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Zhao J, Wei M, Guo M, Wang M, Niu H, Xu T, Zhou Y. GSK3: A potential target and pending issues for treatment of Alzheimer's disease. CNS Neurosci Ther 2024; 30:e14818. [PMID: 38946682 PMCID: PMC11215492 DOI: 10.1111/cns.14818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 05/21/2024] [Accepted: 05/27/2024] [Indexed: 07/02/2024] Open
Abstract
Glycogen synthase kinase-3 (GSK3), consisting of GSK3α and GSK3β subtypes, is a complex protein kinase that regulates numerous substrates. Research has observed increased GSK3 expression in the brains of Alzheimer's disease (AD) patients and models. AD is a neurodegenerative disorder with diverse pathogenesis and notable cognitive impairments, characterized by Aβ aggregation and excessive tau phosphorylation. This article provides an overview of GSK3's structure and regulation, extensively analyzing its relationship with AD factors. GSK3 overactivation disrupts neural growth, development, and function. It directly promotes tau phosphorylation, regulates amyloid precursor protein (APP) cleavage, leading to Aβ formation, and directly or indirectly triggers neuroinflammation and oxidative damage. We also summarize preclinical research highlighting the inhibition of GSK3 activity as a primary therapeutic approach for AD. Finally, pending issues like the lack of highly specific and affinity-driven GSK3 inhibitors, are raised and expected to be addressed in future research. In conclusion, GSK3 represents a target in AD treatment, filled with hope, challenges, opportunities, and obstacles.
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Affiliation(s)
- Jiahui Zhao
- School of Basic Medical SciencesZhejiang Chinese Medical UniversityHangzhouChina
| | - Mengying Wei
- College of Pharmaceutical SciencesZhejiang UniversityHangzhouChina
- Future Health Laboratory, Innovation Center of Yangtze River DeltaZhejiang UniversityJiaxingChina
| | - Minsong Guo
- College of Pharmaceutical SciencesZhejiang UniversityHangzhouChina
- Cangnan County Qiushi Innovation Research Institute of Traditional Chinese MedicineWenzhouChina
| | - Mengyao Wang
- School of Basic Medical SciencesZhejiang Chinese Medical UniversityHangzhouChina
| | - Hongxia Niu
- School of Basic Medical SciencesZhejiang Chinese Medical UniversityHangzhouChina
- Key Laboratory of Blood‐stasis‐toxin Syndrome of Zhejiang ProvinceHangzhouChina
| | - Tengfei Xu
- College of Pharmaceutical SciencesZhejiang UniversityHangzhouChina
- Cangnan County Qiushi Innovation Research Institute of Traditional Chinese MedicineWenzhouChina
| | - Yuan Zhou
- School of Basic Medical SciencesZhejiang Chinese Medical UniversityHangzhouChina
- Key Laboratory of Blood‐stasis‐toxin Syndrome of Zhejiang ProvinceHangzhouChina
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2
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Fazakerley DJ, van Gerwen J, Cooke KC, Duan X, Needham EJ, Díaz-Vegas A, Madsen S, Norris DM, Shun-Shion AS, Krycer JR, Burchfield JG, Yang P, Wade MR, Brozinick JT, James DE, Humphrey SJ. Phosphoproteomics reveals rewiring of the insulin signaling network and multi-nodal defects in insulin resistance. Nat Commun 2023; 14:923. [PMID: 36808134 PMCID: PMC9938909 DOI: 10.1038/s41467-023-36549-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 02/07/2023] [Indexed: 02/19/2023] Open
Abstract
The failure of metabolic tissues to appropriately respond to insulin ("insulin resistance") is an early marker in the pathogenesis of type 2 diabetes. Protein phosphorylation is central to the adipocyte insulin response, but how adipocyte signaling networks are dysregulated upon insulin resistance is unknown. Here we employ phosphoproteomics to delineate insulin signal transduction in adipocyte cells and adipose tissue. Across a range of insults causing insulin resistance, we observe a marked rewiring of the insulin signaling network. This includes both attenuated insulin-responsive phosphorylation, and the emergence of phosphorylation uniquely insulin-regulated in insulin resistance. Identifying dysregulated phosphosites common to multiple insults reveals subnetworks containing non-canonical regulators of insulin action, such as MARK2/3, and causal drivers of insulin resistance. The presence of several bona fide GSK3 substrates among these phosphosites led us to establish a pipeline for identifying context-specific kinase substrates, revealing widespread dysregulation of GSK3 signaling. Pharmacological inhibition of GSK3 partially reverses insulin resistance in cells and tissue explants. These data highlight that insulin resistance is a multi-nodal signaling defect that includes dysregulated MARK2/3 and GSK3 activity.
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Affiliation(s)
- Daniel J Fazakerley
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia.
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK.
| | - Julian van Gerwen
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Kristen C Cooke
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Xiaowen Duan
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Elise J Needham
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Alexis Díaz-Vegas
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Søren Madsen
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Dougall M Norris
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Amber S Shun-Shion
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - James R Krycer
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
- QIMR Berghofer Medical Research Institute, Brisbane, QL, Australia
- Faculty of Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, QL, Australia
| | - James G Burchfield
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Pengyi Yang
- Charles Perkins Centre, School of Mathematics and Statistics, University of Sydney, Sydney, NSW, 2006, Australia
- Computational Systems Biology Group, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, 2145, Australia
| | - Mark R Wade
- Lilly Research Laboratories, Division of Eli Lilly and Company, Indianapolis, IN, USA
| | - Joseph T Brozinick
- Lilly Research Laboratories, Division of Eli Lilly and Company, Indianapolis, IN, USA
| | - David E James
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia.
- Sydney Medical School, University of Sydney, Sydney, 2006, Australia.
| | - Sean J Humphrey
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia.
- Murdoch Children's Research Institute, The Royal Children's Hospital, Melbourne, VIC, 3052, Australia.
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3
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Wenger K, Viode A, Schlaffner CN, van Zalm P, Cheng L, Dellovade T, Langlois X, Bannon A, Chang R, Connors TR, Oakley D, Renard B, Rappsilber J, Hyman B, Steen H, Steen JA. Common mouse models of tauopathy reflect early but not late human disease. Mol Neurodegener 2023; 18:10. [PMID: 36732784 PMCID: PMC9893608 DOI: 10.1186/s13024-023-00601-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 01/25/2023] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Mouse models that overexpress human mutant Tau (P301S and P301L) are commonly used in preclinical studies of Alzheimer's Disease (AD) and while several drugs showed therapeutic effects in these mice, they were ineffective in humans. This leads to the question to which extent the murine models reflect human Tau pathology on the molecular level. METHODS We isolated insoluble, aggregated Tau species from two common AD mouse models during different stages of disease and characterized the modification landscape of the aggregated Tau using targeted and untargeted mass spectrometry-based proteomics. The results were compared to human AD and to human patients that suffered from early onset dementia and that carry the P301L Tau mutation. RESULTS Both mouse models accumulate insoluble Tau species during disease. The Tau aggregation is driven by progressive phosphorylation within the proline rich domain and the C-terminus of the protein. This is reflective of early disease stages of human AD and of the pathology of dementia patients carrying the P301L Tau mutation. However, Tau ubiquitination and acetylation, which are important to late-stage human AD are not represented in the mouse models. CONCLUSION AD mouse models that overexpress human Tau using risk mutations are a suitable tool for testing drug candidates that aim to intervene in the early formation of insoluble Tau species promoted by increased phosphorylation of Tau.
