1
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Kodiha M, Azad N, Chu S, Crampton N, Stochaj U. Oxidative stress and signaling through EGFR and PKA pathways converge on the nuclear transport factor RanBP1. Eur J Cell Biol 2024; 103:151376. [PMID: 38011756 DOI: 10.1016/j.ejcb.2023.151376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 11/01/2023] [Accepted: 11/17/2023] [Indexed: 11/29/2023] Open
Abstract
Nuclear protein trafficking requires the soluble transport factor RanBP1. The subcellular distribution of RanBP1 is dynamic, as the protein shuttles between the nucleus and cytoplasm. To date, the signaling pathways regulating RanBP1 subcellular localization are poorly understood. During interphase, RanBP1 resides mostly in the cytoplasm. We show here that oxidative stress concentrates RanBP1 in the nucleus, and our study defines the underlying mechanisms. Specifically, RanBP1's cysteine residues are not essential for its oxidant-induced relocation. Furthermore, our pharmacological approaches uncover that signaling mediated by epidermal growth factor receptor (EGFR) and protein kinase A (PKA) control RanBP1 localization during stress. In particular, pharmacological inhibitors of EGFR or PKA diminish the oxidant-dependent relocation of RanBP1. Mutant analysis identified serine 60 and tyrosine 103 as regulators of RanBP1 nuclear accumulation during oxidant exposure. Taken together, our results define RanBP1 as a target of oxidative stress and a downstream effector of EGFR and PKA signaling routes. This positions RanBP1 at the intersection of important cellular signaling circuits.
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Affiliation(s)
- Mohamed Kodiha
- Department of Physiology McGill University, Montreal H3G 1Y6, Canada
| | - Nabila Azad
- Department of Physiology McGill University, Montreal H3G 1Y6, Canada
| | - Siwei Chu
- Department of Physiology McGill University, Montreal H3G 1Y6, Canada
| | - Noah Crampton
- Department of Physiology McGill University, Montreal H3G 1Y6, Canada
| | - Ursula Stochaj
- Department of Physiology McGill University, Montreal H3G 1Y6, Canada.
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2
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Martin-Vega A, Cobb MH. Navigating the ERK1/2 MAPK Cascade. Biomolecules 2023; 13:1555. [PMID: 37892237 PMCID: PMC10605237 DOI: 10.3390/biom13101555] [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: 09/30/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 10/29/2023] Open
Abstract
The RAS-ERK pathway is a fundamental signaling cascade crucial for many biological processes including proliferation, cell cycle control, growth, and survival; common across all cell types. Notably, ERK1/2 are implicated in specific processes in a context-dependent manner as in stem cells and pancreatic β-cells. Alterations in the different components of this cascade result in dysregulation of the effector kinases ERK1/2 which communicate with hundreds of substrates. Aberrant activation of the pathway contributes to a range of disorders, including cancer. This review provides an overview of the structure, activation, regulation, and mutational frequency of the different tiers of the cascade; with a particular focus on ERK1/2. We highlight the importance of scaffold proteins that contribute to kinase localization and coordinate interaction dynamics of the kinases with substrates, activators, and inhibitors. Additionally, we explore innovative therapeutic approaches emphasizing promising avenues in this field.
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Affiliation(s)
- Ana Martin-Vega
- Department of Pharmacology, UT Southwestern Medical Center, 6001 Forest Park Rd., Dallas, TX 75390, USA;
| | - Melanie H. Cobb
- Department of Pharmacology, UT Southwestern Medical Center, 6001 Forest Park Rd., Dallas, TX 75390, USA;
- Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, 6001 Forest Park Rd., Dallas, TX 75390, USA
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3
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Ulengin-Talkish I, Cyert MS. A cellular atlas of calcineurin signaling. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119366. [PMID: 36191737 PMCID: PMC9948804 DOI: 10.1016/j.bbamcr.2022.119366] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 09/25/2022] [Accepted: 09/27/2022] [Indexed: 11/06/2022]
Abstract
Intracellular Ca2+ signals are temporally controlled and spatially restricted. Signaling occurs adjacent to sites of Ca2+ entry and/or release, where Ca2+-dependent effectors and their substrates co-localize to form signaling microdomains. Here we review signaling by calcineurin, the Ca2+/calmodulin regulated protein phosphatase and target of immunosuppressant drugs, Cyclosporin A and FK506. Although well known for its activation of the adaptive immune response via NFAT dephosphorylation, systematic mapping of human calcineurin substrates and regulators reveals unexpected roles for this versatile phosphatase throughout the cell. We discuss calcineurin function, with an emphasis on where signaling occurs and mechanisms that target calcineurin and its substrates to signaling microdomains, especially binding of cognate short linear peptide motifs (SLiMs). Calcineurin is ubiquitously expressed and regulates events at the plasma membrane, other intracellular membranes, mitochondria, the nuclear pore complex and centrosomes/cilia. Based on our expanding knowledge of localized CN actions, we describe a cellular atlas of Ca2+/calcineurin signaling.
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Affiliation(s)
| | - Martha S Cyert
- Department of Biology, Stanford University, Stanford, CA 94035, United States.
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4
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Vazquez-Sandoval A, Velez-delValle C, Hernández-Mosqueira C, Marsch-Moreno M, Ayala-Sumuano JT, Kuri-Harcuch W. FAM129B is a cooperative protein that regulates adipogenesis. Biochem Biophys Res Commun 2023; 638:66-75. [PMID: 36442234 DOI: 10.1016/j.bbrc.2022.11.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/08/2022] [Accepted: 11/14/2022] [Indexed: 11/21/2022]
Abstract
FAM129B is one of Niban-like proteins described in neoplastic cells and implicated in melanoma cell invasion, but no reports have been published on FAM129B and cell differentiation. We show that FAM129B is early and transiently expressed and crucial for 3T3-F442A adipogenesis. Fam129b is expressed downstream of the early genes Cebpb, Klf4, Klf5 and Srebf1a, but upstream of Pparg2 since knockdown of Fam129b blocked Pparg2 expression and adipose differentiation. Glycogen synthase kinase 3 beta activity, a crucial kinase for adipogenesis, and the ERK1/2 are involved in FAM129B phosphorylation as part of the adipogenic program. Phosphorylated FAM129B is crucial for Pparg2 expression and the lipogenic gene expression downstream of Pparg2, and hence for adipogenesis. Fam129b knockdown reduced adipocyte cluster formation and size, regulating commitment and clonal amplification. In vivo, BAT, inguinal and epidydimal fat expressed Fam129b, suggesting a role in adipose tissue development. We conclude that FAM129B is a cooperative protein that regulates differentiation during the early stages of adipogenesis.
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Affiliation(s)
- Alfredo Vazquez-Sandoval
- Department of Cell Biology, Center of Research and Advanced Studies (CINVESTAV), IPN Avenida Instituto Politécnico Nacional 2508, Mexico City, CP 07360, Mexico
| | - Cristina Velez-delValle
- Department of Cell Biology, Center of Research and Advanced Studies (CINVESTAV), IPN Avenida Instituto Politécnico Nacional 2508, Mexico City, CP 07360, Mexico
| | - Claudia Hernández-Mosqueira
- Department of Cell Biology, Center of Research and Advanced Studies (CINVESTAV), IPN Avenida Instituto Politécnico Nacional 2508, Mexico City, CP 07360, Mexico
| | - Meytha Marsch-Moreno
- Department of Cell Biology, Center of Research and Advanced Studies (CINVESTAV), IPN Avenida Instituto Politécnico Nacional 2508, Mexico City, CP 07360, Mexico
| | - Jorge-Tonatiuh Ayala-Sumuano
- Department of Cell Biology, Center of Research and Advanced Studies (CINVESTAV), IPN Avenida Instituto Politécnico Nacional 2508, Mexico City, CP 07360, Mexico; Department of Biomedical Research, IDIX Biotech, Avenida de Los Portones 1151, Queretaro, CP 76100, Mexico
| | - Walid Kuri-Harcuch
- Department of Cell Biology, Center of Research and Advanced Studies (CINVESTAV), IPN Avenida Instituto Politécnico Nacional 2508, Mexico City, CP 07360, Mexico.
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5
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Lizcano-Perret B, Lardinois C, Wavreil F, Hauchamps P, Herinckx G, Sorgeloos F, Vertommen D, Gatto L, Michiels T. Cardiovirus leader proteins retarget RSK kinases toward alternative substrates to perturb nucleocytoplasmic traffic. PLoS Pathog 2022; 18:e1011042. [PMID: 36508477 PMCID: PMC9779665 DOI: 10.1371/journal.ppat.1011042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 12/22/2022] [Accepted: 12/01/2022] [Indexed: 12/14/2022] Open
Abstract
Proteins from some unrelated pathogens, including small RNA viruses of the family Picornaviridae, large DNA viruses such as Kaposi sarcoma-associated herpesvirus and even bacteria of the genus Yersinia can recruit cellular p90-ribosomal protein S6 kinases (RSKs) through a common linear motif and maintain the kinases in an active state. On the one hand, pathogens' proteins might hijack RSKs to promote their own phosphorylation (direct target model). On the other hand, some data suggested that pathogens' proteins might dock the hijacked RSKs toward a third interacting partner, thus redirecting the kinase toward a specific substrate. We explored the second hypothesis using the Cardiovirus leader protein (L) as a paradigm. The L protein is known to trigger nucleocytoplasmic trafficking perturbation, which correlates with hyperphosphorylation of phenylalanine-glycine (FG)-nucleoporins (FG-NUPs) such as NUP98. Using a biotin ligase fused to either RSK or L, we identified FG-NUPs as primary partners of the L-RSK complex in infected cells. An L protein mutated in the central RSK-interaction motif was readily targeted to the nuclear envelope whereas an L protein mutated in the C-terminal domain still interacted with RSK but failed to interact with the nuclear envelope. Thus, L uses distinct motifs to recruit RSK and to dock the L-RSK complex toward the FG-NUPs. Using an analog-sensitive RSK2 mutant kinase, we show that, in infected cells, L can trigger RSK to use NUP98 and NUP214 as direct substrates. Our data therefore illustrate a novel virulence mechanism where pathogens' proteins hijack and retarget cellular protein kinases toward specific substrates, to promote their replication or to escape immunity.
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Affiliation(s)
- Belén Lizcano-Perret
- Molecular Virology unit, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Cécile Lardinois
- Molecular Virology unit, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Fanny Wavreil
- Molecular Virology unit, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Philippe Hauchamps
- Computational Biology and Bioinformatics unit, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Gaëtan Herinckx
- MASSPROT platform, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Frédéric Sorgeloos
- Molecular Virology unit, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Didier Vertommen
- MASSPROT platform, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Laurent Gatto
- Computational Biology and Bioinformatics unit, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Thomas Michiels
- Molecular Virology unit, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
- * E-mail:
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6
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Lucas RM, Luo L, Stow JL. ERK1/2 in immune signalling. Biochem Soc Trans 2022; 50:1341-1352. [PMID: 36281999 PMCID: PMC9704528 DOI: 10.1042/bst20220271] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 10/07/2022] [Accepted: 10/10/2022] [Indexed: 07/30/2023]
Abstract
Extracellular signal-related kinases 1 and 2 (ERK1/2) are the final components of the mitogen-activated protein kinase (MAPK) phosphorylation cascade, an integral module in a diverse array of signalling pathways for shaping cell behaviour and fate. More recently, studies have shown that ERK1/2 plays an essential role downstream of immune receptors to elicit inflammatory gene expression in response to infection and cell or tissue damage. Much of this work has studied ERK1/2 activation in Toll-like receptor (TLR) pathways, providing mechanistic insights into its recruitment, compartmentalisation and activation in cells of the innate immune system. In this review, we summarise the typical activation of ERK1/2 in growth factor receptor pathways before discussing its known roles in immune cell signalling with a focus downstream of TLRs. We examine emerging research uncovering evidence of dysfunctional ERK1/2 signalling in inflammatory diseases and discuss the potential therapeutic benefit of targeting ERK1/2 pathways in inflammation.
