Global Analysis of Neuronal Phosphoproteome Regulation by Chondroitin Sulfate Proteoglycans
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{"title"=>"Global Analysis of Neuronal Phosphoproteome Regulation by Chondroitin Sulfate Proteoglycans", "type"=>"journal", "authors"=>[{"first_name"=>"Panpan", "last_name"=>"Yu", "scopus_author_id"=>"55588038500"}, {"first_name"=>"Trairak", "last_name"=>"Pisitkun", "scopus_author_id"=>"6507728111"}, {"first_name"=>"Guanghui", "last_name"=>"Wang", "scopus_author_id"=>"56239490700"}, {"first_name"=>"Rong", "last_name"=>"Wang", "scopus_author_id"=>"55624749900"}, {"first_name"=>"Yasuhiro", "last_name"=>"Katagiri", "scopus_author_id"=>"7102168133"}, {"first_name"=>"Marjan", "last_name"=>"Gucek", "scopus_author_id"=>"6603624874"}, {"first_name"=>"Mark A.", "last_name"=>"Knepper", "scopus_author_id"=>"35478273500"}, {"first_name"=>"Herbert M.", "last_name"=>"Geller", "scopus_author_id"=>"7006352412"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"84875058793", "pmid"=>"23527152", "scopus"=>"2-s2.0-84875058793", "pui"=>"368539637", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0059285"}, "id"=>"f947b570-4b5f-3198-ba5f-62f75f28caeb", "abstract"=>"Chondroitin sulfate proteoglycans (CSPGs) are major components of the extracellular matrix which mediate inhibition of axonal regeneration after injury to the central nervous system (CNS). Several neuronal receptors for CSPGs have recently been identified; however, the signaling pathways by which CSPGs restrict axonal growth are still largely unknown. In this study, we applied quantitative phosphoproteomics to investigate the global changes in protein phosphorylation induced by CSPGs in primary neurons. In combination with isobaric Tags for Relative and Absolute Quantitation (iTRAQ) labeling, strong cation exchange chromatography (SCX) fractionation, immobilized metal affinity chromatography (IMAC) and LC-MS/MS, we identified and quantified 2214 unique phosphopeptides corresponding to 1118 phosphoproteins, with 118 changing significantly in abundance with CSPG treatment. The proteins that were regulated by CSPGs included key components of synaptic vesicle trafficking, axon guidance mediated by semaphorins, integrin signaling, cadherin signaling and EGF receptor signaling pathways. A significant number of the regulated proteins are cytoskeletal and related proteins that have been implicated in regulating neurite growth. Another highly represented protein category regulated by CSPGs is nucleic acid binding proteins involved in RNA post-transcriptional regulation. Together, by screening the overall phosphoproteome changes induced by CSPGs, this data expand our understanding of CSPG signaling, which provides new insights into development of strategies for overcoming CSPG inhibition and promoting axonal regeneration after CNS injury.", "link"=>"http://www.mendeley.com/research/global-analysis-neuronal-phosphoproteome-regulation-chondroitin-sulfate-proteoglycans", "reader_count"=>11, "reader_count_by_academic_status"=>{"Researcher"=>3, "Student > Ph. D. Student"=>7, "Student > Bachelor"=>1}, "reader_count_by_user_role"=>{"Researcher"=>3, "Student > Ph. D. Student"=>7, "Student > Bachelor"=>1}, "reader_count_by_subject_area"=>{"Materials Science"=>1, "Agricultural and Biological Sciences"=>9, "Medicine and Dentistry"=>1}, "reader_count_by_subdiscipline"=>{"Materials Science"=>{"Materials Science"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>9}}, "reader_count_by_country"=>{"United States"=>1, "Germany"=>1}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/990103", "https://ndownloader.figshare.com/files/990104", "https://ndownloader.figshare.com/files/990105"], "description"=>"<div><p>Chondroitin sulfate proteoglycans (CSPGs) are major components of the extracellular matrix which mediate inhibition of axonal regeneration after injury to the central nervous system (CNS). Several neuronal receptors for CSPGs have recently been identified; however, the signaling pathways by which CSPGs restrict axonal growth are still largely unknown. In this study, we applied quantitative phosphoproteomics to investigate the global changes in protein phosphorylation induced by CSPGs in primary neurons. In combination with isobaric Tags for Relative and Absolute Quantitation (iTRAQ) labeling, strong cation exchange chromatography (SCX) fractionation, immobilized metal affinity chromatography (IMAC) and LC-MS/MS, we identified and quantified 2214 unique phosphopeptides corresponding to 1118 phosphoproteins, with 118 changing significantly in abundance with CSPG treatment. The proteins that were regulated by CSPGs included key components of synaptic vesicle trafficking, axon guidance mediated by semaphorins, integrin signaling, cadherin signaling and EGF receptor signaling pathways. A significant number of the regulated proteins are cytoskeletal and related proteins that have been implicated in regulating neurite growth. Another highly represented protein category regulated by CSPGs is nucleic acid binding proteins involved in RNA post-transcriptional regulation. Together, by screening the overall phosphoproteome changes induced by CSPGs, this data expand our understanding of CSPG signaling, which provides new insights into development of strategies for overcoming CSPG inhibition and promoting axonal regeneration after CNS injury.