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Affiliation(s)
- Kathrin Wenger
- F.M. Kirby Neurobiology Center, Department of Neurobiology, Boston Children’s Hospital and Harvard, Medical School; Center for Life Science, RM 12030, 3 Blackfan Circle, Boston, MA 02115 USA
| | - Arthur Viode
- Departments of Pathology, Boston Children’s Hospital and Harvard Medical School, Boston, MA USA
| | - Christoph N. Schlaffner
- Departments of Pathology, Boston Children’s Hospital and Harvard Medical School, Boston, MA USA
- Data Analytics and Computational Statistics, Hasso-Plattner-Institute, Faculty of Digital Engineering; University of Potsdam, Potsdam, Germany
| | - Patrick van Zalm
- Departments of Pathology, Boston Children’s Hospital and Harvard Medical School, Boston, MA USA
| | - Long Cheng
- F.M. Kirby Neurobiology Center, Department of Neurobiology, Boston Children’s Hospital and Harvard, Medical School; Center for Life Science, RM 12030, 3 Blackfan Circle, Boston, MA 02115 USA
| | | | | | | | - Rui Chang
- AbbVie, Cambridge Research Center, Cambridge, MA USA
| | - Theresa R. Connors
- Massachusetts Alzheimer’s Disease Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA USA
| | - Derek Oakley
- Massachusetts Alzheimer’s Disease Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA USA
| | - Bernhard Renard
- Data Analytics and Computational Statistics, Hasso-Plattner-Institute, Faculty of Digital Engineering; University of Potsdam, Potsdam, Germany
| | - Juri Rappsilber
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Bradley Hyman
- Massachusetts Alzheimer’s Disease Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA USA
| | - Hanno Steen
- Departments of Pathology, Boston Children’s Hospital and Harvard Medical School, Boston, MA USA
- Neurobiology Program, Boston Children’s Hospital, Boston, MA USA
| | - Judith A. Steen
- F.M. Kirby Neurobiology Center, Department of Neurobiology, Boston Children’s Hospital and Harvard, Medical School; Center for Life Science, RM 12030, 3 Blackfan Circle, Boston, MA 02115 USA
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Kuraoka S, Higashi H, Yanagihara Y, Sonawane AR, Mukai S, Mlynarchik AK, Whelan MC, Hottiger MO, Nasir W, Delanghe B, Aikawa M, Singh SA. A Novel Spectral Annotation Strategy Streamlines Reporting of mono-ADP-ribosylated Peptides Derived from Mouse Liver and Spleen in Response to IFN-γ. Mol Cell Proteomics 2021; 21:100153. [PMID: 34592425 PMCID: PMC9014395 DOI: 10.1016/j.mcpro.2021.100153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 09/09/2021] [Accepted: 09/21/2021] [Indexed: 12/13/2022] Open
Abstract
Mass-spectrometry-enabled ADP-ribosylation workflows are developing rapidly, providing researchers a variety of ADP-ribosylome enrichment strategies and mass spectrometric acquisition options. Despite the growth spurt in upstream technologies, systematic ADP-ribosyl (ADPr) peptide mass spectral annotation methods are lacking. HCD-dependent ADP-ribosylome studies are common, but the resulting MS2 spectra are complex, owing to a mixture of b/y-ions and the m/p-ion peaks representing one or more dissociation events of the ADPr moiety (m-ion) and peptide (p-ion). In particular, p-ions that dissociate further into one or more fragment ions can dominate HCD spectra but are not recognized by standard spectral annotation workflows. As a result, annotation strategies that are solely reliant upon the b/y-ions result in lower spectral scores that in turn reduce the number of reportable ADPr peptides. To improve the confidence of spectral assignments, we implemented an ADPr peptide annotation and scoring strategy. All MS2 spectra are scored for the ADPr m-ions, but once spectra are assigned as an ADPr peptide, they are further annotated and scored for the p-ions. We implemented this novel workflow to ADPr peptides enriched from the liver and spleen isolated from mice post 4 h exposure to systemic IFN-γ. HCD collision energy experiments were first performed on the Orbitrap Fusion Lumos and the Q Exactive, with notable ADPr peptide dissociation properties verified with CID (Lumos). The m-ion and p-ion series score distributions revealed that ADPr peptide dissociation properties vary markedly between instruments and within instrument collision energy settings, with consequences on ADPr peptide reporting and amino acid localization. Consequentially, we increased the number of reportable ADPr peptides by 25% (liver) and 17% (spleen) by validation and the inclusion of lower confidence ADPr peptide spectra. This systematic annotation strategy will streamline future reporting of ADPr peptides that have been sequenced using any HCD/CID-based method. An annotation method to identify and score ADP-ribosyl (ADPr) peptide MS2 spectra. The m-ion score monitors the dissociation of the ADPr modification. The p-ion score monitors the dissociation of the peptide plus residual ADPr fragment. The p-ion score increased reportable ADPr peptide numbers in mouse tissues.
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Affiliation(s)
- Shiori Kuraoka
- Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Department of Medicine, Brigham Women's Hospital, Harvard Medical School, Boston, MA, United States
| | - Hideyuki Higashi
- Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Department of Medicine, Brigham Women's Hospital, Harvard Medical School, Boston, MA, United States
| | - Yoshihiro Yanagihara
- Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Department of Medicine, Brigham Women's Hospital, Harvard Medical School, Boston, MA, United States
| | - Abhijeet R Sonawane
- Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Department of Medicine, Brigham Women's Hospital, Harvard Medical School, Boston, MA, United States; Center for Excellence in Vascular Biology, Division of Cardiovascular Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
| | - Shin Mukai
- Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Department of Medicine, Brigham Women's Hospital, Harvard Medical School, Boston, MA, United States
| | - Andrew K Mlynarchik
- Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Department of Medicine, Brigham Women's Hospital, Harvard Medical School, Boston, MA, United States
| | - Mary C Whelan
- Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Department of Medicine, Brigham Women's Hospital, Harvard Medical School, Boston, MA, United States
| | - Michael O Hottiger
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Waqas Nasir
- Thermo Fisher Scientific (Bremen) GmbH, Bremen, Germany
| | | | - Masanori Aikawa
- Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Department of Medicine, Brigham Women's Hospital, Harvard Medical School, Boston, MA, United States; Center for Excellence in Vascular Biology, Division of Cardiovascular Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States; Channing Division of Network Medicine, Department of Medicine, Brigham Women's Hospital, Harvard Medical School, Boston, MA, United States.
| | - Sasha A Singh
- Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Department of Medicine, Brigham Women's Hospital, Harvard Medical School, Boston, MA, United States.
