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Voukali E, Veetil NK, Němec P, Stopka P, Vinkler M. Comparison of plasma and cerebrospinal fluid proteomes identifies gene products guiding adult neurogenesis and neural differentiation in birds. Sci Rep 2021; 11:5312. [PMID: 33674647 PMCID: PMC7935914 DOI: 10.1038/s41598-021-84274-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 02/10/2021] [Indexed: 11/27/2022] Open
Abstract
Cerebrospinal fluid (CSF) proteins regulate neurogenesis, brain homeostasis and participate in signalling during neuroinflammation. Even though birds represent valuable models for constitutive adult neurogenesis, current proteomic studies of the avian CSF are limited to chicken embryos. Here we use liquid chromatography-tandem mass spectrometry (nLC-MS/MS) to explore the proteomic composition of CSF and plasma in adult chickens (Gallus gallus) and evolutionarily derived parrots: budgerigar (Melopsittacus undulatus) and cockatiel (Nymphicus hollandicus). Because cockatiel lacks a complete genome information, we compared the cross-species protein identifications using the reference proteomes of three model avian species: chicken, budgerigar and zebra finch (Taeniopygia guttata) and found the highest identification rates when mapping against the phylogenetically closest species, the budgerigar. In total, we identified 483, 641 and 458 unique proteins consistently represented in the CSF and plasma of all chicken, budgerigar and cockatiel conspecifics, respectively. Comparative pathways analyses of CSF and blood plasma then indicated clusters of proteins involved in neurogenesis, neural development and neural differentiation overrepresented in CSF in each species. This study provides the first insight into the proteomics of adult avian CSF and plasma and brings novel evidence supporting the adult neurogenesis in birds.
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Affiliation(s)
- Eleni Voukali
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44, Prague, Czech Republic.
| | - Nithya Kuttiyarthu Veetil
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44, Prague, Czech Republic
| | - Pavel Němec
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44, Prague, Czech Republic
| | - Pavel Stopka
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44, Prague, Czech Republic
| | - Michal Vinkler
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44, Prague, Czech Republic.
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江 银, 朱 新, 唐 思, 吴 兆, 雷 鹏, 刘 月. [Study on expression and mechanism of serum differential proteins after rush immunotherapy of allergic rhinitis]. LIN CHUANG ER BI YAN HOU TOU JING WAI KE ZA ZHI = JOURNAL OF CLINICAL OTORHINOLARYNGOLOGY, HEAD, AND NECK SURGERY 2020; 34:683-689. [PMID: 32842198 PMCID: PMC10127927 DOI: 10.13201/j.issn.2096-7993.2020.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Indexed: 06/11/2023]
Abstract
Objective:To detect the expression of differentially expressed proteins in serum of patients with allergic rhinitis who were allergic to dust mites before and after 6-day rush immunotherapy. The three differentially expressed proteins, CRP, CTHRC1 and WDR89, were detected and identified. The immunoregulatory effects and significance of these three differentially expressed proteins in rush immunotherapy of allergic rhinitis were analyzed and discussed. Method:The serum samples of 15 patients with allergic rhinitis, 15 patients with rush immunotherapy and 10 patients with healthy control group were collected. The samples were studied by isobaric tags for relative and absolute quantitation(iTRAQ) technique. The related differential proteins were determined by two-dimensional gel electrophoresis and mass spectrometry, and the rationality of the screened differential proteins was tested and verified by Cluster3.0 software and Java TreeView software. Finally, the selected CRP, CTHRC1 and WDR89 proteins were identified by enzyme-linked immunosorbent assay(ELISA). Result:In this study, 893 proteins were detected and 53 differential proteins were identified. Compared with healthy control group, 24 proteins which was statistically significant were found in allergic rhinitis group, which were closely related to the occurrence of allergic rhinitis, including 10 up-regulated proteins and 14 down-regulated proteins. Compared with the allergic rhinitis group, patients with allergic rhinitis underwent 6 days of rush immunotherapy. There were 29 proteins whose expression of proteins with a difference of P value of less than 0.05 and 1.2 times higher, which were related to the effect after the incremental phase of rush immunotherapy was completed, of which 12 were up-regulated and 17 were down-regulated. Compared with healthy control group, the expression of up-regulated of allergic rhinitis group and the expression of down-regulated protein after 6 days of rush immunotherapy were CTHRC1, WDR89; Compared with healthy control group, AR group was down-regulated and the expression of up-regulated protein after 6 days of rush immunotherapy was CRP. CRP, CTHRC1 and WDR89 proteins were identified by enzyme linked immunosorbent assay(ELISA), and it was found that the differential expression of CTHRC1 and WDR89 in AR and RIT was statistically significant(P<0.05), but the differential expression of serum CRP in AR and RIT was not statistically significant(P>0.05). Conclusion:Serum protein CTHRC1 and WDR89 are closely related to the pathogenesis of allergic rhinitis, and played a role in the regulation of rush immunotherapy, while serum protein CRP has no significant effect on AR and RIT.
