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      Cerebrospinal Fluid Proteomic Profiles in Patients with Postherpetic Neuralgia

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          Abstract

          The intrinsic mechanism of postherpetic neuralgia (PHN) remains unclear. Herein, we aimed to seek the hub proteins in the cerebrospinal fluid (CSF), which display significant changes between the PHN and nonpainful patients (Control). First, the proteomic results showed that compared with the Control-CSF, there were 100 upregulated and 50 downregulated differentially expressed proteins (DEPs) in the PHN-CSF. Besides, functional analyses including gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and gene set enrichment analysis (GSEA) revealed that biological processes and pathways including complement activation, infection, coagulation, and lipid metabolism were activated, while synaptic organization was suppressed. Next, the protein–protein interaction (PPI) analysis indicated that increased PLG, F2, APOA1, APOA2, SERPINC1, and KNG1 and reduced APOE, which were all enriched in the top pathways according to the KEGG analysis, were defined as hub proteins. Finally, three of the hub proteins, such as PLG, APOA1, and APOE, were reconfirmed in a larger cohort using both enzyme-linked immunosorbent assay (ELISA) and Western blotting methods. Above all, the results indicated that PLG, APOA1, and APOE and their involved processes such as infection, inflammation, cholesterol metabolism, and coagulation shall be potential therapeutic approaches. (The raw mass spectrometry proteome data and search results have been deposited to the iProx-integrated Proteome Resources ( http://www.iprox.cn) with the data set identifier IPX0007372000.)

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          Most cited references55

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          clusterProfiler: an R package for comparing biological themes among gene clusters.

          Increasing quantitative data generated from transcriptomics and proteomics require integrative strategies for analysis. Here, we present an R package, clusterProfiler that automates the process of biological-term classification and the enrichment analysis of gene clusters. The analysis module and visualization module were combined into a reusable workflow. Currently, clusterProfiler supports three species, including humans, mice, and yeast. Methods provided in this package can be easily extended to other species and ontologies. The clusterProfiler package is released under Artistic-2.0 License within Bioconductor project. The source code and vignette are freely available at http://bioconductor.org/packages/release/bioc/html/clusterProfiler.html.
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            Universal sample preparation method for proteome analysis.

            We describe a method, filter-aided sample preparation (FASP), which combines the advantages of in-gel and in-solution digestion for mass spectrometry-based proteomics. We completely solubilized the proteome in sodium dodecyl sulfate, which we then exchanged by urea on a standard filtration device. Peptides eluted after digestion on the filter were pure, allowing single-run analyses of organelles and an unprecedented depth of proteome coverage.
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              jvenn: an interactive Venn diagram viewer

              Background Venn diagrams are commonly used to display list comparison. In biology, they are widely used to show the differences between gene lists originating from different differential analyses, for instance. They thus allow the comparison between different experimental conditions or between different methods. However, when the number of input lists exceeds four, the diagram becomes difficult to read. Alternative layouts and dynamic display features can improve its use and its readability. Results jvenn is a new JavaScript library. It processes lists and produces Venn diagrams. It handles up to six input lists and presents results using classical or Edwards-Venn layouts. User interactions can be controlled and customized. Finally, jvenn can easily be embeded in a web page, allowing to have dynamic Venn diagrams. Conclusions jvenn is an open source component for web environments helping scientists to analyze their data. The library package, which comes with full documentation and an example, is freely available at http://bioinfo.genotoul.fr/jvenn.
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                Author and article information

                Journal
                J Proteome Res
                J Proteome Res
                pr
                jprobs
                Journal of Proteome Research
                American Chemical Society
                1535-3893
                1535-3907
                15 November 2023
                01 December 2023
                : 22
                : 12
                : 3879-3892
                Affiliations
                []Department of Pain Management, The Second Xiangya Hospital, Central South University , Changsha 410011, China
                []Department of Anesthesiology, The Second Xiangya Hospital, Central South University , Changsha, Hunan 410011, China
                [§ ]Clinical Research Center for Pain Medicine in Hunan Province , Changsha, Hunan 410011, China
                []Hunan Province Center for Clinical Anesthesia and Anesthesiology, Research Institute of Central South University , Changsha, Hunan 410083, China
                []Bourns Engineering, The University of California , Riverside, California 92521, United States
                Author notes
                [* ]Email: wangyaping6568@ 123456csu.edu.cn . Fax: +86 073185295970.
                [* ]Email: yangl0410smu@ 123456163.com . Fax: +86 073185295970.
                Author information
                https://orcid.org/0000-0002-9318-9812
                Article
                10.1021/acs.jproteome.3c00547
                10696610
                37966014
                810f0fe6-d2e4-45cc-b3f9-7f217ab56cb0
                © 2023 The Authors. Published by American Chemical Society

                Permits non-commercial access and re-use, provided that author attribution and integrity are maintained; but does not permit creation of adaptations or other derivative works ( https://creativecommons.org/licenses/by-nc-nd/4.0/).

                History
                : 29 August 2023
                : 01 November 2023
                : 24 October 2023
                Funding
                Funded by: Health Commission of Hunan Province, doi 10.13039/100017695;
                Award ID: HNA202101002
                Funded by: Hunan Province, doi NA;
                Award ID: 2020SK2079
                Funded by: Natural Science Foundation of Hunan Province, doi 10.13039/501100004735;
                Award ID: 2020JJ4811
                Categories
                Article
                Custom metadata
                pr3c00547
                pr3c00547

                Molecular biology
                postherpetic neuralgia,cerebrospinal fluid,proteomics,differential expressed proteins,central nervous system

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