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Dowling P, Zweyer M, Sabir H, Henry M, Meleady P, Swandulla D, Ohlendieck K. Mass spectrometry-based proteomic characterization of the middle-aged mouse brain for animal model research of neuromuscular diseases. Eur J Transl Myol 2023; 33:11553. [PMID: 37545360 PMCID: PMC10583138 DOI: 10.4081/ejtm.2023.11553] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 07/28/2023] [Indexed: 08/08/2023] Open
Abstract
Neuromuscular diseases with primary muscle wasting symptoms may also display multi-systemic changes in the body and exhibit secondary pathophysiological alterations in various non-muscle tissues. In some cases, this includes proteome-wide alterations and/or adaptations in the central nervous system. Thus, in order to provide an improved bioanalytical basis for the comprehensive evaluation of animal models that are routinely used in muscle research, this report describes the mass spectrometry-based proteomic characterization of the mouse brain. Crude tissue extracts were examined by bottom-up proteomics and detected 4558 distinct protein species. The detailed analysis of the brain proteome revealed the presence of abundant cellular proteoforms in the neuronal cytoskeleton, as well as various brain region enriched proteins, including markers of the cerebral cortex, cerebellum, hippocampus and the olfactory bulb. Neuroproteomic markers of specific cell types in the brain were identified in association with various types of neurons and glia cells. Markers of subcellular structures were established for the plasmalemma, nucleus, endoplasmic reticulum, mitochondria and other crucial organelles, as well as synaptic components that are involved in presynaptic vesicle docking, neurotransmitter release and synapse remodelling.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland; Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Co. Kildare.
| | - Margit Zweyer
- Department of Neonatology and Paediatric Intensive Care, Children's Hospital, University of Bonn, Bonn, Germany; German Centre for Neurodegenerative Diseases, University of Bonn, Bonn.
| | - Hemmen Sabir
- Department of Neonatology and Paediatric Intensive Care, Children's Hospital, University of Bonn, Bonn, Germany; German Centre for Neurodegenerative Diseases, University of Bonn, Bonn.
| | - Michael Henry
- National Institute for Cellular Biotechnology, Dublin City University, Dublin.
| | - Paula Meleady
- National Institute for Cellular Biotechnology, Dublin City University, Dublin.
| | - Dieter Swandulla
- Institute of Physiology, Medical Faculty, University of Bonn, Bonn.
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland; Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Co. Kildare.
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2
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Collins ES, Butt AQ, Gibson DS, Dunn MJ, Fearon U, van Kuijk AW, Gerlag DM, Pontifex E, Veale DJ, Tak PP, FitzGerald O, Pennington SR. A clinically based protein discovery strategy to identify potential biomarkers of response to anti-TNF-α treatment of psoriatic arthritis. Proteomics Clin Appl 2015; 10:645-62. [PMID: 26108918 DOI: 10.1002/prca.201500051] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 06/05/2015] [Accepted: 06/22/2015] [Indexed: 12/19/2022]
Abstract
PURPOSE Psoriatic arthritis (PsA) can be treated using biologic therapies targeting biomolecules such as tumor necrosis factor alpha, interleukins (IL)-17 and IL-23. Although 70% PsA patients respond well to therapy, 30% patients show no or limited clinical improvement. Biomarkers that predict response to therapy would help to avoid unnecessary use of expensive biologics in nonresponding patients and enable alternative treatments to be explored. EXPERIMENTAL DESIGN Patient synovial tissue samples from two clinical studies were analysed using difference in-gel electrophoresis-based proteomics to identify protein expression differences in response to anti-TNF-α treatment. Subsequent multiplexed MRM measurements were used to verify potential biomarkers. RESULTS A total of 119 proteins were differentially expressed (p<0.05) in response to anti-TNF-α treatment and 25 proteins were differentially expressed (p<0.05) between "good responders" and "poor responders". From these differentially expressed proteins, MRM assays were developed for four proteins to explore their potential as treatment predictive biomarkers. CONCLUSION AND CLINICAL RELEVANCE Gel-based proteomics strategy has demonstrated differential protein expression in synovial tissue of PsA patients, in response to anti-TNF-α treatment. Development of multiplex MRM assays to these differentially expressed proteins has the potential to predict response to therapy and allow alternative, more effective treatments to be explored sooner.
