CSF Proteomics Identifies Specific and Shared Pathways for Multiple Sclerosis Clinical Subtypes
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{"title"=>"CSF proteomics identifies specific and shared pathways for multiple sclerosis clinical subtypes", "type"=>"journal", "authors"=>[{"first_name"=>"Timucin", "last_name"=>"Avsar", "scopus_author_id"=>"55318846300"}, {"first_name"=>"Ilknur", "last_name"=>"Melis Durasi", "scopus_author_id"=>"56638695800"}, {"first_name"=>"Ugur", "last_name"=>"Uygunoglu", "scopus_author_id"=>"36708802800"}, {"first_name"=>"Melih", "last_name"=>"Tutuncu", "scopus_author_id"=>"42462558200"}, {"first_name"=>"Nuri", "last_name"=>"Onat Demirci", "scopus_author_id"=>"56638692000"}, {"first_name"=>"Sabahattin", "last_name"=>"Saip", "scopus_author_id"=>"55372483000"}, {"first_name"=>"O.", "last_name"=>"Ugur Sezerman", "scopus_author_id"=>"36125855600"}, {"first_name"=>"Aksel", "last_name"=>"Siva", "scopus_author_id"=>"7004131839"}, {"first_name"=>"Eda", "last_name"=>"Tahir Turanli", "scopus_author_id"=>"37032225800"}], "year"=>2015, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"25942430", "doi"=>"10.1371/journal.pone.0122045", "sgr"=>"84929096088", "scopus"=>"2-s2.0-84929096088", "issn"=>"19326203", "pui"=>"604276463"}, "id"=>"267f4e05-42e5-31a4-9b01-48c2b6cef8e1", "abstract"=>"Multiple sclerosis (MS) is an immune-mediated, neuro-inflammatory, demyelinating and neurodegenerative disease of the central nervous system (CNS) with a heterogeneous clinical presentation and course. There is a remarkable phenotypic heterogeneity in MS, and the molecular mechanisms underlying it remain unknown. We aimed to investigate further the etiopathogenesis related molecular pathways in subclinical types of MS using proteomic and bioinformatics approaches in cerebrospinal fluids of patients with clinically isolated syndrome, relapsing remitting MS and progressive MS (n=179). Comparison of disease groups with controls revealed a total of 151 proteins that are differentially expressed in clinically different MS subtypes. KEGG analysis using PANOGA tool revealed the disease related pathways including aldosterone-regulated sodium reabsorption (p=8.02x10-5) which is important in the immune cell migration, renin-angiotensin (p=6.88x10-5) system that induces Th17 dependent immunity, notch signaling (p=1.83x10-10) pathway indicating the activated remyelination and vitamin digestion and absorption pathways (p=1.73x10-5). An emerging theme from our studies is that whilst all MS clinical forms share common biological pathways, there are also clinical subtypes specific and pathophysiology related pathways which may have further therapeutic implications.", "link"=>"http://www.mendeley.com/research/csf-proteomics-identifies-specific-shared-pathways-multiple-sclerosis-clinical-subtypes", "reader_count"=>18, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Researcher"=>4, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>3, "Student > Postgraduate"=>1, "Student > Master"=>2, "Other"=>2, "Student > Bachelor"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Researcher"=>4, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>3, "Student > Postgraduate"=>1, "Student > Master"=>2, "Other"=>2, "Student > Bachelor"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Mathematics"=>1, "Medicine and Dentistry"=>8, "Agricultural and Biological Sciences"=>3, "Neuroscience"=>2, "Pharmacology, Toxicology and Pharmaceutical Science"=>2, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>8}, "Neuroscience"=>{"Neuroscience"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>3}, "Computer Science"=>{"Computer Science"=>1}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>1}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>2}}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/2053230"], "description"=>"<p>This flowchart summarizes our approach in identification of MS related molecular pathways using a combination of two-dimensional gel electrophoresis and mass spectroscopy, with bioinformatics analysis.</p>", "links"=>[], "tags"=>["Multiple Sclerosis Clinical Subtypes Multiple sclerosis", "cerebrospinal fluids", "151 proteins", "Shared Pathways", "neurodegenerative disease", "phenotypic heterogeneity", "Th 17", "subclinical types", "PANOGA tool", "bioinformatics approaches", "MS subtypes", "forms share", "disease groups", "KEGG analysis", "CSF Proteomics Identifies", "cell migration", "vitamin digestion", "cns", "absorption pathways"], "article_id"=>1404702, "categories"=>["Biological Sciences"], "users"=>["Timucin Avsar", "İlknur Melis Durası", "Uğur Uygunoğlu", "Melih Tutuncu", "Nuri Onat Demirci", "Sabahattin Saip", "O. Uğur Sezerman", "Aksel Siva", "Eda Tahir Turanlı"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0122045.g001", "stats"=>{"downloads"=>0, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Overview_and_design_of_the_study_/1404702", "title"=>"Overview and design of the study.