1
|
Rubio FJ, Olivares DE, Dunn C, Zhang S, Hilaire EM, Henry A, Mejias-Aponte C, Nogueras-Ortiz CJ, Selvam PV, Cruz FC, Madangopal R, Morales M, Hope BT. Flow Cytometry of Synaptoneurosomes (FCS) Reveals Increased Ribosomal S6 and Calcineurin Proteins in Activated Medial Prefrontal Cortex to Nucleus Accumbens Synapses. J Neurosci 2023; 43:4217-4233. [PMID: 37160369 PMCID: PMC10255002 DOI: 10.1523/jneurosci.0927-22.2023] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 04/11/2023] [Accepted: 04/14/2023] [Indexed: 05/11/2023] Open
Abstract
Learning and behavior activate cue-specific patterns of sparsely distributed cells and synapses called ensembles that undergo memory-encoding engram alterations. While Fos is often used to label selectively activated cell bodies and identify neuronal ensembles, there is no comparable endogenous marker to label activated synapses and identify synaptic ensembles. For the purpose of identifying candidate synaptic activity markers, we optimized a flow cytometry of synaptoneurosome (FCS) procedure for assessing protein alterations in activated synapses from male and female rats. After injecting yellow fluorescent protein (YFP)-expressing adeno-associated virus into medial prefrontal cortex (mPFC) to label terminals in nucleus accumbens (NAc) of rats, we injected 20 mg/kg cocaine in a novel context (cocaine+novelty) to activate synapses, and prepared NAc synaptoneurosomes 0-60 min following injections. For FCS, we used commercially available antibodies to label presynaptic and postsynaptic markers synaptophysin and PSD-95 as well as candidate markers of synaptic activity [activity-regulated cytoskeleton protein (Arc), CaMKII and phospho-CaMKII, ribosomal protein S6 (S6) and phospho-S6, and calcineurin and phospho-calcineurin] in YFP-labeled synaptoneurosomes. Cocaine+novelty increased the percentage of S6-positive synaptoneurosomes at 5-60 min and calcineurin-positive synaptoneurosomes at 5-10 min. Electron microscopy verified that S6 and calcineurin levels in synaptoneurosomes were increased 10 min after cocaine+novelty. Pretreatment with the anesthetic chloral hydrate blocked cocaine+novelty-induced S6 and calcineurin increases in synaptoneurosomes, and novel context exposure alone (without cocaine) increased S6, both of which indicate that these increases were due to neural activity per se. Overall, FCS can be used to study protein alterations in activated synapses coming from specifically labeled mPFC projections to NAc.SIGNIFICANCE STATEMENT Memories are formed during learning and are stored in the brain by long-lasting molecular and cellular alterations called engrams formed within specific patterns of cue-activated neurons called neuronal ensembles. While Fos has been used to identify activated ensemble neurons and the engrams within them, we have not had a similar marker for activated synapses that can be used to identify synaptic engrams. Here we developed a procedure for high-throughput in-line analysis of flow cytometry of synaptoneurosome (FCS) and found that ribosomal S6 protein and calcineurin were increased in activated mPFC-NAc synapses. FCS can be used to study protein alterations in activated synapses within specifically labeled circuits.
Collapse
Affiliation(s)
- F Javier Rubio
- Neuronal Ensembles in Addiction Section, Behavioral Neuroscience Research Branch, Intramural Research Program/National Institute on Drug Abuse/National Institutes of Health, Baltimore, Maryland 21224
| | - Daniel E Olivares
- Neuronal Ensembles in Addiction Section, Behavioral Neuroscience Research Branch, Intramural Research Program/National Institute on Drug Abuse/National Institutes of Health, Baltimore, Maryland 21224
| | - Christopher Dunn
- Flow Cytometry Unit, Intramural Research Program/National Institute on Aging/National Institutes of Health, Baltimore, Maryland 21224
| | - Shiliang Zhang
- Confocal and Electron Microscopy Core, Intramural Research Program/National Institute on Drug Abuse/National Institutes of Health, Baltimore, Maryland 21224
| | - Elias M Hilaire
- Neuronal Ensembles in Addiction Section, Behavioral Neuroscience Research Branch, Intramural Research Program/National Institute on Drug Abuse/National Institutes of Health, Baltimore, Maryland 21224
| | - Akeem Henry
- Neuronal Ensembles in Addiction Section, Behavioral Neuroscience Research Branch, Intramural Research Program/National Institute on Drug Abuse/National Institutes of Health, Baltimore, Maryland 21224
| | - Carlos Mejias-Aponte
- Confocal and Electron Microscopy Core, Intramural Research Program/National Institute on Drug Abuse/National Institutes of Health, Baltimore, Maryland 21224
| | - Carlos J Nogueras-Ortiz
- Laboratory of Clinical Investigation, Intramural Research Program, National Institute on Aging, NIH, Baltimore, Maryland 21224
| | - Pooja V Selvam
- Neuronal Ensembles in Addiction Section, Behavioral Neuroscience Research Branch, Intramural Research Program/National Institute on Drug Abuse/National Institutes of Health, Baltimore, Maryland 21224
| | - Fabio C Cruz
- Neuronal Ensembles in Addiction Section, Behavioral Neuroscience Research Branch, Intramural Research Program/National Institute on Drug Abuse/National Institutes of Health, Baltimore, Maryland 21224
- Department of Pharmacology, Escola Paulista de Medicina, Universidade Federal de São Paulo, CEP 04023-062, São Paulo, Brazil
| | - Rajtarun Madangopal
- Neuronal Ensembles in Addiction Section, Behavioral Neuroscience Research Branch, Intramural Research Program/National Institute on Drug Abuse/National Institutes of Health, Baltimore, Maryland 21224
| | - Marisela Morales
- Neuronal Networks Section, Integrative Neuroscience Research Branch, Intramural Research Program/National Institute on Drug Abuse/National Institutes of Health, Baltimore, Maryland 21224
| | - Bruce T Hope
- Neuronal Ensembles in Addiction Section, Behavioral Neuroscience Research Branch, Intramural Research Program/National Institute on Drug Abuse/National Institutes of Health, Baltimore, Maryland 21224
| |
Collapse
|
2
|
Butt E, Howard CM, Raman D. LASP1 in Cellular Signaling and Gene Expression: More than Just a Cytoskeletal Regulator. Cells 2022; 11:cells11233817. [PMID: 36497077 PMCID: PMC9741313 DOI: 10.3390/cells11233817] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/24/2022] [Accepted: 11/24/2022] [Indexed: 11/30/2022] Open
Abstract
LIM and SH3 protein 1 was originally identified as a structural cytoskeletal protein with scaffolding function. However, recent data suggest additional roles in cell signaling and gene expression, especially in tumor cells. These novel functions are primarily regulated by the site-specific phosphorylation of LASP1. This review will focus on specific phosphorylation-dependent interaction between LASP1 and cellular proteins that orchestrate primary tumor progression and metastasis. More specifically, we will describe the role of LASP1 in chemokine receptor, and PI3K/AKT signaling. We outline the nuclear role for LASP1 in terms of epigenetics and transcriptional regulation and modulation of oncogenic mRNA translation. Finally, newly identified roles for the cytoskeletal function of LASP1 next to its known canonical F-actin binding properties are included.
Collapse
Affiliation(s)
- Elke Butt
- Institute of Experimental Biochemistry II, University Clinic Wuerzburg, 97080 Wuerzburg, Germany
- Correspondence: (E.B.); (D.R.); Tel.: +49-(0)931-201-48333 (E.B.); +1-419-383-4616 (D.R.)
| | - Cory M. Howard
- Department of Cell and Cancer Biology, College of Medicine and Life Sciences, University of Toledo, MS 1010, Toledo, OH 43614, USA
| | - Dayanidhi Raman
- Department of Cell and Cancer Biology, College of Medicine and Life Sciences, University of Toledo, MS 1010, Toledo, OH 43614, USA
- Correspondence: (E.B.); (D.R.); Tel.: +49-(0)931-201-48333 (E.B.); +1-419-383-4616 (D.R.)
| |
Collapse
|
3
|
van Gelder CAGH, Altelaar M. Neuroproteomics of the Synapse: Subcellular Quantification of Protein Networks and Signaling Dynamics. Mol Cell Proteomics 2021; 20:100087. [PMID: 33933679 PMCID: PMC8167277 DOI: 10.1016/j.mcpro.2021.100087] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/21/2021] [Accepted: 04/26/2021] [Indexed: 01/21/2023] Open
Abstract
One of the most fascinating features of the brain is its ability to adapt to its surroundings. Synaptic plasticity, the dynamic mechanism of functional and structural alterations in synaptic strength, is essential for brain functioning and underlies a variety of processes such as learning and memory. Although the molecular mechanisms underlying such rapid plasticity are not fully understood, a consensus exists on the important role of proteins. The study of these neuronal proteins using neuroproteomics has increased rapidly in the last decades, and advancements in MS-based proteomics have broadened our understanding of neuroplasticity exponentially. In this review, we discuss the trends in MS-based neuroproteomics for the study of synaptic protein-protein interactions and protein signaling dynamics, with a focus on sample types, different labeling and enrichment approaches, and data analysis and interpretation. We highlight studies from the last 5 years, with a focus on synapse structure, composition, functioning, or signaling and finally discuss some recent developments that could further advance the field of neuroproteomics.
Collapse
Affiliation(s)
- Charlotte A G H van Gelder
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Maarten Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands.
| |
Collapse
|
4
|
Lleó A, Núñez-Llaves R, Alcolea D, Chiva C, Balateu-Paños D, Colom-Cadena M, Gomez-Giro G, Muñoz L, Querol-Vilaseca M, Pegueroles J, Rami L, Lladó A, Molinuevo JL, Tainta M, Clarimón J, Spires-Jones T, Blesa R, Fortea J, Martínez-Lage P, Sánchez-Valle R, Sabidó E, Bayés À, Belbin O. Changes in Synaptic Proteins Precede Neurodegeneration Markers in Preclinical Alzheimer's Disease Cerebrospinal Fluid. Mol Cell Proteomics 2019; 18:546-560. [PMID: 30606734 PMCID: PMC6398205 DOI: 10.1074/mcp.ra118.001290] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Indexed: 01/08/2023] Open
Abstract
A biomarker of synapse loss, an early event in Alzheimer's disease (AD) pathophysiology that precedes neuronal death and symptom onset, would be a much-needed prognostic biomarker. With direct access to the brain interstitial fluid, the cerebrospinal fluid (CSF) is a potential source of synapse-derived proteins. In this study, we aimed to identify and validate novel CSF biomarkers of synapse loss in AD. Discovery: Combining shotgun proteomics of the CSF with an exhaustive search of the literature and public databases, we identified 251 synaptic proteins, from which we selected 22 for further study. Verification: Twelve proteins were discarded because of poor detection by Selected Reaction Monitoring (SRM). We confirmed the specific expression of 9 of the remaining proteins (Calsynytenin-1, GluR2, GluR4, Neurexin-2A, Neurexin-3A, Neuroligin-2, Syntaxin-1B, Thy-1, Vamp-2) at the human synapse using Array Tomography microscopy and biochemical fractionation methods. Exploration: Using SRM, we monitored these 9 synaptic proteins (20 peptides) in a cohort of CSF from cognitively normal controls and subjects in the pre-clinical and clinical AD stages (n = 80). Compared with controls, peptides from 8 proteins were elevated 1.3 to 1.6-fold (p < 0.04) in prodromal AD patients. Validation: Elevated levels of a GluR4 peptide at the prodromal stage were replicated (1.3-fold, p = 0.04) in an independent cohort (n = 60). Moreover, 7 proteins were reduced at preclinical stage 1 (0.6 to 0.8-fold, p < 0.04), a finding that was replicated (0.7 to 0.8-fold, p < 0.05) for 6 proteins in a third cohort (n = 38). In a cross-cohort meta-analysis, 6 synaptic proteins (Calsyntenin-1, GluR4, Neurexin-2A, Neurexin-3A, Syntaxin-1B and Thy-1) were reduced 0.8-fold (p < 0.05) in preclinical AD, changes that precede clinical symptoms and CSF markers of neurodegeneration. Therefore, these proteins could have clinical value for assessing disease progression, especially in preclinical stages of AD.