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Affiliation(s)
- Richard M. Lucas
- Institute for Molecular Bioscience (IMB) and Centre for Inflammation and Disease Research, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Lin Luo
- Institute for Molecular Bioscience (IMB) and Centre for Inflammation and Disease Research, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Jennifer L. Stow
- Institute for Molecular Bioscience (IMB) and Centre for Inflammation and Disease Research, The University of Queensland, St Lucia, QLD 4072, Australia
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7
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Cellular Stress Induces Nucleocytoplasmic Transport Deficits Independent of Stress Granules. Biomedicines 2022; 10:biomedicines10051057. [PMID: 35625794 PMCID: PMC9138870 DOI: 10.3390/biomedicines10051057] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 02/05/2023] Open
Abstract
Stress granules are non-membrane bound granules temporarily forming in the cytoplasm in response to stress. Proteins of the nucleocytoplasmic transport machinery were found in these stress granules and it was suggested that stress granules contribute to the nucleocytoplasmic transport defects in several neurodegenerative disorders, including amyotrophic lateral sclerosis (ALS). The aim of this study was to investigate whether there is a causal link between stress granule formation and nucleocytoplasmic transport deficits. Therefore, we uncoupled stress granule formation from cellular stress while studying nuclear import. This was carried out by preventing cells from assembling stress granules despite being subjected to cellular stress either by knocking down both G3BP1 and G3BP2 or by pharmacologically inhibiting stress granule formation. Conversely, we induced stress granules by overexpressing G3BP1 in the absence of cellular stress. In both conditions, nuclear import was not affected demonstrating that stress granule formation is not a direct cause of stress-induced nucleocytoplasmic transport deficits.
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8
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Zhang T, Fassl A, Vaites LP, Fu S, Sicinski P, Paulo JA, Gygi SP. Interrogating Kinase-Substrate Relationships with Proximity Labeling and Phosphorylation Enrichment. J Proteome Res 2022; 21:494-506. [PMID: 35044772 PMCID: PMC9142857 DOI: 10.1021/acs.jproteome.1c00865] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Kinases govern many cellular responses through the reversible transfer of a phosphate moiety to their substrates. However, pairing a substrate with a kinase is challenging. In proximity labeling experiments, proteins proximal to a target protein are marked by biotinylation, and mass spectrometry can be used for their identification. Here, we combine ascorbate peroxidase (APEX) proximity labeling and a phosphorylation enrichment-based workflow, Phospho-APEX (pAPEX), to rapidly identify phosphorylated and biotinylated neighbor proteins which can be considered for candidate substrates. The pAPEX strategy enriches and quantifies differences in proximity for proteins and phosphorylation sites proximal to an APEX2-tagged kinase under the kinase "ON" and kinase "OFF" conditions. As a proof of concept, we identified candidate substrates of MAPK1 in HEK293T and HCT116 cells and candidate substrates of PKA in HEK293T cells. In addition to many known substrates, C15orf39 was identified and confirmed as a novel MAPK1 substrate. In all, we adapted the proximity labeling-based platform to accommodate phosphorylation analysis for kinase substrate identification.
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Affiliation(s)
- Tian Zhang
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Anne Fassl
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Laura P. Vaites
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Sipei Fu
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Piotr Sicinski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Joao A. Paulo
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Steven P. Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
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9
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Diehl JN, Hibshman PS, Ozkan-Dagliyan I, Goodwin CM, Howard SV, Cox AD, Der CJ. Targeting the ERK mitogen-activated protein kinase cascade for the treatment of KRAS-mutant pancreatic cancer. Adv Cancer Res 2022; 153:101-130. [PMID: 35101228 DOI: 10.1016/bs.acr.2021.07.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Mutational activation of the KRAS oncogene is found in ~95% of pancreatic ductal adenocarcinoma (PDAC), the major form of pancreatic cancer. With substantial experimental evidence that continued aberrant KRAS function is essential for the maintenance of PDAC tumorigenic growth, the National Cancer Institute has identified the development of effective anti-KRAS therapies as one of four major initiatives for pancreatic cancer research. The recent clinical success in the development of an anti-KRAS therapy targeting one specific KRAS mutant (G12C) supports the significant potential impact of anti-KRAS therapies. However, KRASG12C mutations comprise only 2% of KRAS mutations in PDAC. Thus, there remains a dire need for additional therapeutic approaches for targeting the majority of KRAS-mutant PDAC. Among the different directions currently being pursued for anti-KRAS drug development, one of the most promising involves inhibitors of the key KRAS effector pathway, the three-tiered RAF-MEK-ERK mitogen-activated protein kinase (MAPK) cascade. We address the promises and challenges of targeting ERK MAPK signaling as an anti-KRAS therapy for PDAC. In particular, we also summarize the key role of the MYC transcription factor and oncoprotein in supporting ERK-dependent growth of KRAS-mutant PDAC.
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Affiliation(s)
- J Nathaniel Diehl
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Priya S Hibshman
- Cell Biology and Physiology Curriculum, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Irem Ozkan-Dagliyan
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Craig M Goodwin
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Sarah V Howard
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Adrienne D Cox
- Cell Biology and Physiology Curriculum, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States; Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States; Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Channing J Der
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States; Cell Biology and Physiology Curriculum, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States; Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.
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10
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Identification and validation of new ERK substrates by phosphoproteomic technologies including Phos-tag SDS-PAGE. J Proteomics 2022; 258:104543. [DOI: 10.1016/j.jprot.2022.104543] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 02/15/2022] [Accepted: 02/15/2022] [Indexed: 11/17/2022]
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11
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Holzer G, De Magistris P, Gramminger C, Sachdev R, Magalska A, Schooley A, Scheufen A, Lennartz B, Tatarek-Nossol M, Lue H, Linder MI, Kutay U, Preisinger C, Moreno-Andres D, Antonin W. The nucleoporin Nup50 activates the Ran guanine nucleotide exchange factor RCC1 to promote NPC assembly at the end of mitosis. EMBO J 2021; 40:e108788. [PMID: 34725842 PMCID: PMC8634129 DOI: 10.15252/embj.2021108788] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 10/06/2021] [Accepted: 10/07/2021] [Indexed: 12/26/2022] Open
Abstract
During mitotic exit, thousands of nuclear pore complexes (NPCs) assemble concomitant with the nuclear envelope to build a transport‐competent nucleus. Here, we show that Nup50 plays a crucial role in NPC assembly independent of its well‐established function in nuclear transport. RNAi‐mediated downregulation in cells or immunodepletion of Nup50 protein in Xenopus egg extracts interferes with NPC assembly. We define a conserved central region of 46 residues in Nup50 that is crucial for Nup153 and MEL28/ELYS binding, and for NPC interaction. Surprisingly, neither NPC interaction nor binding of Nup50 to importin α/β, the GTPase Ran, or chromatin is crucial for its function in the assembly process. Instead, an N‐terminal fragment of Nup50 can stimulate the Ran GTPase guanine nucleotide exchange factor RCC1 and NPC assembly, indicating that Nup50 acts via the Ran system in NPC reformation at the end of mitosis. In support of this conclusion, Nup50 mutants defective in RCC1 binding and stimulation cannot replace the wild‐type protein in in vitro NPC assembly assays, whereas excess RCC1 can compensate the loss of Nup50.
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Affiliation(s)
- Guillaume Holzer
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, Aachen, Germany
| | - Paola De Magistris
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, Aachen, Germany.,Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
| | - Cathrin Gramminger
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
| | - Ruchika Sachdev
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
| | - Adriana Magalska
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
| | - Allana Schooley
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
| | - Anja Scheufen
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, Aachen, Germany
| | - Birgitt Lennartz
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, Aachen, Germany
| | - Marianna Tatarek-Nossol
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, Aachen, Germany
| | - Hongqi Lue
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, Aachen, Germany
| | | | - Ulrike Kutay
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Christian Preisinger
- Proteomics Facility, Interdisciplinary Centre for Clinical Research (IZKF), Medical School, RWTH Aachen University, Aachen, Germany
| | - Daniel Moreno-Andres
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, Aachen, Germany
| | - Wolfram Antonin
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, Aachen, Germany
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12
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Ogata K, Tsai CF, Ishihama Y. Nanoscale Solid-Phase Isobaric Labeling for Multiplexed Quantitative Phosphoproteomics. J Proteome Res 2021; 20:4193-4202. [PMID: 34292731 DOI: 10.1021/acs.jproteome.1c00444] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We established a workflow for highly sensitive multiplexed quantitative phosphoproteomics using a nanoscale solid-phase tandem mass tag (TMT) labeling reactor. Phosphopeptides were first enriched by titanium oxide chromatography and then labeled with isobaric TMT reagents in a StageTip packed with hydrophobic polymer-based sorbents. We found that TMT-labeled singly phosphorylated peptides tend to flow through the titanium oxide column. Therefore, TMT labeling should be performed after the enrichment step from tryptic peptides, resulting in the need for microscale reactions with small amounts of phosphopeptides. Using an optimized protocol for tens to hundreds of nanograms of phosphopeptides, we obtained a nearly 10-fold increase in sensitivity compared to the conventional solution-based TMT protocol. We demonstrate that this nanoscale phosphoproteomics protocol works for 50 μg of HeLa proteins treated with selumetinib, and we successfully quantified the selumetinib-regulated phosphorylated sites on a proteome scale. The MS raw data files have been deposited with the ProteomeXchange Consortium via the jPOST partner repository (https://jpostdb.org) with the data set identifier PXD025536.
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Affiliation(s)
- Kosuke Ogata
- Department of Molecular & Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Chia-Feng Tsai
- Department of Molecular & Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Yasushi Ishihama
- Department of Molecular & Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan.,Laboratory of Clinical and Analytical Chemistry, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan
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13
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ERK1/2: An Integrator of Signals That Alters Cardiac Homeostasis and Growth. BIOLOGY 2021; 10:biology10040346. [PMID: 33923899 PMCID: PMC8072600 DOI: 10.3390/biology10040346] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/15/2021] [Accepted: 04/16/2021] [Indexed: 12/24/2022]
Abstract
Integration of cellular responses to extracellular cues is essential for cell survival and adaptation to stress. Extracellular signal-regulated kinase (ERK) 1 and 2 serve an evolutionarily conserved role for intracellular signal transduction that proved critical for cardiomyocyte homeostasis and cardiac stress responses. Considering the importance of ERK1/2 in the heart, understanding how these kinases operate in both normal and disease states is critical. Here, we review the complexity of upstream and downstream signals that govern ERK1/2-dependent regulation of cardiac structure and function. Particular emphasis is given to cardiomyocyte hypertrophy as an outcome of ERK1/2 activation regulation in the heart.
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14
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Barbosa R, Acevedo LA, Marmorstein R. The MEK/ERK Network as a Therapeutic Target in Human Cancer. Mol Cancer Res 2021; 19:361-374. [PMID: 33139506 PMCID: PMC7925338 DOI: 10.1158/1541-7786.mcr-20-0687] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 10/01/2020] [Accepted: 10/27/2020] [Indexed: 11/16/2022]
Abstract
The RAS-RAF-MEK-ERK pathway is the most well-studied of the MAPK cascades and is critical for cell proliferation, differentiation, and survival. Abnormalities in regulation resulting from mutations in components of this pathway, particularly in upstream proteins, RAS and RAF, are responsible for a significant fraction of human cancers and nearly all cutaneous melanomas. Activation of receptor tyrosine kinases by growth factors and various extracellular signals leads to the sequential activation of RAS, RAF, MEK, and finally ERK, which activates numerous transcription factors and facilitates oncogenesis in the case of aberrant pathway activation. While extensive studies have worked to elucidate the activation mechanisms and structural components of upstream MAPK components, comparatively less attention has been directed toward the kinases, MEK and ERK, due to the infrequency of oncogenic-activating mutations in these kinases. However, acquired drug resistance has become a major issue in the treatment of RAS- and RAF-mutated cancers. Targeting the terminal kinases in the MAPK cascade has shown promise for overcoming many of these resistance mechanisms and improving treatment options for patients with MAPK-aberrant cancers. Here, we will describe the role of MEK and ERK in MAPK signaling and summarize the current understanding of their interaction and activation mechanisms. We will also discuss existing approaches for targeting MEK and ERK, and the benefits of alternative strategies. Areas requiring further exploration will be highlighted to guide future research endeavors and aid in the development of alternative therapeutic strategies to combat surmounting drug resistance in treating MAPK-mediated cancers. VISUAL OVERVIEW: http://mcr.aacrjournals.org/content/molcanres/19/3/361/F1.large.jpg.