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-05-05 03:22:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/2053243", "https://ndownloader.figshare.com/files/2053245", "https://ndownloader.figshare.com/files/2053246", "https://ndownloader.figshare.com/files/2053247"], "description"=>"<div><p>Multiple sclerosis (MS) is an immune-mediated, neuro-inflammatory, demyelinating and neurodegenerative disease of the central nervous system (CNS) with a heterogeneous clinical presentation and course. There is a remarkable phenotypic heterogeneity in MS, and the molecular mechanisms underlying it remain unknown. We aimed to investigate further the etiopathogenesis related molecular pathways in subclinical types of MS using proteomic and bioinformatics approaches in cerebrospinal fluids of patients with clinically isolated syndrome, relapsing remitting MS and progressive MS (n=179). Comparison of disease groups with controls revealed a total of 151 proteins that are differentially expressed in clinically different MS subtypes. KEGG analysis using PANOGA tool revealed the disease related pathways including aldosterone-regulated sodium reabsorption (p=8.02x10<sup>-5</sup>) which is important in the immune cell migration, renin-angiotensin (p=6.88x10<sup>-5</sup>) system that induces Th17 dependent immunity, notch signaling (p=1.83x10<sup>-10</sup>) pathway indicating the activated remyelination and vitamin digestion and absorption pathways (p=1.73x10<sup>-5</sup>). An emerging theme from our studies is that whilst all MS clinical forms share common biological pathways, there are also clinical subtypes specific and pathophysiology related pathways which may have further therapeutic implications.</p></div>", "links"=>[], "tags"=>["Multiple Sclerosis Clinical Subtypes Multiple sclerosis", "cerebrospinal fluids", "151 proteins", "Shared Pathways", "neurodegenerative disease", "phenotypic heterogeneity", "Th 17", "subclinical types", "PANOGA tool", "bioinformatics approaches", "MS subtypes", "forms share", "disease groups", "KEGG analysis", "CSF Proteomics Identifies", "cell migration", "vitamin digestion", "cns", "absorption pathways"], "article_id"=>1404716, "categories"=>["Biological Sciences"], "users"=>["Timucin Avsar", "İlknur Melis Durası", "Uğur Uygunoğlu", "Melih Tutuncu", "Nuri Onat Demirci", "Sabahattin Saip", "O. Uğur Sezerman", "Aksel Siva", "Eda Tahir Turanlı"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0122045.s001", "https://dx.doi.org/10.1371/journal.pone.0122045.s002", "https://dx.doi.org/10.1371/journal.pone.0122045.s003", "https://dx.doi.org/10.1371/journal.pone.0122045.s004"], "stats"=>{"downloads"=>0, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_CSF_Proteomics_Identifies_Specific_and_Shared_Pathways_for_Multiple_Sclerosis_Clinical_Subtypes_/1404716", "title"=>"CSF Proteomics Identifies Specific and Shared Pathways for Multiple Sclerosis Clinical Subtypes", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-05-05 03:22:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/2053238"], "description"=>"<p>Analysis with in the CIS subgroup revealed the important pathways in the transmission of disease subtypes. MS suggestive CIS (MSs-CIS) group indicated the importance of Aldosterone regulated sodium reabsorption pathway. Single attack (SA-MS) showed the increased activation of NOD-like receptor signaling pathway and clinically definite MS (CDMS) showed shared pathways with RRMS and CIS subtypes.</p><p>Molecular pathways and associated proteins revealed by CIS subgroup analysis.</p>", "links"=>[], "tags"=>["Multiple Sclerosis Clinical Subtypes Multiple sclerosis", "cerebrospinal fluids", "151 proteins", "Shared Pathways", "neurodegenerative disease", "phenotypic heterogeneity", "Th 17", "subclinical types", "PANOGA tool", "bioinformatics approaches", "MS subtypes", "forms share", "disease groups", "KEGG analysis", "CSF Proteomics Identifies", "cell migration", "vitamin digestion", "cns", "absorption pathways"], "article_id"=>1404710, "categories"=>["Biological Sciences"], "users"=>["Timucin Avsar", "İlknur Melis Durası", "Uğur Uygunoğlu", "Melih Tutuncu", "Nuri Onat Demirci", "Sabahattin Saip", "O. Uğur Sezerman", "Aksel Siva", "Eda Tahir Turanlı"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0122045.t005", "stats"=>{"downloads"=>0, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Molecular_pathways_and_associated_proteins_revealed_by_CIS_subgroup_analysis_/1404710", "title"=>"Molecular pathways and associated proteins revealed by CIS subgroup analysis.