Collapse
Affiliation(s)
- Alberto Lleó
- From the ‡Memory Unit, Neurology Department, Hospital de la Santa Creu i Sant Pau, 08025 Barcelona, Spain;
- §Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain
| | - Raúl Núñez-Llaves
- §Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain
- ¶Biomedical Research Institute Sant Pau (IIB Sant Pau), 08025Barcelona, Spain
| | - Daniel Alcolea
- From the ‡Memory Unit, Neurology Department, Hospital de la Santa Creu i Sant Pau, 08025 Barcelona, Spain
- §Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain
| | - Cristina Chiva
- ‖Proteomics Unit, Center for Genomics Regulation, Barcelona Institute of Science and Technology, 08003 Barcelona
- **University Pompeu Fabra, 08003 Barcelona
| | | | - Martí Colom-Cadena
- §Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain
- ¶Biomedical Research Institute Sant Pau (IIB Sant Pau), 08025Barcelona, Spain
| | - Gemma Gomez-Giro
- ¶Biomedical Research Institute Sant Pau (IIB Sant Pau), 08025Barcelona, Spain
| | - Laia Muñoz
- §Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain
- ¶Biomedical Research Institute Sant Pau (IIB Sant Pau), 08025Barcelona, Spain
| | - Marta Querol-Vilaseca
- §Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain
- ¶Biomedical Research Institute Sant Pau (IIB Sant Pau), 08025Barcelona, Spain
| | - Jordi Pegueroles
- §Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain
- ¶Biomedical Research Institute Sant Pau (IIB Sant Pau), 08025Barcelona, Spain
| | - Lorena Rami
- ‡‡Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Department, Hospital Clínic-Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS), 08015 Barcelona, Spain
| | - Albert Lladó
- ‡‡Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Department, Hospital Clínic-Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS), 08015 Barcelona, Spain
| | - José L Molinuevo
- ‡‡Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Department, Hospital Clínic-Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS), 08015 Barcelona, Spain
| | - Mikel Tainta
- §§Department of Neurology, Center for Research and Advanced Therapies, CITA-Alzheimer Foundation, 20009 San Sebastian, Spain
- ¶¶Servicio de Neurologia, Organización Sanitaria Integrada Goierri-Alto Urola, Osakidetza, Zumárraga, España
| | - Jordi Clarimón
- §Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain
- ¶Biomedical Research Institute Sant Pau (IIB Sant Pau), 08025Barcelona, Spain
| | - Tara Spires-Jones
- ‖‖Centre for Discovery Brain Sciences and UK Dementia Research Institute, University of Edinburgh EH8 9JZ, UK
| | - Rafael Blesa
- From the ‡Memory Unit, Neurology Department, Hospital de la Santa Creu i Sant Pau, 08025 Barcelona, Spain
- §Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain
| | - Juan Fortea
- From the ‡Memory Unit, Neurology Department, Hospital de la Santa Creu i Sant Pau, 08025 Barcelona, Spain
- §Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain
| | - Pablo Martínez-Lage
- §§Department of Neurology, Center for Research and Advanced Therapies, CITA-Alzheimer Foundation, 20009 San Sebastian, Spain
| | - Raquel Sánchez-Valle
- ‡‡Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Department, Hospital Clínic-Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS), 08015 Barcelona, Spain
| | - Eduard Sabidó
- ‖Proteomics Unit, Center for Genomics Regulation, Barcelona Institute of Science and Technology, 08003 Barcelona
- **University Pompeu Fabra, 08003 Barcelona
| | - Àlex Bayés
- ***Molecular Physiology of the Synapse Laboratory, Biomedical Research Institute Sant Pau (IIB Sant Pau), 08025, Barcelona, Spain
- ‡‡‡Universitat Autònoma de Barcelona, 08193 Bellaterra (Cerdanyola del Vallès), Spain
| | - Olivia Belbin
- §Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain;
- ¶Biomedical Research Institute Sant Pau (IIB Sant Pau), 08025Barcelona, Spain
| |
Collapse
|
5
|
Pandya NJ, Koopmans F, Slotman JA, Paliukhovich I, Houtsmuller AB, Smit AB, Li KW. Correlation profiling of brain sub-cellular proteomes reveals co-assembly of synaptic proteins and subcellular distribution. Sci Rep 2017; 7:12107. [PMID: 28935861 PMCID: PMC5608747 DOI: 10.1038/s41598-017-11690-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 08/21/2017] [Indexed: 12/13/2022] Open
Abstract
Protein correlation profiling might assist in defining co-assembled proteins and subcellular distribution. Here, we quantified the proteomes of five biochemically isolated mouse brain cellular sub-fractions, with emphasis on synaptic compartments, from three brain regions, hippocampus, cortex and cerebellum. We demonstrated the expected co-fractionation of canonical synaptic proteins belonging to the same functional groups. The enrichment profiles also suggested the presence of many novel pre- and post-synaptic proteins. Using super-resolution microscopy on primary neuronal culture we confirmed the postsynaptic localization of PLEKHA5 and ADGRA1. We further detected profound brain region specific differences in the extent of enrichment for some functionally associated proteins. This is exemplified by different AMPA receptor subunits and substantial differences in sub-fraction distribution of their potential interactors, which implicated the differences of AMPA receptor complex compositions. This resource aids the identification of proteins partners and subcellular distribution of synaptic proteins.
Collapse
Affiliation(s)
- Nikhil J Pandya
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Frank Koopmans
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Johan A Slotman
- Optical Imaging Center, Department of Pathology, Erasmus Medical Center, 3015 GE, Rotterdam, Netherlands
| | - Iryna Paliukhovich
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Adriaan B Houtsmuller
- Optical Imaging Center, Department of Pathology, Erasmus Medical Center, 3015 GE, Rotterdam, Netherlands
| | - August B Smit
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Ka Wan Li
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
| |
Collapse
|
6
|
Baucum AJ. Proteomic Analysis of Postsynaptic Protein Complexes Underlying Neuronal Plasticity. ACS Chem Neurosci 2017; 8:689-701. [PMID: 28211672 DOI: 10.1021/acschemneuro.7b00008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Normal neuronal communication and synaptic plasticity at glutamatergic synapses requires dynamic regulation of postsynaptic molecules. Protein expression and protein post-translational modifications regulate protein interactions that underlie this organization. In this Review, we highlight data obtained over the last 20 years that have used qualitative and quantitative proteomics-based approaches to identify postsynaptic protein complexes. Herein, we describe how these proteomics studies have helped lay the foundation for understanding synaptic physiology and perturbations in synaptic signaling observed in different pathologies. We also describe emerging technologies that can be useful in these analyses. We focus on protein complexes associated with the highly abundant and functionally critical proteins: calcium/calmodulin-dependent protein kinase II, the N-methyl-d-aspartate, and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid glutamate receptors, and postsynaptic density protein of 95 kDa.
Collapse
Affiliation(s)
- Anthony J. Baucum
- Department of Biology, Stark Neurosciences
Research Institute, Indiana University-Purdue University Indianapolis, 723 W. Michigan St., Indianapolis, Indiana 46202, United States
| |
Collapse
|
7
|
Bayés À, Collins MO, Reig-Viader R, Gou G, Goulding D, Izquierdo A, Choudhary JS, Emes RD, Grant SGN. Evolution of complexity in the zebrafish synapse proteome. Nat Commun 2017; 8:14613. [PMID: 28252024 PMCID: PMC5337974 DOI: 10.1038/ncomms14613] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 01/15/2017] [Indexed: 11/09/2022] Open
Abstract
The proteome of human brain synapses is highly complex and is mutated in over 130 diseases. This complexity arose from two whole-genome duplications early in the vertebrate lineage. Zebrafish are used in modelling human diseases; however, its synapse proteome is uncharacterized, and whether the teleost-specific genome duplication (TSGD) influenced complexity is unknown. We report the characterization of the proteomes and ultrastructure of central synapses in zebrafish and analyse the importance of the TSGD. While the TSGD increases overall synapse proteome complexity, the postsynaptic density (PSD) proteome of zebrafish has lower complexity than mammals. A highly conserved set of ∼1,000 proteins is shared across vertebrates. PSD ultrastructural features are also conserved. Lineage-specific proteome differences indicate that vertebrate species evolved distinct synapse types and functions. The data sets are a resource for a wide range of studies and have important implications for the use of zebrafish in modelling human synaptic diseases.
Collapse
Affiliation(s)
- Àlex Bayés
- Molecular Physiology of the Synapse Laboratory, Biomedical Research Institute Sant Pau (IIB Sant Pau), Sant Antoni Maria Claret 167, 08025 Barcelona, Spain
- Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193 Bellaterra, Spain
| | - Mark O. Collins
- Department of Biomedical Science, The Centre for Membrane Interactions and Dynamics, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Rita Reig-Viader
- Molecular Physiology of the Synapse Laboratory, Biomedical Research Institute Sant Pau (IIB Sant Pau), Sant Antoni Maria Claret 167, 08025 Barcelona, Spain
- Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193 Bellaterra, Spain
| | - Gemma Gou
- Molecular Physiology of the Synapse Laboratory, Biomedical Research Institute Sant Pau (IIB Sant Pau), Sant Antoni Maria Claret 167, 08025 Barcelona, Spain
- Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193 Bellaterra, Spain
| | - David Goulding
- Pathogen Genomics, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Abril Izquierdo
- School of Veterinary Medicine and Science, University of Nottingham. Sutton Bonington Campus, Leicestershire LE12 5RD, UK
| | - Jyoti S. Choudhary
- Proteomic Mass Spectrometry, The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Richard D. Emes
- School of Veterinary Medicine and Science, University of Nottingham. Sutton Bonington Campus, Leicestershire LE12 5RD, UK
- Advanced Data Analysis Centre, University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, UK
| | - Seth G. N. Grant
- Genes to Cognition Programme, Centre for Clinical Brain Science, University of Edinburgh, Edinburgh EH16 4SB, UK
| |
Collapse
|
8
|
Kolodziej A, Smalla KH, Richter S, Engler A, Pielot R, Dieterich DC, Tischmeyer W, Naumann M, Kähne T. High Resolution Quantitative Synaptic Proteome Profiling of Mouse Brain Regions After Auditory Discrimination Learning. J Vis Exp 2016. [PMID: 28060347 PMCID: PMC5226410 DOI: 10.3791/54992] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The molecular synaptic mechanisms underlying auditory learning and memory remain largely unknown. Here, the workflow of a proteomic study on auditory discrimination learning in mice is described. In this learning paradigm, mice are trained in a shuttle box Go/NoGo-task to discriminate between rising and falling frequency-modulated tones in order to avoid a mild electric foot-shock. The protocol involves the enrichment of synaptosomes from four brain areas, namely the auditory cortex, frontal cortex, hippocampus, and striatum, at different stages of training. Synaptic protein expression patterns obtained from trained mice are compared to naïve controls using a proteomic approach. To achieve sufficient analytical depth, samples are fractionated in three different ways prior to mass spectrometry, namely 1D SDS-PAGE/in-gel digestion, in-solution digestion and phospho-peptide enrichment. High-resolution proteomic analysis on a mass spectrometer and label-free quantification are used to examine synaptic protein profiles in phospho-peptide-depleted and phospho-peptide-enriched fractions of synaptosomal protein samples. A commercial software package is utilized to reveal proteins and phospho-peptides with significantly regulated relative synaptic abundance levels (trained/naïve controls). Common and differential regulation modes for the synaptic proteome in the investigated brain regions of mice after training were observed. Subsequently, meta-analyses utilizing several databases are employed to identify underlying cellular functions and biological pathways.