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5
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Schlaffner CN, Kahnert K, Muntel J, Chauhan R, Renard BY, Steen JA, Steen H. FLEXIQuant-LF to quantify protein modification extent in label-free proteomics data. eLife 2020; 9:e58783. [PMID: 33284109 PMCID: PMC7721442 DOI: 10.7554/elife.58783] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 11/23/2020] [Indexed: 12/22/2022] Open
Abstract
Improvements in LC-MS/MS methods and technology have enabled the identification of thousands of modified peptides in a single experiment. However, protein regulation by post-translational modifications (PTMs) is not binary, making methods to quantify the modification extent crucial to understanding the role of PTMs. Here, we introduce FLEXIQuant-LF, a software tool for large-scale identification of differentially modified peptides and quantification of their modification extent without knowledge of the types of modifications involved. We developed FLEXIQuant-LF using label-free quantification of unmodified peptides and robust linear regression to quantify the modification extent of peptides. As proof of concept, we applied FLEXIQuant-LF to data-independent-acquisition (DIA) data of the anaphase promoting complex/cyclosome (APC/C) during mitosis. The unbiased FLEXIQuant-LF approach to assess the modification extent in quantitative proteomics data provides a better understanding of the function and regulation of PTMs. The software is available at https://github.com/SteenOmicsLab/FLEXIQuantLF.
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Affiliation(s)
- Christoph N Schlaffner
- F.M. Kirby Neurobiology Center, Boston Children’s HospitalBostonUnited States
- Department of Neurology, Harvard Medical SchoolBostonUnited States
| | - Konstantin Kahnert
- Department of Pathology, Boston Children’s HospitalBostonUnited States
- Bioinformatics Unit (MF1), Robert Koch InstituteBerlinGermany
- Department of Medical Biotechnology, Institute of Biotechnology, Technische Universität BerlinBerlinGermany
| | - Jan Muntel
- Department of Pathology, Boston Children’s HospitalBostonUnited States
- Department of Pathology, Harvard Medical SchoolBostonUnited States
| | - Ruchi Chauhan
- F.M. Kirby Neurobiology Center, Boston Children’s HospitalBostonUnited States
| | - Bernhard Y Renard
- Bioinformatics Unit (MF1), Robert Koch InstituteBerlinGermany
- Data Analytics and Computational Statistics, Hasso-Plattner-Institute, Faculty of Digital Engineering, University of PotsdamPotsdamGermany
| | - Judith A Steen
- F.M. Kirby Neurobiology Center, Boston Children’s HospitalBostonUnited States
- Department of Neurology, Harvard Medical SchoolBostonUnited States
| | - Hanno Steen
- Department of Pathology, Boston Children’s HospitalBostonUnited States
- Department of Pathology, Harvard Medical SchoolBostonUnited States
- Precision Vaccines Program, Boston Children’s HospitalBostonUnited States
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6
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Comparative phosphoproteomic analysis of BR-defective mutant reveals a key role of GhSK13 in regulating cotton fiber development. SCIENCE CHINA-LIFE SCIENCES 2020; 63:1905-1917. [PMID: 32632733 DOI: 10.1007/s11427-020-1728-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 05/12/2020] [Indexed: 02/07/2023]
Abstract
Brassinosteroid (BR), a steroid phytohormone, whose signaling transduction pathways include a series of phosphorylation and dephosphorylation events, and GSK3s are the main negative regulator kinases. BRs have been shown to play vital roles in cotton fiber elongation. However, the underlying mechanism is still elusive. In this study, fibers of a BR-defective mutant Pagoda 1 (pag1), and its corresponding wild-type (ZM24) were selected for a comparative global phosphoproteome analysis at critical developmental time points: fast-growing stage (10 days after pollination (DPA)) and secondary cell wall synthesis stage (20 DPA). Based on the substrate characteristics of GSK3, 900 potential substrates were identified. Their GO and KEGG annotation results suggest that BR functions in fiber development by regulating GhSKs (GSK3s of Gossypium hirsutum L.) involved microtubule cytoskeleton organization, and pathways of glucose, sucrose and lipid metabolism. Further experimental results revealed that among the GhSK members identified, GhSK13 not only plays a role in BR signaling pathway, but also functions in developing fiber by respectively interacting with an AP2-like ethylene-responsive factor GhAP2L, a nuclear transcription factor Gh_DNF_YB19, and a homeodomain zipper member GhHDZ5. Overall, our phosphoproteomic research advances the understanding of fiber development controlled by BR signal pathways especially through GhSKs, and also offers numbers of target proteins for improving cotton fiber quality.