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-05-05 03:22:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/2053235"], "description"=>"<p>Molecular pathways and associated proteins in CIS subtype were shown. Individual protein list of each CIS patients were processed and compared with control samples regarding their fold changes. Table shows the targeted KEGG pathways with the database ID and names. P values were given with the Bonferroni Corrections. ‘Times found’ indicates the co-occurrence of target proteins in subnetworks. Other pathway-associated proteins that are not found in subnetworks were also listed. Regarding the common and shared pathways, proteasome pathway is only found in CIS subtype.</p><p>Molecular pathways and associated proteins in CIS subtype.</p>", "links"=>[], "tags"=>["Multiple Sclerosis Clinical Subtypes Multiple sclerosis", "cerebrospinal fluids", "151 proteins", "Shared Pathways", "neurodegenerative disease", "phenotypic heterogeneity", "Th 17", "subclinical types", "PANOGA tool", "bioinformatics approaches", "MS subtypes", "forms share", "disease groups", "KEGG analysis", "CSF Proteomics Identifies", "cell migration", "vitamin digestion", "cns", "absorption pathways"], "article_id"=>1404707, "categories"=>["Biological Sciences"], "users"=>["Timucin Avsar", "İlknur Melis Durası", "Uğur Uygunoğlu", "Melih Tutuncu", "Nuri Onat Demirci", "Sabahattin Saip", "O. Uğur Sezerman", "Aksel Siva", "Eda Tahir Turanlı"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0122045.t002", "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Molecular_pathways_and_associated_proteins_in_CIS_subtype_/1404707", "title"=>"Molecular pathways and associated proteins in CIS subtype.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-05-05 03:22:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/2053234"], "description"=>"<p>* The time between first clinical attack and last examination</p><p>** The time between first and last examination</p><p>*** PMS samples were obtained from our biobank</p><p>Study groups with case and control samples were summarized in terms of demographical and clinical information. Age at analysis, age of disease onset, gender, expanded disability status scale (EDSS), disease duration which indicates the time between first clinical attack and last examination, follow-up period which indicates the time between first and last examination and finally CSF IgG index, which is calculated as IgG to CSF albumin ratio compared to the serum IgG to serum albumin ratio, were summarized. NonMS control samples consisted of acute headache and pseudotumour cerebri patients whereas, other neurological disease (OND) consisted of neuro-Behçet disease, neuro-sarcoidosis and polyneuropathies.</p><p>Clinical and demographical data of study group.</p>", "links"=>[], "tags"=>["Multiple Sclerosis Clinical Subtypes Multiple sclerosis", "cerebrospinal fluids", "151 proteins", "Shared Pathways", "neurodegenerative disease", "phenotypic heterogeneity", "Th 17", "subclinical types", "PANOGA tool", "bioinformatics approaches", "MS subtypes", "forms share", "disease groups", "KEGG analysis", "CSF Proteomics Identifies", "cell migration", "vitamin digestion", "cns", "absorption pathways"], "article_id"=>1404706, "categories"=>["Biological Sciences"], "users"=>["Timucin Avsar", "İlknur Melis Durası", "Uğur Uygunoğlu", "Melih Tutuncu", "Nuri Onat Demirci", "Sabahattin Saip", "O. Uğur Sezerman", "Aksel Siva", "Eda Tahir Turanlı"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0122045.t001", "stats"=>{"downloads"=>0, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Clinical_and_demographical_data_of_study_group_/1404706", "title"=>"Clinical and demographical data of study group.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-05-05 03:22:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/2053237"], "description"=>"<p>Molecular pathways and associated proteins in PMS subtype were shown. Individual protein list of each PMS patients were processed and compared with control samples regarding their fold changes. Table shows the targeted KEGG pathways with the database ID and names. P values were given with the Bonferroni Corrections. ‘Times found’ indicates the co-occurrence of target proteins in subnetworks. Other pathway-associated proteins that are not found in subnetworks were also listed.</p><p>Molecular pathways and associated proteins in PMS subtype.</p>", "links"=>[], "tags"=>["Multiple Sclerosis Clinical Subtypes Multiple sclerosis", "cerebrospinal fluids", "151 proteins", "Shared Pathways", "neurodegenerative disease", "phenotypic heterogeneity", "Th 17", "subclinical types", "PANOGA tool", "bioinformatics approaches", "MS subtypes", "forms share", "disease groups", "KEGG analysis", "CSF Proteomics Identifies", "cell migration", "vitamin digestion", "cns", "absorption pathways"], "article_id"=>1404709, "categories"=>["Biological Sciences"], "users"=>["Timucin Avsar", "İlknur Melis Durası", "Uğur Uygunoğlu", "Melih Tutuncu", "Nuri Onat Demirci", "Sabahattin Saip", "O. Uğur Sezerman", "Aksel Siva", "Eda Tahir Turanlı"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0122045.t004", "stats"=>{"downloads"=>0, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Molecular_pathways_and_associated_proteins_in_PMS_subtype_/1404709", "title"=>"Molecular pathways and associated proteins in PMS subtype.