Collapse
Affiliation(s)
| | | | - Sandra Richter
- Institute of Experimental Internal Medicine, Medical School, Otto von Guericke University Magdeburg
| | | | - Rainer Pielot
- Leibniz Institute for Neurobiology (LIN); Institute of Pharmacology and Toxicology, Medical School, Otto von Guericke University
| | - Daniela C Dieterich
- Institute of Pharmacology and Toxicology, Medical School, Otto von Guericke University
| | | | - Michael Naumann
- Institute of Experimental Internal Medicine, Medical School, Otto von Guericke University Magdeburg
| | - Thilo Kähne
- Institute of Experimental Internal Medicine, Medical School, Otto von Guericke University Magdeburg;
| |
Collapse
|
9
|
Dieterich DC, Kreutz MR. Proteomics of the Synapse--A Quantitative Approach to Neuronal Plasticity. Mol Cell Proteomics 2016; 15:368-81. [PMID: 26307175 PMCID: PMC4739661 DOI: 10.1074/mcp.r115.051482] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 07/29/2015] [Indexed: 11/06/2022] Open
Abstract
The advances in mass spectrometry based proteomics in the past 15 years have contributed to a deeper appreciation of protein networks and the composition of functional synaptic protein complexes. However, research on protein dynamics underlying core mechanisms of synaptic plasticity in brain lag far behind. In this review, we provide a synopsis on proteomic research addressing various aspects of synaptic function. We discuss the major topics in the study of protein dynamics of the chemical synapse and the limitations of current methodology. We highlight recent developments and the future importance of multidimensional proteomics and metabolic labeling. Finally, emphasis is given on the conceptual framework of modern proteomics and its current shortcomings in the quest to gain a deeper understanding of synaptic plasticity.
Collapse
Affiliation(s)
- Daniela C Dieterich
- From the ‡Institute for Pharmacology and Toxicology, Otto-von-Guericke University Magdeburg, Germany; Research Group Neuralomics, Leibniz Institute for Neurobiology Magdeburg, Germany; ¶Center for Behavioral Brain Sciences (CBBS), Magdeburg, Germany.
| | - Michael R Kreutz
- §RG Neuroplasticity, Leibniz Institute for Neurobiology, Magdeburg, Germany; ¶Center for Behavioral Brain Sciences (CBBS), Magdeburg, Germany.
| |
Collapse
|
10
|
Jankowska U, Latosinska A, Skupien-Rabian B, Swiderska B, Dziedzicka-Wasylewska M, Kedracka-Krok S. Optimized procedure of extraction, purification and proteomic analysis of nuclear proteins from mouse brain. J Neurosci Methods 2015; 261:1-9. [PMID: 26698226 DOI: 10.1016/j.jneumeth.2015.12.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 12/02/2015] [Accepted: 12/02/2015] [Indexed: 11/19/2022]
Abstract
BACKGROUND The cell nucleus is a highly dynamic subcellular compartment performing crucial processes for functioning and administration of the cell. Proteomic analysis of isolated nuclear fraction enables in-depth insight into these processes leading to better understanding of physiological and pathological state of the brain. There is no universal method for nuclear proteome investigation and each biological material needs individual optimization. An additional difficulty is the large amount of nucleic acids, which impairs isoelectrofocusing of proteins and shotgun mass spectrometry analysis of complex peptide samples. NEW METHOD We performed the first comprehensive optimization of intact nuclei isolation from mouse brain in combination with nuclear protein purification prior to two-dimensional gel electrophoresis (2DE) and gel-free proteomic analysis. RESULTS Application of sonication, digestion with nuclease and protein precipitation with acetone allowed to obtain high quality 2DE gels. Shotgun mass spectrometry analysis of isolated proteins proved an enrichment in nuclear proteins. The 66.4% of 265 identified proteins had assigned nucleus localization in UniProt database. Gene Ontology analysis using DAVID platform revealed the highest fold enrichment in spliceosome (24.5), nuclear periphery (12.4) and nuclear matrix (11.3). COMPARISON WITH EXISTING METHODS The proposed procedure is tailored to mouse brain tissue nuclear subproteome investigation. The quality of isolated nuclei, the effectiveness of the protein purification, efficiency of protein recovery after precipitation and overall method reproducibility was taken into detailed consideration. CONCLUSIONS The elaborated procedure could be further applied for in-depth proteomic analysis of molecular processes occurring in the mouse brain nucleus.
Collapse
Affiliation(s)
- Urszula Jankowska
- Department of Structural Biology, Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Agnieszka Latosinska
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Bozena Skupien-Rabian
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Bianka Swiderska
- Department of Structural Biology, Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland; Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Marta Dziedzicka-Wasylewska
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Sylwia Kedracka-Krok
- Department of Structural Biology, Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland; Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.
| |
Collapse
|
11
|
Eising E, de Leeuw C, Min JL, Anttila V, Verheijen MHG, Terwindt GM, Dichgans M, Freilinger T, Kubisch C, Ferrari MD, Smit AB, de Vries B, Palotie A, van den Maagdenberg AMJM, Posthuma D. Involvement of astrocyte and oligodendrocyte gene sets in migraine. Cephalalgia 2015; 36:640-7. [DOI: 10.1177/0333102415618614] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 10/26/2015] [Indexed: 01/13/2023]
Abstract
Background Migraine is a common episodic brain disorder characterized by recurrent attacks of severe unilateral headache and additional neurological symptoms. Two main migraine types can be distinguished based on the presence of aura symptoms that can accompany the headache: migraine with aura and migraine without aura. Multiple genetic and environmental factors confer disease susceptibility. Recent genome-wide association studies (GWAS) indicate that migraine susceptibility genes are involved in various pathways, including neurotransmission, which have already been implicated in genetic studies of monogenic familial hemiplegic migraine, a subtype of migraine with aura. Methods To further explore the genetic background of migraine, we performed a gene set analysis of migraine GWAS data of 4954 clinic-based patients with migraine, as well as 13,390 controls. Curated sets of synaptic genes and sets of genes predominantly expressed in three glial cell types (astrocytes, microglia and oligodendrocytes) were investigated. Discussion Our results show that gene sets containing astrocyte- and oligodendrocyte-related genes are associated with migraine, which is especially true for gene sets involved in protein modification and signal transduction. Observed differences between migraine with aura and migraine without aura indicate that both migraine types, at least in part, seem to have a different genetic background.
Collapse
Affiliation(s)
- Else Eising
- Department of Human Genetics, Leiden University Medical Centre, The Netherlands
| | - Christiaan de Leeuw
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, The Netherlands
- Institute for Computing and Information Sciences, Radboud University, The Netherlands
| | - Josine L Min
- MRC Integrative Epidemiology Unit, University of Bristol, UK
| | - Verneri Anttila
- Analytical and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, USA
| | - Mark HG Verheijen
- Department of Molecular and Cellular Neurobiology, Centre for Neurogenomics and Cognitive Research, Neuroscience, Campus Amsterdam, VU University, The Netherlands
| | - Gisela M Terwindt
- Department of Neurology, Leiden University Medical Centre, The Netherlands
| | - Martin Dichgans
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians-Universität, Germany
- Munich Cluster for Systems Neurology (SyNergy), Germany
| | - Tobias Freilinger
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians-Universität, Germany
- Department of Neurology and Epileptology and Hertie-Institute for Clinical Brain Research, University of Tübingen, Germany
| | - Christian Kubisch
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Germany
| | - Michel D Ferrari
- Department of Neurology, Leiden University Medical Centre, The Netherlands
| | - August B Smit
- Department of Molecular and Cellular Neurobiology, Centre for Neurogenomics and Cognitive Research, Neuroscience, Campus Amsterdam, VU University, The Netherlands
| | - Boukje de Vries
- Department of Human Genetics, Leiden University Medical Centre, The Netherlands
| | - Aarno Palotie
- Analytical and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, USA
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, UK
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Finland
| | - Arn MJM van den Maagdenberg
- Department of Human Genetics, Leiden University Medical Centre, The Netherlands
- Department of Neurology, Leiden University Medical Centre, The Netherlands
| | - Danielle Posthuma
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, The Netherlands
- Department of Clinical Genetics, VU University Medical Centre, The Netherlands
| | | |
Collapse
|
12
|
de Leeuw C, Goudriaan A, Smit AB, Yu D, Mathews CA, Scharf JM, Verheijen MHG, Posthuma D. Involvement of astrocyte metabolic coupling in Tourette syndrome pathogenesis. Eur J Hum Genet 2015; 23:1519-22. [PMID: 25735483 PMCID: PMC4613465 DOI: 10.1038/ejhg.2015.22] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 12/11/2014] [Accepted: 01/20/2015] [Indexed: 01/02/2023] Open
Abstract
Tourette syndrome is a heritable neurodevelopmental disorder whose pathophysiology remains unknown. Recent genome-wide association studies suggest that it is a polygenic disorder influenced by many genes of small effect. We tested whether these genes cluster in cellular function by applying gene-set analysis using expert curated sets of brain-expressed genes in the current largest available Tourette syndrome genome-wide association data set, involving 1285 cases and 4964 controls. The gene sets included specific synaptic, astrocytic, oligodendrocyte and microglial functions. We report association of Tourette syndrome with a set of genes involved in astrocyte function, specifically in astrocyte carbohydrate metabolism. This association is driven primarily by a subset of 33 genes involved in glycolysis and glutamate metabolism through which astrocytes support synaptic function. Our results indicate for the first time that the process of astrocyte-neuron metabolic coupling may be an important contributor to Tourette syndrome pathogenesis.
Collapse
Affiliation(s)
- Christiaan de Leeuw
- Department of Complex Trait Genetics, VU University Medical Center, Amsterdam, The Netherlands
- Institute for Computing and Information Sciences, Radboud University, Nijmegen, The Netherlands
| | - Andrea Goudriaan
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, Amsterdam, The Netherlands
| | - August B Smit
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, Amsterdam, The Netherlands
| | - Dongmei Yu
- Psychiatric and Neurodevelopmental Genetics Unit, Departments of Psychiatry and Neurology, Center for Human Genetics Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Carol A Mathews
- Department of Psychiatry, Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Jeremiah M Scharf
- Psychiatric and Neurodevelopmental Genetics Unit, Departments of Psychiatry and Neurology, Center for Human Genetics Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Division of Cognitive and Behavioral Neurology, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Mark H G Verheijen
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, Amsterdam, The Netherlands
| | - Danielle Posthuma
- Department of Complex Trait Genetics, VU University Medical Center, Amsterdam, The Netherlands
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, Amsterdam, The Netherlands
- Department of Child and Adolescent Psychiatry, Erasmus University Rotterdam, Sophia Child Hospital, Rotterdam, The Netherlands
| |
Collapse
|
13
|
Orth MF, Cazes A, Butt E, Grunewald TGP. An update on the LIM and SH3 domain protein 1 (LASP1): a versatile structural, signaling, and biomarker protein. Oncotarget 2015; 6:26-42. [PMID: 25622104 PMCID: PMC4381576 DOI: 10.18632/oncotarget.3083] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 12/28/2014] [Indexed: 01/15/2023] Open
Abstract
The gene encoding the LIM and SH3 domain protein (LASP1) was cloned two decades ago from a cDNA library of breast cancer metastases. As the first protein of a class comprising one N-terminal LIM and one C-terminal SH3 domain, LASP1 founded a new LIM-protein subfamily of the nebulin group. Since its discovery LASP1 proved to be an extremely versatile protein because of its exceptional structure allowing interaction with various binding partners, its ubiquitous expression in normal tissues, albeit with distinct expression patterns, and its ability to transmit signals from the cytoplasm into the nucleus. As a result, LASP1 plays key roles in cell structure, physiological processes, and cell signaling. Furthermore, LASP1 overexpression contributes to cancer aggressiveness hinting to a potential value of LASP1 as a cancer biomarker. In this review we summarize published data on structure, regulation, function, and expression pattern of LASP1, with a focus on its role in human cancer and as a biomarker protein. In addition, we provide a comprehensive transcriptome analysis of published microarrays (n=2,780) that illustrates the expression profile of LASP1 in normal tissues and its overexpression in a broad range of human cancer entities.