</p> </div>", "links"=>[], "tags"=>["neuronal", "phosphoproteome", "chondroitin", "sulfate", "proteoglycans"], "article_id"=>654298, "categories"=>["Biochemistry", "Neuroscience", "Genetics"], "users"=>["Panpan Yu", "Trairak Pisitkun", "Guanghui Wang", "Rong Wang", "Yasuhiro Katagiri", "Marjan Gucek", "Mark A. Knepper", "Herbert M. Geller"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0059285.s001", "https://dx.doi.org/10.1371/journal.pone.0059285.s002", "https://dx.doi.org/10.1371/journal.pone.0059285.s003"], "stats"=>{"downloads"=>4, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Global_Analysis_of_Neuronal_Phosphoproteome_Regulation_by_Chondroitin_Sulfate_Proteoglycans__/654298", "title"=>"Global Analysis of Neuronal Phosphoproteome Regulation by Chondroitin Sulfate Proteoglycans", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-03-19 08:13:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/990098"], "description"=>"<p>(<b>A</b>) Phosphorylation motif distribution for increased phosphopeptides by CSPG treatment. (<b>B</b>) Phosphorylation motif distribution for decreased phosphopeptides by CSPG treatment. (<b>C</b>) Sequence logos showing overrepresented phosphorylation motifs in 41 phosphopeptides significantly increase by CSPGs. (<b>D</b>) Sequence logos showing overrepresented phosphorylation motifs in 77 phosphopeptides significantly decreased by CSPGs.</p>", "links"=>[], "tags"=>["changed"], "article_id"=>654293, "categories"=>["Biochemistry", "Neuroscience", "Genetics"], "users"=>["Panpan Yu", "Trairak Pisitkun", "Guanghui Wang", "Rong Wang", "Yasuhiro Katagiri", "Marjan Gucek", "Mark A. Knepper", "Herbert M. Geller"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0059285.g003", "stats"=>{"downloads"=>0, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Motif_analysis_of_significantly_changed_phosphopeptides_/654293", "title"=>"Motif analysis of significantly changed phosphopeptides.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-19 08:12:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/990093"], "description"=>"<p>(<b>A</b>) Strategy used for iTRAQ-based quantitative phosphoproteomics of CSPG-treated mouse CGNs. <i>CGN</i>, cerebellar granule neuron; <i>SCX</i>, strong cation exchange chromatography; <i>IMAC</i>, immobilized metal affinity chromatography. (<b>B</b>) Distribution of changes for all quantified phosphopeptides. (<b>C</b>) A volcano plot shows the differentially regulated phosphopeptides. The horizontal line marks the threshold at1.301 = -log (<i>p = </i>0.05) and the vertical dash lines represent the positions with ratios of Mean+1SD and Mean-1SD. Using the dual criterions of p<0.05 and change>1SD, 77 phosphopeptides were defined as decreased (green) and 41 were increased (red) by CSPGs.</p>", "links"=>[], "tags"=>["phosphoproteomic"], "article_id"=>654288, "categories"=>["Biochemistry", "Neuroscience", "Genetics"], "users"=>["Panpan Yu", "Trairak Pisitkun", "Guanghui Wang", "Rong Wang", "Yasuhiro Katagiri", "Marjan Gucek", "Mark A. Knepper", "Herbert M. Geller"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0059285.g001", "stats"=>{"downloads"=>0, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Overview_of_phosphoproteomic_profiling_/654288", "title"=>"Overview of phosphoproteomic profiling.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-19 08:10:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/1007394"], "description"=>"<p>List of phosphopeptides that show significant changes in abundance in response to CSPG treatment with mean log<sub>2</sub> (CSPG/Control) >0.5 or<−0.5.</p>", "links"=>[], "tags"=>["phosphopeptides", "abundance", "cspg"], "article_id"=>668014, "categories"=>["Biochemistry", "Neuroscience", "Genetics"], "users"=>["Panpan Yu", "Trairak Pisitkun", "Guanghui Wang", "Rong Wang", "Yasuhiro Katagiri", "Marjan Gucek", "Mark A. Knepper", "Herbert M. Geller"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0059285.t001", "stats"=>{"downloads"=>2, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_List_of_phosphopeptides_that_show_significant_changes_in_abundance_in_response_to_CSPG_treatment_with_mean_log_2_CSPG_Control_gt_0_5_or_lt_8722_0_5_/668014", "title"=>"List of phosphopeptides that show significant changes in abundance in response to CSPG treatment with mean log<sub>2</sub> (CSPG/Control) >0.5 or<−0.5.