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Affiliation(s)
- Renee Barbosa
- School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Lucila A Acevedo
- Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ronen Marmorstein
- Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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15
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The ERK mitogen-activated protein kinase signaling network: the final frontier in RAS signal transduction. Biochem Soc Trans 2021; 49:253-267. [PMID: 33544118 DOI: 10.1042/bst20200507] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 12/30/2020] [Accepted: 01/08/2021] [Indexed: 12/11/2022]
Abstract
The RAF-MEK-ERK mitogen-activated protein kinase (MAPK) cascade is aberrantly activated in a diverse set of human cancers and the RASopathy group of genetic developmental disorders. This protein kinase cascade is one of the most intensely studied cellular signaling networks and has been frequently targeted by the pharmaceutical industry, with more than 30 inhibitors either approved or under clinical evaluation. The ERK-MAPK cascade was originally depicted as a serial and linear, unidirectional pathway that relays extracellular signals, such as mitogenic stimuli, through the cytoplasm to the nucleus. However, we now appreciate that this three-tiered protein kinase cascade is a central core of a complex network with dynamic signaling inputs and outputs and autoregulatory loops. Despite our considerable advances in understanding the ERK-MAPK network, the ability of cancer cells to adapt to the inhibition of key nodes reveals a level of complexity that remains to be fully understood. In this review, we summarize important developments in our understanding of the ERK-MAPK network and identify unresolved issues for ongoing and future study.
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16
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Zhang W, Watanabe R, Konishi HA, Fujiwara T, Yoshimura SH, Kumeta M. Redox-Sensitive Cysteines Confer Proximal Control of the Molecular Crowding Barrier in the Nuclear Pore. Cell Rep 2020; 33:108484. [PMID: 33326779 DOI: 10.1016/j.celrep.2020.108484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 09/01/2020] [Accepted: 11/13/2020] [Indexed: 10/22/2022] Open
Abstract
The nuclear pore complex forms a highly crowded selective barrier with intrinsically disordered regions at the nuclear membrane to coordinate nucleocytoplasmic molecular communications. Although oxidative stress is known to alter the barrier function, the molecular mechanism underlying this adaptive control of the nuclear pore complex remains unknown. Here we uncover a systematic control of the crowding barrier within the nuclear pore in response to various redox environments. Direct measurements of the crowding states using a crowding-sensitive FRET (Förster resonance energy transfer) probe reveal specific roles of the nuclear pore subunits that adjust the degree of crowding in response to different redox conditions, by adaptively forming or disrupting redox-sensitive disulfide bonds. Relationships between crowding control and the barrier function of the nuclear pore are investigated by single-molecular fluorescence measurements of nuclear transport. Based on these findings, we propose a proximal control model of molecular crowding in vivo that is dynamically regulated at the molecular level.
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Affiliation(s)
- Wanzhen Zhang
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
| | - Ryuji Watanabe
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
| | - Hide A Konishi
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan; Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, NY 10065, USA
| | - Takahiro Fujiwara
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto 606-8501, Japan
| | - Shige H Yoshimura
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
| | - Masahiro Kumeta
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan.
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17
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Wigington CP, Roy J, Damle NP, Yadav VK, Blikstad C, Resch E, Wong CJ, Mackay DR, Wang JT, Krystkowiak I, Bradburn DA, Tsekitsidou E, Hong SH, Kaderali MA, Xu SL, Stearns T, Gingras AC, Ullman KS, Ivarsson Y, Davey NE, Cyert MS. Systematic Discovery of Short Linear Motifs Decodes Calcineurin Phosphatase Signaling. Mol Cell 2020; 79:342-358.e12. [PMID: 32645368 DOI: 10.1016/j.molcel.2020.06.029] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 03/24/2020] [Accepted: 05/26/2020] [Indexed: 12/17/2022]
Abstract
Short linear motifs (SLiMs) drive dynamic protein-protein interactions essential for signaling, but sequence degeneracy and low binding affinities make them difficult to identify. We harnessed unbiased systematic approaches for SLiM discovery to elucidate the regulatory network of calcineurin (CN)/PP2B, the Ca2+-activated phosphatase that recognizes LxVP and PxIxIT motifs. In vitro proteome-wide detection of CN-binding peptides, in vivo SLiM-dependent proximity labeling, and in silico modeling of motif determinants uncovered unanticipated CN interactors, including NOTCH1, which we establish as a CN substrate. Unexpectedly, CN shows SLiM-dependent proximity to centrosomal and nuclear pore complex (NPC) proteins-structures where Ca2+ signaling is largely uncharacterized. CN dephosphorylates human and yeast NPC proteins and promotes accumulation of a nuclear transport reporter, suggesting conserved NPC regulation by CN. The CN network assembled here provides a resource to investigate Ca2+ and CN signaling and demonstrates synergy between experimental and computational methods, establishing a blueprint for examining SLiM-based networks.
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Affiliation(s)
| | - Jagoree Roy
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Nikhil P Damle
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Vikash K Yadav
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Cecilia Blikstad
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Eduard Resch
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine and Pharmacology TMP, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Cassandra J Wong
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada
| | - Douglas R Mackay
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Jennifer T Wang
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Izabella Krystkowiak
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | | | | | - Su Hyun Hong
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Malika Amyn Kaderali
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Shou-Ling Xu
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Tim Stearns
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, M5S 3H7 ON, Canada
| | - Katharine S Ullman
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Ylva Ivarsson
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Norman E Davey
- Division of Cancer Biology, The Institute of Cancer Research, 237 Fullham Road, London SW3 6JB, UK
| | - Martha S Cyert
- Department of Biology, Stanford University, Stanford, CA, USA.
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18
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ERK signalling: a master regulator of cell behaviour, life and fate. Nat Rev Mol Cell Biol 2020; 21:607-632. [PMID: 32576977 DOI: 10.1038/s41580-020-0255-7] [Citation(s) in RCA: 452] [Impact Index Per Article: 113.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/07/2020] [Indexed: 12/13/2022]
Abstract
The proteins extracellular signal-regulated kinase 1 (ERK1) and ERK2 are the downstream components of a phosphorelay pathway that conveys growth and mitogenic signals largely channelled by the small RAS GTPases. By phosphorylating widely diverse substrates, ERK proteins govern a variety of evolutionarily conserved cellular processes in metazoans, the dysregulation of which contributes to the cause of distinct human diseases. The mechanisms underlying the regulation of ERK1 and ERK2, their mode of action and their impact on the development and homeostasis of various organisms have been the focus of much attention for nearly three decades. In this Review, we discuss the current understanding of this important class of kinases. We begin with a brief overview of the structure, regulation, substrate recognition and subcellular localization of ERK1 and ERK2. We then systematically discuss how ERK signalling regulates six fundamental cellular processes in response to extracellular cues. These processes are cell proliferation, cell survival, cell growth, cell metabolism, cell migration and cell differentiation.
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19
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Tabuchi Y, Maekawa K, Torigoe M, Furusawa Y, Hirano T, Minagawa S, Yunoki T, Hayashi A. HIKESHI silencing can enhance mild hyperthermia sensitivity in human oral squamous cell carcinoma HSC‑3 cells. Int J Mol Med 2020; 46:58-66. [PMID: 32377716 PMCID: PMC7255474 DOI: 10.3892/ijmm.2020.4591] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 03/09/2020] [Indexed: 12/11/2022] Open
Abstract
Hyperthermia (HT) is considered to be of value as a treatment modality in various cancers. However, the acquisition of thermotolerance in cancer cells due to the induction of heat shock proteins (HSPs) makes HT less effective. Recent findings have indicated that heat shock protein nuclear import factor hikeshi (HIKESHI), also referred to as C11orf73, acts as a nuclear import carrier of Hsp70 under heat stress conditions. The aim of the present study was to determine whether knockdown (KD) of HIKESHI by small interfering RNA (siRNA) can potentiate mild HT (MHT) sensitivity in human oral squamous cell carcinoma (OSCC) HSC‑3 cells. The mRNA and protein expression of HIKESHI was found to be markedly suppressed in HSC‑3 cells treated with siRNA for HIKESHI (siHIKE). Silencing HIKESHI significantly decreased the cell viability under MHT conditions (42˚C for 90 min). Immunocytochemical and western blot analyses clearly demonstrated that Hsp70 protein translocated from the cytoplasm to the nucleus under MHT conditions, and this translocation was significantly inhibited in cells treated with siHIKE. Treatment of the cells with MHT transiently increased the phosphorylation level of extracellular signal‑regulated kinase (ERK)2. Furthermore, the phosphorylation was sustained in HIKESHI‑KD cells under MHT conditions, and this sustained phosphorylation was abolished by pretreatment with U0126, an inhibitor of mitogen‑activated protein kinase/ERK. In addition, U0126 significantly decreased the viability of cells treated with the combination of HIKESHI‑KD and MHT. The data of the present study suggest that HIKESHI silencing enhanced the sensitivity of human OSCC HSC‑3 cells to MHT.
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Affiliation(s)
- Yoshiaki Tabuchi
- Division of Molecular Genetics Research, Life Science Research Center, University of Toyama, Toyama 930‑0194, Japan
| | - Keita Maekawa
- Division of Molecular Genetics Research, Life Science Research Center, University of Toyama, Toyama 930‑0194, Japan
| | - Misako Torigoe
- Department of Ophthalmology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama 930‑0194, Japan
| | - Yukihiro Furusawa
- Department of Liberal Arts and Sciences, Toyama Prefectural University, Toyama 939‑0398, Japan
| | - Tetsushi Hirano
- Division of Molecular Genetics Research, Life Science Research Center, University of Toyama, Toyama 930‑0194, Japan
| | - Satsuki Minagawa
- Division of Molecular Genetics Research, Life Science Research Center, University of Toyama, Toyama 930‑0194, Japan
| | - Tatsuya Yunoki
- Department of Ophthalmology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama 930‑0194, Japan
| | - Atsushi Hayashi
- Department of Ophthalmology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama 930‑0194, Japan
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20
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Sugiyama N. Mass Spectrometry-Based Discovery of in vitro Kinome Substrates. ACTA ACUST UNITED AC 2020; 9:A0082. [PMID: 32547896 PMCID: PMC7242781 DOI: 10.5702/massspectrometry.a0082] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 02/10/2020] [Indexed: 12/28/2022]
Abstract
Protein phosphorylation mediated by protein kinases is one of the most significant posttranslational modifications in many biological events. The function and physiological substrates of specific protein kinases, which are highly associated with known signal transduction elements or therapeutic targets, have been extensively studied using various approaches; however, most protein kinases have not yet been characterized. In recent decades, many techniques have been developed for the identification of in vitro and physiological substrates of protein kinases. In this review, I summarize recent studies profiling the characteristics of kinases using mass spectrometry-based proteomics, focusing on the large-scale identification of in vitro substrates of the human kinome using a quantitative phosphoproteomics approach.