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Affiliation(s)
- 银丽 江
- 南昌大学第二附属医院耳鼻咽喉头颈外科(南昌,330006)Department of Otolaryngology and Head Neck Surgery, the Second Affiliated Hospital of Nanchang University, Nanchang, 330006, China
| | - 新华 朱
- 南昌大学第二附属医院耳鼻咽喉头颈外科(南昌,330006)Department of Otolaryngology and Head Neck Surgery, the Second Affiliated Hospital of Nanchang University, Nanchang, 330006, China
| | - 思艺 唐
- 南昌大学第二附属医院耳鼻咽喉头颈外科(南昌,330006)Department of Otolaryngology and Head Neck Surgery, the Second Affiliated Hospital of Nanchang University, Nanchang, 330006, China
| | - 兆坤 吴
- 南昌大学第二附属医院耳鼻咽喉头颈外科(南昌,330006)Department of Otolaryngology and Head Neck Surgery, the Second Affiliated Hospital of Nanchang University, Nanchang, 330006, China
| | - 鹏太 雷
- 南昌大学第二附属医院耳鼻咽喉头颈外科(南昌,330006)Department of Otolaryngology and Head Neck Surgery, the Second Affiliated Hospital of Nanchang University, Nanchang, 330006, China
| | - 月辉 刘
- 南昌大学第二附属医院耳鼻咽喉头颈外科(南昌,330006)Department of Otolaryngology and Head Neck Surgery, the Second Affiliated Hospital of Nanchang University, Nanchang, 330006, China
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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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Demartini DR, Schilling LP, da Costa JC, Carlini CR. Alzheimer's and Parkinson's diseases: an environmental proteomic point of view. J Proteomics 2014; 104:24-36. [PMID: 24751585 DOI: 10.1016/j.jprot.2014.04.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 04/07/2014] [Accepted: 04/10/2014] [Indexed: 11/25/2022]
Abstract
Alzheimer's and Parkinson's diseases are severe neurodegenerative conditions triggered by complex biochemical routes. Many groups are currently pursuing the search for valuable biomarkers to either perform early diagnostic or to follow the disease's progress. Several studies have reported relevant findings regarding environmental issues and the progression of such diseases. Here the etiology and mechanisms of these diseases are briefly reviewed. Approaches that might reveal candidate biomarkers and environmental stressors associated to the diseases were analyzed under a proteomic perspective. This article is part of a Special Issue entitled: Environmental and structural proteomics.
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Affiliation(s)
- Diogo Ribeiro Demartini
- Center of Biotechnology, Federal University of Rio Grande do Sul, Av. Bento Gonçalves 9500, Prédio 43431, Sala 214, 91501-970 Porto Alegre, RS, Brazil.
| | - Lucas Porcello Schilling
- Brain Institute of Rio Grande do Sul, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Av. Ipiranga 6690, 90610-000 Porto Alegre, RS, Brazil
| | - Jaderson Costa da Costa
- Brain Institute of Rio Grande do Sul, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Av. Ipiranga 6690, 90610-000 Porto Alegre, RS, Brazil.
