1
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Luna Coronell JA, Sergelen K, Hofer P, Gyurján I, Brezina S, Hettegger P, Leeb G, Mach K, Gsur A, Weinhäusel A. The Immunome of Colon Cancer: Functional In Silico Analysis of Antigenic Proteins Deduced from IgG Microarray Profiling. GENOMICS PROTEOMICS & BIOINFORMATICS 2018; 16:73-84. [PMID: 29505855 PMCID: PMC6000238 DOI: 10.1016/j.gpb.2017.10.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 10/01/2017] [Accepted: 10/19/2017] [Indexed: 01/16/2023]
Abstract
Characterization of the colon cancer immunome and its autoantibody signature from differentially-reactive antigens (DIRAGs) could provide insights into aberrant cellular mechanisms or enriched networks associated with diseases. The purpose of this study was to characterize the antibody profile of plasma samples from 32 colorectal cancer (CRC) patients and 32 controls using proteins isolated from 15,417 human cDNA expression clones on microarrays. 671 unique DIRAGs were identified and 632 were more highly reactive in CRC samples. Bioinformatics analyses reveal that compared to control samples, the immunoproteomic IgG profiling of CRC samples is mainly associated with cell death, survival, and proliferation pathways, especially proteins involved in EIF2 and mTOR signaling. Ribosomal proteins (e.g., RPL7, RPL22, and RPL27A) and CRC-related genes such as APC, AXIN1, E2F4, MSH2, PMS2, and TP53 were highly enriched. In addition, differential pathways were observed between the CRC and control samples. Furthermore, 103 DIRAGs were reported in the SEREX antigen database, demonstrating our ability to identify known and new reactive antigens. We also found an overlap of 7 antigens with 48 “CRC genes.” These data indicate that immunomics profiling on protein microarrays is able to reveal the complexity of immune responses in cancerous diseases and faithfully reflects the underlying pathology.
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Affiliation(s)
| | - Khulan Sergelen
- Molecular Diagnostics, AIT - Austrian Institute of Technology, A-1190 Vienna, Austria
| | - Philipp Hofer
- Department of Medicine I, Institute of Cancer Research, Comprehensive Cancer Center, Medical University Vienna, A-1090 Vienna, Austria
| | - István Gyurján
- Molecular Diagnostics, AIT - Austrian Institute of Technology, A-1190 Vienna, Austria
| | - Stefanie Brezina
- Department of Medicine I, Institute of Cancer Research, Comprehensive Cancer Center, Medical University Vienna, A-1090 Vienna, Austria
| | - Peter Hettegger
- Molecular Diagnostics, AIT - Austrian Institute of Technology, A-1190 Vienna, Austria
| | - Gernot Leeb
- Hospital Oberpullendorf, A-7350, Oberpullendorf, Austria
| | - Karl Mach
- Hospital Oberpullendorf, A-7350, Oberpullendorf, Austria
| | - Andrea Gsur
- Department of Medicine I, Institute of Cancer Research, Comprehensive Cancer Center, Medical University Vienna, A-1090 Vienna, Austria
| | - Andreas Weinhäusel
- Molecular Diagnostics, AIT - Austrian Institute of Technology, A-1190 Vienna, Austria.
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2
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Abstract
Proteomics and lipidomics are powerful tools to the large-scale study of proteins and lipids, respectively. Several methods can be employed with particular benefits and limitations in the study of human brain. This is a review of the rationale use of current techniques with particular attention to limitations and pitfalls inherent to each one of the techniques, and more importantly, to their use in the study of post-mortem brain tissue. These aspects are cardinal to avoid false interpretations, errors and unreal expectancies. Other points are also stressed as exemplified in the analysis of human neurodegenerative diseases which are manifested by disease-, region-, and stage-specific modifications commonly in the context of aging. Information about certain altered protein clusters and proteins oxidatively damaged is summarized for Alzheimer and Parkinson diseases.
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Affiliation(s)
- Isidro Ferrer
- Pathologic Anatomy Service, Institute of Neuropathology, Bellvitge University Hospital; Department of Pathology and Experimental Therapeutics, Faculty of Medicine, University of Barcelona; and Network Center of Biomedical Research on Neurodegenerative Diseases, Institute Carlos III; Hospitalet de Llobregat, Llobregat, Spain.
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3
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Pabba M, Scifo E, Kapadia F, Nikolova YS, Ma T, Mechawar N, Tseng GC, Sibille E. Resilient protein co-expression network in male orbitofrontal cortex layer 2/3 during human aging. Neurobiol Aging 2017; 58:180-190. [PMID: 28750307 DOI: 10.1016/j.neurobiolaging.2017.06.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 06/23/2017] [Accepted: 06/24/2017] [Indexed: 12/19/2022]
Abstract
The orbitofrontal cortex (OFC) is vulnerable to normal and pathologic aging. Currently, layer resolution large-scale proteomic studies describing "normal" age-related alterations at OFC are not available. Here, we performed a large-scale exploratory high-throughput mass spectrometry-based protein analysis on OFC layer 2/3 from 15 "young" (15-43 years) and 18 "old" (62-88 years) human male subjects. We detected 4193 proteins and identified 127 differentially expressed (DE) proteins (p-value ≤0.05; effect size >20%), including 65 up- and 62 downregulated proteins (e.g., GFAP, CALB1). Using a previously described categorization of biological aging based on somatic tissues, that is, peripheral "hallmarks of aging," and considering overlap in protein function, we show the highest representation of altered cell-cell communication (54%), deregulated nutrient sensing (39%), and loss of proteostasis (35%) in the set of OFC layer 2/3 DE proteins. DE proteins also showed a significant association with several neurologic disorders; for example, Alzheimer's disease and schizophrenia. Notably, despite age-related changes in individual protein levels, protein co-expression modules were remarkably conserved across age groups, suggesting robust functional homeostasis. Collectively, these results provide biological insight into aging and associated homeostatic mechanisms that maintain normal brain function with advancing age.
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Affiliation(s)
- Mohan Pabba
- Campbell Family Mental Health Research Institute of CAMH, Neurobiology of Depression and Aging, Toronto, Ontario, Canada
| | - Enzo Scifo
- Campbell Family Mental Health Research Institute of CAMH, Neurobiology of Depression and Aging, Toronto, Ontario, Canada
| | - Fenika Kapadia
- Campbell Family Mental Health Research Institute of CAMH, Neurobiology of Depression and Aging, Toronto, Ontario, Canada
| | - Yuliya S Nikolova
- Campbell Family Mental Health Research Institute of CAMH, Neurobiology of Depression and Aging, Toronto, Ontario, Canada
| | - Tianzhou Ma
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Naguib Mechawar
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Verdun, Quebec, Canada; Department of Psychiatry, McGill University, Montréal, Quebec, Canada
| | - George C Tseng
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA; Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Etienne Sibille
- Campbell Family Mental Health Research Institute of CAMH, Neurobiology of Depression and Aging, Toronto, Ontario, Canada; Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada.
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4
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Martín-Aragón S, Villar Á, Benedí J. Age-dependent effects of esculetin on mood-related behavior and cognition from stressed mice are associated with restoring brain antioxidant status. Prog Neuropsychopharmacol Biol Psychiatry 2016; 65:1-16. [PMID: 26290950 DOI: 10.1016/j.pnpbp.2015.08.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2015] [Revised: 08/06/2015] [Accepted: 08/12/2015] [Indexed: 12/20/2022]
Abstract
Dietary antioxidants might exert an important role in the aging process by relieving oxidative damage, a likely cause of age-associated brain dysfunctions. This study aims to investigate the influence of esculetin (6,7-dihydroxycoumarin), a naturally occurring antioxidant in the diet, on mood-related behaviors and cognitive function and its relation with age and brain oxidative damage. Behavioral tests were employed in 11-, 17- and 22-month-old male C57BL/6J mice upon an oral 35day-esculetin treatment (25mg/kg). Activity of antioxidant enzymes, GSH and GSSG levels, GSH/GSSG ratio, and mitochondrial function were analyzed in brain cortex at the end of treatment in order to assess the oxidative status related to mouse behavior. Esculetin treatment attenuated the increased immobility time and enhanced the diminished climbing time in the forced swim task elicited by acute restraint stress (ARS) in the 11- and 17-month-old mice versus their counterpart controls. Furthermore, ARS caused an impairment of contextual memory in the step-through passive avoidance both in mature adult and aged mice which was partially reversed by esculetin only in the 11-month-old mice. Esculetin was effective to prevent the ARS-induced oxidative stress mostly in mature adult mice by restoring antioxidant enzyme activities, augmenting the GSH/GSSG ratio and increasing cytochrome c oxidase (COX) activity in cortex. Modulation of the mood-related behavior and cognitive function upon esculetin treatment in a mouse model of ARS depends on age and is partly due to the enhancement of redox status and levels of COX activity in cortex.