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Affiliation(s)
- Naoyuki Sugiyama
- Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
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21
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Taylor CA, Cormier KW, Keenan SE, Earnest S, Stippec S, Wichaidit C, Juang YC, Wang J, Shvartsman SY, Goldsmith EJ, Cobb MH. Functional divergence caused by mutations in an energetic hotspot in ERK2. Proc Natl Acad Sci U S A 2019; 116:15514-15523. [PMID: 31296562 PMCID: PMC6681740 DOI: 10.1073/pnas.1905015116] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The most frequent extracellular signal-regulated kinase 2 (ERK2) mutation occurring in cancers is E322K (E-K). ERK2 E-K reverses a buried charge in the ERK2 common docking (CD) site, a region that binds activators, inhibitors, and substrates. Little is known about the cellular consequences associated with this mutation, other than apparent increases in tumor resistance to pathway inhibitors. ERK2 E-K, like the mutation of the preceding aspartate (ERK2 D321N [D-N]) known as the sevenmaker mutation, causes increased activity in cells and evades inactivation by dual-specificity phosphatases. As opposed to findings in cancer cells, in developmental assays in Drosophila, only ERK2 D-N displays a significant gain of function, revealing mutation-specific phenotypes. The crystal structure of ERK2 D-N is indistinguishable from that of wild-type protein, yet this mutant displays increased thermal stability. In contrast, the crystal structure of ERK2 E-K reveals profound structural changes, including disorder in the CD site and exposure of the activation loop phosphorylation sites, which likely account for the decreased thermal stability of the protein. These contiguous mutations in the CD site of ERK2 are both required for docking interactions but lead to unpredictably different functional outcomes. Our results suggest that the CD site is in an energetically strained configuration, and this helps drive conformational changes at distal sites on ERK2 during docking interactions.
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Affiliation(s)
- Clinton A Taylor
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390
| | - Kevin W Cormier
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390
| | - Shannon E Keenan
- Department of Chemical and Biological Engineering, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
| | - Svetlana Earnest
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390
| | - Steve Stippec
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390
| | - Chonlarat Wichaidit
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390
| | - Yu-Chi Juang
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390
| | - Junmei Wang
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390
| | - Stanislav Y Shvartsman
- Department of Chemical and Biological Engineering, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
| | | | - Melanie H Cobb
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390;
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22
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Global view of the RAF-MEK-ERK module and its immediate downstream effectors. Sci Rep 2019; 9:10865. [PMID: 31350469 PMCID: PMC6659682 DOI: 10.1038/s41598-019-47245-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 07/09/2019] [Indexed: 12/22/2022] Open
Abstract
Small molecule inhibitors of BRAF and MEK have proven effective at inhibiting tumor growth in melanoma patients, however this efficacy is limited due to the almost universal development of drug resistance. To provide advanced insight into the signaling responses that occur following kinase inhibition we have performed quantitative (phospho)-proteomics of human melanoma cells treated with either dabrafenib, a BRAF inhibitor; trametinib, a MEK inhibitor or SCH772984, an ERK inhibitor. Over nine experiments we identified 7827 class I phosphorylation sites on 4960 proteins. This included 54 phosphorylation sites that were significantly down-modulated after exposure to all three inhibitors, 34 of which have not been previously reported. Functional analysis of these novel ERK targets identified roles for them in GTPase activity and regulation, apoptosis and cell-cell adhesion. Comparison of the results presented here with previously reported phosphorylation sites downstream of ERK showed a limited degree of overlap suggesting that ERK signaling responses may be highly cell line and cue specific. In addition we identified 26 phosphorylation sites that were only responsive to dabrafenib. We provide further orthogonal experimental evidence for 3 of these sites in human embryonic kidney cells over-expressing BRAF as well as further computational insights using KinomeXplorer. The validated phosphorylation sites were found to be involved in actin regulation, which has been proposed as a novel mechanism for inhibiting resistance development. These results would suggest that the linearity of the BRAF-MEK-ERK module is at least context dependent.
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23
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Biological Rationale for Targeting MEK/ERK Pathways in Anti-Cancer Therapy and to Potentiate Tumour Responses to Radiation. Int J Mol Sci 2019; 20:ijms20102530. [PMID: 31126017 PMCID: PMC6567863 DOI: 10.3390/ijms20102530] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 05/16/2019] [Accepted: 05/21/2019] [Indexed: 02/07/2023] Open
Abstract
ERK1 and ERK2 (ERKs), two extracellular regulated kinases (ERK1/2), are evolutionary-conserved and ubiquitous serine-threonine kinases involved in regulating cell signalling in normal and pathological tissues. The expression levels of these kinases are almost always different, with ERK2 being the more prominent. ERK1/2 activation is fundamental for the development and progression of cancer. Since their discovery, much research has been dedicated to their role in mitogen-activated protein kinases (MAPK) pathway signalling and in their activation by mitogens and mutated RAF or RAS in cancer cells. In order to gain a better understanding of the role of ERK1/2 in MAPK pathway signalling, many studies have been aimed at characterizing ERK1/2 splicing isoforms, mutants, substrates and partners. In this review, we highlight the differences between ERK1 and ERK2 without completely discarding the hypothesis that ERK1 and ERK2 exhibit functional redundancy. The main goal of this review is to shed light on the role of ERK1/2 in targeted therapy and radiotherapy and highlight the importance of identifying ERK inhibitors that may overcome acquired resistance. This is a highly relevant therapeutic issue that needs to be addressed to combat tumours that rely on constitutively active RAF and RAS mutants and the MAPK pathway.
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24
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Breitenbach T, Lorenz K, Dandekar T. How to Steer and Control ERK and the ERK Signaling Cascade Exemplified by Looking at Cardiac Insufficiency. Int J Mol Sci 2019; 20:E2179. [PMID: 31052520 PMCID: PMC6539830 DOI: 10.3390/ijms20092179] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 04/16/2019] [Accepted: 04/24/2019] [Indexed: 12/13/2022] Open
Abstract
Mathematical optimization framework allows the identification of certain nodes within a signaling network. In this work, we analyzed the complex extracellular-signal-regulated kinase 1 and 2 (ERK1/2) cascade in cardiomyocytes using the framework to find efficient adjustment screws for this cascade that is important for cardiomyocyte survival and maladaptive heart muscle growth. We modeled optimal pharmacological intervention points that are beneficial for the heart, but avoid the occurrence of a maladaptive ERK1/2 modification, the autophosphorylation of ERK at threonine 188 (ERK Thr 188 phosphorylation), which causes cardiac hypertrophy. For this purpose, a network of a cardiomyocyte that was fitted to experimental data was equipped with external stimuli that model the pharmacological intervention points. Specifically, two situations were considered. In the first one, the cardiomyocyte was driven to a desired expression level with different treatment strategies. These strategies were quantified with respect to beneficial effects and maleficent side effects and then which one is the best treatment strategy was evaluated. In the second situation, it was shown how to model constitutively activated pathways and how to identify drug targets to obtain a desired activity level that is associated with a healthy state and in contrast to the maleficent expression pattern caused by the constitutively activated pathway. An implementation of the algorithms used for the calculations is also presented in this paper, which simplifies the application of the presented framework for drug targeting, optimal drug combinations and the systematic and automatic search for pharmacological intervention points. The codes were designed such that they can be combined with any mathematical model given by ordinary differential equations.
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Affiliation(s)
- Tim Breitenbach
- Biozentrum, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany.
| | - Kristina Lorenz
- Institute of Pharmacology and Toxicology, Versbacher Straße 9, 97078 Würzburg, Germany.
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44139 Dortmund, Germany.
| | - Thomas Dandekar
- Biozentrum, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany.
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25
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Abstract
Nuclear pore complexes (NPCs) mediate nucleocytoplasmic exchange. They are exceptionally large protein complexes that fuse the inner and outer nuclear membranes to form channels across the nuclear envelope. About 30 different protein components, termed nucleoporins, assemble in multiple copies into an intricate cylindrical architecture. Here, we review our current knowledge of the structure of nucleoporins and how those come together in situ. We delineate architectural principles on several hierarchical organization levels, including isoforms, posttranslational modifications, nucleoporins, and higher-order oligomerization of nucleoporin subcomplexes. We discuss how cells exploit this modularity to faithfully assemble NPCs.
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Affiliation(s)
- Bernhard Hampoelz
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany; , ,
| | - Amparo Andres-Pons
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany; , , .,Current affiliation: Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland;
| | - Panagiotis Kastritis
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany; , , .,Current affiliation: ZIK HALOmem, Martin Luther University of Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Martin Beck
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany; , , .,Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.,Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
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26
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El Husseini N, Hales BF. The Roles of P53 and Its Family Proteins, P63 and P73, in the DNA Damage Stress Response in Organogenesis-Stage Mouse Embryos. Toxicol Sci 2019; 162:439-449. [PMID: 29228353 DOI: 10.1093/toxsci/kfx270] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Members of the P53 transcription factor family, P53, P63, and P73, play important roles in normal development and in regulating the expression of genes that control apoptosis and cell cycle progression in response to genotoxic stress. P53 is involved in the DNA damage response pathway that is activated by hydroxyurea in organogenesis-stage murine embryos. The extent to which P63 and P73 contribute to this stress response is not known. To address this question, we examined the roles of P53, P63, and P73 in mediating the response of Trp53-positive and Trp53-deficient murine embryos to a single dose of hydroxyurea (400 mg/kg) on gestational day 9. Hydroxyurea treatment downregulated the expression of Trp63 and upregulated Trp73 in the absence of effects on the levels of Trp53 transcripts; Trp73 upregulation was P53-dependent. At the protein level, hydroxyurea treatment increased the levels and phosphorylation of P53 in the absence of effects on P63 and P73. Upregulation of the expression of genes that regulate cell cycle arrest and apoptosis, Cdkn1a, Rb1, Fas, Trp53inp1, and Pmaip1, was P53-dependent in hydroxyurea-treated embryos. The increase in cleaved caspase-3 and cleaved mammalian sterile-20-like-1 kinase levels induced by hydroxyurea was also P53-dependent; in contrast, the increase in phosphorylated H2AX, a marker of DNA double-strand breaks, in response to hydroxyurea treatment was only partially P53-dependent. Together, our data show that P53 is the principal P53 family member that is activated in the embryonic DNA damage response.
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Affiliation(s)
- Nazem El Husseini
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Barbara F Hales
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec H3G 1Y6, Canada
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27
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The Effect of FG-Nup Phosphorylation on NPC Selectivity: A One-Bead-Per-Amino-Acid Molecular Dynamics Study. Int J Mol Sci 2019; 20:ijms20030596. [PMID: 30704069 PMCID: PMC6387328 DOI: 10.3390/ijms20030596] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 01/21/2019] [Accepted: 01/23/2019] [Indexed: 01/16/2023] Open
Abstract
Nuclear pore complexes (NPCs) are large protein complexes embedded in the nuclear envelope separating the cytoplasm from the nucleoplasm in eukaryotic cells. They function as selective gates for the transport of molecules in and out of the nucleus. The inner wall of the NPC is coated with intrinsically disordered proteins rich in phenylalanine-glycine repeats (FG-repeats), which are responsible for the intriguing selectivity of NPCs. The phosphorylation state of the FG-Nups is controlled by kinases and phosphatases. In the current study, we extended our one-bead-per-amino-acid (1BPA) model for intrinsically disordered proteins to account for phosphorylation. With this, we performed molecular dynamics simulations to probe the effect of phosphorylation on the Stokes radius of isolated FG-Nups, and on the structure and transport properties of the NPC. Our results indicate that phosphorylation causes a reduced attraction between the residues, leading to an extension of the FG-Nups and the formation of a significantly less dense FG-network inside the NPC. Furthermore, our simulations show that upon phosphorylation, the transport rate of inert molecules increases, while that of nuclear transport receptors decreases, which can be rationalized in terms of modified hydrophobic, electrostatic, and steric interactions. Altogether, our models provide a molecular framework to explain how extensive phosphorylation of FG-Nups decreases the selectivity of the NPC.