Collapse
Affiliation(s)
- Martin F Orth
- Institute for Clinical Biochemistry and Pathobiochemistry, University Clinic of Würzburg, Grombühlstrasse, Würzburg, Germany
| | - Alex Cazes
- Institute for Clinical Biochemistry and Pathobiochemistry, University Clinic of Würzburg, Grombühlstrasse, Würzburg, Germany
| | - Elke Butt
- Institute for Clinical Biochemistry and Pathobiochemistry, University Clinic of Würzburg, Grombühlstrasse, Würzburg, Germany
| | - Thomas G P Grunewald
- Laboratory for Pediatric Sarcoma Biology, Institute of Pathology of the LMU Munich, Thalkirchner Strasse, Munich, Germany
| |
Collapse
|
14
|
Lowenthal MS, Markey SP, Dosemeci A. Quantitative mass spectrometry measurements reveal stoichiometry of principal postsynaptic density proteins. J Proteome Res 2015; 14:2528-38. [PMID: 25874902 DOI: 10.1021/acs.jproteome.5b00109] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Quantitative studies are presented of postsynaptic density (PSD) fractions from rat cerebral cortex with the ultimate goal of defining the average copy numbers of proteins in the PSD complex. Highly specific and selective isotope dilution mass spectrometry assays were developed using isotopically labeled polypeptide concatemer internal standards. Interpretation of PSD protein stoichiometry was achieved as a molar ratio with respect to PSD-95 (SAP-90, DLG4), and subsequently, copy numbers were estimated using a consensus literature value for PSD-95. Average copy numbers for several proteins at the PSD were estimated for the first time, including those for AIDA-1, BRAGs, and densin. Major findings include evidence for the high copy number of AIDA-1 in the PSD (144 ± 30)-equivalent to that of the total GKAP family of proteins (150 ± 27)-suggesting that AIDA-1 is an element of the PSD scaffold. The average copy numbers for NMDA receptor sub-units were estimated to be 66 ± 18, 27 ± 9, and 45 ± 15, respectively, for GluN1, GluN2A, and GluN2B, yielding a total of 34 ± 10 NMDA channels. Estimated average copy numbers for AMPA channels and their auxiliary sub-units TARPs were 68 ± 36 and 144 ± 38, respectively, with a stoichiometry of ∼1:2, supporting the assertion that most AMPA receptors anchor to the PSD via TARP sub-units. This robust, quantitative analysis of PSD proteins improves upon and extends the list of major PSD components with assigned average copy numbers in the ongoing effort to unravel the complex molecular architecture of the PSD.
Collapse
Affiliation(s)
- Mark S Lowenthal
- †Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Sanford P Markey
- †Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States.,‡Laboratory of Neurotoxicology, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Ayse Dosemeci
- §Laboratory of Neurobiology, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892, United States
| |
Collapse
|
15
|
Laßek M, Weingarten J, Volknandt W. The synaptic proteome. Cell Tissue Res 2014; 359:255-65. [PMID: 25038742 DOI: 10.1007/s00441-014-1943-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 06/04/2014] [Indexed: 11/29/2022]
Abstract
Synapses are focal hot spots for signal transduction and plasticity in the brain. A synapse comprises an axon terminus, the presynapse, the synaptic cleft containing extracellular matrix proteins as well as adhesion molecules, and the postsynaptic density as target structure for chemical signaling. The proteomes of the presynaptic and postsynaptic active zones control neurotransmitter release and perception. These tasks demand short- and long-term structural and functional dynamics of the synapse mediated by its proteinaceous inventory. This review addresses subcellular fractionation protocols and the related proteomic approaches to the various synaptic subcompartments with an emphasis on the presynaptic active zone (PAZ). Furthermore, it discusses major constituents of the PAZ including the amyloid precursor protein family members. Numerous proteins regulating the rearrangement of the cytoskeleton are indicative of the functional and structural dynamics of the pre- and postsynapse. The identification of protein candidates of the synapse provides the basis for further analyzing the interaction of synaptic proteins with their targets, and the effect of their deletion opens novel insights into the functional role of these proteins in neuronal communication. The knowledge of the molecular interactome is also a prerequisite for understanding numerous neurodegenerative diseases.
Collapse
Affiliation(s)
- Melanie Laßek
- Molecular and Cellular Neurobiology, Goethe University, Frankfurt, Germany
| | | | | |
Collapse
|
16
|
Li KW, Jimenez CR. Synapse proteomics: current status and quantitative applications. Expert Rev Proteomics 2014; 5:353-60. [DOI: 10.1586/14789450.5.2.353] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
|
17
|
Tribl F, Meyer HE, Marcus K. Analysis of organelles within the nervous system: impact on brain and organelle functions. Expert Rev Proteomics 2014; 5:333-51. [DOI: 10.1586/14789450.5.2.333] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
|
18
|
Schmidt O, Schulenborg T, Meyer HE, Marcus K, Hamacher M. How proteomics reveals potential biomarkers in brain diseases. Expert Rev Proteomics 2014; 2:901-13. [PMID: 16307519 DOI: 10.1586/14789450.2.6.901] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The brain is complex, and so are the proteomics studies of brain tissue and its diseases, including Alzheimer's Disease, Parkinson's Disease and schizophrenia. In this review, general considerations and strategies of proteomics technologies, the advantages and challenges as well as the special needs for brain tissue are described and summarized. In addition, the results of the first studies are presented including a quality evaluation of the candidate proteins for these diseases. A paragraph is dedicated to the efforts of standardization in this field.
Collapse
Affiliation(s)
- Oliver Schmidt
- Ruhr-Universitaet Bochum, Medizinisches Proteom-Center, ZKF E.141, Universitaetsstrasse 150, D-44801 Bochum, Germany.
| | | | | | | | | |
Collapse
|
19
|
Kadakkuzha BM, Puthanveettil SV. Genomics and proteomics in solving brain complexity. MOLECULAR BIOSYSTEMS 2013; 9:1807-21. [PMID: 23615871 PMCID: PMC6425491 DOI: 10.1039/c3mb25391k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The human brain is extraordinarily complex, composed of billions of neurons and trillions of synaptic connections. Neurons are organized into circuit assemblies that are modulated by specific interneurons and non-neuronal cells, such as glia and astrocytes. Data on human genome sequences predicts that each of these cells in the human brain has the potential of expressing ∼20 000 protein coding genes and tens of thousands of noncoding RNAs. A major challenge in neuroscience is to determine (1) how individual neurons and circuitry utilize this potential during development and maturation of the nervous system, and for higher brain functions such as cognition, and (2) how this potential is altered in neurological and psychiatric disorders. In this review, we will discuss how recent advances in next generation sequencing, proteomics and bioinformatics have transformed our understanding of gene expression and the functions of neural circuitry, memory storage, and disorders of cognition.
Collapse
Affiliation(s)
- Beena M Kadakkuzha
- Department of Neuroscience, The Scripps Research Institute, Scripps Florida 130 Scripps Way, Jupiter, FL 33458, USA
| | | |
Collapse
|
20
|
Craft GE, Chen A, Nairn AC. Recent advances in quantitative neuroproteomics. Methods 2013; 61:186-218. [PMID: 23623823 PMCID: PMC3891841 DOI: 10.1016/j.ymeth.2013.04.008] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2012] [Revised: 03/29/2013] [Accepted: 04/13/2013] [Indexed: 01/07/2023] Open
Abstract
The field of proteomics is undergoing rapid development in a number of different areas including improvements in mass spectrometric platforms, peptide identification algorithms and bioinformatics. In particular, new and/or improved approaches have established robust methods that not only allow for in-depth and accurate peptide and protein identification and modification, but also allow for sensitive measurement of relative or absolute quantitation. These methods are beginning to be applied to the area of neuroproteomics, but the central nervous system poses many specific challenges in terms of quantitative proteomics, given the large number of different neuronal cell types that are intermixed and that exhibit distinct patterns of gene and protein expression. This review highlights the recent advances that have been made in quantitative neuroproteomics, with a focus on work published over the last five years that applies emerging methods to normal brain function as well as to various neuropsychiatric disorders including schizophrenia and drug addiction as well as of neurodegenerative diseases including Parkinson's disease and Alzheimer's disease. While older methods such as two-dimensional polyacrylamide electrophoresis continued to be used, a variety of more in-depth MS-based approaches including both label (ICAT, iTRAQ, TMT, SILAC, SILAM), label-free (label-free, MRM, SWATH) and absolute quantification methods, are rapidly being applied to neurobiological investigations of normal and diseased brain tissue as well as of cerebrospinal fluid (CSF). While the biological implications of many of these studies remain to be clearly established, that there is a clear need for standardization of experimental design and data analysis, and that the analysis of protein changes in specific neuronal cell types in the central nervous system remains a serious challenge, it appears that the quality and depth of the more recent quantitative proteomics studies is beginning to shed light on a number of aspects of neuroscience that relates to normal brain function as well as of the changes in protein expression and regulation that occurs in neuropsychiatric and neurodegenerative disorders.
Collapse
Affiliation(s)
- George E Craft
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, 06508
| | - Anshu Chen
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, 06508
| | - Angus C Nairn
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, 06508
- Yale/NIDA Neuroproteomics Center, Yale University School of Medicine, New Haven, CT, 06508
| |
Collapse
|
21
|
Zhang Y, Fonslow BR, Shan B, Baek MC, Yates JR. Protein analysis by shotgun/bottom-up proteomics. Chem Rev 2013; 113:2343-94. [PMID: 23438204 PMCID: PMC3751594 DOI: 10.1021/cr3003533] [Citation(s) in RCA: 1029] [Impact Index Per Article: 85.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Yaoyang Zhang
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bryan R. Fonslow
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bing Shan
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Moon-Chang Baek
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Molecular Medicine, Cell and Matrix Biology Research Institute, School of Medicine, Kyungpook National University, Daegu 700-422, Republic of Korea
| | - John R. Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| |
Collapse
|
22
|
Joo J, Lee S, Nah SS, Kim YO, Kim DS, Shim SH, Hwangbo Y, Kim HK, Kwon JT, Kim JW, Song HY, Kim HJ. Lasp1 is down-regulated in NMDA receptor antagonist-treated mice and implicated in human schizophrenia susceptibility. J Psychiatr Res 2013; 47:105-12. [PMID: 23040864 DOI: 10.1016/j.jpsychires.2012.09.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 09/13/2012] [Accepted: 09/14/2012] [Indexed: 11/29/2022]
Abstract
Mice treated with MK-801, a non-competitive antagonist of the N-methyl-d-aspartic (NMDA) acid receptor, are important animal models for schizophrenia studies. In the present study, we compared protein expression levels in the hippocampus of mice treated with MK-801 (0.6 mg/kg) or saline once daily for 7 days. Changes in the proteome were detected by two-dimensional electrophoresis, and the six proteins exhibiting differential expression were identified by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry. Down-regulation of one of these proteins, Lasp1 (LIM and SH3 protein 1), in MK-801-treated mice was confirmed by western blotting and immunohistochemical analyses. Lasp1 is a multidomain protein that may recruit signaling molecules to the actin-based cytoskeleton and is known to concentrate in synaptic sites of hippocampal neurons. We next investigated whether polymorphisms in the human LASP1 gene were associated with schizophrenia in the Korean population. A single-nucleotide polymorphism in the LASP1 gene promoter region was associated with schizophrenia susceptibility. Our results suggest that LASP1 might be associated with NMDA receptor antagonism and schizophrenia susceptibility and, thus, might be involved in the pathophysiology of schizophrenia.