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Affiliation(s)
- Sagrario Martín-Aragón
- Departamento de Farmacología, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza Ramón y Cajal s/n, 28040 Madrid, Spain.
| | - Ángel Villar
- Departamento de Farmacología, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza Ramón y Cajal s/n, 28040 Madrid, Spain
| | - Juana Benedí
- Departamento de Farmacología, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza Ramón y Cajal s/n, 28040 Madrid, Spain
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5
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Häggmark A, Schwenk JM, Nilsson P. Neuroproteomic profiling of human body fluids. Proteomics Clin Appl 2015; 10:485-502. [PMID: 26286680 DOI: 10.1002/prca.201500065] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 07/17/2015] [Accepted: 08/12/2015] [Indexed: 12/11/2022]
Abstract
Analysis of protein expression and abundance provides a possibility to extend the current knowledge on disease-associated processes and pathways. The human brain is a complex organ and dysfunction or damage can give rise to a variety of neurological diseases. Although many proteins potentially reflecting disease progress are originating from brain, the scarce availability of human tissue material has lead to utilization of body fluids such as cerebrospinal fluid and blood in disease-related research. Within the most common neurological disorders, much effort has been spent on studying the role of a few hallmark proteins in disease pathogenesis but despite extensive investigation, the signatures they provide seem insufficient to fully understand and predict disease progress. In order to expand the view the field of neuroproteomics has lately emerged alongside developing technologies, such as affinity proteomics and mass spectrometry, for multiplexed and high-throughput protein profiling. Here, we provide an overview of how such technologies have been applied to study neurological disease and we also discuss some important considerations concerning discovery of disease-associated profiles.
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Affiliation(s)
- Anna Häggmark
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Jochen M Schwenk
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Peter Nilsson
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Stockholm, Sweden
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Bauernfeind AL, Reyzer ML, Caprioli RM, Ely JJ, Babbitt CC, Wray GA, Hof PR, Sherwood CC. High spatial resolution proteomic comparison of the brain in humans and chimpanzees. J Comp Neurol 2015; 523:2043-61. [PMID: 25779868 DOI: 10.1002/cne.23777] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 02/03/2015] [Accepted: 03/11/2015] [Indexed: 12/30/2022]
Abstract
We performed high-throughput mass spectrometry at high spatial resolution from individual regions (anterior cingulate and primary motor, somatosensory, and visual cortices) and layers of the neocortex (layers III, IV, and V) and cerebellum (granule cell layer), as well as the caudate nucleus in humans and chimpanzees. A total of 39 mass spectrometry peaks were matched with probable protein identifications in both species, allowing for comparison in expression. We explored how the pattern of protein expression varies across regions and cortical layers to provide insights into the differences in molecular phenotype of these neural structures between species. The expression of proteins differed principally in a region- and layer-specific pattern, with more subtle differences between species. Specifically, human and chimpanzee brains were similar in their distribution of proteins related to the regulation of transcription and enzyme activity but differed in their expression of proteins supporting aerobic metabolism. Whereas most work assessing molecular expression differences in the brains of primates has been performed on gene transcripts, this dataset extends current understanding of the differential molecular expression that may underlie human cognitive specializations.
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Affiliation(s)
- Amy L Bauernfeind
- Department of Anatomy and Neurobiology, Washington University School of Medicine, St. Louis, Missouri, 63110.,Department of Anthropology, Washington University in St. Louis, St. Louis, Missouri, 63130.,Department of Anthropology, The George Washington University, Washington, DC, 20052
| | - Michelle L Reyzer
- Mass Spectrometry Research Center, Vanderbilt University Medical Center, Nashville, Tennessee, 37232.,Department of Biochemistry, Vanderbilt University Medical Center, Nashville, Tennessee, 37232
| | - Richard M Caprioli
- Mass Spectrometry Research Center, Vanderbilt University Medical Center, Nashville, Tennessee, 37232.,Department of Biochemistry, Vanderbilt University Medical Center, Nashville, Tennessee, 37232
| | - John J Ely
- MAEBIOS-TM, Alamogordo, New Mexico, 88310
| | - Courtney C Babbitt
- Department of Biology, University of Massachusetts Amherst, Amherst, Massachusetts 01003
| | - Gregory A Wray
- Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina, 27708.,Department of Biology, Duke University, Durham, North Carolina, 27708.,Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, 27708
| | - Patrick R Hof
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, 10029.,New York Consortium in Evolutionary Primatology, New York, New York
| | - Chet C Sherwood
- Department of Anthropology, The George Washington University, Washington, DC, 20052
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7
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Fernández-Irigoyen J, Zelaya MV, Perez-Valderrama E, Santamaría E. New insights into the human brain proteome: Protein expression profiling of deep brain stimulation target areas. J Proteomics 2015; 127:395-405. [PMID: 25845585 DOI: 10.1016/j.jprot.2015.03.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 02/09/2015] [Accepted: 03/19/2015] [Indexed: 12/30/2022]
Abstract
UNLABELLED Deep brain stimulation (DBS) is a neurosurgical procedure that provides therapeutic benefits for movement and affective disorders. The nucleus basalis of Meynert (NBM) and substantia nigra (SN) are considered target areas to apply DBS. Even though the degeneration of NBM and SN underlies the cognitive decline observed in neurological diseases, the protein knowledge derived from both areas is scarce. We have characterized the proteome present in both subcortical brain areas using the Triple TOF 5600 mass spectrometer, identifying 2775 and 3469 proteoforms in NBM and SN respectively. Data mining of MS-generated proteomic data have revealed that: i) 675 proteins tend to localize to synaptic ending, ii) 61% of the global dataset is also present in human CSF and/or plasma, and iii) 894 proteins have not been previously identified in healthy brain by MS. The correlation of NBM and SN proteomic expression profiles with human brain transcriptome data available at Allen Brain Atlas has revealed protein evidence for 250 genes considered with brain-wide expression and 112 genes with region-specific expression in human brain. In addition, protein datasets have been classified according to their chromosomal origin, increasing the current proteome coverage in healthy human brain. BIOLOGICAL SIGNIFICANCE The nucleus basalis of Meynert and substantia nigra are brain areas of clinical interest to apply the deep brain stimulation (DBS) technology in neurosurgery. Our proteomic characterization has revealed 675 proteins involved in the regulation of synaptic transmission, electrical machinery, and neurotransmitter release in both DBS target areas. Moreover, 2599 identified proteins present capacity to be secreted to the CSF and plasma. Our data contribute to a further step towards the characterization of the anatomical atlas of the human brain proteome, detecting 652 proteins that are common between different basal ganglia structures. This article is part of a Special Issue entitled: HUPO 2014.
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Affiliation(s)
- Joaquín Fernández-Irigoyen
- ProteoRed-ISCIII, Proteomics Unit, Clinical Neuroproteomics Group, Navarrabiomed, Fundación Miguel Servet, Instituto de Investigación Sanitaria de Navarra (IDISNA), 31008 Pamplona, Spain
| | - María Victoria Zelaya
- ProteoRed-ISCIII, Proteomics Unit, Clinical Neuroproteomics Group, Navarrabiomed, Fundación Miguel Servet, Instituto de Investigación Sanitaria de Navarra (IDISNA), 31008 Pamplona, Spain; Neurological Tissue Bank, Navarrabiomed, Fundación Miguel Servet, 31008 Pamplona, Spain
| | - Estela Perez-Valderrama
- ProteoRed-ISCIII, Proteomics Unit, Clinical Neuroproteomics Group, Navarrabiomed, Fundación Miguel Servet, Instituto de Investigación Sanitaria de Navarra (IDISNA), 31008 Pamplona, Spain
| | - Enrique Santamaría
- ProteoRed-ISCIII, Proteomics Unit, Clinical Neuroproteomics Group, Navarrabiomed, Fundación Miguel Servet, Instituto de Investigación Sanitaria de Navarra (IDISNA), 31008 Pamplona, Spain.