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Flores K, Yadav SS, Katz AA, Seger R. The Nuclear Translocation of Mitogen-Activated Protein Kinases: Molecular Mechanisms and Use as Novel Therapeutic Target. Neuroendocrinology 2019; 108:121-131. [PMID: 30261516 DOI: 10.1159/000494085] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 09/26/2018] [Indexed: 11/19/2022]
Abstract
The mitogen-activated protein kinase (MAPK) cascades are central signaling pathways that play a central role in the regulation of most stimulated cellular processes including proliferation, differentiation, stress response and apoptosis. Currently 4 such cascades are known, each termed by its downstream MAPK components: the extracellular signal-regulated kinase 1/2 (ERK1/2), cJun-N-terminal kinase (JNK), p38 and ERK5. One of the hallmarks of these cascades is the stimulated nuclear translocation of their MAPK components using distinct mechanisms. ERK1/2 are shuttled into the nucleus by importin7, JNK and p38 by a dimer of importin3 with either importin9 or importin7, and ERK5 by importin-α/β. Dysregulation of these cascades often results in diseases, including cancer and inflammation, as well as developmental and neurological disorders. Much effort has been invested over the years in developing inhibitors to the MAPK cascades to combat these diseases. Although some inhibitors are already in clinical use or clinical trials, their effects are hampered by development of resistance or adverse side-effects. Recently, our group developed 2 myristoylated peptides: EPE peptide, which inhibits the interaction of ERK1/2 with importin7, and PERY peptide, which prevents JNK/p38 interaction with either importin7 or importin9. These peptides block the nuclear translocation of their corresponding kinases, resulting in prevention of several cancers, while the PERY peptide also inhibits inflammation-induced diseases. These peptides provide a proof of concept for the use of the nuclear translocation of MAPKs as therapeutic targets for cancer and/or inflammation.
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Affiliation(s)
- Karen Flores
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Suresh Singh Yadav
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Arieh A Katz
- Department of Integrative Biomedical Sciences and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Rony Seger
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot,
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Phosphoproteomic identification and functional characterization of protein kinase substrates by 2D-DIGE and Phos-tag PAGE. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:57-61. [DOI: 10.1016/j.bbapap.2018.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 05/30/2018] [Accepted: 06/01/2018] [Indexed: 12/22/2022]
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30
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Hey F, Andreadi C, Noble C, Patel B, Jin H, Kamata T, Straatman K, Luo J, Balmanno K, Jones DT, Collins VP, Cook SJ, Caunt CJ, Pritchard C. Over-expressed, N-terminally truncated BRAF is detected in the nucleus of cells with nuclear phosphorylated MEK and ERK. Heliyon 2018; 4:e01065. [PMID: 30603699 PMCID: PMC6304467 DOI: 10.1016/j.heliyon.2018.e01065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 09/12/2018] [Accepted: 12/14/2018] [Indexed: 12/31/2022] Open
Abstract
BRAF is a cytoplasmic protein kinase, which activates the MEK-ERK signalling pathway. Deregulation of the pathway is associated with the presence of BRAF mutations in human cancer, the most common being V600E BRAF, although structural rearrangements, which remove N-terminal regulatory sequences, have also been reported. RAF-MEK-ERK signalling is normally thought to occur in the cytoplasm of the cell. However, in an investigation of BRAF localisation using fluorescence microscopy combined with subcellular fractionation of Green Fluorescent Protein (GFP)-tagged proteins expressed in NIH3T3 cells, surprisingly, we detected N-terminally truncated BRAF (ΔBRAF) in both nuclear and cytoplasmic compartments. In contrast, ΔCRAF and full-length, wild-type BRAF (WTBRAF) were detected at lower levels in the nucleus while full-length V600EBRAF was virtually excluded from this compartment. Similar results were obtained using ΔBRAF tagged with the hormone-binding domain of the oestrogen receptor (hbER) and with the KIAA1549-ΔBRAF translocation mutant found in human pilocytic astrocytomas. Here we show that GFP-ΔBRAF nuclear translocation does not involve a canonical Nuclear Localisation Signal (NLS), but is suppressed by N-terminal sequences. Nuclear GFP-ΔBRAF retains MEK/ERK activating potential and is associated with the accumulation of phosphorylated MEK and ERK in the nucleus. In contrast, full-length GFP-WTBRAF and GFP-V600EBRAF are associated with the accumulation of phosphorylated ERK but not phosphorylated MEK in the nucleus. These data have implications for cancers bearing single nucleotide variants or N-terminal deleted structural variants of BRAF.
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Affiliation(s)
- Fiona Hey
- Department of Molecular Cell Biology, University of Leicester, Lancaster Road, Leicester LE1 9HN, UK
| | - Catherine Andreadi
- Leicester Cancer Research Centre, Clinical Sciences Building, University of Leicester, Leicester Royal Infirmary, Leicester LE2 7LX, UK
| | - Catherine Noble
- Department of Molecular Cell Biology, University of Leicester, Lancaster Road, Leicester LE1 9HN, UK
| | - Bipin Patel
- Department of Molecular Cell Biology, University of Leicester, Lancaster Road, Leicester LE1 9HN, UK
| | - Hong Jin
- Department of Molecular Cell Biology, University of Leicester, Lancaster Road, Leicester LE1 9HN, UK
| | - Tamihiro Kamata
- Leicester Cancer Research Centre, Clinical Sciences Building, University of Leicester, Leicester Royal Infirmary, Leicester LE2 7LX, UK
| | - Kees Straatman
- Core Biotechnology Services, University of Leicester, Lancaster Road, Leicester LE1 9HN, UK
| | - Jinli Luo
- Leicester Cancer Research Centre, Clinical Sciences Building, University of Leicester, Leicester Royal Infirmary, Leicester LE2 7LX, UK
| | - Kathryn Balmanno
- Signalling Laboratory, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - David T.W. Jones
- Department of Pathology, Division of Molecular Histopathology, University of Cambridge, Cambridge CB2 0QQ, UK
| | - V. Peter Collins
- Department of Pathology, Division of Molecular Histopathology, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Simon J. Cook
- Signalling Laboratory, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Christopher J. Caunt
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Catrin Pritchard
- Leicester Cancer Research Centre, Clinical Sciences Building, University of Leicester, Leicester Royal Infirmary, Leicester LE2 7LX, UK
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31
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Jin DZ, Mao LM, Wang JQ. The Role of Extracellular Signal-Regulated Kinases (ERK) in the Regulation of mGlu5 Receptors in Neurons. J Mol Neurosci 2018; 66:629-638. [PMID: 30430306 PMCID: PMC6312115 DOI: 10.1007/s12031-018-1193-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 10/01/2018] [Indexed: 12/21/2022]
Abstract
The metabotropic glutamate (mGlu) receptor 5 is a G protein-coupled receptor and is densely expressed in the mammalian brain. Like other glutamate receptors, mGlu5 receptors are tightly regulated by posttranslational modifications such as phosphorylation, although underlying mechanisms are incompletely investigated. In this study, we investigated the role of a prime kinase, extracellular signal-regulated kinase 1 (ERK1), in the phosphorylation and regulation of mGlu5 receptors in vitro and in striatal neurons. We found that recombinant ERK1 proteins directly bound to the C-terminal tail (CT) of mGlu5 receptors in vitro. Endogenous ERK1 also interacted with mGlu5 receptor proteins in adult rat striatal neurons in vivo. The kinase showed the ability to phosphorylate mGlu5 receptors. A serine residue in the distal region of mGlu5 CT was found to be a primary phosphorylation site sensitive to ERK1. In functional studies, we found that pharmacological inhibition of ERK with an inhibitor U0126 reduced the efficacy of mGlu5 receptors in stimulating production of cytoplasmic inositol-1,4,5-triphosphate, a major downstream conventional signaling event, in striatal neurons under normal conditions. These results identify mGlu5 as a new biochemical substrate of ERK1. The kinase can interact with and phosphorylate an intracellular domain of mGlu5 receptors in striatal neurons and thereby control its signaling efficacy.
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Affiliation(s)
- Dao-Zhong Jin
- Department of Biomedical Sciences, School of Medicine, University of Missouri-Kansas City, 2411 Holmes Street, Kansas City, MO, 64108, USA.
| | - Li-Min Mao
- Department of Biomedical Sciences, School of Medicine, University of Missouri-Kansas City, 2411 Holmes Street, Kansas City, MO, 64108, USA
| | - John Q Wang
- Department of Biomedical Sciences, School of Medicine, University of Missouri-Kansas City, 2411 Holmes Street, Kansas City, MO, 64108, USA.
- Department of Anesthesiology, School of Medicine, University of Missouri-Kansas City, 2411 Holmes Street, Kansas City, MO, 64108, USA.
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McCloskey A, Ibarra A, Hetzer MW. Tpr regulates the total number of nuclear pore complexes per cell nucleus. Genes Dev 2018; 32:1321-1331. [PMID: 30228202 PMCID: PMC6169833 DOI: 10.1101/gad.315523.118] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 07/23/2018] [Indexed: 01/16/2023]
Abstract
In this study, McCloskey et al. investigated the underlying mechanisms that control how many nuclear transport channels are assembled into a given nuclear envelope. Their results show that depletion of the NPC basket protein Tpr, but not Nup153, dramatically increases the total NPC number in various cell types and provide insight into a critical role of the nucleoporin Tpr in coordinating signal transduction pathways during cell proliferation and the dynamic organization of the nucleus. The total number of nuclear pore complexes (NPCs) per nucleus varies greatly between different cell types and is known to change during cell differentiation and cell transformation. However, the underlying mechanisms that control how many nuclear transport channels are assembled into a given nuclear envelope remain unclear. Here, we report that depletion of the NPC basket protein Tpr, but not Nup153, dramatically increases the total NPC number in various cell types. This negative regulation of Tpr occurs via a phosphorylation cascade of extracellular signal-regulated kinase (ERK), the central kinase of the mitogen-activated protein kinase (MAPK) pathway. Tpr serves as a scaffold for ERK to phosphorylate the nucleoporin (Nup) Nup153, which is critical for early stages of NPC biogenesis. Our results reveal a critical role of the Nup Tpr in coordinating signal transduction pathways during cell proliferation and the dynamic organization of the nucleus.
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Affiliation(s)
- Asako McCloskey
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92130, USA
| | - Arkaitz Ibarra
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92130, USA
| | - Martin W Hetzer
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92130, USA
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33
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Eblen ST. Extracellular-Regulated Kinases: Signaling From Ras to ERK Substrates to Control Biological Outcomes. Adv Cancer Res 2018; 138:99-142. [PMID: 29551131 DOI: 10.1016/bs.acr.2018.02.004] [Citation(s) in RCA: 125] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The extracellular-regulated kinases ERK1 and ERK2 are evolutionarily conserved, ubiquitous serine-threonine kinases that are involved in regulating cellular signaling in both normal and pathological conditions. Their expression is critical for development and their hyperactivation is a major factor in cancer development and progression. Since their discovery as one of the major signaling mediators activated by mitogens and Ras mutation, we have learned much about their regulation, including their activation, binding partners and substrates. In this review I will discuss some of what has been discovered about the members of the Ras to ERK pathway, including regulation of their activation by growth factors and cell adhesion pathways. Looking downstream of ERK activation I will also highlight some of the many ERK substrates that have been discovered, including those involved in feedback regulation, cell migration and cell cycle progression through the control of transcription, pre-mRNA splicing and protein synthesis.
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Affiliation(s)
- Scott T Eblen
- Medical University of South Carolina, Charleston, SC, United States.