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Affiliation(s)
- Emily S Collins
- School of Medicine and Medical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland.,Department of Rheumatology, St Vincent's University Hospital, Elm Park, Dublin, Ireland
| | - Aisha Q Butt
- School of Medicine and Medical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - David S Gibson
- Northern Ireland Centre for Stratified Medicine, University of Ulster, C-TRIC, Londonderry, UK
| | - Michael J Dunn
- School of Medicine and Medical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Ursula Fearon
- School of Medicine and Medical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland.,Department of Rheumatology, St Vincent's University Hospital, Elm Park, Dublin, Ireland
| | - Arno W van Kuijk
- Department of Clinical Immunology and Rheumatology, F4-105, Academic Medical Centre/University of Amsterdam, Amsterdam, The Netherlands
| | - Danielle M Gerlag
- Department of Clinical Immunology and Rheumatology, F4-105, Academic Medical Centre/University of Amsterdam, Amsterdam, The Netherlands
| | - Eliza Pontifex
- Department of Rheumatology, St Vincent's University Hospital, Elm Park, Dublin, Ireland
| | - Douglas J Veale
- School of Medicine and Medical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland.,Department of Rheumatology, St Vincent's University Hospital, Elm Park, Dublin, Ireland
| | - Paul P Tak
- Department of Clinical Immunology and Rheumatology, F4-105, Academic Medical Centre/University of Amsterdam, Amsterdam, The Netherlands
| | - Oliver FitzGerald
- School of Medicine and Medical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland.,Department of Rheumatology, St Vincent's University Hospital, Elm Park, Dublin, Ireland
| | - Stephen R Pennington
- School of Medicine and Medical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland
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Föcking M, Opstelten R, Prickaerts J, Steinbusch HWM, Dunn MJ, van den Hove DLA, Cotter DR. Proteomic investigation of the hippocampus in prenatally stressed mice implicates changes in membrane trafficking, cytoskeletal, and metabolic function. Dev Neurosci 2014; 36:432-42. [PMID: 25138076 DOI: 10.1159/000365327] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 06/17/2014] [Indexed: 11/19/2022] Open
Abstract
Prenatal stress influences the development of the fetal brain and so contributes to the risk of the development of psychiatric disorders in later life. The hippocampus is particularly sensitive to prenatal stress, and robust abnormalities have been described in the hippocampus in schizophrenia and depression. The aim of this study was to determine whether prenatal stress is associated with distinct patterns of differential protein expression in the hippocampus using a validated mouse model. We therefore performed a comparative proteomic study assessing female hippocampal samples from 8 prenatally stressed mice and 8 control mice. Differential protein expression was assessed using 2-dimensional difference in gel electrophoresis and subsequent mass spectrometry. The observed changes in a selected group of differentially expressed proteins were confirmed by Western blotting. In comparison to controls, 47 protein spots (38 individual proteins) were found to be differentially expressed in the hippocampus of prenatally stressed mice. Functional grouping of these proteins revealed that prenatal stress influenced the expression of proteins involved in brain development, cytoskeletal composition, stress response, and energy metabolism. Western blotting was utilized to validate the changes in calretinin, hippocalcin, profilin-1 and the signal-transducing adaptor molecule STAM1. Septin-5 could not be validated via Western blotting due to methodological issues. Closer investigation of the validated proteins also pointed to an interesting role for membrane trafficking deficits mediated by prenatal stress. Our findings demonstrate that prenatal stress leads to altered hippocampal protein expression, implicating numerous molecular pathways that may provide new targets for psychotropic drug development.