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8
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Fernandez-Irigoyen J, Labarga A, Zabaleta A, de Morentin XM, Perez-Valderrama E, Zelaya MV, Santamaria E. Toward defining the anatomo-proteomic puzzle of the human brain: An integrative analysis. Proteomics Clin Appl 2015; 9:796-807. [PMID: 25418211 DOI: 10.1002/prca.201400127] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 10/17/2014] [Accepted: 11/18/2014] [Indexed: 01/18/2023]
Abstract
The human brain is exceedingly complex, constituted by billions of neurons and trillions of synaptic connections that, in turn, define ∼900 neuroanatomical subdivisions in the adult brain (Hawrylycz et al. An anatomically comprehensive atlas of the human brain transcriptome. Nature 2012, 489, 391-399). The human brain transcriptome has revealed specific regional transcriptional signatures that are regulated in a spatiotemporal manner, increasing the complexity of the structural and molecular organization of this organ (Kang et al. Spatio-temporal transcriptome of the human brain. Nature 2011, 478, 483-489). During the last decade, neuroproteomics has emerged as a powerful approach to profile neural proteomes using shotgun-based MS, providing complementary information about protein content and function at a global level. Here, we revise recent proteome profiling studies performed in human brain, with special emphasis on proteome mapping of anatomical macrostructures, specific subcellular compartments, and cerebrospinal fluid. Moreover, we have performed an integrative functional analysis of the protein compilation derived from these large-scale human brain proteomic studies in order to obtain a comprehensive view of human brain biology. Finally, we also discuss the potential contribution of our meta-analysis to the Chromosome-centric Human Proteome Project initiative.
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Affiliation(s)
- Joaquín Fernandez-Irigoyen
- Clinical Neuroproteomics Group, Proteomics Unit, Proteored-ISCIII, Navarrabiomed, Fundación Miguel Servet, Pamplona, Spain
| | - Alberto Labarga
- Bioinformatics Unit, Navarrabiomed, Fundación Miguel Servet, Pamplona, Spain
| | - Aintzane Zabaleta
- Biofunctional Nanomaterials Laboratory, CIC Biomagune, San Sebastian, Spain
| | - Xabier Martínez de Morentin
- Clinical Neuroproteomics Group, Proteomics Unit, Proteored-ISCIII, Navarrabiomed, Fundación Miguel Servet, Pamplona, Spain
| | - Estela Perez-Valderrama
- Clinical Neuroproteomics Group, Proteomics Unit, Proteored-ISCIII, Navarrabiomed, Fundación Miguel Servet, Pamplona, Spain
| | | | - Enrique Santamaria
- Clinical Neuroproteomics Group, Proteomics Unit, Proteored-ISCIII, Navarrabiomed, Fundación Miguel Servet, Pamplona, Spain
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9
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Shi M, Movius J, Dator R, Aro P, Zhao Y, Pan C, Lin X, Bammler TK, Stewart T, Zabetian CP, Peskind ER, Hu SC, Quinn JF, Galasko DR, Zhang J. Cerebrospinal fluid peptides as potential Parkinson disease biomarkers: a staged pipeline for discovery and validation. Mol Cell Proteomics 2015; 14:544-55. [PMID: 25556233 DOI: 10.1074/mcp.m114.040576] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Finding robust biomarkers for Parkinson disease (PD) is currently hampered by inherent technical limitations associated with imaging or antibody-based protein assays. To circumvent the challenges, we adapted a staged pipeline, starting from our previous proteomic profiling followed by high-throughput targeted mass spectrometry (MS), to identify peptides in human cerebrospinal fluid (CSF) for PD diagnosis and disease severity correlation. In this multicenter study consisting of training and validation sets, a total of 178 subjects were randomly selected from a retrospective cohort, matching age and sex between PD patients, healthy controls, and neurological controls with Alzheimer disease (AD). From ∼14,000 unique peptides displaying differences between PD and healthy control in proteomic investigations, 126 peptides were selected based on relevance and observability in CSF using bioinformatic analysis and MS screening, and then quantified by highly accurate and sensitive selected reaction monitoring (SRM) in the CSF of 30 PD patients versus 30 healthy controls (training set), followed by diagnostic (receiver operating characteristics) and disease severity correlation analyses. The most promising candidates were further tested in an independent cohort of 40 PD patients, 38 AD patients, and 40 healthy controls (validation set). A panel of five peptides (derived from SPP1, LRP1, CSF1R, EPHA4, and TIMP1) was identified to provide an area under curve (AUC) of 0.873 (sensitivity = 76.7%, specificity = 80.0%) for PD versus healthy controls in the training set. The performance was essentially confirmed in the validation set (AUC = 0.853, sensitivity = 82.5%, specificity = 82.5%). Additionally, this panel could also differentiate the PD and AD groups (AUC = 0.990, sensitivity = 95.0%, specificity = 97.4%). Furthermore, a combination of two peptides belonging to proteins TIMP1 and APLP1 significantly correlated with disease severity as determined by the Unified Parkinson's Disease Rating Scale motor scores in both the training (r = 0.381, p = 0.038)j and the validation (r = 0.339, p = 0.032) sets. The novel panel of CSF peptides, if validated in independent cohorts, could be used to assist in clinical diagnosis of PD and has the potential to help monitoring or predicting disease progression.
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Affiliation(s)
- Min Shi
- From the ‡Department of Pathology, University of Washington School of Medicine, Seattle, Washington 98104
| | - James Movius
- From the ‡Department of Pathology, University of Washington School of Medicine, Seattle, Washington 98104
| | - Romel Dator
- From the ‡Department of Pathology, University of Washington School of Medicine, Seattle, Washington 98104
| | - Patrick Aro
- From the ‡Department of Pathology, University of Washington School of Medicine, Seattle, Washington 98104
| | - Yanchun Zhao
- From the ‡Department of Pathology, University of Washington School of Medicine, Seattle, Washington 98104
| | - Catherine Pan
- From the ‡Department of Pathology, University of Washington School of Medicine, Seattle, Washington 98104
| | - Xiangmin Lin
- From the ‡Department of Pathology, University of Washington School of Medicine, Seattle, Washington 98104; §School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Theo K Bammler
- ¶Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington 98195
| | - Tessandra Stewart
- From the ‡Department of Pathology, University of Washington School of Medicine, Seattle, Washington 98104
| | - Cyrus P Zabetian
- ‖Geriatric and Parkinson's Disease Research, Education, and Clinical Centers, Veterans Affairs Puget Sound Health Care System, Seattle, Washington 98108; **Department of Neurology, University of Washington School of Medicine, Seattle, Washington 98195
| | - Elaine R Peskind
- ‡‡Department of Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, Washington 98195; §§Mental Illness Research, Education, and Clinical Center, Veterans Affairs Puget Sound Health Care System, Seattle, Washington 98108
| | - Shu-Ching Hu
- ‖Geriatric and Parkinson's Disease Research, Education, and Clinical Centers, Veterans Affairs Puget Sound Health Care System, Seattle, Washington 98108; **Department of Neurology, University of Washington School of Medicine, Seattle, Washington 98195
| | - Joseph F Quinn
- ¶¶Department of Neurology, Oregon Health and Science University, Portland, Oregon 97239
| | - Douglas R Galasko
- ‖‖Department of Neurosciences, University of California at San Diego, La Jolla, California 92093
| | - Jing Zhang
- From the ‡Department of Pathology, University of Washington School of Medicine, Seattle, Washington 98104;
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10
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Buddhala C, Campbell MC, Perlmutter JS, Kotzbauer PT. Correlation between decreased CSF α-synuclein and Aβ₁₋₄₂ in Parkinson disease. Neurobiol Aging 2015; 36:476-84. [PMID: 25212463 PMCID: PMC4268043 DOI: 10.1016/j.neurobiolaging.2014.07.043] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 07/14/2014] [Accepted: 07/30/2014] [Indexed: 02/07/2023]
Abstract
Accumulation of misfolded α-synuclein (α-syn) protein in Lewy bodies and neurites is the cardinal pathologic feature of Parkinson disease (PD), but abnormal deposition of other proteins may also play a role. Cerebrospinal fluid (CSF) levels of proteins known to accumulate in PD may provide insight into disease-associated changes in protein metabolism and their relationship to disease progression. We measured CSF α-syn, amyloid β₁₋₄₂ (Aβ₁₋₄₂), and tau from 77 nondemented PD and 30 control participants. CSF α-syn and Aβ₁₋₄₂ were significantly lower in PD compared with controls. In contrast with increased CSF tau in Alzheimer disease, CSF tau did not significantly differ between PD and controls. CSF protein levels did not significantly correlate with ratings of motor function or performance on neuropsychological testing. As expected, CSF Aβ₁₋₄₂ inversely correlated with [(11)C]-Pittsburgh compound B (PiB) mean cortical binding potential, with PiB(+) PD participants having lower CSF Aβ₁₋₄₂ compared with PiB(-) PD participants. Furthermore, CSF α-syn positively correlated with Aβ₁₋₄₂ in PD participants but not in controls, suggesting a pathophysiologic connection between the metabolisms of these proteins in PD.