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34
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Sales Gil R, de Castro IJ, Berihun J, Vagnarelli P. Protein phosphatases at the nuclear envelope. Biochem Soc Trans 2018; 46:173-182. [PMID: 29432143 PMCID: PMC5818667 DOI: 10.1042/bst20170139] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 12/07/2017] [Accepted: 12/11/2017] [Indexed: 12/14/2022]
Abstract
The nuclear envelope (NE) is a unique topological structure formed by lipid membranes (Inner and Outer Membrane: IM and OM) interrupted by open channels (Nuclear Pore complexes). Besides its well-established structural role in providing a physical separation between the genome and the cytoplasm and regulating the exchanges between the two cellular compartments, it has become quite evident in recent years that the NE also represents a hub for localized signal transduction. Mechanical, stress, or mitogen signals reach the nucleus and trigger the activation of several pathways, many effectors of which are processed at the NE. Therefore, the concept of the NE acting just as a barrier needs to be expanded to embrace all the dynamic processes that are indeed associated with it. In this context, dynamic protein association and turnover coupled to reversible post-translational modifications of NE components can provide important clues on how this integrated cellular machinery functions as a whole. Reversible protein phosphorylation is the most used mechanism to control protein dynamics and association in cells. Keys to the reversibility of the system are protein phosphatases and the regulation of their activity in space and time. As the NE is clearly becoming an interesting compartment for the control and transduction of several signalling pathways, in this review we will focus on the role of Protein Phosphatases at the NE since the significance of this class of proteins in this context has been little explored.
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Affiliation(s)
- Raquel Sales Gil
- College of Health and Life Science, Research Institute for Environment Health and Society, Brunel University London, London UB8 3PH, U.K
| | - Ines J de Castro
- Department of Infectious Diseases, Integrative Virology, University Hospital Heidelberg and German Center for Infection Research (DZIF), Heidelberg 69120, Germany
| | - Jerusalem Berihun
- College of Health and Life Science, Research Institute for Environment Health and Society, Brunel University London, London UB8 3PH, U.K
| | - Paola Vagnarelli
- College of Health and Life Science, Research Institute for Environment Health and Society, Brunel University London, London UB8 3PH, U.K.
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35
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Cutler AA, Jackson JB, Corbett AH, Pavlath GK. Non-equivalence of nuclear import among nuclei in multinucleated skeletal muscle cells. J Cell Sci 2018; 131:jcs.207670. [PMID: 29361530 DOI: 10.1242/jcs.207670] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 12/21/2017] [Indexed: 01/01/2023] Open
Abstract
Skeletal muscle is primarily composed of large myofibers containing thousands of post-mitotic nuclei distributed throughout a common cytoplasm. Protein production and localization in specialized myofiber regions is crucial for muscle function. Myonuclei differ in transcriptional activity and protein accumulation, but how these differences among nuclei sharing a cytoplasm are achieved is unknown. Regulated nuclear import of proteins is one potential mechanism for regulating transcription spatially and temporally in individual myonuclei. The best-characterized nuclear localization signal (NLS) in proteins is the classical NLS (cNLS), but many other NLS motifs exist. We examined cNLS and non-cNLS reporter protein import using multinucleated muscle cells generated in vitro, revealing that cNLS and non-cNLS nuclear import differs among nuclei in the same cell. Investigation of cNLS nuclear import rates in isolated myofibers ex vivo confirmed differences in nuclear import rates among myonuclei. Analyzing nuclear import throughout myogenesis revealed that cNLS and non-cNLS import varies during differentiation. Taken together, our results suggest that both spatial and temporal regulation of nuclear import pathways are important in muscle cell differentiation and protein regionalization in myofibers.
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Affiliation(s)
- Alicia A Cutler
- Department of Pharmacology, Emory University, Atlanta, GA 30322, USA.,Graduate Program in Biochemistry, Cell and Developmental Biology, Emory University, Atlanta, GA 30322, USA
| | | | - Anita H Corbett
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Grace K Pavlath
- Department of Pharmacology, Emory University, Atlanta, GA 30322, USA
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36
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Hazawa M, Lin DC, Kobayashi A, Jiang YY, Xu L, Dewi FRP, Mohamed MS, Hartono, Nakada M, Meguro-Horike M, Horike SI, Koeffler HP, Wong RW. ROCK-dependent phosphorylation of NUP62 regulates p63 nuclear transport and squamous cell carcinoma proliferation. EMBO Rep 2017; 19:73-88. [PMID: 29217659 DOI: 10.15252/embr.201744523] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 10/26/2017] [Accepted: 11/06/2017] [Indexed: 01/02/2023] Open
Abstract
p63, more specifically its ΔNp63α isoform, plays essential roles in squamous cell carcinomas (SCCs), yet the mechanisms controlling its nuclear transport remain unknown. Nucleoporins (NUPs) are a family of proteins building nuclear pore complexes (NPC) and mediating nuclear transport across the nuclear envelope. Recent evidence suggests a cell type-specific function for certain NUPs; however, the significance of NUPs in SCC biology remains unknown. In this study, we show that nucleoporin 62 (NUP62) is highly expressed in stratified squamous epithelia and is further elevated in SCCs. Depletion of NUP62 inhibits proliferation and augments differentiation of SCC cells. The impaired ability to maintain the undifferentiated status is associated with defects in ΔNp63α nuclear transport. We further find that differentiation-inducible Rho kinase reduces the interaction between NUP62 and ΔNp63α by phosphorylation of phenylalanine-glycine regions of NUP62, attenuating ΔNp63α nuclear import. Our results characterize NUP62 as a gatekeeper for ΔNp63α and uncover its role in the control of cell fate through regulation of ΔNp63α nuclear transport in SCC.
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Affiliation(s)
- Masaharu Hazawa
- Cell-Bionomics Research Unit, Innovative Integrated Bio-Research Core, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Ishikawa, Japan .,Laboratory of Molecular Cell Biology, School of Natural System, Institute of Science and Engineering, Kanazawa University, Kanazawa, Ishikawa, Japan.,WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University Kakuma-machi, Kanazawa, Japan
| | - De-Chen Lin
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Division of Hematology/Oncology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Akiko Kobayashi
- Laboratory of Molecular Cell Biology, School of Natural System, Institute of Science and Engineering, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Yan-Yi Jiang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Liang Xu
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Firli Rahmah Primula Dewi
- Laboratory of Molecular Cell Biology, School of Natural System, Institute of Science and Engineering, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Mahmoud Shaaban Mohamed
- Laboratory of Molecular Cell Biology, School of Natural System, Institute of Science and Engineering, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Hartono
- Laboratory of Molecular Cell Biology, School of Natural System, Institute of Science and Engineering, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Mitsutoshi Nakada
- Cell-Bionomics Research Unit, Innovative Integrated Bio-Research Core, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Ishikawa, Japan.,Department of Neurosurgery, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Makiko Meguro-Horike
- Advanced Science Research Center, Institute for Gene Research, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Shin-Ichi Horike
- Cell-Bionomics Research Unit, Innovative Integrated Bio-Research Core, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Ishikawa, Japan.,Advanced Science Research Center, Institute for Gene Research, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - H Phillip Koeffler
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Division of Hematology/Oncology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Richard W Wong
- Cell-Bionomics Research Unit, Innovative Integrated Bio-Research Core, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Ishikawa, Japan .,Laboratory of Molecular Cell Biology, School of Natural System, Institute of Science and Engineering, Kanazawa University, Kanazawa, Ishikawa, Japan.,WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University Kakuma-machi, Kanazawa, Japan
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37
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Tanimura S, Takeda K. ERK signalling as a regulator of cell motility. J Biochem 2017; 162:145-154. [PMID: 28903547 DOI: 10.1093/jb/mvx048] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 05/17/2017] [Indexed: 01/21/2023] Open
Abstract
Cell motility is regulated by multiple processes, including cell protrusion, cell retraction, cell-matrix adhesion, polarized exocytosis and polarized vesicle trafficking, each of which is spatiotemporally controlled by various intracellular signalling pathways. Dysregulation of cell motility leads to pathological conditions, such as tumour invasion and metastasis. Accumulating evidence has revealed that extracellular signal-regulated kinase (ERK) signalling is one of the critical regulators of cell motility, although it is classically known as an important regulator of cell proliferation, differentiation and survival through regulation of gene expression. ERK and its downstream kinase, p90 ribosomal S6 kinase (RSK), dynamically regulate cell motility mainly through direct phosphorylation of various molecules that are not necessarily involved in the regulation of gene transcription and translation. In this review, we summarize how ERK signalling regulates cell motility by focusing on the components of the cell motility machinery that are directly regulated by ERK or RSK.
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Affiliation(s)
- Susumu Tanimura
- Department of Cell Regulation, Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Kohsuke Takeda
- Department of Cell Regulation, Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
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38
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Pott LL, Hagemann S, Reis H, Lorenz K, Bracht T, Herold T, Skryabin BV, Megger DA, Kälsch J, Weber F, Sitek B, Baba HA. Eukaryotic elongation factor 2 is a prognostic marker and its kinase a potential therapeutic target in HCC. Oncotarget 2017; 8:11950-11962. [PMID: 28060762 PMCID: PMC5355317 DOI: 10.18632/oncotarget.14447] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 12/18/2016] [Indexed: 11/25/2022] Open
Abstract
Hepatocellular carcinoma is a cancer with increasing incidence and largely refractory to current anticancer drugs. Since Sorafenib, a multikinase inhibitor has shown modest efficacy in advanced hepatocellular carcinoma additional treatments are highly needed. Protein phosphorylation via kinases is an important post-translational modification to regulate cell homeostasis including proliferation and apoptosis. Therefore kinases are valuable targets in cancer therapy. To this end we performed 2D differential gel electrophoresis and mass spectrometry analysis of phosphoprotein-enriched lysates of tumor and corresponding non-tumorous liver samples to detect differentially abundant phosphoproteins to screen for novel kinases as potential drug targets. We identified 34 differentially abundant proteins in phosphoprotein enriched lysates. Expression and distribution of the candidate protein eEF2 and its phosphorylated isoform was validated immunohistochemically on 78 hepatocellular carcinoma and non-tumorous tissue samples. Validation showed that total eEF2 and phosphorylated eEF2 at threonine 56 are prognostic markers for overall survival of HCC-patients. The activity of the regulating eEF2 kinase, compared between tumor and non-tumorous tissue lysates by in vitro kinase assays, is more than four times higher in tumor tissues. Functional analyzes regarding eEF2 kinase were performed in JHH5 cells with CRISPR/Cas9 mediated eEF2 kinase knock out. Proliferation and growth is decreased in eEF2 kinase knock out cells.
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Affiliation(s)
- Leona L Pott
- Institute of Pathology, University of Duisburg-Essen, Essen, Germany.,Medizinisches Proteom-Center, Ruhr-University Bochum, Bochum, Germany
| | - Sascha Hagemann
- Institute of Pathology, University of Duisburg-Essen, Essen, Germany
| | - Henning Reis
- Institute of Pathology, University of Duisburg-Essen, Essen, Germany
| | - Kristina Lorenz
- Institute of Pharmacology, University of Wuerzburg, Wuerzburg, Germany.,Leibniz-Institut für Analytische Wissenschaften -ISAS-e.V., Dortmund, Germany.,West German Heart and Vascular Center, University of Duisburg-Essen, Essen, Germany
| | - Thilo Bracht
- Medizinisches Proteom-Center, Ruhr-University Bochum, Bochum, Germany
| | - Thomas Herold
- Institute of Pathology, University of Duisburg-Essen, Essen, Germany
| | - Boris V Skryabin
- Transgenic Animal and Genetic Engineering Models (TRAM), Westphalian Wilhelms University, Muenster, Germany
| | - Dominik A Megger
- Medizinisches Proteom-Center, Ruhr-University Bochum, Bochum, Germany
| | - Julia Kälsch
- Institute of Pathology, University of Duisburg-Essen, Essen, Germany.,Department of Gastroenterology and Hepatology, University of Duisburg-Essen, Essen, Germany
| | - Frank Weber
- Department of General, Visceral and Transplantation Surgery, University of Duisburg-Essen, Essen, Germany
| | - Barbara Sitek
- Medizinisches Proteom-Center, Ruhr-University Bochum, Bochum, Germany
| | - Hideo A Baba
- Institute of Pathology, University of Duisburg-Essen, Essen, Germany
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39
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Ünal EB, Uhlitz F, Blüthgen N. A compendium of ERK targets. FEBS Lett 2017; 591:2607-2615. [PMID: 28675784 DOI: 10.1002/1873-3468.12740] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 06/28/2017] [Accepted: 06/29/2017] [Indexed: 12/20/2022]
Abstract
The RAF-MEK-ERK cascade is one of the most studied signaling pathways as it controls many vital cellular programs. There has been an immense amount of effort to determine ERK target proteins involved in regulating these programs. Classical biochemical and genetic approaches have elicited hundreds of direct ERK substrates, and with the advent of phospho-proteomic technologies, numerous studies have expanded the number of ERK target proteins. Here, we compile a comprehensive ERK target phospho-site archive, in which we gathered information from various research studies, and we provide this archive as an online database to form a searchable compendium of ERK targets.