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Affiliation(s)
- Melanie Föcking
- Department of Psychiatry, Royal College of Surgeons in Ireland, Beaumont Hospital, Dublin, Ireland
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4
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Laeremans A, Van de Plas B, Clerens S, Van den Bergh G, Arckens L, Hu TT. Protein expression dynamics during postnatal mouse brain development. J Exp Neurosci 2013; 7:61-74. [PMID: 25157209 PMCID: PMC4089830 DOI: 10.4137/jen.s12453] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
We explored differential protein expression profiles in the mouse forebrain at different stages of postnatal development, including 10-day (P10), 30-day (P30), and adult (Ad) mice, by large-scale screening of proteome maps using two-dimensional difference gel electrophoresis. Mass spectrometry analysis resulted in the identification of 251 differentially expressed proteins. Most molecular changes were observed between P10 compared to both P30 and Ad. Computational ingenuity pathway analysis (IPA) confirmed these proteins as crucial molecules in the biological function of nervous system development. Moreover, IPA revealed Semaphorin signaling in neurons and the protein ubiquitination pathway as essential canonical pathways in the mouse forebrain during postnatal development. For these main biological pathways, the transcriptional regulation of the age-dependent expression of selected proteins was validated by means of in situ hybridization. In conclusion, we suggest that proteolysis and neurite outgrowth guidance are key biological processes, particularly during early brain maturation.
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Affiliation(s)
- Annelies Laeremans
- Laboratory of Neuroplasticity and Neuroproteomics, KU Leuven, Leuven, Belgium
| | - Babs Van de Plas
- Laboratory of Neuroplasticity and Neuroproteomics, KU Leuven, Leuven, Belgium
| | - Stefan Clerens
- Laboratory of Neuroplasticity and Neuroproteomics, KU Leuven, Leuven, Belgium. ; Group of Food & Bio-based Products, AgResearch Ltd., Christchurch, New Zealand
| | - Gert Van den Bergh
- Laboratory of Neuroplasticity and Neuroproteomics, KU Leuven, Leuven, Belgium. ; Laboratory of Biological Psychology, KU Leuven, Leuven, Belgium
| | - Lutgarde Arckens
- Laboratory of Neuroplasticity and Neuroproteomics, KU Leuven, Leuven, Belgium
| | - Tjing-Tjing Hu
- Laboratory of Neuroplasticity and Neuroproteomics, KU Leuven, Leuven, Belgium
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5
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Ottis P, Topic B, Loos M, Li KW, de Souza A, Schulz D, Smit AB, Huston JP, Korth C. Aging-induced proteostatic changes in the rat hippocampus identify ARP3, NEB2 and BRAG2 as a molecular circuitry for cognitive impairment. PLoS One 2013; 8:e75112. [PMID: 24069387 PMCID: PMC3777897 DOI: 10.1371/journal.pone.0075112] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 08/10/2013] [Indexed: 11/28/2022] Open
Abstract
Disturbed proteostasis as a particular phenotype of the aging organism has been advanced in C. elegans experiments and is also conceived to underlie neurodegenerative diseases in humans. Here, we investigated whether particular changes in non-disease related proteostasis can be identified in the aged mammalian brain, and whether a particular signature of aberrant proteostasis is related to behavioral performance of learning and memory. Young (adult, n = 30) and aged (2 years, n = 50) Wistar rats were tested in the Morris Water Maze (MWM) to distinguish superior and inferior performers. For both young and old rats, the best and worst performers in the MWM were selected and the insoluble proteome, termed aggregome, was purified from the hippocampus as evidence for aberrant proteostasis. Quantitative proteomics (iTRAQ) was performed. The aged inferior performers were considered as a model for spontaneous, age-associated cognitive impairment. Whereas variability of the insoluble proteome increased with age, absolute changes in the levels of insoluble proteins were small compared to the findings in the whole C. elegans insoluble proteome. However, we identified proteins with aberrant proteostasis in aging. For the cognitively impaired rats, we identified a changed molecular circuitry of proteins selectively involved in F-actin remodeling, synapse building and long-term depression: actin related protein 3 (ARP3), neurabin II (NEB2) and IQ motif and SEC7 domain-containing protein 1 (BRAG2). We demonstrate that aberrant proteostasis is a specific phenotype of brain aging in mammals. We identify a distinct molecular circuitry where changes in proteostasis are characteristic for poor learning and memory performance in the wild type, aged rat. Our findings 1. establish the search for aberrant proteostasis as a successful strategy to identify neuronal dysfunction in deficient cognitive behavior, 2. reveal a previously unknown functional network of proteins (ARP3, NEB2, BRAG2) involved in age-associated cognitive dysfunction.