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Affiliation(s)
- Chandana Buddhala
- Department of Neurology, Washington University School of Medicine, St Louis, MO, USA; Department of Developmental Biology, Washington University School of Medicine, St Louis, MO, USA; Hope Center for Neurological Disorders, Washington University School of Medicine, St Louis, MO, USA
| | - Meghan C Campbell
- Department of Neurology, Washington University School of Medicine, St Louis, MO, USA; Department of Radiology, Washington University School of Medicine, St Louis, MO, USA
| | - Joel S Perlmutter
- Department of Neurology, Washington University School of Medicine, St Louis, MO, USA; Hope Center for Neurological Disorders, Washington University School of Medicine, St Louis, MO, USA; Department of Radiology, Washington University School of Medicine, St Louis, MO, USA; Department of Anatomy and Neurobiology, Washington University School of Medicine, St Louis, MO, USA; Program in Occupational Therapy, Washington University School of Medicine, St Louis, MO, USA; Program in Physical Therapy, Washington University School of Medicine, St Louis, MO, USA
| | - Paul T Kotzbauer
- Department of Neurology, Washington University School of Medicine, St Louis, MO, USA; Department of Developmental Biology, Washington University School of Medicine, St Louis, MO, USA; Hope Center for Neurological Disorders, Washington University School of Medicine, St Louis, MO, USA.
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11
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Licker V, Burkhard PR. Proteomics as a new paradigm to tackle Parkinson’s disease research challenges. TRANSLATIONAL PROTEOMICS 2014. [DOI: 10.1016/j.trprot.2014.08.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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12
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Fernández-Irigoyen J, Zelaya MV, Tuñon T, Santamaría E. Anatomo-proteomic characterization of human basal ganglia: focus on striatum and globus pallidus. Mol Brain 2014; 7:83. [PMID: 25406675 PMCID: PMC4236423 DOI: 10.1186/s13041-014-0083-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 11/04/2014] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The basal ganglia (BG) are a complex network of subcortical nuclei involved in the coordination and integration of the motor activity. Although these independent anatomical structures are functionally related, the proteome present in each isolated nucleus remains largely unexplored. In order to analyse the BG proteome in a large-scale format, we used a multi-dimensional fractionation approach which combines isolation of anatomically-defined nuclei, and protein/peptide chromatographic fractionation strategies coupled to mass spectrometry. RESULTS Using this workflow, we have obtained a proteomic expression profile across striatum and globus pallidus structures among which 1681 proteins were located in caudate nucleus (CN), 1329 in putamen, 1419 in medial globus pallidus (GPi), and 1480 in lateral globus pallidus (GPe), establishing a BG reference proteome to a depth of 2979 unique proteins. Protein interactome mapping highlighted significant clustering of common proteins in striatal and pallidal structures, contributing to oxidative phosphorylation, protein degradation and neurotrophin signalling pathways. In silico analyses emphasized specific pathways represented in striatal and pallidal structures highlighting 5-hydroxytryptamine degradation, synaptic vesicle trafficking, and dopamine, metabotropic glutamate and muscarinic acetylcholine receptor pathways. Additional bioinformatic analyses also revealed that: i) nearly 4% of identified proteins have been previously associated to neurodegenerative syndromes, ii) 11% of protein set tends to localize to synaptic terminal, and iii) 20% of identified proteins were also localized in cerebrospinal fluid (CSF). CONCLUSIONS Overall, the anatomo-proteomic profiling of BG complements the anatomical atlas of the human brain transcriptome, increasing our knowledge about the molecular basis of the BG and the etiology of the movement disorders.
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Affiliation(s)
- Joaquín Fernández-Irigoyen
- />Clinical Neuroproteomics Group, Proteomics Unit, Proteored-ISCIII, Navarrabiomed, Fundación Miguel Servet, Irunlarrea Street, 31008 Pamplona, Spain
| | - María Victoria Zelaya
- />Neurological Tissue Bank, Navarrabiomed, Fundación Miguel Servet, 31008 Pamplona, Spain
| | - Teresa Tuñon
- />Pathological Anatomy Department, Navarra Hospital Complex, Pamplona, Spain
| | - Enrique Santamaría
- />Clinical Neuroproteomics Group, Proteomics Unit, Proteored-ISCIII, Navarrabiomed, Fundación Miguel Servet, Irunlarrea Street, 31008 Pamplona, Spain
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Fernández-Irigoyen J, Zelaya MV, Santamaría E. Applying mass spectrometry-based qualitative proteomics to human amygdaloid complex. Front Cell Neurosci 2014; 8:80. [PMID: 24688456 PMCID: PMC3960493 DOI: 10.3389/fncel.2014.00080] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 02/27/2014] [Indexed: 11/13/2022] Open
Abstract
The amygdaloid complex is a key brain structure involved in the expression of behaviors and emotions such as learning, fear, and anxiety. Brain diseases including depression, epilepsy, autism, schizophrenia, and Alzheimer's disease, have been associated with amygdala dysfunction. For several decades, neuroanatomical, neurophysiological, volumetric, and cognitive approaches have been the gold standard techniques employed to characterize the amygdala functionality. However, little attention has been focused specifically on the molecular composition of the human amygdala from the perspective of proteomics. We have performed a global proteome analysis employing protein and peptide fractionation methods followed by nano-liquid chromatography tandem mass spectrometry (nanoLC-MS/MS), detecting expression of at least 1820 protein species in human amygdala, corresponding to 1814 proteins which represent a nine-fold increase in proteome coverage with respect to previous proteomic profiling of the rat amygdala. Gene ontology analysis were used to determine biological process represented in human amygdala highlighting molecule transport, nucleotide binding, and oxidoreductase and GTPase activities. Bioinformatic analyses have revealed that nearly 4% of identified proteins have been previously associated to neurodegenerative syndromes, and 26% of amygdaloid proteins were also found to be present in cerebrospinal fluid (CSF). In particular, a subset of amygdaloid proteins was mainly involved in axon guidance, synaptic vesicle release, L1CAM interactome, and signaling pathways transduced by NGF and NCAM1. Taken together, our data contributes to the repertoire of the human brain proteome, serving as a reference library to provide basic information for understanding the neurobiology of the human amygdala.