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-03-18 02:13:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/1007372"], "description"=>"<p>Main Networks and the associated phosphoproteins that were regulated by CSPGs as analyzed by IPA from Ingenuity System.</p>", "links"=>[], "tags"=>["networks", "phosphoproteins", "regulated", "cspgs", "ipa", "ingenuity"], "article_id"=>667991, "categories"=>["Biochemistry", "Neuroscience", "Genetics"], "users"=>["Panpan Yu", "Trairak Pisitkun", "Guanghui Wang", "Rong Wang", "Yasuhiro Katagiri", "Marjan Gucek", "Mark A. Knepper", "Herbert M. Geller"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0059285.t002", "stats"=>{"downloads"=>1, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Main_Networks_and_the_associated_phosphoproteins_that_were_regulated_by_CSPGs_as_analyzed_by_IPA_from_Ingenuity_System_/667991", "title"=>"Main Networks and the associated phosphoproteins that were regulated by CSPGs as analyzed by IPA from Ingenuity System.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-03-18 02:13:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/990101"], "description"=>"<p>(<b>A</b>) The phosphorylation level of cofilin (pS3) and the amount of total protein expression at different time course after CSPG treatment; (<b>B</b>) The phosphorylation level of GSK3β (pY216) and the amount of its total protein expression at different time course after CSPG treatment.</p>", "links"=>[], "tags"=>["blot", "cofilin", "phosphorylation", "regulated"], "article_id"=>654296, "categories"=>["Biochemistry", "Neuroscience", "Genetics"], "users"=>["Panpan Yu", "Trairak Pisitkun", "Guanghui Wang", "Rong Wang", "Yasuhiro Katagiri", "Marjan Gucek", "Mark A. Knepper", "Herbert M. Geller"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0059285.g005", "stats"=>{"downloads"=>0, "page_views"=>31, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Western_blot_analysis_of_cofilin_pS3_and_GSK3_946_pY216_phosphorylation_regulated_by_CSPGs_/654296", "title"=>"Western blot analysis of cofilin (pS3) and GSK3β (pY216) phosphorylation regulated by CSPGs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-19 08:12:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/990099"], "description"=>"<p>PANTHER Pathway terms were extracted for each phosphopeptide that changed significantly with CSPGs and compared with pathway terms for all identified peptides which were used as background. The gene names for the corresponding phosphoproteins that changed with CSPGs are listed for each pathway. Only the pathways that contained more than one identified protein are included.</p>", "links"=>[], "tags"=>["pathways", "regulated"], "article_id"=>654294, "categories"=>["Biochemistry", "Neuroscience", "Genetics"], "users"=>["Panpan Yu", "Trairak Pisitkun", "Guanghui Wang", "Rong Wang", "Yasuhiro Katagiri", "Marjan Gucek", "Mark A. Knepper", "Herbert M. Geller"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0059285.g004", "stats"=>{"downloads"=>0, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Signaling_pathways_regulated_by_CSPGs_/654294", "title"=>"Signaling pathways regulated by CSPGs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-19 08:12:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/990096"], "description"=>"<p>(<b>A</b>) Gene ontology analysis of changed phosphoproteins using PANTHER program. (<b>B</b>) Subdivision of the category cytoskeletal protein (PC00085) in (A). (<b>C</b>) Subdivision of the category nucleic acid binding (PC00171) in (A). (<b>D</b>) Significance of biological functions refers to the –log (p-value) obtained by the Ingenuity program. The top 20 biological functions with significant enrichment are shown. Threshold is at 1.031 = -log (p = 0.05).</p>", "links"=>[], "tags"=>["classification", "changed"], "article_id"=>654291, "categories"=>["Biochemistry", "Neuroscience", "Genetics"], "users"=>["Panpan Yu", "Trairak Pisitkun", "Guanghui Wang", "Rong Wang", "Yasuhiro Katagiri", "Marjan Gucek", "Mark A. Knepper", "Herbert M. Geller"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0059285.g002", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Protein_classification_of_significantly_changed_phosphoproteins_/654291", "title"=>"Protein classification of significantly changed phosphoproteins.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-19 08:11:33"}

PMC Usage Stats | Further Information

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Relative Metric

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