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Affiliation(s)
- Philipp Ottis
- Department of Neuropathology, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany
| | - Bianca Topic
- Center for Behavioral Neuroscience, Department Experimental Psychology, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany
| | - Maarten Loos
- Department of Molecular and Cellular Neurobiology, Faculty of Earth and Life Sciences, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, Amsterdam, The Netherlands
- Synaptologics B.V., Amsterdam, The Netherlands
| | - Ka Wan Li
- Department of Molecular and Cellular Neurobiology, Faculty of Earth and Life Sciences, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, Amsterdam, The Netherlands
| | - Angelica de Souza
- Center for Behavioral Neuroscience, Department Experimental Psychology, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany
| | - Daniela Schulz
- Center for Behavioral Neuroscience, Department Experimental Psychology, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany
| | - August B. Smit
- Department of Molecular and Cellular Neurobiology, Faculty of Earth and Life Sciences, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, Amsterdam, The Netherlands
| | - Joseph P. Huston
- Center for Behavioral Neuroscience, Department Experimental Psychology, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany
| | - Carsten Korth
- Department of Neuropathology, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany
- * E-mail:
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6
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Föcking M, Chen WQ, Dicker P, Dunn MJ, Lubec G, Cotter DR. Proteomic analysis of human hippocampus shows differential protein expression in the different hippocampal subfields. Proteomics 2012; 12:2477-81. [DOI: 10.1002/pmic.201200031] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Melanie Föcking
- Department of Psychiatry; Royal College of Surgeons in Ireland; Dublin; Ireland
| | - Wei-Qiang Chen
- Department of Pediatrics; Medical University of Vienna; Vienna; Austria
| | - Patrick Dicker
- Department of Epidemiology; Royal College of Surgeons in Ireland; Dublin; Ireland
| | - Michael J. Dunn
- Proteome Research Centre; UCD Conway Institute of Biomolecular and Biomedical Research, School of Medicine and Medical Sciences; Dublin; Ireland
| | - Gert Lubec
- Department of Pediatrics; Medical University of Vienna; Vienna; Austria
| | - David R. Cotter
- Department of Psychiatry; Royal College of Surgeons in Ireland; Dublin; Ireland
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7
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Vanguilder HD, Freeman WM. The hippocampal neuroproteome with aging and cognitive decline: past progress and future directions. Front Aging Neurosci 2011; 3:8. [PMID: 21647399 PMCID: PMC3102218 DOI: 10.3389/fnagi.2011.00008] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Accepted: 05/12/2011] [Indexed: 01/12/2023] Open
Abstract
Although steady progress on understanding brain aging has been made over recent decades through standard anatomical, immunohistochemical, and biochemical techniques, the biological basis of non-neurodegenerative cognitive decline with aging remains to be determined. This is due in part to technical limitations of traditional approaches, in which only a small fraction of neurobiologically relevant proteins, mRNAs or metabolites can be assessed at a time. With the development and refinement of proteomic technologies that enable simultaneous quantitative assessment of hundreds to thousands of proteins, neuroproteomic studies of brain aging and cognitive decline are becoming more widespread. This review focuses on the contributions of neuroproteomic investigations to advances in our understanding of age-related deficits of hippocampus-dependent spatial learning and memory. Accumulating neuroproteomic data demonstrate that hippocampal aging involves common themes of dysregulated metabolism, increased oxidative stress, altered protein processing, and decreased synaptic function. Additionally, growing evidence suggests that cognitive decline does not represent a "more aged" phenotype, but rather is associated with specific neuroproteomic changes that occur in addition to age-related alterations. Understanding if and how age-related changes in the hippocampal neuroproteome contribute to cognitive decline and elucidating the pathways and processes that lead to cognitive decline are critical objectives that remain to be achieved. Progress in the field and challenges that remain to be addressed with regard to animal models, behavioral testing, and proteomic reporting are also discussed.