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Affiliation(s)
| | - María V Zelaya
- Neurological Tissue Bank, Navarrabiomed, Fundación Miguel Servet Pamplona, Spain
| | - Enrique Santamaría
- Clinical Neuroproteomics Group, Proteomics Unit, Navarrabiomed, Fundación Miguel Servet Pamplona, Spain
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14
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Datta A, Akatsu H, Heese K, Sze SK. Quantitative clinical proteomic study of autopsied human infarcted brain specimens to elucidate the deregulated pathways in ischemic stroke pathology. J Proteomics 2013; 91:556-68. [PMID: 24007662 DOI: 10.1016/j.jprot.2013.08.017] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Revised: 08/15/2013] [Accepted: 08/20/2013] [Indexed: 11/26/2022]
Abstract
UNLABELLED Ischemic stroke, still lacking an effective neuroprotective therapy is the third leading cause of global mortality and morbidity. Here, we have applied an 8-plex iTRAQ-based 2D-LC-MS/MS strategy to study the commonly regulated infarct proteome from three different brain regions (putamen, thalamus and the parietal lobe) of female Japanese patients. Infarcts were compared with age-, post-mortem interval- and location-matched control specimens. The iTRAQ experiment confidently identified 1520 proteins with 0.1% false discovery rate. Bioinformatics data mining and immunochemical validation of pivotal perturbed proteins revealed a global failure of the cellular energy metabolism in the infarcted tissues as seen by the parallel down-regulation of proteins related to glycolysis, pyruvate dehydrogenase complex, TCA cycle and oxidative phosphorylation. The concomitant down-regulation of all participating proteins (SLC25A11, SLC25A12, GOT2 and MDH2) of malate-aspartate shuttle might be responsible for the metabolic in-coordination between the cytosol and mitochondria resulting in the failure of energy metabolism. The levels of proteins related to reactive gliosis (VIM, GFAP) and anti-inflammatory response (ANXA1, ANXA2) showed an increasing trend. The elevation of ferritin (FTL, FTH1) may indicate an iron-mediated oxidative imbalance aggravating the mitochondrial failure and neurotoxicity. The deregulated proteins could be useful as potential therapeutic targets or biomarkers for ischemic stroke. BIOLOGICAL SIGNIFICANCE Clinical proteomics of stroke has been lagging behind other areas of clinical proteomics like Alzheimer's disease or schizophrenia. Our study is the first quantitative clinical proteomics study where iTRAQ-2D-LC-MS/MS has been utilized in the area of ischemic stroke to obtain a comparative profile of human ischemic infarcts and age-, sex-, location- and post-mortem interval-matched control brain specimens. Different pathological attributes of ischemic stroke well-known through basic and pre-clinical research such as failure of cellular energy metabolism, reactive gliosis, activation of anti-inflammatory response and aberrant iron metabolism have been observed at the bedside. Our dataset could act as a reference for similar studies done in the future using ischemic brain samples from various brain banks across the world. A meta-analysis of these studies could help to map the pathological proteome specific to ischemic stroke that will guide the scientific community to better evaluate the pros and cons of the pre-clinical models for efficacy and mechanistic studies. Infarct being the core of injury should have the most intense regulation for several key proteins involved in the pathophysiology of ischemic stroke. Hence, a part of the up-regulated proteome could leak into the general circulation that may offer candidates of interest as potential biomarkers. In support of our proposed hypothesis, we report ferritin in the current study as one of the most elevated proteins in the infarct, which has been documented as a biomarker in the context of ischemic stroke by an independent study. Overall, our approach has the potential to identify probable therapeutic targets and biomarkers in the area of ischemic stroke.
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Affiliation(s)
- Arnab Datta
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
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15
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Ferrer I, López-Gonzalez I, Carmona M, Dalfó E, Pujol A, Martínez A. Neurochemistry and the non-motor aspects of PD. Neurobiol Dis 2012; 46:508-26. [PMID: 22737710 DOI: 10.1016/j.nbd.2011.10.019] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022] Open
Abstract
Parkinson disease (PD) is a systemic disease with variegated non-motor deficits and neurological symptoms, including impaired olfaction, autonomic failure, cognitive impairment and psychiatric symptoms, in addition to the classical motor symptoms. Many non-motor symptoms appear before or in parallel with motor deficits and then worsen with disease progression. Although there is a relationship, albeit not causal, between motor symptoms and the presence of Lewy bodies (LBs) and neurites filled with abnormal α-synuclein, other neurological alterations are independent of the amount of α-synuclein inclusions in neurons and neurites, thereby indicating that different mechanisms probably converge in the degenerative process. This may apply to complex alterations interfering with olfactory and autonomic nervous systemfunctions, emotions, sleep regulation, and behavioral, cognitive and mental performance. Involvement of the cerebral cortex leading to impaired behavior and cognition is related to several convergent altered factors including: a. dopaminergic, noradrenergic, serotoninergic and cholinergic cortical innervation; b. synapses; c. cortical metabolism; d. mitochondrial function and energy production; e. oxidative damage; f. transcription; g. protein expression; h. lipid composition; and i. ubiquitin–proteasome system and autophagy, among others. This complex situation indicates that multiple subcellular failure in selected cell populations is difficult to reconcilewith a reductionistic scenario of a single causative cascade of events leading to non-motor symptoms in PD. Furthermore, these alterationsmay appear at early stages of the disease and may precede the appearance of substantial irreversible cell loss by years. These observations have important implications in the design of therapeutic approaches geared to prevention and treatment of PD.
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Affiliation(s)
- I Ferrer
- Institute of Neuropathology, Service of Pathology, University Hospital of Bellvitge, Spain.
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16
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Bakulski KM, Dolinoy DC, Sartor MA, Paulson HL, Konen JR, Lieberman AP, Albin RL, Hu H, Rozek LS. Genome-wide DNA methylation differences between late-onset Alzheimer's disease and cognitively normal controls in human frontal cortex. J Alzheimers Dis 2012; 29:571-88. [PMID: 22451312 DOI: 10.3233/jad-2012-111223] [Citation(s) in RCA: 173] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Evidence supports a role for epigenetic mechanisms in the pathogenesis of late-onset Alzheimer's disease (LOAD), but little has been done on a genome-wide scale to identify potential sites involved in disease. This study investigates human postmortem frontal cortex genome-wide DNA methylation profiles between 12 LOAD and 12 cognitively normal age- and gender-matched subjects. Quantitative DNA methylation is determined at 27,578 CpG sites spanning 14,475 genes via the Illumina Infinium HumanMethylation27 BeadArray. Data are analyzed using parallel linear models adjusting for age and gender with empirical Bayes standard error methods. Gene-specific technical and functional validation is performed on an additional 13 matched pair samples, encompassing a wider age range. Analysis reveals 948 CpG sites representing 918 unique genes as potentially associated with LOAD disease status pending confirmation in additional study populations. Across these 948 sites the subtle mean methylation difference between cases and controls is 2.9%. The CpG site with a minimum false discovery rate located in the promoter of the gene Transmembrane Protein 59 (TMEM59) is 7.3% hypomethylated in cases. Methylation at this site is functionally associated with tissue RNA and protein levels of the TMEM59 gene product. The TMEM59 gene identified from our discovery approach was recently implicated in amyloid-β protein precursor post-translational processing, supporting a role for epigenetic change in LOAD pathology. This study demonstrates widespread, modest discordant DNA methylation in LOAD-diseased tissue independent from DNA methylation changes with age. Identification of epigenetic biomarkers of LOAD risk may allow for the development of novel diagnostic and therapeutic targets.
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Affiliation(s)
- Kelly M Bakulski
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
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17
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Luna Coronell JA, Syed P, Sergelen K, Gyurján I, Weinhäusel A. The current status of cancer biomarker research using tumour-associated antigens for minimal invasive and early cancer diagnostics. J Proteomics 2012; 76 Spec No.:102-15. [PMID: 22842156 DOI: 10.1016/j.jprot.2012.07.022] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Revised: 06/22/2012] [Accepted: 07/16/2012] [Indexed: 11/30/2022]
Abstract
Tumour-associated antigens (TAA) can be detected prior to clinical diagnosis and thus would be ideal biomarkers for early detection of cancer using only a few microliters of a patient's serum. In this article we provide a summary of TAA screening and serum-profiling conducted for breast, prostate, lung and colon cancers. Different methodological approaches, including SEREX, SERPA, and phage display for TAA identification and TAA panels are summarised, and a revision of array based techniques is provided. The most promising studies performed on these cancers (performed with 80-400 serum samples, including controls) obtained sensitivities in a range of 44-95% and specificities of 80-100%. From the various studies reviewed, only one performed cross validation (AUC=0.71) in a prostate cancer study. Thus, albeit receiver operation characteristics are very promising, cross validation of most studies is still missing. Additionally, the concerted action of research groups for standardization of serum-TAA testing and cross validation is required. Along with today's technological options, the chances of establishing TAA biomarkers are now higher than ever before. This may also be true for confirmation and validation of already existing data, which is a prerequisite for implementation of TAA biomarkers into clinical diagnostics. This article is part of a Special Issue entitled: Integrated omics.
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Affiliation(s)
- Johana A Luna Coronell
- Molecular Diagnostics, AIT Austrian Institute of Technology GmbH, Muthgasse 11, 1190 Vienna, Austria.