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7
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Hampel H, Lista S, Mango D, Nisticò R, Perry G, Avila J, Hernandez F, Geerts H, Vergallo A. Lithium as a Treatment for Alzheimer’s Disease: The Systems Pharmacology Perspective. J Alzheimers Dis 2019; 69:615-629. [DOI: 10.3233/jad-190197] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Harald Hampel
- Sorbonne University, GRC n° 21, Alzheimer Precision Medicine (APM), AP-HP, Pitié-Salpêtrière Hospital, Boulevard de l’hôpital, F-75013, Paris, France
| | - Simone Lista
- Sorbonne University, GRC n° 21, Alzheimer Precision Medicine (APM), AP-HP, Pitié-Salpêtrière Hospital, Boulevard de l’hôpital, F-75013, Paris, France
- Brain & Spine Institute (ICM), INSERM U 1127, CNRS UMR 7225, Boulevard de l’hôpital, F-75013, Paris, France
- Institute of Memory and Alzheimer’s Disease (IM2A), Department of Neurology, Pitié-Salpêtrière Hospital, AP-HP, Boulevard de l’hôpital, F-75013, Paris, France
| | - Dalila Mango
- Laboratory of Neuropharmacology, European Brain Research Institute, Rita Levi-Montalcini Foundation, Rome, Italy
| | - Robert Nisticò
- Laboratory of Neuropharmacology, European Brain Research Institute, Rita Levi-Montalcini Foundation, Rome, Italy
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - George Perry
- College of Sciences, One UTSA Circle, The University of Texas at San Antonio, San Antonio, TX, USA
| | - Jesus Avila
- Centro de Biologia Molecular “Severo Ochoa”, Consejo Superior de Investigaciones, Cientificas, Universidad Autonoma de Madrid, C/ Nicolas Cabrera, 1. Campus de Cantoblanco, 28049, Madrid, Spain
- Networking Research Center on Neurodegenerative, Diseases (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - Felix Hernandez
- Centro de Biologia Molecular “Severo Ochoa”, Consejo Superior de Investigaciones, Cientificas, Universidad Autonoma de Madrid, C/ Nicolas Cabrera, 1. Campus de Cantoblanco, 28049, Madrid, Spain
- Networking Research Center on Neurodegenerative, Diseases (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - Hugo Geerts
- In silico Biosciences, Computational Neuropharmacology, Berwyn, PA, USA
| | - Andrea Vergallo
- Sorbonne University, GRC n° 21, Alzheimer Precision Medicine (APM), AP-HP, Pitié-Salpêtrière Hospital, Boulevard de l’hôpital, F-75013, Paris, France
- Brain & Spine Institute (ICM), INSERM U 1127, CNRS UMR 7225, Boulevard de l’hôpital, F-75013, Paris, France
- Institute of Memory and Alzheimer’s Disease (IM2A), Department of Neurology, Pitié-Salpêtrière Hospital, AP-HP, Boulevard de l’hôpital, F-75013, Paris, France
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8
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Narumi R, Masuda K, Tomonaga T, Adachi J, Ueda HR, Shimizu Y. Cell-free synthesis of stable isotope-labeled internal standards for targeted quantitative proteomics. Synth Syst Biotechnol 2018; 3:97-104. [PMID: 29900422 PMCID: PMC5995455 DOI: 10.1016/j.synbio.2018.02.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 02/16/2018] [Accepted: 02/18/2018] [Indexed: 01/04/2023] Open
Abstract
High-sensitivity mass spectrometry approaches using selected reaction monitoring (SRM) or multiple reaction monitoring (MRM) methods are powerful tools for targeted quantitative proteomics-based investigation of dynamics in specific biological systems. Both high-sensitivity detection of low-abundance proteins and their quantification using this technique employ stable isotope-labeled peptide internal standards. Currently, there are various ways for preparing standards, including chemical peptide synthesis, cellular protein expression, and cell-free protein or peptide synthesis. Cell-free protein synthesis (CFPS) or in vitro translation (IVT) systems in particular provide high-throughput and low-cost preparation methods, and various cell types and reconstituted forms are now commercially available. Herein, we review the use of such systems for precise and reliable protein quantification.
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Affiliation(s)
- Ryohei Narumi
- Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8, Satio-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Keiko Masuda
- Laboratory for Single Cell Mass Spectrometry, RIKEN Quantitative Biology Center (QBiC), 6-2-3, Furuedai, Suita, Osaka 565-0874, Japan
| | - Takeshi Tomonaga
- Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8, Satio-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Jun Adachi
- Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8, Satio-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Hiroki R. Ueda
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center (QBiC), 6-2-3, Furuedai, Suita, Osaka 565-0874, Japan
| | - Yoshihiro Shimizu
- Laboratory for Single Cell Mass Spectrometry, RIKEN Quantitative Biology Center (QBiC), 6-2-3, Furuedai, Suita, Osaka 565-0874, Japan
- Laboratory for Cell-Free Protein Synthesis, RIKEN Quantitative Biology Center (QBiC), 6-2-3, Furuedai, Suita, Osaka 565-0874, Japan
- Corresponding author. Laboratory for Cell-Free Protein Synthesis, RIKEN Quantitative Biology Center (QBiC), 6-2-3, Furuedai, Suita, Osaka 565-0874, Japan.
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9
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Lee LH, Andraski AB, Pieper B, Higashi H, Sacks FM, Aikawa M, Singh SA. Automation of PRM-dependent D3-Leu tracer enrichment in HDL to study the metabolism of apoA-I, LCAT and other apolipoproteins. Proteomics 2017; 17. [PMID: 27862954 DOI: 10.1002/pmic.201600085] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 10/09/2016] [Accepted: 11/04/2016] [Indexed: 12/22/2022]
Abstract
We developed an automated quantification workflow for PRM-enabled detection of D3-Leu labeled apoA-I in high-density lipoprotein (HDL) isolated from humans. Subjects received a bolus injection of D3-Leu and blood was drawn at eight time points over three days. HDL was isolated and separated into six size fractions for subsequent proteolysis and PRM analysis for the detection of D3-Leu signal from ∼0.03 to 0.6% enrichment. We implemented an intensity-based quantification approach that takes advantage of high-resolution/accurate mass PRM scans to identify the D3-Leu 2HM3 ion from non-specific peaks. Our workflow includes five modules for extracting the targeted PRM peak intensities (XPIs): Peak centroiding, noise removal, fragment ion matching using Δm/z windows, nine intensity quantification options, and validation and visualization outputs. We optimized the XPI workflow using in vitro synthesized and clinical samples of D0/D3-Leu labeled apoA-I. Three subjects' apoA-I enrichment curves in six HDL size fractions, and LCAT, apoA-II and apoE from two size fractions were generated within a few hours. Our PRM strategy and automated quantification workflow will expedite the turnaround of HDL apoA-I metabolism data in clinical studies that aim to understand and treat the mechanisms behind dyslipidemia.
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Affiliation(s)
- Lang Ho Lee
- Center for Interdisciplinary Cardiovascular Sciences, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Allison B Andraski
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Brett Pieper
- Center for Interdisciplinary Cardiovascular Sciences, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Hideyuki Higashi
- Center for Interdisciplinary Cardiovascular Sciences, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Frank M Sacks
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Masanori Aikawa
- Center for Interdisciplinary Cardiovascular Sciences, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Sasha A Singh
- Center for Interdisciplinary Cardiovascular Sciences, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
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10
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Hermida MA, Dinesh Kumar J, Leslie NR. GSK3 and its interactions with the PI3K/AKT/mTOR signalling network. Adv Biol Regul 2017; 65:5-15. [PMID: 28712664 DOI: 10.1016/j.jbior.2017.06.003] [Citation(s) in RCA: 282] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 06/23/2017] [Indexed: 01/01/2023]
Abstract
Glycogen Synthase Kinase-3 (GSK3 or GSK-3) is a promiscuous protein kinase and its phosphorylation of its diverse substrates has major influences on many areas of physiology and pathology, including cellular metabolism, lineage commitment and neuroscience. GSK3 was one of the first identified substrates of the heavily studied oncogenic kinase AKT, phosphorylation by which inhibits GSK3 activity via the formation of an autoinhibitory pseudosubstrate sequence. This has led to investigation of the role of GSK3 inhibition as a key component of the cellular responses to growth factors and insulin, which stimulate the class I PI 3-Kinases and in turn AKT activity and GSK3 phosphorylation. GSK3 has been shown to phosphorylate several upstream and downstream components of the PI3K/AKT/mTOR signalling network, including AKT itself, RICTOR, TSC1 and 2, PTEN and IRS1 and 2, with the potential to apply feedback control within the network. However, it has been clear for some time that functionally distinct, insulated pools of GSK3 exist which are regulated independently, so that for some GSK3 substrates such as β-catenin, phosphorylation by GSK3 is not controlled by input from PI3K and AKT. Instead, as almost all GSK3 substrates require a priming phosphorylated residue to be 4 amino acids C-terminal to the Ser/Thr phosphorylated by GSK3, the predominant form of regulation of the activity of GSK3 often appears to be through control over these priming events, specific to individual substrates. Therefore, a major role of GSK3 can be viewed as an amplifier of the electrostatic effects on protein function which are caused by these priming phosphorylation events. Here we discuss these different aspects to GSK3 regulation and function, and the functions of GSK3 as it integrates with signalling through the PI3K-AKT-mTOR signalling axis.