Collapse
Affiliation(s)
- Jaesoon Joo
- Department of Microbiology, College of Medicine, Soonchunhyang University, Cheonan 330-090, Republic of Korea
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
23
|
Smalla KH, Klemmer P, Wyneken U. Isolation of the Postsynaptic Density: A Specialization of the Subsynaptic Cytoskeleton. THE CYTOSKELETON 2013. [DOI: 10.1007/978-1-62703-266-7_11] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
24
|
Lips ES, Cornelisse LN, Toonen RF, Min JL, Hultman CM, the International Schizophrenia Consortium 13, Holmans PA, O'Donovan MC, Purcell SM, Smit AB, Verhage M, Sullivan PF, Visscher PM, Posthuma D. Functional gene group analysis identifies synaptic gene groups as risk factor for schizophrenia. Mol Psychiatry 2012; 17:996-1006. [PMID: 21931320 PMCID: PMC3449234 DOI: 10.1038/mp.2011.117] [Citation(s) in RCA: 124] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Revised: 07/21/2011] [Accepted: 08/01/2011] [Indexed: 01/08/2023]
Abstract
Schizophrenia is a highly heritable disorder with a polygenic pattern of inheritance and a population prevalence of ~1%. Previous studies have implicated synaptic dysfunction in schizophrenia. We tested the accumulated association of genetic variants in expert-curated synaptic gene groups with schizophrenia in 4673 cases and 4965 healthy controls, using functional gene group analysis. Identifying groups of genes with similar cellular function rather than genes in isolation may have clinical implications for finding additional drug targets. We found that a group of 1026 synaptic genes was significantly associated with the risk of schizophrenia (P=7.6 × 10(-11)) and more strongly associated than 100 randomly drawn, matched control groups of genetic variants (P<0.01). Subsequent analysis of synaptic subgroups suggested that the strongest association signals are derived from three synaptic gene groups: intracellular signal transduction (P=2.0 × 10(-4)), excitability (P=9.0 × 10(-4)) and cell adhesion and trans-synaptic signaling (P=2.4 × 10(-3)). These results are consistent with a role of synaptic dysfunction in schizophrenia and imply that impaired intracellular signal transduction in synapses, synaptic excitability and cell adhesion and trans-synaptic signaling play a role in the pathology of schizophrenia.
Collapse
Affiliation(s)
- E S Lips
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, Amsterdam, The Netherlands
| | - L N Cornelisse
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, Amsterdam, The Netherlands
| | - R F Toonen
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, Amsterdam, The Netherlands
| | - J L Min
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, Amsterdam, The Netherlands
| | - C M Hultman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Neuroscience, Psychiatry, Ulleråker, Uppsala University, Uppsala, Sweden
| | - the International Schizophrenia Consortium13
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, Amsterdam, The Netherlands
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Neuroscience, Psychiatry, Ulleråker, Uppsala University, Uppsala, Sweden
- School of Medicine, Department of Psychological Medicine, School of Medicine, Cardiff University, Cardiff, UK
- Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA
- Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, Amsterdam, The Netherlands
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
- Queensland Statistical Genetics Laboratory, Queensland Institute of Medical Research, Brisbane, QLD, Australia
- Department of Medical Genomics, VU Medical Center, Neuroscience Campus, Amsterdam, The Netherlands
| | - P A Holmans
- School of Medicine, Department of Psychological Medicine, School of Medicine, Cardiff University, Cardiff, UK
| | - M C O'Donovan
- School of Medicine, Department of Psychological Medicine, School of Medicine, Cardiff University, Cardiff, UK
| | - S M Purcell
- Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA
| | - A B Smit
- Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, Amsterdam, The Netherlands
| | - M Verhage
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, Amsterdam, The Netherlands
| | - P F Sullivan
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - P M Visscher
- Queensland Statistical Genetics Laboratory, Queensland Institute of Medical Research, Brisbane, QLD, Australia
| | - D Posthuma
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, Amsterdam, The Netherlands
- Department of Medical Genomics, VU Medical Center, Neuroscience Campus, Amsterdam, The Netherlands
| |
Collapse
|
25
|
MacDonald ML, Ciccimaro E, Prakash A, Banerjee A, Seeholzer SH, Blair IA, Hahn CG. Biochemical fractionation and stable isotope dilution liquid chromatography-mass spectrometry for targeted and microdomain-specific protein quantification in human postmortem brain tissue. Mol Cell Proteomics 2012; 11:1670-81. [PMID: 22942359 DOI: 10.1074/mcp.m112.021766] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Synaptic architecture and its adaptive changes require numerous molecular events that are both highly ordered and complex. A majority of neuropsychiatric illnesses are complex trait disorders, in which multiple etiologic factors converge at the synapse via many signaling pathways. Investigating the protein composition of synaptic microdomains from human patient brain tissues will yield valuable insights into the interactions of risk genes in many disorders. These types of studies in postmortem tissues have been limited by the lack of proper study paradigms. Thus, it is necessary not only to develop strategies to quantify protein and post-translational modifications at the synapse, but also to rigorously validate them for use in postmortem human brain tissues. In this study we describe the development of a liquid chromatography-selected reaction monitoring method, using a stable isotope-labeled neuronal proteome standard prepared from the brain tissue of a stable isotope-labeled mouse, for the multiplexed quantification of target synaptic proteins in mammalian samples. Additionally, we report the use of this method to validate a biochemical approach for the preparation of synaptic microdomain enrichments from human postmortem prefrontal cortex. Our data demonstrate that a targeted mass spectrometry approach with a true neuronal proteome standard facilitates accurate and precise quantification of over 100 synaptic proteins in mammalian samples, with the potential to quantify over 1000 proteins. Using this method, we found that protein enrichments in subcellular fractions prepared from human postmortem brain tissue were strikingly similar to those prepared from fresh mouse brain tissue. These findings demonstrate that biochemical fractionation methods paired with targeted proteomic strategies can be used in human brain tissues, with important implications for the study of neuropsychiatric disease.
Collapse
Affiliation(s)
- Matthew L MacDonald
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | | | | | | | | | | | | |
Collapse
|
26
|
Pielot R, Smalla KH, Müller A, Landgraf P, Lehmann AC, Eisenschmidt E, Haus UU, Weismantel R, Gundelfinger ED, Dieterich DC. SynProt: A Database for Proteins of Detergent-Resistant Synaptic Protein Preparations. Front Synaptic Neurosci 2012; 4:1. [PMID: 22737123 PMCID: PMC3382120 DOI: 10.3389/fnsyn.2012.00001] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Accepted: 05/29/2012] [Indexed: 11/13/2022] Open
Abstract
Chemical synapses are highly specialized cell–cell contacts for communication between neurons in the CNS characterized by complex and dynamic protein networks at both synaptic membranes. The cytomatrix at the active zone (CAZ) organizes the apparatus for the regulated release of transmitters from the presynapse. At the postsynaptic side, the postsynaptic density constitutes the machinery for detection, integration, and transduction of the transmitter signal. Both pre- and postsynaptic protein networks represent the molecular substrates for synaptic plasticity. Their function can be altered both by regulating their composition and by post-translational modification of their components. For a comprehensive understanding of synaptic networks the entire ensemble of synaptic proteins has to be considered. To support this, we established a comprehensive database for synaptic junction proteins (SynProt database) primarily based on proteomics data obtained from biochemical preparations of detergent-resistant synaptic junctions. The database currently contains 2,788 non-redundant entries of rat, mouse, and some human proteins, which mainly have been manually extracted from 12 proteomic studies and annotated for synaptic subcellular localization. Each dataset is completed with manually added information including protein classifiers as well as automatically retrieved and updated information from public databases (UniProt and PubMed). We intend that the database will be used to support modeling of synaptic protein networks and rational experimental design.
Collapse
Affiliation(s)
- Rainer Pielot
- Department of Neurochemistry and Molecular Biology, Leibniz Institute for Neurobiology Magdeburg, Germany
| | | | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Costain WJ, Haqqani AS, Rasquinha I, Giguere MS, Slinn J, Zurakowski B, Stanimirovic DB. Proteomic analysis of synaptosomal protein expression reveals that cerebral ischemia alters lysosomal Psap processing. Proteomics 2011; 10:3272-91. [PMID: 20718007 DOI: 10.1002/pmic.200900447] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Cerebral ischemia (CI) induces dramatic changes in synaptic structure and function that precedes delayed post-ischemic neuronal death. Here, a proteomic analysis was used to identify the effects of focal CI on synaptosomal protein levels. Contralateral and ipsilateral synaptosomes, prepared from adult mice subjected to 60 min middle cerebral artery occlusion, were isolated following 3, 6 and 20 h of reperfusion. Synaptosomal protein samples (n=3) were labeled using the cleavable ICAT system prior to analysis with nanoLC-MS/MS. Each sample was analyzed by LC-MS to identify differential expressions using InDEPT software and differentially expressed peptides were identified by targeted LC-MS/MS. A total of 62 differentially expressed proteins were identified and Gene Ontology classification (cellular component) indicated that the majority of the proteins were located in the mitochondria and other components consistent with synaptic localization. The observed alterations in synaptic protein levels poorly correlated with gene expression, indicating the involvement of post-transcriptional regulatory mechanisms in determining post-ischemic synaptic protein content. Additionally, immunohistochemistry analysis of prosaposin (Psap) and saposin C (SapC) indicates that CI disrupts Psap processing and glycosphingolipid metabolism. These results demonstrate that the synapse is adversely affected by CI and may play a role in mediating post-ischemic neuronal viability.
Collapse
Affiliation(s)
- Willard J Costain
- Glycosyltransferases and Neuroglycomics, Institute for Biological Sciences, National Research Council, Ottawa, ON, Canada.
| | | | | | | | | | | | | |
Collapse
|
28
|
Jiang L, Fang J, Moore DS, Gogichaeva NV, Galeva NA, Michaelis ML, Zaidi A. Age-associated changes in synaptic lipid raft proteins revealed by two-dimensional fluorescence difference gel electrophoresis. Neurobiol Aging 2010; 31:2146-59. [PMID: 19118924 PMCID: PMC2904836 DOI: 10.1016/j.neurobiolaging.2008.11.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2008] [Revised: 10/06/2008] [Accepted: 11/18/2008] [Indexed: 01/19/2023]
Abstract
Brain aging is associated with a progressive decline in cognitive function though the molecular mechanisms remain unknown. Functional changes in brain neurons could be due to age-related alterations in levels of specific proteins critical for information processing. Specialized membrane microdomains known as 'lipid rafts' contain protein complexes involved in many signal transduction processes. This study was undertaken to determine if two-dimensional fluorescence difference gel electrophoresis (2D DIGE) analysis of proteins in synaptic membrane lipid rafts revealed age-dependent alterations in levels of raft proteins. Five pairs of young and aged rat synaptic membrane rafts were subjected to DIGE separation, followed by image analysis and identification of significantly altered proteins. Of 1046 matched spots on DIGE gels, 94 showed statistically significant differences in levels between old and young rafts, and 87 of these were decreased in aged rafts. The 41 most significantly altered (p<0.03) proteins included several synaptic proteins involved in energy metabolism, redox homeostasis, and cytoskeletal structure. This may indicate a disruption in bioenergetic balance and redox homeostasis in synaptic rafts with brain aging. Differential levels of representative identified proteins were confirmed by immunoblot analysis. Our findings provide novel pathways in investigations of mechanisms that may contribute to altered neuronal function in aging brain.