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18
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Tau protein and beta-amyloid(1-42) CSF levels in different phenotypes of Parkinson's disease. J Neural Transm (Vienna) 2011; 119:353-62. [PMID: 21892760 DOI: 10.1007/s00702-011-0708-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2011] [Accepted: 08/20/2011] [Indexed: 10/17/2022]
Abstract
Parkinson's disease (PD) is a neurodegenerative disorder with highly heterogeneous clinical manifestations. This fact has prompted many attempts to divide PD patients into clinical subgroups. This could lead to a better recognition of pathogenesis, improving targeted treatment and the prognosis of PD patients. The aim of the present study was to obtain cerebrospinal fluid (CSF) samples in PD patients and to search for a relationship between neurodegenerative CSF markers (tau protein, beta-amyloid(1-42) and index tau protein/beta-amyloid(1-42)) and the clinical subtypes. PD patients were divided into three subgroups: early disease onset (EDO), tremor-dominant PD (TD-PD), and non-tremor dominant PD (NT-PD) according to the previously published classification. Neurodegenerative markers in the CSF were assessed in these three groups of patients suffering from PD (EDO-17, TD-15, NT-16 patients) and in a control group (CG) of 19 patients suffering from non-degenerative neurological diseases and 18 patients with Alzheimer's disease (AD). The NT-PD patients were found to have significantly higher levels of CSF tau protein and index tau/beta than the control subjects and other Parkinsonian subgroups, but no significant differences in these markers were found between AD and NT-PD patients. In the context of more rapid clinical progression and more pronounced neuropathological changes in the NT-PD patient group, our results corroborate the opinion that CSF level of tau protein may be regarded as a potential laboratory marker of the presence and severity of neurodegeneration.
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19
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Martins-de-Souza D, Guest PC, Steeb H, Pietsch S, Rahmoune H, Harris LW, Bahn S. Characterizing the proteome of the human dorsolateral prefrontal cortex by shotgun mass spectrometry. Proteomics 2011; 11:2347-53. [DOI: 10.1002/pmic.201000718] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Revised: 01/12/2011] [Accepted: 03/03/2011] [Indexed: 11/08/2022]
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20
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Ly L, Wasinger VC. Protein and peptide fractionation, enrichment and depletion: Tools for the complex proteome. Proteomics 2011; 11:513-34. [DOI: 10.1002/pmic.201000394] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Revised: 10/03/2010] [Accepted: 10/18/2010] [Indexed: 12/28/2022]
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21
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Abstract
Cognitive impairment, including dementia, is commonly seen in those afflicted with Parkinson disease (PD), particularly at advanced disease stages. Pathologically, PD with dementia (PD-D) is most often associated with the presence of cortical Lewy bodies, as is the closely related dementia with Lewy bodies (DLB). Both PD-D and DLB are also frequently complicated by the presence of neurofibrillary tangles and amyloid plaques, features most often attributed to Alzheimer disease. Biomarkers are urgently needed to differentiate among these disease processes and predict dementia in PD as well as monitor responses of patients to new therapies. A few clinical assessments, along with structural and functional neuroimaging, have been utilized in the last few years with some success in this area. Additionally, a number of other strategies have been employed to identify biochemical/molecular biomarkers associated with cognitive impairment and dementia in PD, e.g. targeted analysis of candidate proteins known to be important to PD pathogenesis and progression in cerebrospinal fluid or blood. Finally, interesting results are emerging from preliminary studies with unbiased and high throughput genomic, proteomic and metabolomic techniques. The current findings and perspectives of applying these strategies and techniques are reviewed in this article, together with potential areas of advancement.
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Affiliation(s)
- Min Shi
- Department of Pathology, University of Washington School of Medicine, Seattle, WA 98104, USA
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22
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Quest for new genomic and proteomic biomarkers in neurology. Transl Neurosci 2011. [DOI: 10.2478/s13380-011-0005-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
AbstractThe possibility of identifying novel biomarkers for neurodegenerative diseases has been greatly enhanced with recent advances in genomics and proteomics. Novel technologies have the potential to hasten the development of new biomarkers useful as predictors of disease etiology and outcome, as well as responsiveness to therapy. Disease-modifying new therapies are very much needed in modern approaches to treatment of neurodegenerative diseases. Current progress in the field encounters a degree of skepticism about the reliability of genomic and proteomic data and its relevance for clinical applications. Standard operating procedures covering sample collection, methodology and statistical analysis need to be fully developed and strictly adhered to in order to assure reproducible and clinically relevant results. Previous studies involving patients with neurodegenerative diseases show promise in using genomic and proteomic approaches for development of new biomarkers. Confirmation of any novel biomarker in multiple independent patient cohorts and correlation of the improvement in biomarker endpoint with clinical improvement in longitudinal patient studies remains crucial for future successful application. We propose that a combination of approaches in biomarker discovery may in the end lead to identification of promising candidates at DNA, RNA, protein and small molecule level.
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23
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Goodwin RJA, Lang AM, Allingham H, Borén M, Pitt AR. Stopping the clock on proteomic degradation by heat treatment at the point of tissue excision. Proteomics 2010; 10:1751-61. [PMID: 20217868 DOI: 10.1002/pmic.200900641] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The effectiveness of rapid and controlled heating of intact tissue to inactivate native enzymatic activity and prevent proteome degradation has been evaluated. Mouse brains were bisected immediately following excision, with one hemisphere being heat treated followed by snap freezing in liquid nitrogen while the other hemisphere was snap frozen immediately. Sections were cut by cryostatic microtome and analyzed by MALDI-MS imaging and minimal label 2-D DIGE, to monitor time-dependent relative changes in intensities of protein and peptide signals. Analysis by MALDI-MS imaging demonstrated that the relative intensities of markers varied across a time course (0-5 min) when the tissues were not stabilized by heat treatment. However, the same markers were seen to be stabilized when the tissues were heat treated before snap freezing. Intensity profiles for proteins indicative of both degradation and stabilization were generated when samples of treated and nontreated tissues were analyzed by 2-D DIGE, with protein extracted before and after a 10-min warming of samples. Thus, heat treatment of tissues at the time of excision is shown to prevent subsequent uncontrolled degradation of tissues at the proteomic level before any quantitative analysis, and to be compatible with downstream proteomic analysis.
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Affiliation(s)
- Richard J A Goodwin
- Division of Integrative and Systems Biology, Faculty of Biomedical and Life Sciences, University of Glasgow, Glasgow, UK
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24
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Caudle WM, Bammler TK, Lin Y, Pan S, Zhang J. Using 'omics' to define pathogenesis and biomarkers of Parkinson's disease. Expert Rev Neurother 2010; 10:925-42. [PMID: 20518609 DOI: 10.1586/ern.10.54] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Although great effort has been put forth to uncover the complex molecular mechanisms exploited in the pathogenesis of Parkinson's disease, a satisfactory explanation remains to be discovered. The emergence of several -omics techniques, transcriptomics, proteomics and metabolomics, have been integral in confirming previously identified pathways that are associated with dopaminergic neurodegeneration and subsequently Parkinson's disease, including mitochondrial and proteasomal function and synaptic neurotransmission. Additionally, these unbiased techniques, particularly in the brain regions uniquely associated with the disease, have greatly enhanced our ability to identify novel pathways, such as axon-guidance, that are potentially involved in Parkinson's pathogenesis. A comprehensive appraisal of the results obtained by different -omics has also reconfirmed the increase in oxidative stress as a common pathway likely to be critical in Parkinson's development/progression. It is hoped that further integration of these techniques will yield a more comprehensive understanding of Parkinson's disease etiology and the biological pathways that mediate neurodegeneration.
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25
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Rostomily RC, Born DE, Beyer RP, Jin J, Alvord EC, Mikheev AM, Matthews RT, Pan C, Khorasani L, Sonnen JA, Montine TJ, Shi M, Zhang J. Quantitative proteomic analysis of oligodendrogliomas with and without 1p/19q deletion. J Proteome Res 2010; 9:2610-8. [PMID: 20337498 DOI: 10.1021/pr100054v] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Approximately 50-80% of oligodendrogliomas demonstrate a combined loss of chromosome 1p and 19q. Chromosome 1p/19q deletion, appearing early in tumorigenesis, is associated with improved clinical outcomes, including response to chemotherapy and radiation. Although many hypotheses have been proposed, the molecular mechanisms underlying improved clinical outcomes with 1p/19q deletion in oligodendrogliomas have not been characterized fully. To investigate the molecular differences between oligodendrogliomas, we employed an unbiased proteomic approach using microcapillary liquid chromatography mass spectrometry, along with a quantitative technique called isotope-coded affinity tags, on patient samples of grade II oligodendrogliomas. Following conventional biochemical separation of pooled tumor tissue from five samples of undeleted and 1p/19q deleted grade II oligodendrogliomas into nuclei-, mitochondria-, and cytosol-enriched fractions, relative changes in protein abundance were quantified. Among the 442 total proteins identified, 163 nonredundant proteins displayed significant changes in relative abundance in at least one of the three fractions between oligodendroglioma with and without 1p/19q deletion. Bioinformatic analyses of differentially regulated proteins supported the potential importance of metabolism and invasion/migration to the codeleted phenotype. A subset of altered proteins, including the pro-invasive extracellular matrix protein BCAN, was further validated by Western blotting as candidate markers for the more aggressive undeleted phenotype. These studies demonstrate the utility of proteomic analysis to identify candidate biological motifs and molecular mechanisms that drive differential malignancy related to 1p19q phenotypes. Future analysis of larger patient samples are warranted to further refine biomarker panels to predict biological behavior and assist in the identification of deleted gene products that define the 1p/19q phenotype.
