Codeletion of 1p and 19q determines distinct gene methylation and expression profiles in IDH-mutated oligodendroglial tumors View Full Text


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

2013-05-21

AUTHORS

Pilar Mur, Manuela Mollejo, Yolanda Ruano, Ángel Rodríguez de Lope, Concepción Fiaño, Juan Fernando García, Javier S. Castresana, Aurelio Hernández-Laín, Juan A. Rey, Bárbara Meléndez

ABSTRACT

Oligodendroglial tumors (OTs) are primary brain tumors that show variable clinical and biological behavior. The 1p/19q codeletion is frequent in these tumors, indicating a better prognosis and/or treatment response. Recently, the prognostically favorable CpG island methylator phenotype (CIMP) in gliomas (G-CIMP+) was associated with mutations in the isocitrate dehydrogenase 1 and isocitrate dehydrogenase 2 (IDH) genes, as opposed to G-CIMP− tumors, highlighting the relevance of epigenetic mechanisms. We performed a whole-genome methylation study in 46 OTs, and a gene expression study of 25 tumors, correlating the methylation and transcriptomic profiles with molecular and clinical variables. Here, we identified two different epigenetic patterns within the previously described main G-CIMP+ profile. Both IDH mutation-associated methylation profiles featured one group of OTs with 1p/19q loss (CD-CIMP+), most of which were pure oligodendrogliomas, and a second group with intact 1p/19q and frequent TP53 mutation (CIMP+), most of which exhibited a mixed histopathology. A third group of OTs lacking the CIMP profile (CIMP−), and with a wild-type IDH and an intact 1p/19q, similar to the G-CIMP− subgroup, was also observed. The three CIMP groups presented a significantly better (CD-CIMP+), intermediate (CIMP+) or worse (CIMP−) prognosis. Furthermore, transcriptomic analyses revealed CIMP-specific gene expression signatures, indicating the impact of genetic status (IDH mutation, 1p/19q codeletion, TP53 mutation) on gene expression, and pointing to candidate biomarkers. Therefore, the CIMP profiles contributed to the identification of subgroups of OTs characterized by different prognoses, histopathologies, molecular features and gene expression signatures, which may help in the classification of OTs. More... »

PAGES

277-289

References to SciGraph publications

  • 2012-05-17. CIC and FUBP1 mutations in oligodendrogliomas, oligoastrocytomas and astrocytomas in ACTA NEUROPATHOLOGICA
  • 2008-11-05. Analysis of the IDH1 codon 132 mutation in brain tumors in ACTA NEUROPATHOLOGICA
  • 2008-12-18. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources in NATURE PROTOCOLS
  • 2012-02-15. IDH1 mutation is sufficient to establish the glioma hypermethylator phenotype in NATURE
  • 2012-10-14. Epigenomic analysis detects widespread gene-body DNA hypomethylation in chronic lymphocytic leukemia in NATURE GENETICS
  • 2009-06-25. Type and frequency of IDH1 and IDH2 mutations are related to astrocytic and oligodendroglial differentiation and age: a study of 1,010 diffuse gliomas in ACTA NEUROPATHOLOGICA
  • 2012-02-15. IDH mutation impairs histone demethylation and results in a block to cell differentiation in NATURE
  • 2011-12-12. Downregulation of PRDX1 by promoter hypermethylation is frequent in 1p/19q-deleted oligodendroglial tumours and increases radio- and chemosensitivity of Hs683 glioma cells in vitro in ONCOGENE
  • 2012-07-19. MGMT methylation analysis of glioblastoma on the Infinium methylation BeadChip identifies two distinct CpG regions associated with gene silencing and outcome, yielding a prediction model for comparisons across datasets, tumor grades, and CIMP-status in ACTA NEUROPATHOLOGICA
  • 2012-01-29. Somatic Histone H3 Alterations in Paediatric Diffuse Intrinsic Pontine Gliomas and Non-Brainstem Glioblastomas in NATURE GENETICS
  • 2007-07-06. The 2007 WHO Classification of Tumours of the Central Nervous System in ACTA NEUROPATHOLOGICA
  • 2012-01-29. Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma in NATURE
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1007/s00401-013-1130-9

    DOI

    http://dx.doi.org/10.1007/s00401-013-1130-9

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1038390505

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/23689617


    Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
    Incoming Citations Browse incoming citations for this publication using opencitations.net

    JSON-LD is the canonical representation for SciGraph data.

    TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

    [
      {
        "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
        "about": [
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/11", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Medical and Health Sciences", 
            "type": "DefinedTerm"
          }, 
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/1103", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Clinical Sciences", 
            "type": "DefinedTerm"
          }, 
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/1109", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Neurosciences", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Brain Neoplasms", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Chromosomes, Human, Pair 1", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Chromosomes, Human, Pair 19", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "DNA Methylation", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Gene Expression Regulation, Neoplastic", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Genome-Wide Association Study", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Humans", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Isocitrate Dehydrogenase", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Kaplan-Meier Estimate", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Oligodendroglioma", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Prognosis", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Transcriptome", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Tumor Suppressor Protein p53", 
            "type": "DefinedTerm"
          }
        ], 
        "author": [
          {
            "affiliation": {
              "alternateName": "Molecular Pathology Research Unit, Department of Pathology, Virgen de la Salud Hospital, Avda. Barber 30, 45004, Toledo, Spain", 
              "id": "http://www.grid.ac/institutes/grid.413514.6", 
              "name": [
                "Molecular Pathology Research Unit, Department of Pathology, Virgen de la Salud Hospital, Avda. Barber 30, 45004, Toledo, Spain"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Mur", 
            "givenName": "Pilar", 
            "id": "sg:person.01244257011.25", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01244257011.25"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Pathology, Virgen de la Salud Hospital, Avda Barber 30, 45004, Toledo, Spain", 
              "id": "http://www.grid.ac/institutes/grid.413514.6", 
              "name": [
                "Molecular Pathology Research Unit, Department of Pathology, Virgen de la Salud Hospital, Avda. Barber 30, 45004, Toledo, Spain", 
                "Department of Pathology, Virgen de la Salud Hospital, Avda Barber 30, 45004, Toledo, Spain"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Mollejo", 
            "givenName": "Manuela", 
            "id": "sg:person.01053746063.57", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01053746063.57"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Pathology (Neuropathology), 12 de Octubre University Hospital, Avda de C\u00f3rdoba s/n, 28041, Madrid, Spain", 
              "id": "http://www.grid.ac/institutes/grid.144756.5", 
              "name": [
                "Department of Pathology (Neuropathology), 12 de Octubre University Hospital, Avda de C\u00f3rdoba s/n, 28041, Madrid, Spain"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Ruano", 
            "givenName": "Yolanda", 
            "id": "sg:person.0715227154.14", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0715227154.14"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Neurosurgery, Puerta del Hierro Hospital, C/Manuel de Falla no 1, Majadahonda, 28222, Madrid, Spain", 
              "id": "http://www.grid.ac/institutes/grid.73221.35", 
              "name": [
                "Department of Neurosurgery, Puerta del Hierro Hospital, C/Manuel de Falla no 1, Majadahonda, 28222, Madrid, Spain"
              ], 
              "type": "Organization"
            }, 
            "familyName": "de Lope", 
            "givenName": "\u00c1ngel Rodr\u00edguez", 
            "id": "sg:person.014022446676.50", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.014022446676.50"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Pathology, University Hospital Complex of Vigo (C.H.U.V.I.), R\u00faa Pizarro, 22, 36204, Vigo, Spain", 
              "id": "http://www.grid.ac/institutes/grid.411855.c", 
              "name": [
                "Department of Pathology, University Hospital Complex of Vigo (C.H.U.V.I.), R\u00faa Pizarro, 22, 36204, Vigo, Spain"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Fia\u00f1o", 
            "givenName": "Concepci\u00f3n", 
            "id": "sg:person.01236307663.37", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01236307663.37"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Pathology, MD Anderson International, C/Arturo Soria 270, 28033, Madrid, Spain", 
              "id": "http://www.grid.ac/institutes/None", 
              "name": [
                "Department of Pathology, MD Anderson International, C/Arturo Soria 270, 28033, Madrid, Spain"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Garc\u00eda", 
            "givenName": "Juan Fernando", 
            "id": "sg:person.013242743702.55", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.013242743702.55"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Brain Tumor Biology Unit, University of Navarra School of Sciences, C/Irunlarrea 1, 31008, Pamplona, Spain", 