Collapse
Affiliation(s)
- Lei Jiang
- Department of Pharmacology and Toxicology, University of Kansas, Lawrence, KS 66045, USA
| | - Jianwen Fang
- Bioinformatics Core Facility, University of Kansas, Lawrence, KS 66047, USA
| | - David S. Moore
- Microscopy and Imaging Laboratory, University of Kansas, Lawrence, KS 66045, USA
| | - Natalia V. Gogichaeva
- Analytical Proteomics Laboratory, Structural Biology Center, University of Kansas, Lawrence, KS 66047, USA
| | - Nadezhda A. Galeva
- Analytical Proteomics Laboratory, Structural Biology Center, University of Kansas, Lawrence, KS 66047, USA
| | - Mary L. Michaelis
- Department of Pharmacology and Toxicology, University of Kansas, Lawrence, KS 66045, USA
| | - Asma Zaidi
- Department of Pharmacology and Toxicology, University of Kansas, Lawrence, KS 66045, USA
- Department of Biochemistry, Kansas City University of Medicine and Biosciences, 1750 Independence Avenue, Kansas City, MO 64106, USA
| |
Collapse
|
29
|
Willis DE, Twiss JL. Regulation of protein levels in subcellular domains through mRNA transport and localized translation. Mol Cell Proteomics 2010; 9:952-62. [PMID: 20167945 DOI: 10.1074/mcp.r900005-mcp200] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Localized protein synthesis is increasingly recognized as a means for polarized cells to modulate protein levels in subcellular regions and the distal reaches of their cytoplasm. The axonal and dendritic processes of neurons represent functional domains of cytoplasm that can be separated from their cell body by vast distances. This separation provides a biological setting where the cell uses locally synthesized proteins to both autonomously respond to stimuli and to retrogradely signal the cell body of events occurring is this distal environment. Other cell types undoubtedly take advantage of this localized mechanism, but these have not proven as amenable for isolation of functional subcellular domains. Consequently, neurons have provided an appealing experimental platform for study of mRNA transport and localized protein synthesis. Molecular biology approaches have shown both the population of mRNAs that can localize into axons and dendrites and an unexpectedly complex regulation of their transport into these processes. Several lines of evidence point to similar complexities and specificity for regulation of mRNA translation at subcellular sites. Proteomics studies are beginning to provide a comprehensive view of the protein constituents of subcellular domains in neurons and other cell types. However, these have currently fallen short of dissecting temporal regulation of new protein synthesis in subcellular sites and mechanisms used to ferry mRNAs to these sites.
Collapse
Affiliation(s)
- Dianna E Willis
- Burke Medical Research Institute, White Plains, New York 10605, USA.
| | | |
Collapse
|
30
|
Ruano D, Abecasis GR, Glaser B, Lips ES, Cornelisse LN, de Jong AP, Evans DM, Smith GD, Timpson NJ, Smit AB, Heutink P, Verhage M, Posthuma D. Functional gene group analysis reveals a role of synaptic heterotrimeric G proteins in cognitive ability. Am J Hum Genet 2010; 86:113-25. [PMID: 20060087 PMCID: PMC2820181 DOI: 10.1016/j.ajhg.2009.12.006] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2009] [Revised: 11/26/2009] [Accepted: 12/04/2009] [Indexed: 01/06/2023] Open
Abstract
Although cognitive ability is a highly heritable complex trait, only a few genes have been identified, explaining relatively low proportions of the observed trait variation. This implies that hundreds of genes of small effect may be of importance for cognitive ability. We applied an innovative method in which we tested for the effect of groups of genes defined according to cellular function (functional gene group analysis). Using an initial sample of 627 subjects, this functional gene group analysis detected that synaptic heterotrimeric guanine nucleotide binding proteins (G proteins) play an important role in cognitive ability (PEMP = 1.9 × 10−4). The association with heterotrimeric G proteins was validated in an independent population sample of 1507 subjects. Heterotrimeric G proteins are central relay factors between the activation of plasma membrane receptors by extracellular ligands and the cellular responses that these induce, and they can be considered a point of convergence, or a “signaling bottleneck.” Although alterations in synaptic signaling processes may not be the exclusive explanation for the association of heterotrimeric G proteins with cognitive ability, such alterations may prominently affect the properties of neuronal networks in the brain in such a manner that impaired cognitive ability and lower intelligence are observed. The reported association of synaptic heterotrimeric G proteins with cognitive ability clearly points to a new direction in the study of the genetic basis of cognitive ability.
Collapse
|
31
|
Lin Y, Li Y, Liu Y, Han W, He Q, Li J, Chen P, Wang X, Liang S. Improvement of gel-separated protein identification by DMF-assisted digestion and peptide recovery after electroblotting. Electrophoresis 2009; 30:3626-35. [DOI: 10.1002/elps.200900070] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
32
|
Luo Y, Blex C, Baessler O, Glinski M, Dreger M, Sefkow M, Köster H. The cAMP capture compound mass spectrometry as a novel tool for targeting cAMP-binding proteins: from protein kinase A to potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channels. Mol Cell Proteomics 2009; 8:2843-56. [PMID: 19741253 PMCID: PMC2816025 DOI: 10.1074/mcp.m900110-mcp200] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The profiling of subproteomes from complex mixtures on the basis of small molecule interactions shared by members of protein families or small molecule interaction domains present in a subset of proteins is an increasingly important approach in functional proteomics. Capture CompoundTM Mass Spectrometry (CCMS) is a novel technology to address this issue. CCs are trifunctional molecules that accomplish the reversible binding of target protein families to a selectivity group (small molecule), covalent capturing of the bound proteins by photoactivated cross-linking through a reactivity group, and pullout of the small molecule-protein complexes through a sorting function, e.g. biotin. Here we present the design, synthesis, and application of a new Capture Compound to target and identify cAMP-binding proteins in complex protein mixtures. Starting with modest amounts of total protein mixture (65–500 μg), we demonstrate that the cAMP-CCs can be used to isolate bona fide cAMP-binding proteins from lysates of Escherichia coli, mammalian HepG2 cells, and subcellular fractions of mammalian brain, respectively. The identified proteins captured by the cAMP-CCs range from soluble cAMP-binding proteins, such as the catabolite gene activator protein from E. coli and regulatory subunits of protein kinase A from mammalian systems, to cAMP-activated potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channels from neuronal membranes and specifically synaptosomal fractions from rat brain. The latter group of proteins has never been identified before in any small molecule protein interaction and mass spectrometry-based proteomics study. Given the modest amount of protein input required, we expect that CCMS using the cAMP-CCs provides a unique tool for profiling cAMP-binding proteins from proteome samples of limited abundance, such as tissue biopsies.
Collapse
Affiliation(s)
- Yan Luo
- GmbH, Volmerstrasse 5, 12489 Berlin, Germany
| | | | | | | | | | | | | |
Collapse
|
33
|
Rajcevic U, Petersen K, Knol JC, Loos M, Bougnaud S, Klychnikov O, Li KW, Pham TV, Wang J, Miletic H, Peng Z, Bjerkvig R, Jimenez CR, Niclou SP. iTRAQ-based proteomics profiling reveals increased metabolic activity and cellular cross-talk in angiogenic compared with invasive glioblastoma phenotype. Mol Cell Proteomics 2009; 8:2595-612. [PMID: 19674965 PMCID: PMC2773724 DOI: 10.1074/mcp.m900124-mcp200] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Malignant gliomas (glioblastoma multiforme) have a poor prognosis with an average patient survival under current treatment regimens ranging between 12 and 14 months. The tumors are characterized by rapid cell growth, extensive neovascularization, and diffuse cellular infiltration of normal brain structures. We have developed a human glioblastoma xenograft model in nude rats that is characterized by a highly infiltrative non-angiogenic phenotype. Upon serial transplantation this phenotype will develop into a highly angiogenic tumor. Thus, we have developed an animal model where we are able to establish two characteristic tumor phenotypes that define human glioblastoma (i.e. diffuse infiltration and high neovascularization). Here we aimed at identifying potential biomarkers expressed by the non-angiogenic and the angiogenic phenotypes and elucidating the molecular pathways involved in the switch from invasive to angiogenic growth. Focusing on membrane-associated proteins, we profiled protein expression during the progression from an invasive to an angiogenic phenotype by analyzing serially transplanted glioma xenografts in rats. Applying isobaric peptide tagging chemistry (iTRAQ) combined with two-dimensional LC and MALDI-TOF/TOF mass spectrometry, we were able to identify several thousand proteins in membrane-enriched fractions of which 1460 were extracted as quantifiable proteins (isoform- and species-specific and present in more than one sample). Known and novel candidate proteins were identified that characterize the switch from a non-angiogenic to a highly angiogenic phenotype. The robustness of the data was corroborated by extensive bioinformatics analysis and by validation of selected proteins on tissue microarrays from xenograft and clinical gliomas. The data point to enhanced intercellular cross-talk and metabolic activity adopted by tumor cells in the angiogenic compared with the non-angiogenic phenotype. In conclusion, we describe molecular profiles that reflect the change from an invasive to an angiogenic brain tumor phenotype. The identified proteins could be further exploited as biomarkers or therapeutic targets for malignant gliomas.
Collapse
Affiliation(s)
- Uros Rajcevic
- Norlux Neuro-Oncology Laboratory, Department of Oncology, Centre de Recherche Public Santé (CRP-Santé), 84 Val Fleuri, L-1526 Luxembourg, Luxembourg
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
34
|
Zhai J, Liu X, Huang Z, Zhu H. RABA (reductive alkylation by acetone): a novel stable isotope labeling approach for quantitative proteomics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2009; 20:1366-77. [PMID: 19419886 PMCID: PMC2731973 DOI: 10.1016/j.jasms.2009.03.027] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/03/2009] [Revised: 03/28/2009] [Accepted: 03/28/2009] [Indexed: 05/27/2023]
Abstract
Quantitative proteomics is challenging and various stable isotope based approaches have been developed to meet the challenge. Hereby we describe a simple, efficient, reliable, and inexpensive method named reductive alkylation by acetone (RABA) to introduce stable isotopes to peptides for quantitative analysis. The RABA method leads to alkylation of N-terminal and lysine amino groups with isopropyl moiety. Using unlabeled (d(0)) and deuterium labeled (d(6)) acetone, a 6 Da mass split is introduced to each isopropyl modification between the light and heavy isotope labeled peptides, which is ideally suited for quantitative analysis. The reaction specificity, stoichiometry, labeling efficiency, and linear range of the RABA method have been thoroughly evaluated in this study using standard peptides, tryptic digest of proteins, as well as human cell lysate. Reliable quantitative results have been consistently obtained in all experiments. We also applied the RABA method to quantitative analysis of proteins in spinal cords of transgenic mouse models of amyotrophic lateral sclerosis. Highly homologous proteins (transgenic human SOD1 and endogenous mouse SOD1) were distinguished and quantified using the method developed in this study. In addition, the quantitative results using the RABA approach were independently validated by Western blot.