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Affiliation(s)
- Miguel A Hermida
- Institute of Biological Chemistry, Biophysics and Bioengineering, School of Engineering and Physical Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK
| | - J Dinesh Kumar
- Institute of Biological Chemistry, Biophysics and Bioengineering, School of Engineering and Physical Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK
| | - Nick R Leslie
- Institute of Biological Chemistry, Biophysics and Bioengineering, School of Engineering and Physical Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK.
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11
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Jayaraman D, Richards AL, Westphall MS, Coon JJ, Ané JM. Identification of the phosphorylation targets of symbiotic receptor-like kinases using a high-throughput multiplexed assay for kinase specificity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:1196-1207. [PMID: 28267253 PMCID: PMC5461195 DOI: 10.1111/tpj.13529] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 02/17/2017] [Accepted: 03/01/2017] [Indexed: 05/29/2023]
Abstract
Detecting the phosphorylation substrates of multiple kinases in a single experiment is a challenge, and new techniques are being developed to overcome this challenge. Here, we used a multiplexed assay for kinase specificity (MAKS) to identify the substrates directly and to map the phosphorylation site(s) of plant symbiotic receptor-like kinases. The symbiotic receptor-like kinases nodulation receptor-like kinase (NORK) and lysin motif domain-containing receptor-like kinase 3 (LYK3) are indispensable for the establishment of root nodule symbiosis. Although some interacting proteins have been identified for these symbiotic receptor-like kinases, very little is known about their phosphorylation substrates. Using this high-throughput approach, we identified several other potential phosphorylation targets for both these symbiotic receptor-like kinases. In particular, we also discovered the phosphorylation of LYK3 by NORK itself, which was also confirmed by pairwise kinase assays. Motif analysis of potential targets for these kinases revealed that the acidic motif xxxsDxxx was common to both of them. In summary, this high-throughput technique catalogs the potential phosphorylation substrates of multiple kinases in a single efficient experiment, the biological characterization of which should provide a better understanding of phosphorylation signaling cascade in symbiosis.
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Affiliation(s)
- Dhileepkumar Jayaraman
- Department of Agronomy, 1575 Linden Drive, University of Wisconsin–Madison, WI 53706, USA
| | - Alicia L. Richards
- Department of Chemistry, 1101 University Avenue, University of Wisconsin–Madison, WI 53706, USA
- Genome Center of Wisconsin, University of Wisconsin–Madison, 425 Henry Mall, WI 53706, USA
| | - Michael S. Westphall
- Department of Chemistry, 1101 University Avenue, University of Wisconsin–Madison, WI 53706, USA
- Genome Center of Wisconsin, University of Wisconsin–Madison, 425 Henry Mall, WI 53706, USA
- Department of Biomolecular Chemistry, University of Wisconsin–Madison, 420 Henry Mall, WI 53706, USA
| | - Joshua J. Coon
- Department of Chemistry, 1101 University Avenue, University of Wisconsin–Madison, WI 53706, USA
- Genome Center of Wisconsin, University of Wisconsin–Madison, 425 Henry Mall, WI 53706, USA
- Department of Biomolecular Chemistry, University of Wisconsin–Madison, 420 Henry Mall, WI 53706, USA
| | - Jean-Michel Ané
- Department of Agronomy, 1575 Linden Drive, University of Wisconsin–Madison, WI 53706, USA
- Department of Bacteriology, 1550 Linden Drive, University of Wisconsin–Madison, WI 53706, USA
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12
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JNK Signaling: Regulation and Functions Based on Complex Protein-Protein Partnerships. Microbiol Mol Biol Rev 2016; 80:793-835. [PMID: 27466283 DOI: 10.1128/mmbr.00043-14] [Citation(s) in RCA: 321] [Impact Index Per Article: 40.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The c-Jun N-terminal kinases (JNKs), as members of the mitogen-activated protein kinase (MAPK) family, mediate eukaryotic cell responses to a wide range of abiotic and biotic stress insults. JNKs also regulate important physiological processes, including neuronal functions, immunological actions, and embryonic development, via their impact on gene expression, cytoskeletal protein dynamics, and cell death/survival pathways. Although the JNK pathway has been under study for >20 years, its complexity is still perplexing, with multiple protein partners of JNKs underlying the diversity of actions. Here we review the current knowledge of JNK structure and isoforms as well as the partnerships of JNKs with a range of intracellular proteins. Many of these proteins are direct substrates of the JNKs. We analyzed almost 100 of these target proteins in detail within a framework of their classification based on their regulation by JNKs. Examples of these JNK substrates include a diverse assortment of nuclear transcription factors (Jun, ATF2, Myc, Elk1), cytoplasmic proteins involved in cytoskeleton regulation (DCX, Tau, WDR62) or vesicular transport (JIP1, JIP3), cell membrane receptors (BMPR2), and mitochondrial proteins (Mcl1, Bim). In addition, because upstream signaling components impact JNK activity, we critically assessed the involvement of signaling scaffolds and the roles of feedback mechanisms in the JNK pathway. Despite a clarification of many regulatory events in JNK-dependent signaling during the past decade, many other structural and mechanistic insights are just beginning to be revealed. These advances open new opportunities to understand the role of JNK signaling in diverse physiological and pathophysiological states.