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Affiliation(s)
- Robert C Rostomily
- Department of Neurological Surgery, Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, Washington 98195-6470, USA.
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26
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Katagiri T, Hatano N, Aihara M, Kawano H, Okamoto M, Liu Y, Izumi T, Maekawa T, Nakamura S, Ishihara T, Shirai M, Mizukami Y. Proteomic analysis of proteins expressing in regions of rat brain by a combination of SDS-PAGE with nano-liquid chromatography-quadrupole-time of flight tandem mass spectrometry. Proteome Sci 2010; 8:41. [PMID: 20659346 PMCID: PMC2918549 DOI: 10.1186/1477-5956-8-41] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2010] [Accepted: 07/27/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Most biological functions controlled by the brain and their related disorders are closely associated with activation in specific regions of the brain. Neuroproteomics has been applied to the analysis of whole brain, and the general pattern of protein expression in all regions has been elucidated. However, the comprehensive proteome of each brain region remains unclear. RESULTS In this study, we carried out comparative proteomics of six regions of the adult rat brain: thalamus, hippocampus, frontal cortex, parietal cortex, occipital cortex, and amygdala using semi-quantitative analysis by Mascot Score of the identified proteins. In order to identify efficiently the proteins that are present in the brain, the proteins were separated by a combination of SDS-PAGE on a C18 column-equipped nano-liquid chromatograph, and analyzed by quadrupole-time of flight-tandem-mass spectrometry. The proteomic data show 2,909 peptides in the rat brain, with more than 200 identified as region-abundant proteins by semi-quantitative analysis. The regions containing the identified proteins are membrane (20.0%), cytoplasm (19.5%), mitochondrion (17.1%), cytoskeleton (8.2%), nucleus (4.7%), extracellular region (3.3%), and other (18.0%). Of the identified proteins, the expressions of glial fibrillary acidic protein, GABA transporter 3, Septin 5, heat shock protein 90, synaptotagmin, heat shock protein 70, and pyruvate kinase were confirmed by immunoblotting. We examined the distributions in rat brain of GABA transporter 3, glial fibrillary acidic protein, and heat shock protein 70 by immunohistochemistry, and found that the proteins are localized around the regions observed by proteomic analysis and immunoblotting. IPA analysis indicates that pathways closely related to the biological functions of each region may be activated in rat brain. CONCLUSIONS These observations indicate that proteomics in each region of adult rat brain may provide a novel way to elucidate biological actions associated with the activation of regions of the brain.
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Affiliation(s)
- Tomoki Katagiri
- Center for Gene Research, Yamaguchi University, Yamaguchi, 755-8505, Japan.
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27
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Lesur A, Varesio E, Hopfgartner G. Protein Quantification by MALDI-Selected Reaction Monitoring Mass Spectrometry Using Sulfonate Derivatized Peptides. Anal Chem 2010; 82:5227-37. [DOI: 10.1021/ac100602d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Antoine Lesur
- Life Sciences Mass Spectrometry, School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| | - Emmanuel Varesio
- Life Sciences Mass Spectrometry, School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| | - Gérard Hopfgartner
- Life Sciences Mass Spectrometry, School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
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28
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Diagnostic cerebrospinal fluid biomarkers for Parkinson's disease: a pathogenetically based approach. Neurobiol Dis 2010; 39:229-41. [PMID: 20451609 PMCID: PMC7126274 DOI: 10.1016/j.nbd.2010.04.020] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2010] [Revised: 04/09/2010] [Accepted: 04/26/2010] [Indexed: 12/21/2022] Open
Abstract
The inaccuracy of the early diagnosis of Parkinson's disease (PD) has been a major incentive for studies aimed at the identification of biomarkers. Brain-derived cerebrospinal fluid (CSF) proteins are potential biomarkers considering the major role that proteins play in PD pathogenesis. In this review, we discuss the current hypotheses about the pathogenesis of PD and identify the most promising candidate biomarkers among the CSF proteins studied so far. The list of potential markers includes proteins involved in various pathogenetic processes, such as oxidative stress and protein aggregation. This list will undoubtedly grow in the near future by application of CSF proteomics and subsequent validation of identified proteins. Probably a single biomarker will not suffice to reach high sensitivity and specificity, because PD is pathogenetically heterogeneous and shares etiological factors with other neurodegenerative diseases. Furthermore, identified candidate biomarkers will have to be thoroughly validated before they can be implemented as diagnostic aids.
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Hwang H, Zhang J, Chung KA, Leverenz JB, Zabetian CP, Peskind ER, Jankovic J, Su Z, Hancock AM, Pan C, Montine TJ, Pan S, Nutt J, Albin R, Gearing M, Beyer RP, Shi M, Zhang J. Glycoproteomics in neurodegenerative diseases. MASS SPECTROMETRY REVIEWS 2010; 29:79-125. [PMID: 19358229 PMCID: PMC2799547 DOI: 10.1002/mas.20221] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Protein glycosylation regulates protein function and cellular distribution. Additionally, aberrant protein glycosylations have been recognized to play major roles in human disorders, including neurodegenerative diseases. Glycoproteomics, a branch of proteomics that catalogs and quantifies glycoproteins, provides a powerful means to systematically profile the glycopeptides or glycoproteins of a complex mixture that are highly enriched in body fluids, and therefore, carry great potential to be diagnostic and/or prognostic markers. Application of this mass spectrometry-based technology to the study of neurodegenerative disorders (e.g., Alzheimer's disease and Parkinson's disease) is relatively new, and is expected to provide insight into the biochemical pathogenesis of neurodegeneration, as well as biomarker discovery. In this review, we have summarized the current understanding of glycoproteins in biology and neurodegenerative disease, and have discussed existing proteomic technologies that are utilized to characterize glycoproteins. Some of the ongoing studies, where glycoproteins isolated from cerebrospinal fluid and human brain are being characterized in Parkinson's disease at different stages versus controls, are presented, along with future applications of targeted validation of brain specific glycoproteins in body fluids.