Collapse
Affiliation(s)
- Jianjun Zhai
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, 741 South Limestone, Lexington, KY 40536
| | - Xiaoyan Liu
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, 741 South Limestone, Lexington, KY 40536
| | - Zhenyu Huang
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, 741 South Limestone, Lexington, KY 40536
| | - Haining Zhu
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, 741 South Limestone, Lexington, KY 40536
| |
Collapse
|
35
|
Yan W, Aebersold R, Raines EW. Evolution of organelle-associated protein profiling. J Proteomics 2009; 72:4-11. [PMID: 19110081 PMCID: PMC2680700 DOI: 10.1016/j.jprot.2008.11.017] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2008] [Revised: 11/17/2008] [Accepted: 11/22/2008] [Indexed: 12/22/2022]
Abstract
Identification of the protein constituents of cell organelles forms the basis for studies to define the roles of specific proteins in organelle structure and functions. Over the past decade, the use of mass spectrometry-based proteomics has dissected various organelles and allowed the association of many novel proteins with particular organelles. This review chronicles the evolution of organelle proteomics technology, and discusses how many limitations, such as organelle heterogeneity and purity, can be avoided with recently developed quantitative profiling approaches. Although many challenges remain, quantitative profiling of organelles holds the promise to begin to address the complex and dynamic shuttling of proteins among organelles that will be critical for application of this advanced technology to disease-based changes in organelle function.
Collapse
Affiliation(s)
- Wei Yan
- Institute for Systems Biology, Seattle, WA 98103, USA
- University of Washington, Department of Pathology, Seattle, WA 98104, USA
| | - Ruedi Aebersold
- Institute for Systems Biology, Seattle, WA 98103, USA
- Institute of Molecular Systems Biology, ETH Zurich and Faculty of Science, University of Zurich, 8093 Zurich, Switzerland
| | - Elaine W. Raines
- University of Washington, Department of Pathology, Seattle, WA 98104, USA
| |
Collapse
|
36
|
A comparison of the synaptic proteome in human chronic schizophrenia and rat ketamine psychosis suggest that prohibitin is involved in the synaptic pathology of schizophrenia. Mol Psychiatry 2008; 13:878-96. [PMID: 18504422 DOI: 10.1038/mp.2008.60] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Many studies in recent years suggest that schizophrenia is a synaptic disease that crucially involves a hypofunction of N-methyl-D-aspartate receptor-mediated signaling. However, at present it is unclear how these pathological processes are reflected in the protein content of the synapse. We have employed two-dimensional gel electrophoresis in conjunction with mass spectrometry to characterize and compare the synaptic proteomes of the human left dorsolateral prefrontal cortex in chronic schizophrenia and of the cerebral cortex of rats treated subchronically with ketamine. We found consistent changes in the synaptic proteomes of human schizophrenics and in rats with induced ketamine psychosis compared to controls. However, commonly regulated proteins between both groups were very limited and only prohibitin was found upregulated in both chronic schizophrenia and the rat ketamine model. Prohibitin, however, could be a new potential marker for the synaptic pathology of schizophrenia and might be causally involved in the disease process.
Collapse
|
37
|
Abstract
Synaptic plasticity is the dynamic regulation of the strength of synaptic communication between nerve cells. It is central to neuronal development as well as experience-dependent remodeling of the adult nervous system as occurs during memory formation. Aberrant forms of synaptic plasticity also accompany a variety of neurological and psychiatric diseases, and unraveling the biological basis of synaptic plasticity has been a major goal in neurobiology research. The biochemical and structural mechanisms underlying different forms of synaptic plasticity are complex, involving multiple signaling cascades, reconfigurations of structural proteins and the trafficking of synaptic proteins. As such, proteomics should be a valuable tool in dissecting the molecular events underlying normal and disease-related forms of plasticity. In fact, progress in this area has been disappointingly slow. We discuss the particular challenges associated with proteomic interrogation of synaptic plasticity processes and outline ways in which we believe proteomics may advance the field over the next few years. We pay particular attention to technical advances being made in small sample proteomics and the advent of proteomic imaging in studying brain plasticity.
Collapse
Affiliation(s)
- Stuart R Cobb
- Division of Neuroscience & Biomedical Systems, Institute of Biomedical & Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK.
| | | |
Collapse
|
38
|
Chew CS, Chen X, Bollag RJ, Isales C, Ding KH, Zhang H. Targeted disruption of the Lasp-1 gene is linked to increases in histamine-stimulated gastric HCl secretion. Am J Physiol Gastrointest Liver Physiol 2008; 295:G37-G44. [PMID: 18483181 PMCID: PMC2494726 DOI: 10.1152/ajpgi.90247.2008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2008] [Accepted: 05/08/2008] [Indexed: 01/31/2023]
Abstract
Lasp-1 (LIM and SH3 domain protein 1) is a multidomain actin-binding protein that is differentially expressed within epithelial tissues and brain. In the gastric mucosa, Lasp-1 is highly expressed in the HCl-secreting parietal cell, where it is prominently localized within the F-actin-rich subcellular regions. Histamine-induced elevation of parietal cell [cAMP]i increases Lasp-1 phosphorylation, which is correlated with activation of HCl secretion. To determine whether Lasp-1 is involved in the regulation of HCl secretion in vivo, we generated a murine model with a targeted disruption of the Lasp-1 gene. Lasp-1-null mice had slightly lower body weights but developed normally and had no overt phenotypic abnormalities. Basal HCl secretion was unaffected by loss of Lasp-1, but histamine stimulation induced a more robust acid secretory response in Lasp-1-null mice compared with wild-type littermates. A similar effect of histamine was observed in isolated gastric glands on the basis of measurements of accumulation of the weak base [14C]aminopyrine. In addition, inhibition of the acid secretory response to histamine by H2 receptor blockade with ranitidine proceeded more slowly in glands from Lasp-1-null mice. These findings support the conclusion that Lasp-1 is involved in the regulation of parietal HCl secretion. We speculate that cAMP-dependent phosphorylation of Lasp-1 alters interactions with F-actin and/or endocytic proteins that interact with Lasp-1, thereby regulating the trafficking/activation of the H+, K+-ATPase (proton pump).
Collapse
Affiliation(s)
- Catherine S Chew
- Institute of Molecular Medicine and Genetics, Medical College of Georgia, Augusta, GA 30912-3175, USA.
| | | | | | | | | | | |
Collapse
|
39
|
Grunewald TGP, Butt E. The LIM and SH3 domain protein family: structural proteins or signal transducers or both? Mol Cancer 2008; 7:31. [PMID: 18419822 PMCID: PMC2359764 DOI: 10.1186/1476-4598-7-31] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2008] [Accepted: 04/17/2008] [Indexed: 12/24/2022] Open
Abstract
LIM and SH3 Protein 1 (LASP-1) was initially identified from a cDNA library of metastatic axillary lymph nodes (MLN) more than a decade ago. It was found to be overexpressed in human breast and ovarian cancer and became the first member of a newly defined LIM-protein subfamily of the nebulin group characterized by the combined presence of LIM and SH3 domains. LASP2, a novel LASP1-related gene was first identified and characterized in silico. Subsequently it proved to be a splice variant of the Nebulin gene and therefore was also termed LIM/nebulette. LASP-1 and -2 are highly conserved in their LIM, nebulin-like and SH3 domains but differ significantly at their linker regions. Both proteins are ubiquitously expressed and involved in cytoskeletal architecture, especially in the organization of focal adhesions. Here we present the first systematic review to summarize all relevant data concerning their domain organization, expression profiles, regulating factors and function. We compile evidence that both, LASP-1 and LASP-2, are important during early embryo- and fetogenesis and are highly expressed in the central nervous system of the adult. However, only LASP-1 seems to participate significantly in neuronal differentiation and plays an important functional role in migration and proliferation of certain cancer cells while the role of LASP-2 is more structural. The increased expression of LASP-1 in breast tumours correlates with high rates of nodal-metastasis and refers to a possible relevance as a prognostic marker.
Collapse
Affiliation(s)
- Thomas GP Grunewald
- Department of Pediatrics, Klinikum rechts der Isar, Technische Universität München, Pediatric Oncology Center, Kölner Platz 1, D-80804 Munich, Germany
| | - Elke Butt
- Institute for Clinical Biochemistry and Pathobiochemistry, University of Wuerzburg, Grombuehlstr. 12, D-97080 Wuerzburg, Germany
| |
Collapse
|
40
|
Corti V, Sanchez-Ruiz Y, Piccoli G, Bergamaschi A, Cannistraci CV, Pattini L, Cerutti S, Bachi A, Alessio M, Malgaroli A. Protein fingerprints of cultured CA3-CA1 hippocampal neurons: comparative analysis of the distribution of synaptosomal and cytosolic proteins. BMC Neurosci 2008; 9:36. [PMID: 18402664 PMCID: PMC2324106 DOI: 10.1186/1471-2202-9-36] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2008] [Accepted: 04/10/2008] [Indexed: 11/21/2022] Open
Abstract
Background All studies aimed at understanding complex molecular changes occurring at synapses face the problem of how a complete view of the synaptic proteome and of its changes can be efficiently met. This is highly desirable when synaptic plasticity processes are analyzed since the structure and the biochemistry of neurons and synapses get completely reshaped. Because most molecular studies of synapses are nowadays mainly or at least in part based on protein extracts from neuronal cultures, this is not a feasible option: these simplified versions of the brain tissue on one hand provide an homogeneous pure population of neurons but on the other yield only tiny amounts of proteins, many orders of magnitude smaller than conventional brain tissue. As a way to overcome this limitation and to find a simple way to screen for protein changes at cultured synapses, we have produced and characterized two dimensional electrophoresis (2DE) maps of the synaptic proteome of CA3-CA1 hippocampal neurons in culture. Results To obtain 2D maps, hippocampal cultures were mass produced and after synaptic maturation, proteins were extracted following subfractionation procedures and separated by 2D gel electrophoresis. Similar maps were obtained for the crude cytosol of cultured neurons and for synaptosomes purified from CA3-CA1 hippocampal tissue. To efficiently compare these different maps some clearly identifiable reference points were molecularly identified by mass spectrometry and immunolabeling methods. This information was used to run a differential analysis and establish homologies and dissimilarities in these 2D protein profiles. Conclusion Because reproducible fingerprints of cultured synapses were clearly obtained, we believe that our mapping effort could represent a simple tool to screen for protein expression and/or protein localization changes in CA3-CA1 hippocampal neurons following plasticity.
Collapse
Affiliation(s)
- Valeria Corti
- Proteome Biochemistry, San Raffaele Scientific Institute, Milan, Italy.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
41
|
DeGiorgis JA, Galbraith JA, Dosemeci A, Chen X, Reese TS. Distribution of the scaffolding proteins PSD-95, PSD-93, and SAP97 in isolated PSDs. ACTA ACUST UNITED AC 2008; 35:239-50. [PMID: 18392731 DOI: 10.1007/s11068-007-9017-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2007] [Revised: 08/14/2007] [Accepted: 08/21/2007] [Indexed: 10/22/2022]
Abstract
We compared the distribution of three scaffolding proteins, all belonging to a family of membrane-associated guanylate kinases, thought to have key roles in the organization of the postsynaptic density (PSD). Isolated PSDs readily adhered to treated glass coverslips where they were labeled with immunogold and rotary shadowed for analysis by EM. The distribution of proteins within individual PSDs were measured by counting and mapping individual immunogold particles. PSD-95, as previously described, is distributed evenly throughout the PSD. We find here that PSD-93 has a nearly identical distribution suggesting that PSD-95 and PSD-93 could perform similar roles. SAP97, in contrast, is concentrated near edges of cleft sides of the PSDs, and in small clumps on their cytoplasmic sides. The homogenous distribution of PSD-95 and PSD-93 throughout the PSD is consistent with their being part of a backbone that stabilizes their various binding partners within the PSD. The distribution of SAP97 confirms that this protein is actually an integral component of the PSD, and suggests that it may have a role in inserting or stabilizing its main binding partner, Glu-R1, at the edge of the PSD.