              "id": "http://www.grid.ac/institutes/grid.5924.a", 
              "name": [
                "Brain Tumor Biology Unit, University of Navarra School of Sciences, C/Irunlarrea 1, 31008, Pamplona, Spain"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Castresana", 
            "givenName": "Javier S.", 
            "id": "sg:person.014444746137.71", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.014444746137.71"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Pathology (Neuropathology), 12 de Octubre University Hospital, Avda de C\u00f3rdoba s/n, 28041, Madrid, Spain", 
              "id": "http://www.grid.ac/institutes/grid.144756.5", 
              "name": [
                "Department of Pathology (Neuropathology), 12 de Octubre University Hospital, Avda de C\u00f3rdoba s/n, 28041, Madrid, Spain"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Hern\u00e1ndez-La\u00edn", 
            "givenName": "Aurelio", 
            "id": "sg:person.01267313104.25", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01267313104.25"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "IdiPaz Research Unit, La Paz University Hospital, Po de la Castellana, 261, 28046, Madrid, Spain", 
              "id": "http://www.grid.ac/institutes/grid.81821.32", 
              "name": [
                "IdiPaz Research Unit, La Paz University Hospital, Po de la Castellana, 261, 28046, Madrid, Spain"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Rey", 
            "givenName": "Juan A.", 
            "id": "sg:person.0755344505.04", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0755344505.04"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Molecular Pathology Research Unit, Department of Pathology, Virgen de la Salud Hospital, Avda. Barber 30, 45004, Toledo, Spain", 
              "id": "http://www.grid.ac/institutes/grid.413514.6", 
              "name": [
                "Molecular Pathology Research Unit, Department of Pathology, Virgen de la Salud Hospital, Avda. Barber 30, 45004, Toledo, Spain"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Mel\u00e9ndez", 
            "givenName": "B\u00e1rbara", 
            "id": "sg:person.0675245363.05", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0675245363.05"
            ], 
            "type": "Person"
          }
        ], 
        "citation": [
          {
            "id": "sg:pub.10.1038/onc.2011.513", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1029204322", 
              "https://doi.org/10.1038/onc.2011.513"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00401-012-1016-2", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1027095253", 
              "https://doi.org/10.1007/s00401-012-1016-2"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nprot.2008.211", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1039987283", 
              "https://doi.org/10.1038/nprot.2008.211"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature10860", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1000103968", 
              "https://doi.org/10.1038/nature10860"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ng.1102", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1048296872", 
              "https://doi.org/10.1038/ng.1102"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature10833", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1039575824", 
              "https://doi.org/10.1038/nature10833"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00401-007-0243-4", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1001430701", 
              "https://doi.org/10.1007/s00401-007-0243-4"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00401-009-0561-9", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1005128955", 
              "https://doi.org/10.1007/s00401-009-0561-9"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ng.2443", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1037664832", 
              "https://doi.org/10.1038/ng.2443"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature10866", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1010733927", 
              "https://doi.org/10.1038/nature10866"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00401-012-0993-5", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1037252294", 
              "https://doi.org/10.1007/s00401-012-0993-5"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00401-008-0455-2", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1047349518", 
              "https://doi.org/10.1007/s00401-008-0455-2"
            ], 
            "type": "CreativeWork"
          }
        ], 
        "datePublished": "2013-05-21", 
        "datePublishedReg": "2013-05-21", 
        "description": "Oligodendroglial tumors (OTs) are primary brain tumors that show variable clinical and biological behavior. The 1p/19q codeletion is frequent in these tumors, indicating a better prognosis and/or treatment response. Recently, the prognostically favorable CpG island methylator phenotype (CIMP) in gliomas (G-CIMP+) was associated with mutations in the isocitrate dehydrogenase 1 and isocitrate dehydrogenase 2 (IDH) genes, as opposed to G-CIMP\u2212 tumors, highlighting the relevance of epigenetic mechanisms. We performed a whole-genome methylation study in 46 OTs, and a gene expression study of 25 tumors, correlating the methylation and transcriptomic profiles with molecular and clinical variables. Here, we identified two different epigenetic patterns within the previously described main G-CIMP+ profile. Both IDH mutation-associated methylation profiles featured one group