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Affiliation(s)
- Evrim B Ünal
- Integrative Research Institute Life Sciences & Institute for Theoretical Biology, Humboldt Universität zu Berlin, Germany.,Institute of Pathology, Charité - Universitätsmedizin Berlin, Germany
| | - Florian Uhlitz
- Integrative Research Institute Life Sciences & Institute for Theoretical Biology, Humboldt Universität zu Berlin, Germany.,Institute of Pathology, Charité - Universitätsmedizin Berlin, Germany
| | - Nils Blüthgen
- Integrative Research Institute Life Sciences & Institute for Theoretical Biology, Humboldt Universität zu Berlin, Germany.,Institute of Pathology, Charité - Universitätsmedizin Berlin, Germany.,Berlin Institute of Health, Germany
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40
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Kubiniok P, Lavoie H, Therrien M, Thibault P. Time-resolved Phosphoproteome Analysis of Paradoxical RAF Activation Reveals Novel Targets of ERK. Mol Cell Proteomics 2017; 16:663-679. [PMID: 28188228 DOI: 10.1074/mcp.m116.065128] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 12/31/2016] [Indexed: 12/19/2022] Open
Abstract
Small molecules targeting aberrant RAF activity, like vemurafenib (PLX4032), are highly effective against cancers harboring the V600E BRAF mutation and are now approved for clinical use against metastatic melanoma. However, in tissues showing elevated RAS activity and in RAS mutant tumors, these inhibitors stimulate RAF dimerization, resulting in inhibitor resistance and downstream "paradoxical" ERK activation. To understand the global signaling response of cancer cells to RAF inhibitors, we profiled the temporal changes of the phosphoproteome of two colon cancer cell lines (Colo205 and HCT116) that respond differently to vemurafenib. Comprehensive data mining and filtering identified a total of 37,910 phosphorylation sites, 660 of which were dynamically modulated upon treatment with vemurafenib. We established that 83% of these dynamic phosphorylation sites were modulated in accordance with the phospho-ERK profile of the two cell lines. Accordingly, kinase substrate prediction algorithms linked most of these dynamic sites to direct ERK1/2-mediated phosphorylation, supporting a low off-target rate for vemurafenib. Functional classification of target proteins indicated the enrichment of known (nuclear pore, transcription factors, and RAS-RTK signaling) and novel (Rho GTPases signaling and actin cytoskeleton) ERK-controlled functions. Our phosphoproteomic data combined with experimental validation established novel dynamic connections between ERK signaling and the transcriptional regulators TEAD3 (Hippo pathway), MKL1, and MKL2 (Rho serum-response elements pathway). We also confirm that an ERK-docking site found in MKL1 is directly antagonized by overlapping actin binding, defining a novel mechanism of actin-modulated phosphorylation. Altogether, time-resolved phosphoproteomics further documented vemurafenib selectivity and identified novel ERK downstream substrates.
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Affiliation(s)
- Peter Kubiniok
- From the ‡Institute for Research in Immunology and Cancer and.,Departments of §Chemistry
| | - Hugo Lavoie
- From the ‡Institute for Research in Immunology and Cancer and
| | - Marc Therrien
- From the ‡Institute for Research in Immunology and Cancer and .,‖Pathology and Cell Biology, and
| | - Pierre Thibault
- From the ‡Institute for Research in Immunology and Cancer and .,Departments of §Chemistry.,‡‡Biochemistry, Université de Montréal, C.P. 6128, Succursale Centreville, Montréal, Québec H3C 3J7, Canada
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41
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Kosako H, Motani K. Global Identification of ERK Substrates by Phosphoproteomics Based on IMAC and 2D-DIGE. Methods Mol Biol 2017; 1487:137-149. [PMID: 27924564 DOI: 10.1007/978-1-4939-6424-6_10] [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] [Indexed: 12/26/2022]
Abstract
Extracellular signal-regulated kinase (ERK) regulates various cellular functions through phosphorylation of numerous downstream substrates, which have not yet been fully characterized. To date, several phosphoproteomic approaches have been employed to identify novel substrates for ERK. In this chapter, we describe a method to globally identify ERK substrates by combining immobilized metal affinity chromatography (IMAC) and two-dimensional difference gel electrophoresis (2D-DIGE) followed by mass spectrometry. Phosphoprotein enrichment by IMAC enables the subsequent detection of many protein spots with different fluorescence intensities between ERK-inhibited and -activated cells in 2D-DIGE analysis. Furthermore, the advanced sensitivity and resolution of liquid chromatography coupled with tandem mass spectrometry allow for a direct identification of proteins obtained from silver-stained 2D-DIGE gels. Validation experiments such as Phos-tag Western blotting are important steps to further elucidate the functional roles of ERK-mediated phosphorylation of these newly identified substrates.
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Affiliation(s)
- Hidetaka Kosako
- Division of Cell Signaling, Fujii Memorial Institute of Medical Sciences, Tokushima University, 3-18-15 Kuramoto-cho, Tokushima, 770-8503, Japan.
| | - Kou Motani
- Division of Cell Signaling, Fujii Memorial Institute of Medical Sciences, Tokushima University, 3-18-15 Kuramoto-cho, Tokushima, 770-8503, Japan
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42
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Abstract
Cells respond to changes in their environment, to developmental cues, and to pathogen aggression through the action of a complex network of proteins. These networks can be decomposed into a multitude of signaling pathways that relay signals from the microenvironment to the cellular components involved in eliciting a specific response. Perturbations in these signaling processes are at the root of multiple pathologies, the most notable of these being cancer. The study of receptor tyrosine kinase (RTK) signaling led to the first description of a mechanism whereby an extracellular signal is transmitted to the nucleus to induce a transcriptional response. Genetic studies conducted in drosophila and nematodes have provided key elements to this puzzle. Here, we briefly discuss the somewhat lesser known contribution of these multicellular organisms to our understanding of what has come to be known as the prototype of signaling pathways. We also discuss the ostensibly much larger network of regulators that has emerged from recent functional genomic investigations of RTK/RAS/ERK signaling.
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Affiliation(s)
- Dariel Ashton-Beaucage
- Institute for Research in Immunology and Cancer, Laboratory of Intracellular Signaling, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montreal, QC, Canada, H3C 3J7
| | - Marc Therrien
- Institute for Research in Immunology and Cancer, Laboratory of Intracellular Signaling, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montreal, QC, Canada, H3C 3J7.
- Département de Pathologie et de Biologie Cellulaire, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montreal, QC, Canada, H3C 3J7.
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43
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Lee MH, Yoon DS. A Phenotype-Based RNAi Screening for Ras-ERK/MAPK Signaling-Associated Stem Cell Regulators in C. elegans. Methods Mol Biol 2017; 1622:207-221. [PMID: 28674811 DOI: 10.1007/978-1-4939-7108-4_15] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Stem cells have the ability to self-renew and to generate differentiated cell types. A regulatory network that controls this balance is critical for stem cell homeostasis and normal animal development. Particularly, Ras-ERK/MAPK signaling pathway is critical for stem cell self-renewal and differentiation in mammals, including humans. Aberrant regulation of Ras-ERK/MAPK signaling pathway results in either stem cell or overproliferation. Therefore, the identification of Ras-ERK/MAPK signaling pathway-associated regulators is critical to understand the mechanism of stem cell (possibly cancer stem cell) control. In this report, using the nematode C. elegans mutants, we developed a methodology for a phenotype-based RNAi screening that identifies stem cell regulator genes associated with Ras-ERK/MAPK signaling within the context of a whole organism. Importantly, this phenotype-based RNAi screening can be applied for other stem cell-associated signaling pathways such as Wnt/β-catenin and Notch using the C. elegans.
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Affiliation(s)
- Myon-Hee Lee
- Division of Hematology/Oncology, Department of Medicine, Brody School of Medicine at East Carolina University, Greenville, NC, 27834, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA.
| | - Dong Suk Yoon
- Division of Hematology/Oncology, Department of Medicine, Brody School of Medicine at East Carolina University, Greenville, NC, 27834, USA
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44
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Mao LM, Wang HH, Wang JQ. Antagonism of Muscarinic Acetylcholine Receptors Alters Synaptic ERK Phosphorylation in the Rat Forebrain. Neurochem Res 2016; 42:1202-1210. [PMID: 28032295 DOI: 10.1007/s11064-016-2157-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 12/08/2016] [Accepted: 12/19/2016] [Indexed: 11/25/2022]
Abstract
Acetylcholine (ACh) is a key transmitter in the mesocorticolimbic circuit. By interacting with muscarinic ACh receptors (mAChR) enriched in the circuit, ACh actively regulates various neuronal and synaptic activities. The extracellular signal-regulated kinase (ERK) is one of members of the mitogen-activated protein kinase family and is subject to the regulation by dopamine receptors, although the regulation of ERKs by limbic mAChRs is poorly understood. In this study, we investigated the role of mAChRs in the regulation of ERK phosphorylation (activation) in the mesocorticolimbic system of adult rat brains in vivo. We targeted a sub-pool of ERKs at synaptic sites. We found that a systemic injection of the mAChR antagonist scopolamine increased phosphorylation of synaptic ERKs in the striatum (caudate putamen and nucleus accumbens) and medial prefrontal cortex (mPFC). Increases in ERK phosphorylation in both forebrain regions were rapid and transient. Notably, pretreatment with a dopamine D1 receptor (D1R) antagonist SCH23390 blocked the scopolamine-stimulated ERK phosphorylation in these brain regions, while a dopamine D2 receptor antagonist eticlopride did not. Scopolamine and SCH23390 did not change the amount of total ERK proteins. These results demonstrate that mAChRs inhibit synaptic ERK phosphorylation in striatal and mPFC neurons under normal conditions. Blockade of this inhibitory mAChR tone leads to the upregulation of ERK phosphorylation likely through a mechanism involving the level of D1R activity.
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Affiliation(s)
- Li-Min Mao
- Department of Basic Medical Science, School of Medicine, University of Missouri-Kansas City, 2411 Holmes Street, Kansas City, MO, 64108, USA
| | - Henry H Wang
- Department of Basic Medical Science, School of Medicine, University of Missouri-Kansas City, 2411 Holmes Street, Kansas City, MO, 64108, USA
| | - John Q Wang
- Department of Basic Medical Science, School of Medicine, University of Missouri-Kansas City, 2411 Holmes Street, Kansas City, MO, 64108, USA. .,Department of Anesthesiology, School of Medicine, University of Missouri-Kansas City, Kansas City, MO, 64108, USA.