| | - Célia Regina Carlini
- Center of Biotechnology, Federal University of Rio Grande do Sul, Av. Bento Gonçalves 9500, Prédio 43431, Sala 214, 91501-970 Porto Alegre, RS, Brazil; Brain Institute of Rio Grande do Sul, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Av. Ipiranga 6690, 90610-000 Porto Alegre, RS, Brazil
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Sui P, Watanabe H, Ossipov MH, Porreca F, Bakalkin G, Bergquist J, Artemenko K. Dimethyl-Labeling-Based Protein Quantification and Pathway Search: A Novel Method of Spinal Cord Analysis Applicable for Neurological Studies. J Proteome Res 2013; 12:2245-52. [DOI: 10.1021/pr4001064] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
| | | | - Michael H. Ossipov
- Department of Pharmacology, University of Arizona Health Sciences Center, Tucson,
Arizona 85724, United States
| | - Frank Porreca
- Department of Pharmacology, University of Arizona Health Sciences Center, Tucson,
Arizona 85724, United States
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Li Q, Jain MR, Chen W, Li H. A multidimensional approach to an in-depth proteomics analysis of transcriptional regulators in neuroblastoma cells. J Neurosci Methods 2013; 216:118-27. [PMID: 23558336 DOI: 10.1016/j.jneumeth.2013.03.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 03/21/2013] [Accepted: 03/24/2013] [Indexed: 12/13/2022]
Abstract
The dynamic regulation of transcriptional events is fundamental to many aspects of neuronal cell functions. However, proteomics methods have not been routinely used in global neuroproteomics analyses of transcriptional regulators because they are much less abundant than the "house-keeping" proteins in cells and tissues. Recent improvements in both biochemical preparations of nuclear proteins and detection sensitivities of proteomics technologies have made the global analysis of nuclear transcriptional regulators possible. We report here an optimised neuroproteomic method for the analysis of transcriptional regulators in the nuclear extracts of SHSY-5Y neuroblastoma cells by combining an improved nuclear protein extraction procedure with multidimensional peptide separation approaches. We found that rigorous removal of cytoplasmic proteins and solubilisation of DNA-associated proteins improved the number of nuclear proteins identified. Furthermore, we discovered that multidimensional peptide separations by either strong cation exchange (SCX) chromatography or electrostatic repulsion-hydrophilic interaction chromatography (ERLIC) analysis detected more than 1800 nuclear proteins, which constitutes one of the largest datasets of nuclear proteins reported for a neuronal cell. Thus, in-depth analysis of transcriptional regulators for studying neurological diseases are increasingly feasible.
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Affiliation(s)
- Qing Li
- Center for Advanced Proteomics Research and Department of Biochemistry and Molecular Biology, UMDNJ-New Jersey Medical School Cancer Center, 205 S. Orange Avenue, F-1226, Newark, NJ 07103, USA
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Evans C, Noirel J, Ow SY, Salim M, Pereira-Medrano AG, Couto N, Pandhal J, Smith D, Pham TK, Karunakaran E, Zou X, Biggs CA, Wright PC. An insight into iTRAQ: where do we stand now? Anal Bioanal Chem 2012; 404:1011-27. [PMID: 22451173 DOI: 10.1007/s00216-012-5918-6] [Citation(s) in RCA: 220] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2012] [Revised: 02/28/2012] [Accepted: 02/29/2012] [Indexed: 01/09/2023]
Abstract
The iTRAQ (isobaric tags for relative and absolute quantification) technique is widely employed in proteomic workflows requiring relative quantification. Here, we review the iTRAQ literature; in particular, we focus on iTRAQ usage in relation to other commonly used quantitative techniques e.g. stable isotope labelling in culture (SILAC), label-free methods and selected reaction monitoring (SRM). As a result, we identify several issues arising with respect to iTRAQ. Perhaps frustratingly, iTRAQ's attractiveness has been undermined by a number of technical and analytical limitations: it may not be truly quantitative, as the changes in abundance reported will generally be underestimated. We discuss weaknesses and strengths of iTRAQ as a methodology for relative quantification in the light of this and other technical issues. We focus on technical developments targeted at iTRAQ accuracy and precision, use of 4-plex over 8-plex reagents and application of iTRAQ to post-translational modification (PTM) workflows. We also discuss iTRAQ in relation to label-free approaches, to which iTRAQ is losing ground.
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Affiliation(s)
- Caroline Evans
- The ChELSI Institute, Chemical and Biological Engineering, The University of Sheffield, Sheffield, UK
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