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13
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Goettsch C, Hutcheson JD, Aikawa M, Iwata H, Pham T, Nykjaer A, Kjolby M, Rogers M, Michel T, Shibasaki M, Hagita S, Kramann R, Rader DJ, Libby P, Singh SA, Aikawa E. Sortilin mediates vascular calcification via its recruitment into extracellular vesicles. J Clin Invest 2016; 126:1323-36. [PMID: 26950419 DOI: 10.1172/jci80851] [Citation(s) in RCA: 169] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 01/21/2016] [Indexed: 12/23/2022] Open
Abstract
Vascular calcification is a common feature of major cardiovascular diseases. Extracellular vesicles participate in the formation of microcalcifications that are implicated in atherosclerotic plaque rupture; however, the mechanisms that regulate formation of calcifying extracellular vesicles remain obscure. Here, we have demonstrated that sortilin is a key regulator of smooth muscle cell (SMC) calcification via its recruitment to extracellular vesicles. Sortilin localized to calcifying vessels in human and mouse atheromata and participated in formation of microcalcifications in SMC culture. Sortilin regulated the loading of the calcification protein tissue nonspecific alkaline phosphatase (TNAP) into extracellular vesicles, thereby conferring its calcification potential. Furthermore, SMC calcification required Rab11-dependent trafficking and FAM20C/casein kinase 2-dependent C-terminal phosphorylation of sortilin. In a murine model, Sort1-deficiency reduced arterial calcification but did not affect bone mineralization. Additionally, transfer of sortilin-deficient BM cells to irradiated atherosclerotic mice did not affect vascular calcification, indicating a primary role of SMC-derived sortilin. Together, the results of this study identify sortilin phosphorylation as a potential therapeutic target for ectopic calcification/microcalcification and may clarify the mechanism that underlies the genetic association between the SORT1 gene locus and coronary artery calcification.
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MESH Headings
- Adaptor Proteins, Vesicular Transport/genetics
- Adaptor Proteins, Vesicular Transport/metabolism
- Alkaline Phosphatase/biosynthesis
- Alkaline Phosphatase/genetics
- Animals
- Calcium-Binding Proteins/genetics
- Calcium-Binding Proteins/metabolism
- Carrier Proteins/biosynthesis
- Carrier Proteins/genetics
- Casein Kinase I/genetics
- Casein Kinase I/metabolism
- Casein Kinase II/metabolism
- Cell-Derived Microparticles/genetics
- Cell-Derived Microparticles/metabolism
- Cells, Cultured
- Extracellular Matrix Proteins/genetics
- Extracellular Matrix Proteins/metabolism
- Humans
- Mice
- Mice, Knockout
- Muscle, Smooth, Vascular/metabolism
- Muscle, Smooth, Vascular/pathology
- Myocytes, Smooth Muscle/metabolism
- Myocytes, Smooth Muscle/pathology
- Phosphorylation
- Plaque, Atherosclerotic/metabolism
- Plaque, Atherosclerotic/pathology
- Protein Transport
- Vascular Calcification/genetics
- Vascular Calcification/metabolism
- Vascular Calcification/pathology
- rab GTP-Binding Proteins/genetics
- rab GTP-Binding Proteins/metabolism
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14
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Beurel E, Grieco SF, Jope RS. Glycogen synthase kinase-3 (GSK3): regulation, actions, and diseases. Pharmacol Ther 2014; 148:114-31. [PMID: 25435019 DOI: 10.1016/j.pharmthera.2014.11.016] [Citation(s) in RCA: 1106] [Impact Index Per Article: 110.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 11/18/2014] [Indexed: 12/23/2022]
Abstract
Glycogen synthase kinase-3 (GSK3) may be the busiest kinase in most cells, with over 100 known substrates to deal with. How does GSK3 maintain control to selectively phosphorylate each substrate, and why was it evolutionarily favorable for GSK3 to assume such a large responsibility? GSK3 must be particularly adaptable for incorporating new substrates into its repertoire, and we discuss the distinct properties of GSK3 that may contribute to its capacity to fulfill its roles in multiple signaling pathways. The mechanisms regulating GSK3 (predominantly post-translational modifications, substrate priming, cellular trafficking, protein complexes) have been reviewed previously, so here we focus on newly identified complexities in these mechanisms, how each of these regulatory mechanism contributes to the ability of GSK3 to select which substrates to phosphorylate, and how these mechanisms may have contributed to its adaptability as new substrates evolved. The current understanding of the mechanisms regulating GSK3 is reviewed, as are emerging topics in the actions of GSK3, particularly its interactions with receptors and receptor-coupled signal transduction events, and differential actions and regulation of the two GSK3 isoforms, GSK3α and GSK3β. Another remarkable characteristic of GSK3 is its involvement in many prevalent disorders, including psychiatric and neurological diseases, inflammatory diseases, cancer, and others. We address the feasibility of targeting GSK3 therapeutically, and provide an update of its involvement in the etiology and treatment of several disorders.
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Affiliation(s)
- Eleonore Beurel
- Department of Psychiatry and Behavioral Sciences, Miller School of Medicine, University of Miami, Miami, FL 33136, United States; Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, United States
| | - Steven F Grieco
- Department of Psychiatry and Behavioral Sciences, Miller School of Medicine, University of Miami, Miami, FL 33136, United States; Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, United States
| | - Richard S Jope
- Department of Psychiatry and Behavioral Sciences, Miller School of Medicine, University of Miami, Miami, FL 33136, United States; Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, United States.
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15
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Tepper K, Biernat J, Kumar S, Wegmann S, Timm T, Hübschmann S, Redecke L, Mandelkow EM, Müller DJ, Mandelkow E. Oligomer formation of tau protein hyperphosphorylated in cells. J Biol Chem 2014; 289:34389-407. [PMID: 25339173 PMCID: PMC4256367 DOI: 10.1074/jbc.m114.611368] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Abnormal phosphorylation (“hyperphosphorylation”) and aggregation of Tau protein are hallmarks of Alzheimer disease and other tauopathies, but their causative connection is still a matter of debate. Tau with Alzheimer-like phosphorylation is also present in hibernating animals, mitosis, or during embryonic development, without leading to pathophysiology or neurodegeneration. Thus, the role of phosphorylation and the distinction between physiological and pathological phosphorylation needs to be further refined. So far, the systematic investigation of highly phosphorylated Tau was difficult because a reliable method of preparing reproducible quantities was not available. Here, we generated full-length Tau (2N4R) in Sf9 cells in a well defined phosphorylation state containing up to ∼20 phosphates as judged by mass spectrometry and Western blotting with phospho-specific antibodies. Despite the high concentration in living Sf9 cells (estimated ∼230 μm) and high phosphorylation, the protein was not aggregated. However, after purification, the highly phosphorylated protein readily formed oligomers, whereas fibrils were observed only rarely. Exposure of mature primary neuronal cultures to oligomeric phospho-Tau caused reduction of spine density on dendrites but did not change the overall cell viability.