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45
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Co-culture Activation of MAP Kinase in Drosophila S2 Cells. Methods Mol Biol 2016. [PMID: 27924571 DOI: 10.1007/978-1-4939-6424-6_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Intercellular communication often involves phosphorylation of signal transduction proteins, including mitogen-activated protein kinases (MAPKs). Immunological detection of phosphorylated MAPK can be used to monitor signaling in vivo, identify novel pathway components, and assess ligand activity. In this chapter, I describe a cell co-culture method to assess activity of cell-bound extracellular ligands that result in phosphorylation of the ERK (extracellular signal-regulated kinase) MAPK in Drosophila. This protocol may be adaptable to other pathways and/or model systems.
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46
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Modeling Cellular Noise Underlying Heterogeneous Cell Responses in the Epidermal Growth Factor Signaling Pathway. PLoS Comput Biol 2016; 12:e1005222. [PMID: 27902699 PMCID: PMC5130170 DOI: 10.1371/journal.pcbi.1005222] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Accepted: 10/25/2016] [Indexed: 12/03/2022] Open
Abstract
Cellular heterogeneity, which plays an essential role in biological phenomena, such as drug resistance and migration, is considered to arise from intrinsic (i.e., reaction kinetics) and extrinsic (i.e., protein variability) noise in the cell. However, the mechanistic effects of these types of noise to determine the heterogeneity of signal responses have not been elucidated. Here, we report that the output of epidermal growth factor (EGF) signaling activity is modulated by cellular noise, particularly by extrinsic noise of particular signaling components in the pathway. We developed a mathematical model of the EGF signaling pathway incorporating regulation between extracellular signal-regulated kinase (ERK) and nuclear pore complex (NPC), which is necessary for switch-like activation of the nuclear ERK response. As the threshold of switch-like behavior is more sensitive to perturbations than the graded response, the effect of biological noise is potentially critical for cell fate decision. Our simulation analysis indicated that extrinsic noise, but not intrinsic noise, contributes to cell-to-cell heterogeneity of nuclear ERK. In addition, we accurately estimated variations in abundance of the signal proteins between individual cells by direct comparison of experimental data with simulation results using Apparent Measurement Error (AME). AME was constant regardless of whether the protein levels varied in a correlated manner, while covariation among proteins influenced cell-to-cell heterogeneity of nuclear ERK, suppressing the variation. Simulations using the estimated protein abundances showed that each protein species has different effects on cell-to-cell variation in the nuclear ERK response. In particular, variability of EGF receptor, Ras, Raf, and MEK strongly influenced cellular heterogeneity, while others did not. Overall, our results indicated that cellular heterogeneity in response to EGF is strongly driven by extrinsic noise, and that such heterogeneity results from variability of particular protein species that function as sensitive nodes, which may contribute to the pathogenesis of human diseases. Individual cell behaviors are controlled by a variety of noise, such as fluctuations in biochemical reactions, protein variability, molecular diffusion, transcriptional noise, cell-to-cell contact, temperature, and pH. Such cellular noise often interferes with signal responses from external stimuli, and such heterogeneity functions in induction of drug resistance, survival, and migration of cells. Thus, heterogeneous cellular responses have positive and negative roles. However, the regulatory mechanisms that produce cellular heterogeneity are unclear. By mathematical modeling and simulations, we investigated how heterogeneous signaling responses are evoked in the EGF signaling pathway and influence the switch-like activation of nuclear ERK. This study demonstrated that cellular heterogeneity of the EGF signaling response is evoked by cell-to-cell variation of particular signaling proteins, such as EGFR, Ras, Raf, and MEK, which act as sensitive nodes in the pathway. These results suggest that signaling responses in individual cells can be predicted from the levels of proteins of sensitive nodes. This study also suggested that proteins of sensitive nodes may serve as cell survival mechanisms.
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47
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Rose JC, Huang PS, Camp ND, Ye J, Leidal AM, Goreshnik I, Trevillian BM, Dickinson MS, Cunningham-Bryant D, Debnath J, Baker D, Wolf-Yadlin A, Maly DJ. A computationally engineered RAS rheostat reveals RAS-ERK signaling dynamics. Nat Chem Biol 2016; 13:119-126. [PMID: 27870838 PMCID: PMC5161653 DOI: 10.1038/nchembio.2244] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 09/08/2016] [Indexed: 01/07/2023]
Abstract
Synthetic protein switches controlled with user-defined inputs are powerful tools for studying and controlling dynamic cellular processes. To date, these approaches have relied primarily on intermolecular regulation. Here, we report a computationally-guided framework for engineering intramolecular regulation of protein function. We utilize this framework to develop Chemically Inducible Activator of RAS (CIAR), a single-component RAS rheostat that directly activates endogenous RAS in response to a small molecule. Using CIAR, we show that direct RAS activation elicits markedly different RAS/ERK signaling dynamics compared to growth factor stimulation, and that these dynamics differ between cell types. We also found that the clinically-approved RAF inhibitor vemurafenib potently primes cells to respond to direct wild-type RAS activation. These results demonstrate the utility of CIAR for quantitatively interrogating RAS signaling. Finally, we demonstrate the general utility of our approach to design intramolecularly-regulated protein tools by applying this methodology to the Rho Family GEFs.
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Affiliation(s)
- John C Rose
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Po-Ssu Huang
- Department of Biochemistry, University of Washington, Seattle, Washington, USA.,Institute for Protein Design, University of Washington, Seattle, Washington, USA
| | - Nathan D Camp
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Jordan Ye
- Department of Pathology and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - Andrew M Leidal
- Department of Pathology and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - Inna Goreshnik
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | | | - Miles S Dickinson
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | | | - Jayanta Debnath
- Department of Pathology and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, Washington, USA.,Institute for Protein Design, University of Washington, Seattle, Washington, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USA
| | | | - Dustin J Maly
- Department of Chemistry, University of Washington, Seattle, Washington, USA.,Department of Biochemistry, University of Washington, Seattle, Washington, USA
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48
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Sun HL, Cui R, Zhou J, Teng KY, Hsiao YH, Nakanishi K, Fassan M, Luo Z, Shi G, Tili E, Kutay H, Lovat F, Vicentini C, Huang HL, Wang SW, Kim T, Zanesi N, Jeon YJ, Lee TJ, Guh JH, Hung MC, Ghoshal K, Teng CM, Peng Y, Croce CM. ERK Activation Globally Downregulates miRNAs through Phosphorylating Exportin-5. Cancer Cell 2016; 30:723-736. [PMID: 27846390 PMCID: PMC5127275 DOI: 10.1016/j.ccell.2016.10.001] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 04/01/2016] [Accepted: 10/03/2016] [Indexed: 02/05/2023]
Abstract
MicroRNAs (miRNA) are mostly downregulated in cancer. However, the mechanism underlying this phenomenon and the precise consequence in tumorigenesis remain obscure. Here we show that ERK suppresses pre-miRNA export from the nucleus through phosphorylation of exportin-5 (XPO5) at T345/S416/S497. After phosphorylation by ERK, conformation of XPO5 is altered by prolyl isomerase Pin1, resulting in reduction of pre-miRNA loading. In liver cancer, the ERK-mediated XPO5 suppression reduces miR-122, increases microtubule dynamics, and results in tumor development and drug resistance. Analysis of clinical specimens further showed that XPO5 phosphorylation is associated with poor prognosis for liver cancer patients. Our study reveals a function of ERK in miRNA biogenesis and suggests that modulation of miRNA export has potential clinical implications.
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Affiliation(s)
- Hui-Lung Sun
- Department of Cancer Biology and Genetics, Ohio State University, Columbus, OH 43210, USA; Pharmacological Institute, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Ri Cui
- Department of Cancer Biology and Genetics, Ohio State University, Columbus, OH 43210, USA
| | - JianKang Zhou
- Department of Thoracic Surgery, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, PR China
| | - Kun-Yu Teng
- Department of Pathology, Ohio State University, Columbus, OH 43210, USA
| | - Yung-Hsuan Hsiao
- Department of Human Sciences, Human Nutrition Program, College of Education and Human Ecology, Ohio State University, Columbus, OH 43210, USA
| | - Kotaro Nakanishi
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210, USA
| | - Matteo Fassan
- Department of Cancer Biology and Genetics, Ohio State University, Columbus, OH 43210, USA; ARC-NET Research Centre, University and Hospital Trust of Verona, Verona 37126, Italy
| | - Zhenghua Luo
- Department of Cancer Biology and Genetics, Ohio State University, Columbus, OH 43210, USA
| | - Guqin Shi
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, Ohio State University, Columbus, OH 43210, USA
| | - Esmerina Tili
- Department of Cancer Biology and Genetics, Ohio State University, Columbus, OH 43210, USA; Department of Anesthesiology, Ohio State University, Columbus, OH 43210, USA
| | - Huban Kutay
- Department of Pathology, Ohio State University, Columbus, OH 43210, USA
| | - Francesca Lovat
- Department of Cancer Biology and Genetics, Ohio State University, Columbus, OH 43210, USA
| | - Caterina Vicentini
- ARC-NET Research Centre, University and Hospital Trust of Verona, Verona 37126, Italy
| | - Han-Li Huang
- The Ph.D. Program for Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
| | - Shih-Wei Wang
- Department of Medicine, Mackay Medical College, New Taipei City 25245, Taiwan
| | - Taewan Kim
- Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Nicola Zanesi
- Department of Cancer Biology and Genetics, Ohio State University, Columbus, OH 43210, USA
| | - Young-Jun Jeon
- Department of Cancer Biology and Genetics, Ohio State University, Columbus, OH 43210, USA
| | - Tae Jin Lee
- Department of Cancer Biology and Genetics, Ohio State University, Columbus, OH 43210, USA
| | - Jih-Hwa Guh
- School of Pharmacy, National Taiwan University, Taipei 10051, Taiwan
| | - Mien-Chie Hung
- Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Graduate Institute of Cancer Biology and Center for Molecular Medicine, China Medical University, Taichung 40402, Taiwan; Department of Biotechnology, Asia University, Taichung 41354, Taiwan
| | - Kalpana Ghoshal
- Department of Pathology, Ohio State University, Columbus, OH 43210, USA
| | - Che-Ming Teng
- Pharmacological Institute, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Yong Peng
- Department of Thoracic Surgery, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, PR China.
| | - Carlo M Croce
- Department of Cancer Biology and Genetics, Ohio State University, Columbus, OH 43210, USA.
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49
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Synaptic ERK2 Phosphorylates and Regulates Metabotropic Glutamate Receptor 1 In Vitro and in Neurons. Mol Neurobiol 2016; 54:7156-7170. [PMID: 27796752 DOI: 10.1007/s12035-016-0225-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 10/13/2016] [Indexed: 12/21/2022]
Abstract
A synaptic pool of extracellular signal-regulated kinases (ERK) controls synaptic transmission, although little is known about its underlying signaling mechanisms. Here, we found that synaptic ERK2 directly binds to postsynaptic metabotropic glutamate receptor 1a (mGluR1a). This binding is direct and the ERK-binding site is located in the intracellular C-terminus (CT) of mGluR1a. Parallel with this binding, ERK2 phosphorylates mGluR1a at a cluster of serine residues in the distal part of mGluR1a-CT. In rat cerebellar neurons, ERK2 interacts with mGluR1a at synaptic sites, and active ERK constitutively phosphorylates mGluR1a under normal conditions. This basal phosphorylation is critical for maintaining adequate surface expression of mGluR1a. ERK is also essential for controlling mGluR1a signaling in triggering distinct postreceptor signaling transduction pathways. In summary, we have demonstrated that mGluR1a is a sufficient substrate of ERK2. ERK that interacts with and phosphorylates mGluR1a is involved in the regulation of the trafficking and signaling of mGluR1.
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50
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Sugiyama N, Ishihama Y. Large-scale profiling of protein kinases for cellular signaling studies by mass spectrometry and other techniques. J Pharm Biomed Anal 2016; 130:264-272. [DOI: 10.1016/j.jpba.2016.05.046] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 05/26/2016] [Accepted: 05/27/2016] [Indexed: 01/26/2023]
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