Collapse
Affiliation(s)
- Joseph A DeGiorgis
- Laboratory of Neurobiology, National Institutes of Health, NINDS, Building 49, Room 3A60, 49 Convent Drive, Bethesda, MD 20892, USA.
| | | | | | | | | |
Collapse
|
42
|
Wang J, Gu Y, Wang L, Hang X, Gao Y, Wang H, Zhang C. HUPO BPP pilot study: A proteomics analysis of the mouse brain of different developmental stages. Proteomics 2007; 7:4008-15. [DOI: 10.1002/pmic.200700341] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
43
|
Miller LC, Sossin WS. The significance of organellar proteomics for the nervous system. Proteomics Clin Appl 2007; 1:1436-45. [PMID: 21136641 DOI: 10.1002/prca.200700366] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2007] [Indexed: 12/16/2022]
Abstract
Organellar proteomics is a useful tool for gaining biological insights about structures in the cell. Here, we discuss the tools used in organellar proteomics and the impact of this technique in understanding nervous system function. We will review insights gained from the proteomes of nervous system-specific organelles such as synaptic vesicles and the postsynaptic density. Moreover, we will show how comparison of proteomes between organelles isolated from the nervous system and from other tissues highlight nervous system-specific functions using the examples of clathrin-coated vesicles and RNA granules.
Collapse
Affiliation(s)
- Linda C Miller
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | | |
Collapse
|
44
|
Li KW, Smit AB. Proteomics of brain synapses and molecular dissection of synaptic subdomains. Proteomics Clin Appl 2007; 1:1476-84. [DOI: 10.1002/prca.200700328] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
45
|
Dosemeci A, Makusky AJ, Jankowska-Stephens E, Yang X, Slotta DJ, Markey SP. Composition of the synaptic PSD-95 complex. Mol Cell Proteomics 2007; 6:1749-60. [PMID: 17623647 PMCID: PMC2096750 DOI: 10.1074/mcp.m700040-mcp200] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Postsynaptic density protein 95 (PSD-95), a specialized scaffold protein with multiple protein interaction domains, forms the backbone of an extensive postsynaptic protein complex that organizes receptors and signal transduction molecules at the synaptic contact zone. Large, detergent-insoluble PSD-95-based postsynaptic complexes can be affinity-purified from conventional PSD fractions using magnetic beads coated with a PSD-95 antibody. In the present study purified PSD-95 complexes were analyzed by LC/MS/MS. A semiquantitative measure of the relative abundances of proteins in the purified PSD-95 complexes and the parent PSD fraction was estimated based on the cumulative ion current intensities of corresponding peptides. The affinity-purified preparation was largely depleted of presynaptic proteins, spectrin, intermediate filaments, and other contaminants prominent in the parent PSD fraction. We identified 525 of the proteins previously reported in parent PSD fractions, but only 288 of these were detected after affinity purification. We discuss 26 proteins that are major components in the PSD-95 complex based upon abundance ranking and affinity co-purification with PSD-95. This subset represents a minimal list of constituent proteins of the PSD-95 complex and includes, in addition to the specialized scaffolds and N-methyl-d-aspartate (NMDA) receptors, an abundance of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors, small G-protein regulators, cell adhesion molecules, and hypothetical proteins. The identification of two Arf regulators, BRAG1 and BRAG2b, as co-purifying components of the complex implies pivotal functions in spine plasticity such as the reorganization of the actin cytoskeleton and insertion and retrieval of proteins to and from the plasma membrane. Another co-purifying protein (Q8BZM2) with two sterile alpha motif domains may represent a novel structural core element of the PSD.
Collapse
Affiliation(s)
- Ayse Dosemeci
- From the Laboratory of Neurobiology, NINDS, National Institutes of Health, Bethesda, Maryland 20892
| | - Anthony J. Makusky
- Laboratory of Neurotoxicology, National Institute of Mental Health, Bethesda, Maryland 20892
| | - Ewa Jankowska-Stephens
- Laboratory of Neurotoxicology, National Institute of Mental Health, Bethesda, Maryland 20892
| | - Xiaoyu Yang
- Laboratory of Neurotoxicology, National Institute of Mental Health, Bethesda, Maryland 20892
| | - Douglas J. Slotta
- Laboratory of Neurotoxicology, National Institute of Mental Health, Bethesda, Maryland 20892
| | - Sanford P. Markey
- Laboratory of Neurotoxicology, National Institute of Mental Health, Bethesda, Maryland 20892
| |
Collapse
|
46
|
A Comprehensive Identification of Synaptic Vesicle Proteins in Rat Brains by cRPLC/MS-MS and 2DE/MALDI-TOF-MS. B KOREAN CHEM SOC 2007. [DOI: 10.5012/bkcs.2007.28.9.1499] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
47
|
Glückmann M, Fella K, Waidelich D, Merkel D, Kruft V, Kramer PJ, Walter Y, Hellmann J, Karas M, Kröger M. Prevalidation of potential protein biomarkers in toxicology using iTRAQ™ reagent technology. Proteomics 2007; 7:1564-74. [PMID: 17443845 DOI: 10.1002/pmic.200600836] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Today, toxicoproteomics still relies mainly on 2-DE followed by MS for detection and identification of proteins, which might characterize a certain state of disease, indicate toxicity or even predict carcinogenicity. We utilized the classical 2-DE/MS approach for the evaluation of early protein biomarkers which are predictive for chemically induced hepatocarcinogenesis in rats. We were able to identify statistically significantly deregulated proteins in N-nitrosomorpholine exposed rat liver tissue. Based on literature data, biological relevance in the early molecular process of hepatocarcinogenicity could be suggested for most of these potential biomarkers. However, in order to ensure reliable results and to create the prerequisites necessary for integration in routine toxicology studies in the future, these protein expression patterns need to be prevalidated using independent technology platforms. In the current study, we evaluated the usefulness of iTRAQ reagent technology (Applied Biosystems, Framingham, USA), a recently introduced MS-based protein quantitation method, for verification of the 2-DE/MS biomarkers. In summary, the regulation of 26 2-DE/MS derived protein biomarkers could be verified. Proteins like HSP 90-beta, annexin A5, ketohexokinase, N-hydroxyarylamine sulfotransferase, ornithine aminotransferase, and adenosine kinase showed highly comparable fold changes using both proteomic quantitation strategies. In addition, iTRAQ analysis delivered further potential biomarkers with biological relevance to the processes of hepatocarcinogenicity: e.g. placental form of glutathione S-transferase (GST-P), carbonic anhydrase, and aflatoxin B1 aldehyde reductase. Our results show both the usefulness of iTRAQ reagent technology for biomarker prevalidation as well as for identification of further potential marker proteins, which are indicative for liver hepatocarcinogenicity.
Collapse
Affiliation(s)
- Matthias Glückmann
- Applied Biosystems, Mass Spectrometry and Proteomics, Darmstadt, Germany
| | | | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Stone JL, Merriman B, Cantor RM, Geschwind DH, Nelson SF. High density SNP association study of a major autism linkage region on chromosome 17. Hum Mol Genet 2007; 16:704-715. [PMID: 17376794 DOI: 10.1093/hmg/ddm015] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A region on chromosome 17 has recently been highlighted as linked to autism (MIM[209850]) in multiple studies and evidence has accumulated suggesting that male-only families (those families that have produced only affected males) provide the major contribution to linkage at this locus. In an attempt to comprehensively test for association of common variants to autism within the region on chromosome 17 defined in Stone et al. (Stone, J.L., Merriman, B., Cantor, R.M., Yonan, A.L., Gilliam, T.C., Geschwind, D.H. and Nelson, S.F. (2004) Evidence for sex-specific risk alleles in autism spectrum disorder. Am. J. Hum. Genet., 75, 1117-1123), a dense panel of single nucleotide polymorphisms (SNPs) was selected across the linkage peak and analyzed in a trio-based study design. SNPs were genotyped in 219 independent trios at an average intermarker distance of 6.1 kb across the 13.7 Mb interval. This provided ~80% coverage of common HapMap variation present in Caucasians, testing exonic, intronic, promoter and intergenic regions, as knowledge of important functional regions within the genome is currently limited. In this comprehensive association study of a linkage region in autism, no single SNP or haplotype association was sufficient to account for the initial linkage signal. Nominally significant single SNP and/or haplotype-based association results were detected in 15 genes, of which, MYO1D, ACCN1 and LASP1 stand out as genes with autism risk alleles requiring further study, with potential GRRs in the range of 1.34-2.29.
Collapse
Affiliation(s)
- Jennifer L Stone
- Department of Human Genetics, University of California, Los Angeles, CA 90095, USA
| | | | | | | | | |
Collapse
|
49
|
Abstract
Synaptic vesicles are key organelles in neurotransmission. Vesicle integral or membrane-associated proteins mediate the various functions the organelle fulfills during its life cycle. These include organelle transport, interaction with the nerve terminal cytoskeleton, uptake and storage of low molecular weight constituents, and the regulated interaction with the pre-synaptic plasma membrane during exo- and endocytosis. Within the past two decades, converging work from several laboratories resulted in the molecular and functional characterization of the proteinaceous inventory of the synaptic vesicle compartment. However, up until recently and due to technical difficulties, it was impossible to screen the entire organelle thoroughly. Recent advances in membrane protein identification and mass spectrometry (MS) have dramatically promoted this field. A comparison of different techniques for elucidating the proteinaceous composition of synaptic vesicles revealed numerous overlaps but also remarkable differences in the protein constituents of the synaptic vesicle compartment, indicating that several protein separation techniques in combination with differing MS approaches are required to identify and characterize the synaptic vesicle proteome. This review highlights the power of various gel separation techniques and MS analyses for the characterization of the proteome of highly purified synaptic vesicles. Furthermore, the newly detected protein assignments to synaptic vesicles, especially those proteins which are new to the inventory of the synaptic vesicle proteome, are critically discussed.
Collapse
Affiliation(s)
- Jacqueline Burré
- Institute of Cell Biology and Neuroscience, Neurochemistry, JW Goethe University, Frankfurt, Germany.
| | | |
Collapse
|
50
|
Munton RP, Tweedie-Cullen R, Livingstone-Zatchej M, Weinandy F, Waidelich M, Longo D, Gehrig P, Potthast F, Rutishauser D, Gerrits B, Panse C, Schlapbach R, Mansuy IM. Qualitative and Quantitative Analyses of Protein Phosphorylation in Naive and Stimulated Mouse Synaptosomal Preparations. Mol Cell Proteomics 2007; 6:283-93. [PMID: 17114649 DOI: 10.1074/mcp.m600046-mcp200] [Citation(s) in RCA: 181] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Activity-dependent protein phosphorylation is a highly dynamic yet tightly regulated process essential for cellular signaling. Although recognized as critical for neuronal functions, the extent and stoichiometry of phosphorylation in brain cells remain undetermined. In this study, we resolved activity-dependent changes in phosphorylation stoichiometry at specific sites in distinct subcellular compartments of brain cells. Following highly sensitive phosphopeptide enrichment using immobilized metal affinity chromatography and mass spectrometry, we isolated and identified 974 unique phosphorylation sites on 499 proteins, many of which are novel. To further explore the significance of specific phosphorylation sites, we used isobaric peptide labels and determined the absolute quantity of both phosphorylated and non-phosphorylated peptides of candidate phosphoproteins and estimated phosphorylation stoichiometry. The analyses of phosphorylation dynamics using differentially stimulated synaptic terminal preparations revealed activity-dependent changes in phosphorylation stoichiometry of target proteins. Using this method, we were able to differentiate between distinct isoforms of Ca2+/calmodulin-dependent protein kinase (CaMKII) and identify a novel activity-regulated phosphorylation site on the glutamate receptor subunit GluR1. Together these data illustrate that mass spectrometry-based methods can be used to determine activity-dependent changes in phosphorylation stoichiometry on candidate phosphopeptides following large scale phosphoproteome analysis of brain tissue.
Collapse
Affiliation(s)
- Richard P Munton
- Brain Research Institute, Medical Faculty of the University of Zürich, Switzerland
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|