
| | - Chido Mpamhanga
- the MRC Technology Centre for Therapeutics Discovery, 1-3 Burtonhole Lane, Mill Hill, London NW7 1AD, United Kingdom
| | - Simon A Osborne
- the MRC Technology Centre for Therapeutics Discovery, 1-3 Burtonhole Lane, Mill Hill, London NW7 1AD, United Kingdom
| | - Ahmad Kamal
- the MRC Technology Centre for Therapeutics Discovery, 1-3 Burtonhole Lane, Mill Hill, London NW7 1AD, United Kingdom
| | - Barbara Saxty
- the MRC Technology Centre for Therapeutics Discovery, 1-3 Burtonhole Lane, Mill Hill, London NW7 1AD, United Kingdom
| | - Ian G Ganley
- From the Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland and
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511
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Abstract
Autophagy is a catabolic degradation process in which cellular proteins and
organelles are engulfed by double-membrane autophagosomes and degraded in lysosomes.
Autophagy has emerged as a critical pathway in tumor development and cancer therapy,
although its precise function remains a conundrum. The current consensus is that
autophagy has a dual role in cancer. On the one hand, autophagy functions as a tumor
suppressor mechanism by preventing the accumulation of damaged organelles and
aggregated proteins. On the other hand, autophagy is a key cell survival mechanism
for established tumors; therefore autophagy inhibition suppresses tumor progression.
Here, we summarize recent progress on the role of autophagy in tumorigenesis and
cancer therapy.
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Affiliation(s)
- Xiaoyong Zhi
- Center for Autophagy Research, Department of
Internal Medicine, University of Texas Southwestern Medical
CenterDallas, Texas
75390USA
| | - Qing Zhong
- Department of Biochemistry, University of
Texas Southwestern Medical CenterDallas, Texas
75390USA
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512
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Yu X, Long YC, Shen HM. Differential regulatory functions of three classes of phosphatidylinositol and phosphoinositide 3-kinases in autophagy. Autophagy 2015; 11:1711-28. [PMID: 26018563 PMCID: PMC4824607 DOI: 10.1080/15548627.2015.1043076] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 04/11/2015] [Accepted: 04/14/2015] [Indexed: 02/06/2023] Open
Abstract
Autophagy is an evolutionarily conserved and exquisitely regulated self-eating cellular process with important biological functions. Phosphatidylinositol 3-kinases (PtdIns3Ks) and phosphoinositide 3-kinases (PI3Ks) are involved in the autophagic process. Here we aim to recapitulate how 3 classes of these lipid kinases differentially regulate autophagy. Generally, activation of the class I PI3K suppresses autophagy, via the well-established PI3K-AKT-MTOR (mechanistic target of rapamycin) complex 1 (MTORC1) pathway. In contrast, the class III PtdIns3K catalytic subunit PIK3C3/Vps34 forms a protein complex with BECN1 and PIK3R4 and produces phosphatidylinositol 3-phosphate (PtdIns3P), which is required for the initiation and progression of autophagy. The class II enzyme emerged only recently as an alternative source of PtdIns3P and autophagic initiator. However, the orthodox paradigm is challenged by findings that the PIK3CB catalytic subunit of class I PI3K acts as a positive regulator of autophagy, and PIK3C3 was thought to be an amino acid sensor for MTOR, which curbs autophagy. At present, a number of PtdIns3K and PI3K inhibitors, including specific PIK3C3 inhibitors, have been developed for suppression of autophagy and for clinical applications in autophagy-related human diseases.
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Affiliation(s)
- Xinlei Yu
- a Department of Biochemistry; Yong Loo Lin School of Medicine, National University of Singapore ; Singapore
| | - Yun Chau Long
- a Department of Biochemistry; Yong Loo Lin School of Medicine, National University of Singapore ; Singapore
| | - Han-Ming Shen
- b Department of Physiology; Yong Loo Lin School of Medicine, National University of Singapore ; Singapore
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513
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Bauckman KA, Owusu-Boaitey N, Mysorekar IU. Selective autophagy: xenophagy. Methods 2014; 75:120-7. [PMID: 25497060 DOI: 10.1016/j.ymeth.2014.12.005] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Revised: 11/30/2014] [Accepted: 12/02/2014] [Indexed: 12/24/2022] Open
Abstract
Xenophagy is an autophagic phenomenon that specifically involves pathogens and other non-host entities. Although the understanding of the relationship between autophagosomes and invading organisms has grown significantly in the past decade, the exact steps to confirm xenophagy has been not been thoroughly defined. Here we describe a methodical approach to confirming autophagy, its interaction with bacterial invasion, as well as the specific type of autophagic formation (i.e. autophagosome, autolysosome, phagolysosome). Further, we argue that xenophagy is not limited to pathogen interaction with autophagosome, but also non-microbial entities such as iron.
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Affiliation(s)
- Kyle A Bauckman
- Department of Obstetrics and Gynecology, Washington University School of Medicine, St. Louis, MO, USA
| | - Nana Owusu-Boaitey
- Department of Obstetrics and Gynecology, Washington University School of Medicine, St. Louis, MO, USA
| | - Indira U Mysorekar
- Department of Obstetrics and Gynecology, Washington University School of Medicine, St. Louis, MO, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
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514
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Bilanges B, Vanhaesebroeck B. Cinderella finds her shoe: the first Vps34 inhibitor uncovers a new PI3K-AGC protein kinase connection. Biochem J 2014; 464:e7-10. [PMID: 25395352 DOI: 10.1042/bj20141218] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Class II/III PI3Ks (phosphoinositide 3-kinases) produce the PtdIns(3)P lipid that is involved in intracellular vesicular trafficking. In contrast with class I PI3Ks, the potential signalling roles of class II/III PI3Ks are poorly understood. In a recent article in the Biochemical Journal, Bago and co-workers report that Vps34 (vacuolar protein sorting 34), the only class III PI3K, controls the activity of SGK3 (serum- and glucocorticoid-regulated protein kinase 3). Like other AGC kinases, the SGKs (SGK1, SGK2 and SGK3) are activated by dual phosphorylation. Unlike its cousins SGK1 and SGK2, SGK3 contains a PtdIns(3)P-binding domain, providing an additional element of regulation. The study by Bago et al. characterizes and makes extensive use of a Novartis Vps34 inhibitor (VPS34-IN1) that inhibits this PI3K isoform with nanomolar potency, without affecting other lipid kinases or more than 300 protein kinases. The authors show that this compound very rapidly reduced PtdIns(3)P levels at the endosome with concomitant loss of SGK3 phosphorylation. Co-inhibition of class I PI3Ks led to a further reduction in SGK3 activity, indicating that class I PI3Ks may also regulate SGK3 activity through an additional, currently unknown, mechanism. It remains to be assessed whether the novel PI3K-protein kinase connection established by this study is subject to acute cellular stimulation or is part of a constitutive housekeeping function. VPS34-IN1 will provide a useful tool to decipher the kinase-dependent functions of Vps34, with acute changes in SGK3 phosphorylation and subcellular localization being new biomarkers of Vps34 activity.
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Affiliation(s)
- Benoit Bilanges
- *UCL Cancer Institute, Paul O'Gorman Building University College London, 72 Huntley Street, London WC1E 6BT, U.K
| | - Bart Vanhaesebroeck
- *UCL Cancer Institute, Paul O'Gorman Building University College London, 72 Huntley Street, London WC1E 6BT, U.K
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