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-05-05 03:22:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/2053236"], "description"=>"<p>Molecular pathways and associated proteins in RRMS subtype were shown. Individual protein list of each RRMS patients were processed and compared with control samples regarding their fold changes. Table shows the targeted KEGG pathways with the database ID and names. P values were given with the Bonferroni Corrections. ‘Times found’ indicates the co-occurrence of target proteins in subnetworks. Other pathway-associated proteins that are not found in subnetworks were also listed. Regarding the common and shared pathways, Pathogenic Escherichia coli infection pathway is only found in RRMS subtype.</p><p>Molecular pathways and associated proteins in RRMS subtype.</p>", "links"=>[], "tags"=>["Multiple Sclerosis Clinical Subtypes Multiple sclerosis", "cerebrospinal fluids", "151 proteins", "Shared Pathways", "neurodegenerative disease", "phenotypic heterogeneity", "Th 17", "subclinical types", "PANOGA tool", "bioinformatics approaches", "MS subtypes", "forms share", "disease groups", "KEGG analysis", "CSF Proteomics Identifies", "cell migration", "vitamin digestion", "cns", "absorption pathways"], "article_id"=>1404708, "categories"=>["Biological Sciences"], "users"=>["Timucin Avsar", "İlknur Melis Durası", "Uğur Uygunoğlu", "Melih Tutuncu", "Nuri Onat Demirci", "Sabahattin Saip", "O. Uğur Sezerman", "Aksel Siva", "Eda Tahir Turanlı"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0122045.t003", "stats"=>{"downloads"=>0, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Molecular_pathways_and_associated_proteins_in_RRMS_subtype_/1404708", "title"=>"Molecular pathways and associated proteins in RRMS subtype.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-05-05 03:22:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/2053233"], "description"=>"<p>Representative 2D-PAGE image of each study group including control, CIS, RRMS and PMS.</p>", "links"=>[], "tags"=>["Multiple Sclerosis Clinical Subtypes Multiple sclerosis", "cerebrospinal fluids", "151 proteins", "Shared Pathways", "neurodegenerative disease", "phenotypic heterogeneity", "Th 17", "subclinical types", "PANOGA tool", "bioinformatics approaches", "MS subtypes", "forms share", "disease groups", "KEGG analysis", "CSF Proteomics Identifies", "cell migration", "vitamin digestion", "cns", "absorption pathways"], "article_id"=>1404705, "categories"=>["Biological Sciences"], "users"=>["Timucin Avsar", "İlknur Melis Durası", "Uğur Uygunoğlu", "Melih Tutuncu", "Nuri Onat Demirci", "Sabahattin Saip", "O. Uğur Sezerman", "Aksel Siva", "Eda Tahir Turanlı"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0122045.g002", "stats"=>{"downloads"=>0, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Representative_2D_PAGE_image_of_each_study_group_including_control_CIS_RRMS_and_PMS_/1404705", "title"=>"Representative 2D-PAGE image of each study group including control, CIS, RRMS and PMS.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-05-05 03:22:45"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"8", "full-text"=>"12", "pdf"=>"7", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"4"}
  • {"unique-ip"=>"11", "full-text"=>"7", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"6", "cited-by"=>"0", "year"=>"2018", "month"=>"6"}
  • {"unique-ip"=>"6", "full-text"=>"5", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"5"}
  • {"unique-ip"=>"17", "full-text"=>"14", "pdf"=>"6", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2018", "month"=>"7"}
  • {"unique-ip"=>"5", "full-text"=>"6", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"8"}
  • {"unique-ip"=>"17", "full-text"=>"12", "pdf"=>"5", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"10"}
  • {"unique-ip"=>"13", "full-text"=>"11", "pdf"=>"5", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2018", "month"=>"12"}
  • {"unique-ip"=>"8", "full-text"=>"9", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"9"}
  • {"unique-ip"=>"23", "full-text"=>"24", "pdf"=>"9", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"3", "cited-by"=>"0", "year"=>"2019", "month"=>"2"}
  • {"unique-ip"=>"10", "full-text"=>"8", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"3"}
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  • {"unique-ip"=>"8", "full-text"=>"10", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}

Relative Metric

{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}
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