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Affiliation(s)
- Hyejin Hwang
- Department of Pathology, University of Washington, Seattle, Washington
| | - Jianpeng Zhang
- Department of Pathology, University of Washington, Seattle, Washington
| | - Kathryn A. Chung
- Department of Neurology, Oregon Health and Science University, Portland, Oregon
| | - James B. Leverenz
- Department of Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, Washington
- Department of Neurology, University of Washington School of Medicine, Seattle, Washington
| | - Cyrus P. Zabetian
- Department of Neurology, University of Washington School of Medicine, Seattle, Washington
| | - Elaine R. Peskind
- Department of Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, Washington
- Department of Neurology, University of Washington School of Medicine, Seattle, Washington
| | - Joseph Jankovic
- Department of Neurology, Baylor College of Medicine, Houston, Texas
| | - Zhen Su
- Department of Pathology, University of Washington, Seattle, Washington
| | - Aneeka M. Hancock
- Department of Pathology, University of Washington, Seattle, Washington
| | - Catherine Pan
- Department of Pathology, University of Washington, Seattle, Washington
| | - Thomas J. Montine
- Department of Pathology, University of Washington, Seattle, Washington
| | - Sheng Pan
- Department of Pathology, University of Washington, Seattle, Washington
| | - John Nutt
- Department of Neurology, Oregon Health and Science University, Portland, Oregon
| | - Roger Albin
- Ann Arbor VAMC GRECC and Department of Neurology, University of Michigan, Ann Arbor, Michigan
| | - Marla Gearing
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia
| | - Richard P. Beyer
- Department of Environmental & Occupational Health Sciences, University of Washington School of Medicine, Seattle, Washington
| | - Min Shi
- Department of Pathology, University of Washington, Seattle, Washington
| | - Jing Zhang
- Department of Pathology, University of Washington, Seattle, Washington
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30
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Proteomics in human Parkinson's disease research. J Proteomics 2009; 73:10-29. [PMID: 19632367 DOI: 10.1016/j.jprot.2009.07.007] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2009] [Revised: 06/25/2009] [Accepted: 07/08/2009] [Indexed: 11/20/2022]
Abstract
During the last decades, considerable advances in the understanding of specific mechanisms underlying neurodegeneration in Parkinson's disease have been achieved, yet neither definite etiology nor unifying sequence of molecular events has been formally established. Current unmet needs in Parkinson's disease research include exploring new hypotheses regarding disease susceptibility, occurrence and progression, identifying reliable diagnostic, prognostic and therapeutic biomarkers, and translating basic research into appropriate disease-modifying strategies. The most popular view proposes that Parkinson's disease results from the complex interplay between genetic and environmental factors and mechanisms believed to be at work include oxidative stress, mitochondrial dysfunction, excitotoxicity, iron deposition and inflammation. More recently, a plethora of data has accumulated pinpointing an abnormal processing of the neuronal protein alpha-synuclein as a pivotal mechanism leading to aggregation, inclusions formation and degeneration. This protein-oriented scenario logically opens the door to the application of proteomic strategies to this field of research. We here review the current literature on proteomics applied to Parkinson's disease research, with particular emphasis on pathogenesis of sporadic Parkinson's disease in humans. We propose the view that Parkinson's disease may be an acquired or genetically-determined brain proteinopathy involving an abnormal processing of several, rather than individual neuronal proteins, and discuss some pre-analytical and analytical developments in proteomics that may help in verifying this concept.
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Shi M, Bradner J, Bammler TK, Eaton DL, Zhang J, Ye Z, Wilson AM, Montine TJ, Pan C, Zhang J. Identification of glutathione S-transferase pi as a protein involved in Parkinson disease progression. THE AMERICAN JOURNAL OF PATHOLOGY 2009; 175:54-65. [PMID: 19498008 DOI: 10.2353/ajpath.2009.081019] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Parkinson disease (PD) typically affects the cortical regions during the later stages of disease, with neuronal loss, gliosis, and formation of diffuse cortical Lewy bodies in a significant portion of patients with dementia. To identify novel proteins involved in PD progression, we prepared synaptosomal fractions from the frontal cortices of pathologically verified PD patients at different stages along with age-matched controls. Protein expression profiles were compared using a robust quantitative proteomic technique. Approximately 100 proteins displayed significant differences in their relative abundances between PD patients at various stages and controls; three of these proteins were validated using independent techniques. One of the confirmed proteins, glutathione S-transferase Pi, was further investigated in cellular models of PD, demonstrating that its level was intimately associated with several critical cellular processes that are directly related to neurodegeneration in PD. These results have, for the first time, suggested that the levels of glutathione S-transferase Pi may play an important role in modulating the progression of PD.
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Affiliation(s)
- Min Shi
- Department of Pathology, University of Washington School of Medicine, Seattle, WA 98104, USA
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Martins-de-Souza D, Maccarrone G, Reckow S, Falkai P, Schmitt A, Turck CW. Shotgun mass spectrometry analysis of the human thalamus proteome. J Sep Sci 2009; 32:1231-6. [DOI: 10.1002/jssc.200900008] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Lasaosa M, Delmotte N, Huber CG, Melchior K, Heinzle E, Tholey A. A 2D reversed-phase × ion-pair reversed-phase HPLC-MALDI TOF/TOF-MS approach for shotgun proteome analysis. Anal Bioanal Chem 2008; 393:1245-56. [DOI: 10.1007/s00216-008-2539-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2008] [Revised: 11/13/2008] [Accepted: 11/21/2008] [Indexed: 10/21/2022]
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Shi M, Caudle WM, Zhang J. Biomarker discovery in neurodegenerative diseases: a proteomic approach. Neurobiol Dis 2008; 35:157-64. [PMID: 18938247 DOI: 10.1016/j.nbd.2008.09.004] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2008] [Revised: 09/04/2008] [Accepted: 09/14/2008] [Indexed: 11/26/2022] Open
Abstract
Biomarkers for neurodegenerative disorders are essential to facilitate disease diagnosis, ideally at early stages, monitor disease progression, and assess response to existing and future treatments. Application of proteomics to the human brain, cerebrospinal fluid and plasma has greatly hastened the unbiased and high-throughput searches for novel biomarkers. There are many steps critical to biomarker discovery, whether for neurodegenerative or other diseases, including sample preparation, protein/peptide separation and identification, as well as independent confirmation and validation. In this review we have summarized current proteomics technologies involved in discovery of biomarkers for neurodegenerative diseases, practical considerations and limitations of several major aspects, as well as the current status of candidate biomarkers revealed by proteomics for Alzheimer and Parkinson diseases.
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Affiliation(s)
- Min Shi
- Department of Pathology, University of Washington School of Medicine, HMC Box 359635, 325 9th Avenue, Seattle, WA 98104, USA
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Caudle WM, Pan S, Shi M, Quinn T, Hoekstra J, Beyer RP, Montine TJ, Zhang J. Proteomic identification of proteins in the human brain: Towards a more comprehensive understanding of neurodegenerative disease. Proteomics Clin Appl 2008; 2:1484-97. [PMID: 21136796 DOI: 10.1002/prca.200800043] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2008] [Indexed: 12/21/2022]
Abstract
Proteomics has revealed itself as a powerful tool in the identification and determination of proteins and their biological significance. More recently, several groups have taken advantage of the high-throughput nature of proteomics in order to gain a more in-depth understanding of the human brain. In turn, this information has provided researchers with invaluable insight into the potential pathways and mechanisms involved in the pathogenesis of several neurodegenerative disorders, e.g., Alzheimer and Parkinson disease. Furthermore, these findings likely will improve methods to diagnose disease and monitor disease progression as well as generate novel targets for therapeutic intervention. Despite these advances, comprehensive understanding of the human brain proteome remains challenging, and requires development of improved sample enrichment, better instrumentation, and innovative analytic techniques. In this review, we will focus on the most recent progress related to identification of proteins in the human brain under normal as well as pathological conditions, mainly Alzheimer and Parkinson disease, their potential application in biomarker discovery, and discuss current advances in protein identification aimed at providing a more comprehensive understanding of the brain.
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Affiliation(s)
- W Michael Caudle
- Department of Pathology, University of Washington School of Medicine, Seattle, WA, USA
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Martins-de-Souza D, Gattaz WF, Schmitt A, Rewerts C, Maccarrone G, Dias-Neto E, Turck CW. Proteome analysis of human dorsolateral prefrontal cortex using shotgun mass spectrometry. J Sep Sci 2008; 31:3122-6. [DOI: 10.1002/jssc.200800224] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Abstract
Parkinson disease (PD) is a progressive neurodegenerative disorder that is considered to affect the brainstem at its early stages and other brain regions, including the limbic system and isocortex, in advanced stages. It has been suggested that PD progression is characterized pathologically by the spreading of Lewy body deposition. To identify novel proteins involved in PD progression, we prepared subcellular fractions from the frontal cortex of pathologically verified PD patients at different stages of disease and Lewy body deposition and from age-matched controls. Protein expression profiles were compared using a robust quantitative proteomic technique called isobaric tagging for relative and absolute quantification in conjunction with mass spectrometry. Approximately 200 proteins were found to display significant differences in their relative abundance between PD patients at various stages and controls. Gene ontology analysis indicated that these altered proteins belonged to many categories (e.g. mitochondrial function and neurotransmission) that were likely critically involved in the pathogenesis of PD. Of those, mortalin, a mitochondrial protein, was decreased in the advanced PD cases and was further validated to be decreased using independent techniques. These results suggest a role for mortalin in PD progression.
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Kitsou E, Pan S, Zhang J, Shi M, Zabeti A, Dickson DW, Albin R, Gearing M, Kashima DT, Wang Y, Beyer RP, Zhou Y, Pan C, Caudle WM, Zhang J. Identification of proteins in human substantia nigra. Proteomics Clin Appl 2008; 2:776-82. [DOI: 10.1002/prca.200800028] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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