of OTs with 1p/19q loss (CD-CIMP+), most of which were pure oligodendrogliomas, and a second group with intact 1p/19q and frequent TP53 mutation (CIMP+), most of which exhibited a mixed histopathology. A third group of OTs lacking the CIMP profile (CIMP\u2212), and with a wild-type IDH and an intact 1p/19q, similar to the G-CIMP\u2212 subgroup, was also observed. The three CIMP groups presented a significantly better (CD-CIMP+), intermediate (CIMP+) or worse (CIMP\u2212) prognosis. Furthermore, transcriptomic analyses revealed CIMP-specific gene expression signatures, indicating the impact of genetic status (IDH mutation, 1p/19q codeletion, TP53 mutation) on gene expression, and pointing to candidate biomarkers. Therefore, the CIMP profiles contributed to the identification of subgroups of OTs characterized by different prognoses, histopathologies, molecular features and gene expression signatures, which may help in the classification of OTs.", 
        "genre": "article", 
        "id": "sg:pub.10.1007/s00401-013-1130-9", 
        "inLanguage": "en", 
        "isAccessibleForFree": false, 
        "isPartOf": [
          {
            "id": "sg:journal.1019073", 
            "issn": [
              "0001-6322", 
              "1432-0533"
            ], 
            "name": "Acta Neuropathologica", 
            "publisher": "Springer Nature", 
            "type": "Periodical"
          }, 
          {
            "issueNumber": "2", 
            "type": "PublicationIssue"
          }, 
          {
            "type": "PublicationVolume", 
            "volumeNumber": "126"
          }
        ], 
        "keywords": [
          "gene expression signatures", 
          "CpG island methylator phenotype", 
          "different epigenetic patterns", 
          "CIMP profiles", 
          "expression signatures", 
          "isocitrate dehydrogenase 2 gene", 
          "gene expression studies", 
          "epigenetic patterns", 
          "epigenetic mechanisms", 
          "transcriptomic analysis", 
          "methylation profiles", 
          "wild-type IDH", 
          "isocitrate dehydrogenase 1", 
          "transcriptomic profiles", 
          "expression studies", 
          "gene expression", 
          "expression profiles", 
          "methylation studies", 
          "genetic status", 
          "gene methylation", 
          "dehydrogenase 1", 
          "methylation", 
          "methylator phenotype", 
          "mutations", 
          "molecular features", 
          "frequent TP53 mutations", 
          "IDH", 
          "mixed histopathology", 
          "genes", 
          "phenotype", 
          "TP53 mutations", 
          "oligodendroglial tumors", 
          "expression", 
          "codeletion", 
          "signatures", 
          "primary brain tumors", 
          "biological behavior", 
          "codeletion of 1p", 
          "identification", 
          "profile", 
          "mechanism", 
          "patterns", 
          "response", 
          "tumors", 
          "biomarkers", 
          "loss", 
          "brain tumors", 
          "study", 
          "analysis", 
          "gliomas", 
          "relevance", 
          "intact 1p/19q", 
          "group", 
          "status", 
          "third group", 
          "oligodendrogliomas", 
          "second group", 
          "impact", 
          "features", 
          "subgroups", 
          "pure oligodendrogliomas", 
          "prognosis", 
          "classification", 
          "worse prognosis", 
          "treatment response", 
          "behavior", 
          "identification of subgroups", 
          "different prognosis", 
          "variables", 
          "histopathology", 
          "better prognosis", 
          "clinical variables", 
          "favorable CpG island methylator phenotype", 
          "island methylator phenotype", 
          "dehydrogenase 2 (IDH) genes", 
          "whole-genome methylation study", 
          "IDH mutation-associated methylation profiles", 
          "mutation-associated methylation profiles", 
          "group of OTs", 
          "CIMP groups", 
          "CIMP-specific gene expression signatures", 
          "classification of OTs", 
          "distinct gene methylation"
        ], 
        "name": "Codeletion of 1p and 19q determines distinct gene methylation and expression profiles in IDH-mutated oligodendroglial tumors", 
        "pagination": "277-289", 
        "productId": [
          {
            "name": "dimensions_id", 
            "type": "PropertyValue", 
            "value": [
              "pub.1038390505"
            ]
          }, 
          {
            "name": "doi", 
            "type": "PropertyValue", 
            "value": [
              "10.1007/s00401-013-1130-9"
            ]
          }, 
          {
            "name": "pubmed_id", 
            "type": "PropertyValue", 
            "value": [
              "23689617"
            ]
          }
        ], 
        "sameAs": [
          "https://doi.org/10.1007/s00401-013-1130-9", 
          "https://app.dimensions.ai/details/publication/pub.1038390505"
        ], 
        "sdDataset": "articles", 
        "sdDatePublished": "2021-11-01T18:20", 
        "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
        "sdPublisher": {
          "name": "Springer Nature - SN SciGraph project", 
          "type": "Organization"
        }, 
        "sdSource": "s3://com-springernature-scigraph/baseset/20211101/entities/gbq_results/article/article_597.jsonl", 
        "type": "ScholarlyArticle", 
        "url": "https://doi.org/10.1007/s00401-013-1130-9"
      }
    ]
     