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Affiliation(s)
- Heather D Vanguilder
- Department of Pharmacology, Penn State College of Medicine, Milton S. Hershey Medical Center Hershey, PA, USA
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8
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Zhang C. Proteomic Studies on the Development of the Central Nervous System and Beyond. Neurochem Res 2010; 35:1487-500. [DOI: 10.1007/s11064-010-0218-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2010] [Indexed: 11/27/2022]
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9
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Dietz L, Bosque A, Pankert P, Ohnesorge S, Merz P, Anel A, Schnölzer M, Thierse HJ. Quantitative DY-maleimide-based proteomic 2-DE-labeling strategies using human skin proteins. Proteomics 2009; 9:4298-308. [PMID: 19693804 DOI: 10.1002/pmic.200900051] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Sensitive differential proteomic analysis is challenging and often limited by distinct labeling or tagging strategies. In this study, we have examined the sensitivity, linearity, and photophysical properties of novel protein labeling DY-maleimide dyes (DY-505-MAL, DY-555-MAL and DY-635-MAL). All MS compatible DY-maleimide dyes exhibited excellent emission spectra, high sensitivity, and high linearity, when applied to standard 1-DE protein analysis. Correspondingly, 2-DE analysis of DY-635-MAL or DY-505-MAL maximal-labeled human keratinocyte proteins displayed remarkably high sensitivity. Compared with a standard fluorescent protein stain, DY-635-MAL or DY-505-MAL 2-DE analysis demonstrated equally high spot quality with an overall increase in the number of spots detectable (up to threefold higher;>1000 spots/gel). However, as determined with a FLA-5100 imaging system, comparative MultiGauge, and Delta2D analysis, not all DY-maleimide dyes possessed DIGE compatible fluorescent emission properties. However, DY-505-MAL and DY-635-MAL were found to be suitable for more complex, time and gel intensive, focused multiplexing analyses. Notably - as demonstrated with allergen-stimulated human skin proteins - defined, singular DY-maleimide dye protein labeling (SDPL) allows high quality, time saving, simple, and reliable differential proteomic examination.
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Affiliation(s)
- Lisa Dietz
- Research Group for Immunology & Proteomics, Department of Dermatology and University Medical Center Mannheim, University of Heidelberg, Mannheim, Germany
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10
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English JA, Dicker P, Föcking M, Dunn MJ, Cotter DR. 2-D DIGE analysis implicates cytoskeletal abnormalities in psychiatric disease. Proteomics 2009; 9:3368-82. [PMID: 19562803 DOI: 10.1002/pmic.200900015] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The mechanisms underlying white matter changes in psychiatric disease are not known. We aimed to characterise the differential protein expression in deep white matter from the dorsolateral prefrontal cortex from 35 schizophrenia, 35 bipolar disorder, and 35 control subjects, from the Stanley Array Collection. We used 2-D DIGE to profile for protein expression changes in the brain. We found 70 protein spots to be significantly differentially expressed between disease and control subjects (ANCOVA, p<0.05), 46 of which were subsequently identified by LC-MS/MS. The proteins identified included novel disease candidates as well as proteins that have previously been reported as abnormal in schizophrenia, thus reinforcing their association with the disease. Furthermore, we confirmed the direction of change for three proteins using ELISA, namely neurofilament-light, amphiphysin II, and Rab-GDP-alpha, in a subset of the Stanley Array Collection. In addition, altered expression of neurofilament-light, amphiphysin II, and Rab-GDP-alpha was not observed in the cortex of mice chronically treated with haloperidol, making it less likely that these alterations are a consequence of neuroleptic medication. The data presented here strongly suggest disruption of the cytoskeleton and its associated signal transduction proteins in schizophrenia, and to a lesser extent in bipolar disorder.