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Affiliation(s)
- Katharina Tepper
- From the DZNE, German Center for Neurodegenerative Diseases, 53175 Bonn, Germany, the CAESAR Research Center, 53175 Bonn, Germany
| | - Jacek Biernat
- From the DZNE, German Center for Neurodegenerative Diseases, 53175 Bonn, Germany, the CAESAR Research Center, 53175 Bonn, Germany
| | - Satish Kumar
- From the DZNE, German Center for Neurodegenerative Diseases, 53175 Bonn, Germany, the CAESAR Research Center, 53175 Bonn, Germany
| | - Susanne Wegmann
- the Department of Biosystems Science and Engineering, ETHZ, 4058 Basel, Switzerland
| | - Thomas Timm
- the Institute of Biochemistry, Faculty of Medicine, Justus-Liebig-University, 35390 Giessen, Germany, and
| | - Sabrina Hübschmann
- From the DZNE, German Center for Neurodegenerative Diseases, 53175 Bonn, Germany, the CAESAR Research Center, 53175 Bonn, Germany
| | - Lars Redecke
- the Joint Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg and University of Lübeck, ℅DESY, 22603 Hamburg, Germany
| | - Eva-Maria Mandelkow
- From the DZNE, German Center for Neurodegenerative Diseases, 53175 Bonn, Germany, the CAESAR Research Center, 53175 Bonn, Germany
| | - Daniel J Müller
- the Department of Biosystems Science and Engineering, ETHZ, 4058 Basel, Switzerland
| | - Eckhard Mandelkow
- From the DZNE, German Center for Neurodegenerative Diseases, 53175 Bonn, Germany, the CAESAR Research Center, 53175 Bonn, Germany,
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16
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Harbers M. Wheat germ systems for cell-free protein expression. FEBS Lett 2014; 588:2762-73. [PMID: 24931374 DOI: 10.1016/j.febslet.2014.05.061] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 05/25/2014] [Accepted: 05/26/2014] [Indexed: 10/25/2022]
Abstract
Cell-free protein expression plays an important role in biochemical research. However, only recent developments led to new methods to rapidly synthesize preparative amounts of protein that make cell-free protein expression an attractive alternative to cell-based methods. In particular the wheat germ system provides the highest translation efficiency among eukaryotic cell-free protein expression approaches and has a very high success rate for the expression of soluble proteins of good quality. As an open in vitro method, the wheat germ system is a preferable choice for many applications in protein research including options for protein labeling and the expression of difficult-to-express proteins like membrane proteins and multiple protein complexes. Here I describe wheat germ cell-free protein expression systems and give examples how they have been used in genome-wide expression studies, preparation of labeled proteins for structural genomics and protein mass spectroscopy, automated protein synthesis, and screening of enzymatic activities. Future directions for the use of cell-free expression methods are discussed.
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Affiliation(s)
- Matthias Harbers
- RIKEN Center for Life Science Technologies, Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa 230-0045, Japan; CellFree Sciences Co., Ltd., 75-1, Ono-cho, Leading Venture Plaza 201, Tsurumi-ku, Yokohama, Kanagawa 230-0046, Japan.
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17
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Singh SA, Winter D, Kirchner M, Chauhan R, Ahmed S, Ozlu N, Tzur A, Steen JA, Steen H. Co-regulation proteomics reveals substrates and mechanisms of APC/C-dependent degradation. EMBO J 2014; 33:385-99. [PMID: 24510915 DOI: 10.1002/embj.201385876] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Using multiplexed quantitative proteomics, we analyzed cell cycle-dependent changes of the human proteome. We identified >4,400 proteins, each with a six-point abundance profile across the cell cycle. Hypothesizing that proteins with similar abundance profiles are co-regulated, we clustered the proteins with abundance profiles most similar to known Anaphase-Promoting Complex/Cyclosome (APC/C) substrates to identify additional putative APC/C substrates. This protein profile similarity screening (PPSS) analysis resulted in a shortlist enriched in kinases and kinesins. Biochemical studies on the kinesins confirmed KIFC1, KIF18A, KIF2C, and KIF4A as APC/C substrates. Furthermore, we showed that the APC/C(CDH1)-dependent degradation of KIFC1 regulates the bipolar spindle formation and proper cell division. A targeted quantitative proteomics experiment showed that KIFC1 degradation is modulated by a stabilizing CDK1-dependent phosphorylation site within the degradation motif of KIFC1. The regulation of KIFC1 (de-)phosphorylation and degradation provides insights into the fidelity and proper ordering of substrate degradation by the APC/C during mitosis.
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Affiliation(s)
- Sasha A Singh
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
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18
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Brumbaugh J, Russell JD, Yu P, Westphall MS, Coon JJ, Thomson JA. NANOG is multiply phosphorylated and directly modified by ERK2 and CDK1 in vitro. Stem Cell Reports 2014; 2:18-25. [PMID: 24678451 PMCID: PMC3966117 DOI: 10.1016/j.stemcr.2013.12.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 12/04/2013] [Accepted: 12/05/2013] [Indexed: 11/28/2022] Open
Abstract
NANOG is a divergent homeobox protein and a core component of the transcriptional circuitry that sustains pluripotency and self-renewal. Although NANOG has been extensively studied on the transcriptional level, little is known regarding its posttranslational regulation, likely due to its low abundance and challenging physical properties. Here, we identify eleven phosphorylation sites on endogenous human NANOG, nine of which mapped to single amino acids. To screen for the signaling molecules that impart these modifications, we developed the multiplexed assay for kinase specificity (MAKS). MAKS simultaneously tests activity for up to ten kinases while directly identifying the substrate and exact site of phosphorylation. Using MAKS, we discovered site-specific phosphorylation by ERK2 and CDK1/CyclinA2, providing a putative link between key signaling pathways and NANOG.
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Affiliation(s)
- Justin Brumbaugh
- Stem Cells and Regenerative Medicine, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Jason D Russell
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Pengzhi Yu
- Stem Cells and Regenerative Medicine, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Michael S Westphall
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA ; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA ; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - James A Thomson
- Stem Cells and Regenerative Medicine, Morgridge Institute for Research, Madison, WI 53715, USA ; Department of Cell & Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA ; Department of Molecular, Cellular & Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
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19
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Villanueva J, Carrascal M, Abian J. Isotope dilution mass spectrometry for absolute quantification in proteomics: Concepts and strategies. J Proteomics 2014; 96:184-99. [DOI: 10.1016/j.jprot.2013.11.004] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 11/01/2013] [Indexed: 12/25/2022]
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20
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Theillet FX, Rose HM, Liokatis S, Binolfi A, Thongwichian R, Stuiver M, Selenko P. Site-specific NMR mapping and time-resolved monitoring of serine and threonine phosphorylation in reconstituted kinase reactions and mammalian cell extracts. Nat Protoc 2013; 8:1416-32. [PMID: 23807285 DOI: 10.1038/nprot.2013.083] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We outline NMR protocols for site-specific mapping and time-resolved monitoring of protein phosphorylation reactions using purified kinases and mammalian cell extracts. These approaches are particularly amenable to intrinsically disordered proteins and unfolded, regulatory protein domains. We present examples for the ¹⁵N isotope-labeled N-terminal transactivation domain of human p53, which is either sequentially reacted with recombinant enzymes or directly added to mammalian cell extracts and phosphorylated by endogenous kinases. Phosphorylation reactions with purified enzymes are set up in minutes, whereas NMR samples in cell extracts are prepared within 1 h. Time-resolved NMR measurements are performed over minutes to hours depending on the activities of the probed kinases. Phosphorylation is quantitatively monitored with consecutive 2D ¹H-¹⁵N band-selective optimized-flip-angle short-transient (SOFAST)-heteronuclear multiple-quantum (HMQC) NMR experiments, which provide atomic-resolution insights into the phosphorylation levels of individual substrate residues and time-dependent changes thereof, thereby offering unique advantages over western blotting and mass spectrometry.