    Download the RDF metadata as:  json-ld nt turtle xml License info

    HOW TO GET THIS DATA PROGRAMMATICALLY:

    JSON-LD is a popular format for linked data which is fully compatible with JSON.

    curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1007/s00401-013-1130-9'

    N-Triples is a line-based linked data format ideal for batch operations.

    curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1007/s00401-013-1130-9'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1007/s00401-013-1130-9'

    RDF/XML is a standard XML format for linked data.

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1007/s00401-013-1130-9'


     

    This table displays all metadata directly associated to this object as RDF triples.

    332 TRIPLES      22 PREDICATES      135 URIs      114 LITERALS      20 BLANK NODES

    Subject Predicate Object
    1 sg:pub.10.1007/s00401-013-1130-9 schema:about N2b0bd04d36b24c6c889143eacdb86d6e
    2 N301026aa176c49a0ba03f58709c84819
    3 N34527e52bc094b20bcc40a04667ea520
    4 N7744daf61cd845a88f716bdd86dd9da3
    5 N9176fb11d8fb485099c93dfd02d9b8aa
    6 N9693dbf36a32473295935cbca6ea300b
    7 Na1835980eff04a3a9a97385f464d942d
    8 Na8eafee786764d5bac61039a75960e34
    9 Nbcb981a584ac48d797b4dd326d5a3ea6
    10 Ne301f59e03704a239b03f6256b57d3f4
    11 Nea250db1e5694f61a7e67802adb92c31
    12 Nf96db07ae49348cc86cec0adc013d3ce
    13 Nff071ade6f2847ecbf1a18f47938a2de
    14 anzsrc-for:11
    15 anzsrc-for:1103
    16 anzsrc-for:1109
    17 schema:author N9d55e383d6e44ba391b92984e791d649
    18 schema:citation sg:pub.10.1007/s00401-007-0243-4
    19 sg:pub.10.1007/s00401-008-0455-2
    20 sg:pub.10.1007/s00401-009-0561-9
    21 sg:pub.10.1007/s00401-012-0993-5
    22 sg:pub.10.1007/s00401-012-1016-2
    23 sg:pub.10.1038/nature10833
    24 sg:pub.10.1038/nature10860
    25 sg:pub.10.1038/nature10866
    26 sg:pub.10.1038/ng.1102
    27 sg:pub.10.1038/ng.2443
    28 sg:pub.10.1038/nprot.2008.211
    29 sg:pub.10.1038/onc.2011.513
    30 schema:datePublished 2013-05-21
    31 schema:datePublishedReg 2013-05-21
    32 schema:description Oligodendroglial tumors (OTs) are primary brain tumors that show variable clinical and biological behavior. The 1p/19q codeletion is frequent in these tumors, indicating a better prognosis and/or treatment response. Recently, the prognostically favorable CpG island methylator phenotype (CIMP) in gliomas (G-CIMP+) was associated with mutations in the isocitrate dehydrogenase 1 and isocitrate dehydrogenase 2 (IDH) genes, as opposed to G-CIMP− tumors, highlighting the relevance of epigenetic mechanisms. We performed a whole-genome methylation study in 46 OTs, and a gene expression study of 25 tumors, correlating the methylation and transcriptomic profiles with molecular and clinical variables. Here, we identified two different epigenetic patterns within the previously described main G-CIMP+ profile. Both IDH mutation-associated methylation profiles featured one group of OTs with 1p/19q loss (CD-CIMP+), most of which were pure oligodendrogliomas, and a second group with intact 1p/19q and frequent TP53 mutation (CIMP+), most of which exhibited a mixed histopathology. A third group of OTs lacking the CIMP profile (CIMP−), and with a wild-type IDH and an intact 1p/19q, similar to the G-CIMP− subgroup, was also observed. The three CIMP groups presented a significantly better (CD-CIMP+), intermediate (CIMP+) or worse (CIMP−) prognosis. Furthermore, transcriptomic analyses revealed CIMP-specific gene expression signatures, indicating the impact of genetic status (IDH mutation, 1p/19q codeletion, TP53 mutation) on gene expression, and pointing to candidate biomarkers. Therefore, the CIMP profiles contributed to the identification of subgroups of OTs characterized by different prognoses, histopathologies, molecular features and gene expression signatures, which may help in the classification of OTs.
    33 schema:genre article
    34 schema:inLanguage en
    35 schema:isAccessibleForFree false
    36 schema:isPartOf N4ebade503d7448719f5ee0b58cdc71d4
    37 N56aedf7700864473b7301988366989e3
    38 sg:journal.1019073
    39 schema:keywords CIMP groups
    40 CIMP profiles
    41 CIMP-specific gene expression signatures
    42 CpG island methylator phenotype
    43 IDH
    44 IDH mutation-associated methylation profiles
    45 TP53 mutations
    46 analysis
    47 behavior
    48 better prognosis
    49 biological behavior
    50 biomarkers
    51 brain tumors
    52 classification
    53 classification of OTs
    54 clinical variables
    55 codeletion
    56 codeletion of 1p
    57 dehydrogenase 1
    58 dehydrogenase 2 (IDH) genes
    59 different epigenetic patterns
    60 different prognosis
    61 distinct gene methylation
    62 epigenetic mechanisms
    63 epigenetic patterns
    64 expression