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Affiliation(s)
- Jane A English
- Department of Psychiatry, Royal College of Surgeons in Ireland, Dublin, Ireland.
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11
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Govender P, Dunn MJ, Donnelly SC. Proteomics and the lung: Analysis of bronchoalveolar lavage fluid. Proteomics Clin Appl 2009; 3:1044-51. [DOI: 10.1002/prca.200900032] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2009] [Revised: 04/03/2009] [Accepted: 04/09/2009] [Indexed: 11/09/2022]
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12
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Neuroproteomics: understanding the molecular organization and complexity of the brain. Nat Rev Neurosci 2009; 10:635-46. [DOI: 10.1038/nrn2701] [Citation(s) in RCA: 146] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Pennington K, Föcking M, McManus CA, Pariante CM, Dunn MJ, Cotter DR. A proteomic investigation of similarities between conventional and herbal antidepressant treatments. J Psychopharmacol 2009; 23:520-30. [PMID: 18562437 DOI: 10.1177/0269881108091075] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Increasing clinical evidence for the effectiveness of herbal antidepressants has led to investigations at the molecular level. Using two-dimensional gel electrophoresis, this study investigated similarities in protein expression between clomipramine, St John's wort and a Chinese herbal formula, xiao-yao-san, often used in mood disorder treatment. HT22 cells, derived from a mouse hippocampal cell line, were treated for 24 h, and protein expression was compared with that of the untreated cells (n = 4/group). Forty-three protein spots were found to be significantly differentially expressed (P < 0.05) in more than one of the treatment groups. Twenty-nine of these were identified using mass spectrometry. The most affected proteins were those involved in the cytoskeleton and energy metabolism, and an up-regulation of vimentin by all three treatments was confirmed by Western blotting. This study provides preliminary evidence for multiple common molecular targets between conventional and alternative antidepressants, which appear to collectively affect neuronal plasticity.
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Affiliation(s)
- K Pennington
- Department of Psychiatry, Royal College of Surgeons in Ireland, Dublin, Ireland.
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14
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Proteomic analysis of membrane microdomain-associated proteins in the dorsolateral prefrontal cortex in schizophrenia and bipolar disorder reveals alterations in LAMP, STXBP1 and BASP1 protein expression. Mol Psychiatry 2009; 14:601-13. [PMID: 18268500 DOI: 10.1038/mp.2008.7] [Citation(s) in RCA: 136] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The dorsolateral prefrontal cortex (dlpfc) is strongly implicated in the pathogenesis of schizophrenia (SCZ) and bipolar disorder (BPD) and, within this region, abnormalities in glutamatergic neurotransmission and synaptic function have been described. Proteins associated with these functions are enriched in membrane microdomains (MM). In the current study, we used two complementary proteomic methods, two-dimensional difference gel electrophoresis and one-dimensional sodium dodecyl sulphate polyacrylamide gel electrophoresis followed by reverse phase-liquid chromatography-tandem mass spectrometry (RP-LC-MS/MS) (gel separation liquid chromatography-tandem mass spectrometry (GeLC-MS/MS)) to assess protein expression in MM in pooled samples of dlpfc from SCZ, BPD and control cases (n=10 per group) from the Stanley Foundation Brain series. We identified 16 proteins altered in one/both disorders using proteomic methods. We selected three proteins with roles in synaptic function (syntaxin-binding protein 1 (STXBP1), brain abundant membrane-attached signal protein 1 (BASP1) and limbic system-associated membrane protein (LAMP)) for validation by western blotting. This revealed significantly increased expression of these proteins in SCZ (STXBP1 (24% difference; P<0.001), BASP1 (40% difference; P<0.05) and LAMP (22% difference; P<0.01)) and BPD (STXBP1 (31% difference; P<0.001), BASP1 (23% difference; P<0.01) and LAMP (20% difference; P<0.01)) in the Stanley brain series (n=20 per group). Further validation in dlpfc from the Harvard brain subseries (n=10 per group) confirmed increased protein expression in SCZ of STXBP1 (18% difference; P<0.0001), BASP1 (14% difference; P<0.0001) but not LAMP (20% difference; P=0.14). No significant differences in STXBP1, BASP1 or LAMP protein expression in BPD dlpfc were observed. This study, through proteomic assessments of MM in dlpfc and validation in two brain series, strongly implicates LAMP, STXBP1 and BASP1 in SCZ and supports the view of a neuritic and synaptic dysfunction in the neuropathology of SCZ.