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Affiliation(s)
- Francois-Xavier Theillet
- In-Cell NMR Laboratory, Department of NMR-supported Structural Biology, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Berlin, Germany
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21
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Hennrich ML, Marino F, Groenewold V, Kops GJPL, Mohammed S, Heck AJR. Universal quantitative kinase assay based on diagonal SCX chromatography and stable isotope dimethyl labeling provides high-definition kinase consensus motifs for PKA and human Mps1. J Proteome Res 2013; 12:2214-24. [PMID: 23510141 DOI: 10.1021/pr400074f] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
In order to understand cellular signaling, a clear understanding of kinase-substrate relationships is essential. Some of these relationships are defined by consensus recognition motifs present in substrates making them amendable for phosphorylation by designated kinases. Here, we explore a method that is based on two sequential steps of strong cation exchange chromatography combined with differential stable isotope labeling, to define kinase consensus motifs with high accuracy. We demonstrate the value of our method by evaluating the motifs of two very distinct kinases: cAMP regulated protein kinase A (PKA) and human monopolar spindle 1 (Mps1) kinase, also known as TTK. PKA is a well-studied basophilic kinase with a relatively well-defined motif and numerous known substrates in vitro and in vivo. Mps1, a kinase involved in chromosome segregation, has been less well characterized. Its substrate specificity is unclear and here we show that Mps1 is an acidophilic kinase with a striking tendency for phosphorylation of threonines. The final outcomes of our work are high-definition kinase consensus motifs for PKA and Mps1. Our generic method, which makes use of proteolytic cell lysates as a source for peptide-substrate libraries, can be implemented for any kinase present in the kinome.
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Affiliation(s)
- Marco L Hennrich
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands
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22
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Rose HM, Stuiver M, Thongwichian R, Theillet FX, Feller SM, Selenko P. Quantitative NMR analysis of Erk activity and inhibition by U0126 in a panel of patient-derived colorectal cancer cell lines. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1396-401. [PMID: 23360766 DOI: 10.1016/j.bbapap.2013.01.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 01/11/2013] [Accepted: 01/18/2013] [Indexed: 01/01/2023]
Abstract
We comparatively analyzed the basal activity of extra-cellular signal-regulated kinase (Erk1/2) in lysates of 10 human colorectal cancer cell lines by semi-quantitative Western blotting and time-resolved NMR spectroscopy. Both methods revealed heterogeneous levels of endogenous Erk1/2 activities in a highly consistent manner. Upon treatment with U0126, an inhibitor of mitogen-activated protein kinase kinase (MEK) acting upstream of Erk1/2, Western-blotting and NMR congruently reported specific modulations of cellular phospho-Erk levels that translated into reduced kinase activities. Results obtained in this study highlight the complementary nature of antibody- and NMR-based phospho-detection techniques. They further exemplify the usefulness of time-resolved NMR measurements in providing fast and quantitative readouts of kinase activities and kinase inhibitor efficacies in native cellular environments. This article is part of a Special Issue entitled: Inhibitors of Protein Kinases (2012).
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Affiliation(s)
- Honor May Rose
- In-Cell NMR Laboratory, Department of NMR-supported Structural Biology, Leibniz Institute of Molecular Pharmacology FMP Berlin, Robert-Rössle Strasse 10, 13125 Berlin, Germany
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23
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Abstract
![]()
Recent advances in peptide-based (bottom-up) quantitative
proteomics
and bioinformatics have opened unprecedented opportunities for extensive
investigation of cellular proteomes and their dynamics. Here we discuss
two approaches currently used to investigate the global dynamics of
phosphorylation based on the isolation of phosphorylated proteins
or peptides. We evaluate the accuracy of these methodologies to grasp
the global dynamics of phosphorylation, and we raise awareness on
ambiguities inherent to these analyses. We conclude that further development
of targeted approaches should prevent inaccurate conclusions about
the nature of biological regulations and in particular kinase-substrate
networks.
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Affiliation(s)
- Mogjiborahman Salek
- T cell Signaling Laboratory, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, United Kingdom.
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24
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Zhang X, Abreu JG, Yokota C, MacDonald BT, Singh S, Coburn KLA, Cheong SM, Zhang MM, Ye QZ, Hang HC, Steen H, He X. Tiki1 is required for head formation via Wnt cleavage-oxidation and inactivation. Cell 2012; 149:1565-77. [PMID: 22726442 DOI: 10.1016/j.cell.2012.04.039] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2011] [Revised: 02/17/2012] [Accepted: 04/09/2012] [Indexed: 10/28/2022]
Abstract
Secreted Wnt morphogens are signaling molecules essential for embryogenesis, pathogenesis, and regeneration and require distinct modifications for secretion, gradient formation, and activity. Whether Wnt proteins can be posttranslationally inactivated during development and homeostasis is unknown. Here we identify, through functional cDNA screening, a transmembrane protein Tiki1 that is expressed specifically in the dorsal Spemann-Mangold Organizer and is required for anterior development during Xenopus embryogenesis. Tiki1 antagonizes Wnt function in embryos and human cells via a TIKI homology domain that is conserved from bacteria to mammals and acts likely as a protease to cleave eight amino-terminal residues of a Wnt protein, resulting in oxidized Wnt oligomers that exhibit normal secretion but minimized receptor-binding capability. Our findings identify a Wnt-specific protease that controls head formation, reveal a mechanism for morphogen inactivation through proteolysis-induced oxidation-oligomerization, and suggest a role of the Wnt amino terminus in evasion of oxidizing inactivation. TIKI proteins may represent potential therapeutic targets.
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Affiliation(s)
- Xinjun Zhang
- The F. M. Kirby Neurobiology Center, Boston Children's Hospital, Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
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