    65 expression profiles
    66 expression signatures
    67 expression studies
    68 favorable CpG island methylator phenotype
    69 features
    70 frequent TP53 mutations
    71 gene expression
    72 gene expression signatures
    73 gene expression studies
    74 gene methylation
    75 genes
    76 genetic status
    77 gliomas
    78 group
    79 group of OTs
    80 histopathology
    81 identification
    82 identification of subgroups
    83 impact
    84 intact 1p/19q
    85 island methylator phenotype
    86 isocitrate dehydrogenase 1
    87 isocitrate dehydrogenase 2 gene
    88 loss
    89 mechanism
    90 methylation
    91 methylation profiles
    92 methylation studies
    93 methylator phenotype
    94 mixed histopathology
    95 molecular features
    96 mutation-associated methylation profiles
    97 mutations
    98 oligodendroglial tumors
    99 oligodendrogliomas
    100 patterns
    101 phenotype
    102 primary brain tumors
    103 profile
    104 prognosis
    105 pure oligodendrogliomas
    106 relevance
    107 response
    108 second group
    109 signatures
    110 status
    111 study
    112 subgroups
    113 third group
    114 transcriptomic analysis
    115 transcriptomic profiles
    116 treatment response
    117 tumors
    118 variables
    119 whole-genome methylation study
    120 wild-type IDH
    121 worse prognosis
    122 schema:name Codeletion of 1p and 19q determines distinct gene methylation and expression profiles in IDH-mutated oligodendroglial tumors
    123 schema:pagination 277-289
    124 schema:productId N3ac31f158bd8468883e90a7a54750a23
    125 Nb8f23766ca2e48a6aba90a998c1b254a
    126 Ncbc8e3fbc1244f1c9217cd7ac104e279
    127 schema:sameAs https://app.dimensions.ai/details/publication/pub.1038390505
    128 https://doi.org/10.1007/s00401-013-1130-9
    129 schema:sdDatePublished 2021-11-01T18:20
    130 schema:sdLicense https://scigraph.springernature.com/explorer/license/
    131 schema:sdPublisher N24ed4d32e4074576bdfb15ec82625ba4
    132 schema:url https://doi.org/10.1007/s00401-013-1130-9
    133 sgo:license sg:explorer/license/
    134 sgo:sdDataset articles
    135 rdf:type schema:ScholarlyArticle
    136 N24ed4d32e4074576bdfb15ec82625ba4 schema:name Springer Nature - SN SciGraph project
    137 rdf:type schema:Organization
    138 N2988abfeadaa4437b270aaf627d20612 rdf:first sg:person.014444746137.71
    139 rdf:rest N8f4e521c27c146e8979625cac47ffdda
    140 N2b0bd04d36b24c6c889143eacdb86d6e schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    141 schema:name Brain Neoplasms
    142 rdf:type schema:DefinedTerm
    143 N301026aa176c49a0ba03f58709c84819 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    144 schema:name Humans
    145 rdf:type schema:DefinedTerm
    146 N34527e52bc094b20bcc40a04667ea520 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    147 schema:name Isocitrate Dehydrogenase
    148 rdf:type schema:DefinedTerm
    149 N368ba6c3326641799fad07c26bd144d4 rdf:first sg:person.013242743702.55
    150 rdf:rest N2988abfeadaa4437b270aaf627d20612
    151 N3ac31f158bd8468883e90a7a54750a23 schema:name doi
    152 schema:value 10.1007/s00401-013-1130-9
    153 rdf:type schema:PropertyValue
    154 N4ebade503d7448719f5ee0b58cdc71d4 schema:issueNumber 2
    155 rdf:type schema:PublicationIssue
    156 N56aedf7700864473b7301988366989e3 schema:volumeNumber 126
    157 rdf:type schema:PublicationVolume
    158 N5e6684da39054d788343e0d89b70c9a1 rdf:first sg:person.01053746063.57
    159 rdf:rest N77bac777a44c4136a4d2c0350b237fdd
    160 N5e7851456941463ebfd133d201256cf6 rdf:first sg:person.0675245363.05
    161 rdf:rest rdf:nil
    162 N7744daf61cd845a88f716bdd86dd9da3 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    163 schema:name Chromosomes, Human, Pair 1
    164 rdf:type schema:DefinedTerm
    165 N77bac777a44c4136a4d2c0350b237fdd rdf:first sg:person.0715227154.14
    166 rdf:rest N9499a94ea3e64ccfa5e9fd2fc4f33ca8
    167 N8f4e521c27c146e8979625cac47ffdda rdf:first sg:person.01267313104.25
    168 rdf:rest Nea3f419d57e34fa281fa92251fa05d8d
    169 N9176fb11d8fb485099c93dfd02d9b8aa schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    170 schema:name DNA Methylation
    171 rdf:type schema:DefinedTerm
    172 N9499a94ea3e64ccfa5e9fd2fc4f33ca8 rdf:first sg:person.014022446676.50
    173 rdf:rest Ne9f9ded4c2e44bd1a8f1ca888a1312ba
    174 N9693dbf36a32473295935cbca6ea300b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    175 schema:name Chromosomes, Human, Pair 19
    176 rdf:type schema:DefinedTerm
    177 N9d55e383d6e44ba391b92984e791d649 rdf:first sg:person.01244257011.25
    178 rdf:rest N5e6684da39054d788343e0d89b70c9a1
    179 Na1835980eff04a3a9a97385f464d942d schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    180 schema:name Oligodendroglioma