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15
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Haque R, Umstead TM, Freeman WM, Floros J, Phelps DS. The impact of surfactant protein-A on ozone-induced changes in the mouse bronchoalveolar lavage proteome. Proteome Sci 2009; 7:12. [PMID: 19323824 PMCID: PMC2666657 DOI: 10.1186/1477-5956-7-12] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2009] [Accepted: 03/26/2009] [Indexed: 12/22/2022] Open
Abstract
Background Ozone is a major component of air pollution. Exposure to this powerful oxidizing agent can cause or exacerbate many lung conditions, especially those involving innate immunity. Surfactant protein-A (SP-A) plays many roles in innate immunity by participating directly in host defense as it exerts opsonin function, or indirectly via its ability to regulate alveolar macrophages and other innate immune cells. The mechanism(s) responsible for ozone-induced pathophysiology, while likely related to oxidative stress, are not well understood. Methods We employed 2-dimensional difference gel electrophoresis (2D-DIGE), a discovery proteomics approach, coupled with MALDI-ToF/ToF to compare the bronchoalveolar lavage (BAL) proteomes in wild type (WT) and SP-A knockout (KO) mice and to assess the impact of ozone or filtered air on the expression of BAL proteins. Using the PANTHER database and the published literature most identified proteins were placed into three functional groups. Results We identified 66 proteins and focused our analysis on these proteins. Many of them fell into three categories: defense and immunity; redox regulation; and protein metabolism, modification and chaperones. In response to the oxidative stress of acute ozone exposure (2 ppm; 3 hours) there were many significant changes in levels of expression of proteins in these groups. Most of the proteins in the redox group were decreased, the proteins involved in protein metabolism increased, and roughly equal numbers of increases and decreases were seen in the defense and immunity group. Responses between WT and KO mice were similar in many respects. However, the percent change was consistently greater in the KO mice and there were more changes that achieved statistical significance in the KO mice, with levels of expression in filtered air-exposed KO mice being closer to ozone-exposed WT mice than to filtered air-exposed WT mice. Conclusion We postulate that SP-A plays a role in reactive oxidant scavenging in WT mice and that its absence in the KO mice in the presence or absence of ozone exposure results in more pronounced, and presumably chronic, oxidative stress.