    181 rdf:type schema:DefinedTerm
    182 Na8eafee786764d5bac61039a75960e34 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    183 schema:name Prognosis
    184 rdf:type schema:DefinedTerm
    185 Nb8f23766ca2e48a6aba90a998c1b254a schema:name dimensions_id
    186 schema:value pub.1038390505
    187 rdf:type schema:PropertyValue
    188 Nbcb981a584ac48d797b4dd326d5a3ea6 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    189 schema:name Transcriptome
    190 rdf:type schema:DefinedTerm
    191 Ncbc8e3fbc1244f1c9217cd7ac104e279 schema:name pubmed_id
    192 schema:value 23689617
    193 rdf:type schema:PropertyValue
    194 Ne301f59e03704a239b03f6256b57d3f4 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    195 schema:name Gene Expression Regulation, Neoplastic
    196 rdf:type schema:DefinedTerm
    197 Ne9f9ded4c2e44bd1a8f1ca888a1312ba rdf:first sg:person.01236307663.37
    198 rdf:rest N368ba6c3326641799fad07c26bd144d4
    199 Nea250db1e5694f61a7e67802adb92c31 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    200 schema:name Tumor Suppressor Protein p53
    201 rdf:type schema:DefinedTerm
    202 Nea3f419d57e34fa281fa92251fa05d8d rdf:first sg:person.0755344505.04
    203 rdf:rest N5e7851456941463ebfd133d201256cf6
    204 Nf96db07ae49348cc86cec0adc013d3ce schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    205 schema:name Kaplan-Meier Estimate
    206 rdf:type schema:DefinedTerm
    207 Nff071ade6f2847ecbf1a18f47938a2de schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    208 schema:name Genome-Wide Association Study
    209 rdf:type schema:DefinedTerm
    210 anzsrc-for:11 schema:inDefinedTermSet anzsrc-for:
    211 schema:name Medical and Health Sciences
    212 rdf:type schema:DefinedTerm
    213 anzsrc-for:1103 schema:inDefinedTermSet anzsrc-for:
    214 schema:name Clinical Sciences
    215 rdf:type schema:DefinedTerm
    216 anzsrc-for:1109 schema:inDefinedTermSet anzsrc-for:
    217 schema:name Neurosciences
    218 rdf:type schema:DefinedTerm
    219 sg:journal.1019073 schema:issn 0001-6322
    220 1432-0533
    221 schema:name Acta Neuropathologica
    222 schema:publisher Springer Nature
    223 rdf:type schema:Periodical
    224 sg:person.01053746063.57 schema:affiliation grid-institutes:grid.413514.6
    225 schema:familyName Mollejo
    226 schema:givenName Manuela
    227 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01053746063.57
    228 rdf:type schema:Person
    229 sg:person.01236307663.37 schema:affiliation grid-institutes:grid.411855.c
    230 schema:familyName Fiaño
    231 schema:givenName Concepción
    232 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01236307663.37
    233 rdf:type schema:Person
    234 sg:person.01244257011.25 schema:affiliation grid-institutes:grid.413514.6
    235 schema:familyName Mur
    236 schema:givenName Pilar
    237 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01244257011.25
    238 rdf:type schema:Person
    239 sg:person.01267313104.25 schema:affiliation grid-institutes:grid.144756.5
    240 schema:familyName Hernández-Laín
    241 schema:givenName Aurelio
    242 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01267313104.25
    243 rdf:type schema:Person
    244 sg:person.013242743702.55 schema:affiliation grid-institutes:None
    245 schema:familyName García
    246 schema:givenName Juan Fernando
    247 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.013242743702.55
    248 rdf:type schema:Person
    249 sg:person.014022446676.50 schema:affiliation grid-institutes:grid.73221.35
    250 schema:familyName de Lope
    251 schema:givenName Ángel Rodríguez
    252 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.014022446676.50
    253 rdf:type schema:Person
    254 sg:person.014444746137.71 schema:affiliation grid-institutes:grid.5924.a
    255 schema:familyName Castresana
    256 schema:givenName Javier S.
    257 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.014444746137.71
    258 rdf:type schema:Person
    259 sg:person.0675245363.05 schema:affiliation grid-institutes:grid.413514.6
    260 schema:familyName Meléndez
    261 schema:givenName Bárbara
    262 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0675245363.05
    263 rdf:type schema:Person
    264 sg:person.0715227154.14 schema:affiliation grid-institutes:grid.144756.5
    265 schema:familyName Ruano
    266 schema:givenName Yolanda
    267 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0715227154.14
    268 rdf:type schema:Person
    269 sg:person.0755344505.04 schema:affiliation grid-institutes:grid.81821.32
    270 schema:familyName Rey
    271 schema:givenName Juan A.
    272 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0755344505.04
    273 rdf:type schema:Person
    274 sg:pub.10.1007/s00401-007-0243-4 schema:sameAs https://app.dimensions.ai/details/publication/pub.1001430701
    275 https://doi.org/10.1007/s00401-007-0243-4
    276 rdf:type schema:CreativeWork
    277 sg:pub.10.1007/s00401-008-0455-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047349518
    278 https://doi.org/10.1007/s00401-008-0455-2
    279 rdf:type schema:CreativeWork
    280 sg:pub.10.1007/s00401-009-0561-9 schema:sameAs https://app.dimensions.ai/details/publication/pub.1005128955
    281 https://doi.org/10.1007/s00401-009-0561-9
    282 rdf:type schema:CreativeWork
    283 sg:pub.10.1007/s00401-012-0993-5 schema:sameAs https://app.dimensions.ai/details/publication/pub.1037252294
    284 https://doi.org/10.1007/s00401-012-0993-5
    285 rdf:type schema:CreativeWork
    286 sg:pub.10.1007/s00401-012-1016-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1027095253
    287 https://doi.org/10.1007/s00401-012-1016-2
    288 rdf:type schema:CreativeWork
    289 sg:pub.10.1038/nature10833 schema:sameAs https://app.dimensions.ai/details/publication/pub.1039575824
    290 https://doi.org/10.1038/nature10833
    291 rdf:type schema:CreativeWork
    292 sg:pub.10.1038/nature10860 schema:sameAs https://app.dimensions.ai/details/publication/pub.1000103968
    293 https://doi.org/10.1038/nature10860
    294 rdf:type schema:CreativeWork
    295 sg:pub.10.1038/nature10866 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010733927
    296 https://doi.org/10.1038/nature10866
    297 rdf:type schema:CreativeWork
    298 sg:pub.10.1038/ng.1102 schema:sameAs https://app.dimensions.ai/details/publication/pub.1048296872
    299 https://doi.org/10.1038/ng.1102
    300 rdf:type schema:CreativeWork
    301 sg:pub.10.1038/ng.2443 schema:sameAs https://app.dimensions.ai/details/publication/pub.1037664832
    302 https://doi.org/10.1038/ng.2443
    303 rdf:type schema:CreativeWork
    304 sg:pub.10.1038/nprot.2008.211 schema:sameAs https://app.dimensions.ai/details/publication/pub.1039987283
    305 https://doi.org/10.1038/nprot.2008.211
    306 rdf:type schema:CreativeWork
    307 sg:pub.10.1038/onc.2011.513 schema:sameAs https://app.dimensions.ai/details/publication/pub.1029204322
    308 https://doi.org/10.1038/onc.2011.513
    309 rdf:type schema:CreativeWork
    310 grid-institutes:None schema:alternateName Department of Pathology, MD Anderson International, C/Arturo Soria 270, 28033, Madrid, Spain
    311 schema:name Department of Pathology, MD Anderson International, C/Arturo Soria 270, 28033, Madrid, Spain
    312 rdf:type schema:Organization
    313 grid-institutes:grid.144756.5 schema:alternateName Department of Pathology (Neuropathology), 12 de Octubre University Hospital, Avda de Córdoba s/n, 28041, Madrid, Spain
    314 schema:name Department of Pathology (Neuropathology), 12 de Octubre University Hospital, Avda de Córdoba s/n, 28041, Madrid, Spain
    315 rdf:type schema:Organization
    316 grid-institutes:grid.411855.c schema:alternateName Department of Pathology, University Hospital Complex of Vigo (C.H.U.V.I.), Rúa Pizarro, 22, 36204, Vigo, Spain
    317 schema:name Department of Pathology, University Hospital Complex of Vigo (C.H.U.V.I.), Rúa Pizarro, 22, 36204, Vigo, Spain
    318 rdf:type schema:Organization
    319 grid-institutes:grid.413514.6 schema:alternateName Department of Pathology, Virgen de la Salud Hospital, Avda Barber 30, 45004, Toledo, Spain
    320 Molecular Pathology Research Unit, Department of Pathology, Virgen de la Salud Hospital, Avda. Barber 30, 45004, Toledo, Spain
    321 schema:name Department of Pathology, Virgen de la Salud Hospital, Avda Barber 30, 45004, Toledo, Spain
    322 Molecular Pathology Research Unit, Department of Pathology, Virgen de la Salud Hospital, Avda. Barber 30, 45004, Toledo, Spain
    323 rdf:type schema:Organization
    324 grid-institutes:grid.5924.a schema:alternateName Brain Tumor Biology Unit, University of Navarra School of Sciences, C/Irunlarrea 1, 31008, Pamplona, Spain
    325 schema:name Brain Tumor Biology Unit, University of Navarra School of Sciences, C/Irunlarrea 1, 31008, Pamplona, Spain
    326 rdf:type schema:Organization
    327 grid-institutes:grid.73221.35 schema:alternateName Department of Neurosurgery, Puerta del Hierro Hospital, C/Manuel de Falla no 1, Majadahonda, 28222, Madrid, Spain
    328 schema:name Department of Neurosurgery, Puerta del Hierro Hospital, C/Manuel de Falla no 1, Majadahonda, 28222, Madrid, Spain
    329 rdf:type schema:Organization
    330 grid-institutes:grid.81821.32 schema:alternateName IdiPaz Research Unit, La Paz University Hospital, Po de la Castellana, 261, 28046, Madrid, Spain
    331 schema:name IdiPaz Research Unit, La Paz University Hospital, Po de la Castellana, 261, 28046, Madrid, Spain
    332 rdf:type schema:Organization
     




    Preview window. Press ESC to close (or click here)


    ...