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Affiliation(s)
- Rizwanul Haque
- Penn State Center for Host defense, Inflammation, and Lung Disease (CHILD) Research and the Department of Pediatrics, Penn State College of Medicine, Hershey, PA, USA
| | - Todd M Umstead
- Penn State Center for Host defense, Inflammation, and Lung Disease (CHILD) Research and the Department of Pediatrics, Penn State College of Medicine, Hershey, PA, USA
| | - Willard M Freeman
- The Department of Pharmacology, Penn State College of Medicine, Hershey, PA, USA
| | - Joanna Floros
- Penn State Center for Host defense, Inflammation, and Lung Disease (CHILD) Research and the Department of Pediatrics, Penn State College of Medicine, Hershey, PA, USA.,The Department of Obstetrics and Gynecology, Penn State College of Medicine, Hershey, PA, USA
| | - David S Phelps
- Penn State Center for Host defense, Inflammation, and Lung Disease (CHILD) Research and the Department of Pediatrics, Penn State College of Medicine, Hershey, PA, USA
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Myung JK, Shim KS, Li L, Höger H, Lubec G. Developmental Brain Protein Level Changes in the C57BL/6J Mouse. J Proteome Res 2009; 8:1207-19. [DOI: 10.1021/pr800990x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Jae-Kyung Myung
- Department of Pediatrics, Medical University of Vienna, Vienna, Austria, and Institute for Animal Genetics, Medical University of Vienna, Himberg, Austria
| | - Ki Shuk Shim
- Department of Pediatrics, Medical University of Vienna, Vienna, Austria, and Institute for Animal Genetics, Medical University of Vienna, Himberg, Austria
| | - Lin Li
- Department of Pediatrics, Medical University of Vienna, Vienna, Austria, and Institute for Animal Genetics, Medical University of Vienna, Himberg, Austria
| | - Harald Höger
- Department of Pediatrics, Medical University of Vienna, Vienna, Austria, and Institute for Animal Genetics, Medical University of Vienna, Himberg, Austria
| | - Gert Lubec
- Department of Pediatrics, Medical University of Vienna, Vienna, Austria, and Institute for Animal Genetics, Medical University of Vienna, Himberg, Austria
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17
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18
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Pennington K, Dicker P, Dunn MJ, Cotter DR. Proteomic analysis reveals protein changes within layer 2 of the insular cortex in schizophrenia. Proteomics 2008; 8:5097-107. [DOI: 10.1002/pmic.200800415] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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19
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Asamoto H, Ichibangase T, Uchikura K, Imai K. Application of an improved proteomics method, fluorogenic derivatization–liquid chromatography–tandem mass spectrometry, to differential analysis of proteins in small regions of mouse brain. J Chromatogr A 2008; 1208:147-55. [DOI: 10.1016/j.chroma.2008.08.078] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2008] [Revised: 08/19/2008] [Accepted: 08/22/2008] [Indexed: 11/25/2022]
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20
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Radwan M, Miller I, Grunert T, Marchetti-Deschmann M, Vogl C, O'Donoghue N, Dunn MJ, Kolbe T, Allmaier G, Gemeiner M, Müller M, Strobl B. The impact of tyrosine kinase 2 (Tyk2) on the proteome of murine macrophages and their response to lipopolysaccharide (LPS). Proteomics 2008; 8:3469-85. [DOI: 10.1002/pmic.200800260] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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21
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Yang S, Liu T, Li S, Zhang X, Ding Q, Que H, Yan X, Wei K, Liu S. Comparative proteomic analysis of brains of naturally aging mice. Neuroscience 2008; 154:1107-20. [DOI: 10.1016/j.neuroscience.2008.04.012] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2008] [Revised: 04/08/2008] [Accepted: 04/09/2008] [Indexed: 11/28/2022]
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22
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Tannu NS, Hemby SE. Two-dimensional fluorescence difference gel electrophoresis for comparative proteomics profiling. Nat Protoc 2007; 1:1732-42. [PMID: 17487156 PMCID: PMC2001252 DOI: 10.1038/nprot.2006.256] [Citation(s) in RCA: 137] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Quantitative proteomics is the workhorse of the modern proteomics initiative. The gel-based and MuDPIT approaches have facilitated vital advances in the measurement of protein expression alterations in normal and disease phenotypic states. The methodological advance in two-dimensional gel electrophoresis (2DGE) has been the multiplexing fluorescent two-dimensional fluorescence difference gel electrophoresis (2D-DIGE). 2D-DIGE is based on direct labeling of lysine groups on proteins with cyanine CyDye DIGE Fluor minimal dyes before isoelectric focusing, enabling the labeling of 2-3 samples with different dyes and electrophoresis of all the samples on the same 2D gel. This capability minimizes spot pattern variability and the number of gels in an experiment while providing simple, accurate and reproducible spot matching. This protocol can be completed in 3-5 weeks depending on the sample size of the experiment and the level of expertise of the investigator.
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Affiliation(s)
- Nilesh S Tannu
- Department of Physiology and Pharmacology, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157, USA
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