MiRNA data for an Integrated genomic analysis of oligodendroglial tumours identifies subgroups of 1p/19q co-deleted oligodendrogliomas
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB11003 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR1039280.fastq.gz | Fastqsanger.gz | |||
| ERR1039290.fastq.gz | Fastqsanger.gz | |||
| ERR1039300.fastq.gz | Fastqsanger.gz | |||
| ERR1039310.fastq.gz | Fastqsanger.gz | |||
| ERR1039320.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 177 |
Similar Datasets
Project description:A Cartes d'Identite des Tumeurs (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net: Oligodendroglial tumours (OT) are a heterogeneous group of gliomas. Three molecular subgroups are currently distinguished based on the IDH mutation and the 1p/19q co-deletion. Here we performed an integrated analysis of the transcriptome, genome and methylome of 156 OT. Beyond the 3 well-known molecular classes, our multi-omics classification revealed 3 subgroups within 1p/19q co-deleted tumours, associated with different expression patterns of oligodendroglial progenitor cell (OPC), astrocytic, oligodendrocytic and neuronal lineage genes. The validity of these 3 subgroups was confirmed on public datasets. The OPC-like group was associated with a more aggressive histological and genomic profile and with MYC activation that occurred through various alterations including MYC locus genomic gain, MYC exon 3 hypo-methylation and down-regulation of microRNA-34b/c. In the lower grade glioma TCGA dataset, the OPC-like group was associated with a poorer outcome independently from histological grade. Our study unravels previously unrecognized heterogeneity among 1p/19q co-deleted tumours.
2016-03-11 | E-MTAB-3901 | biostudies-arrayexpress
Project description:A Cartes d'Identite des Tumeurs (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net: Oligodendroglial tumours (OT) are a heterogeneous group of gliomas. Three molecular subgroups are currently distinguished based on the IDH mutation and the 1p/19q co-deletion. Here we performed an integrated analysis of the transcriptome, genome and methylome of 156 OT. Beyond the 3 well-known molecular classes, our multi-omics classification revealed 3 subgroups within 1p/19q co-deleted tumours, associated with different expression patterns of oligodendroglial progenitor cell (OPC), astrocytic, oligodendrocytic and neuronal lineage genes. The validity of these 3 subgroups was confirmed on public datasets. The OPC-like group was associated with a more aggressive histological and genomic profile and with MYC activation that occurred through various alterations including MYC locus genomic gain, MYC exon 3 hypo-methylation and down-regulation of microRNA-34b/c. In the lower grade glioma TCGA dataset, the OPC-like group was associated with a poorer outcome independently from histological grade. Our study unravels previously unrecognized heterogeneity among 1p/19q co-deleted tumours.
2016-03-11 | E-MTAB-3896 | biostudies-arrayexpress
Project description:'A Cartes d''Identite des Tumeurs (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net: Oligodendroglial tumours (OT) are a heterogeneous group of gliomas. Three molecular subgroups are currently distinguished based on the IDH mutation and the 1p/19q co-deletion. Here we performed an integrated analysis of the transcriptome, genome and methylome of 156 OT. Beyond the 3 well-known molecular classes, our multi-omics classification revealed 3 subgroups within 1p/19q co-deleted tumours, associated with different expression patterns of oligodendroglial progenitor cell (OPC), astrocytic, oligodendrocytic and neuronal lineage genes. The validity of these 3 subgroups was confirmed on public datasets. The OPC-like group was associated with a more aggressive histological and genomic profile and with MYC activation that occurred through various alterations including MYC locus genomic gain, MYC exon 3 hypo-methylation and down-regulation of microRNA-34b/c. In the lower grade glioma TCGA dataset, the OPC-like group was associated with a poorer outcome independently from histological grade. Our study unravels previously unrecognized heterogeneity among 1p/19q co-deleted tumours.'
2016-06-15 | E-MTAB-3902 | biostudies-arrayexpress
Project description:A Cartes d'Identite des Tumeurs (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net: Oligodendroglial tumours (OT) are a heterogeneous group of gliomas. Three molecular subgroups are currently distinguished based on the IDH mutation and the 1p/19q co-deletion. Here we performed an integrated analysis of the transcriptome, genome and methylome of 156 OT. Beyond the 3 well-known molecular classes, our multi-omics classification revealed 3 subgroups within 1p/19q co-deleted tumours, associated with different expression patterns of oligodendroglial progenitor cell (OPC), astrocytic, oligodendrocytic and neuronal lineage genes. The validity of these 3 subgroups was confirmed on public datasets. The OPC-like group was associated with a more aggressive histological and genomic profile and with MYC activation that occurred through various alterations including MYC locus genomic gain, MYC exon 3 hypo-methylation and down-regulation of microRNA-34b/c. In the lower grade glioma TCGA dataset, the OPC-like group was associated with a poorer outcome independently from histological grade. Our study unravels previously unrecognized heterogeneity among 1p/19q co-deleted tumours.
2016-03-11 | E-MTAB-3907 | biostudies-arrayexpress
Project description:A Cartes d'Identite des Tumeurs (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net: Oligodendroglial tumours (OT) are a heterogeneous group of gliomas. Three molecular subgroups are currently distinguished based on the IDH mutation and the 1p/19q co-deletion. Here we performed an integrated analysis of the transcriptome, genome and methylome of 156 OT. Beyond the 3 well-known molecular classes, our multi-omics classification revealed 3 subgroups within 1p/19q co-deleted tumours, associated with different expression patterns of oligodendroglial progenitor cell (OPC), astrocytic, oligodendrocytic and neuronal lineage genes. The validity of these 3 subgroups was confirmed on public datasets. The OPC-like group was associated with a more aggressive histological and genomic profile and with MYC activation that occurred through various alterations including MYC locus genomic gain, MYC exon 3 hypo-methylation and down-regulation of microRNA-34b/c. In the lower grade glioma TCGA dataset, the OPC-like group was associated with a poorer outcome independently from histological grade. Our study unravels previously unrecognized heterogeneity among 1p/19q co-deleted tumours.
2016-03-11 | E-MTAB-3905 | biostudies-arrayexpress
Project description:Oligodendroglioma is a primary central nervous system tumor classified by the presence of isocitrate dehydrogenase (IDH) mutations and codeletion of 1p/19q. Here we describe the generation of an IDH-mutant 1p/19q-codeleted oligodendroglioma mouse model using in utero electroporation. We identified IDH1R132H, PIK3CAE545K, CicKO, Fubp1KO and Cdkn2aKO as the optimal combination (termed OligoCdkn2a) to drive fully penetrant tumors that histologically resemble human grade II/III IDH-mutant, 1p/19q-codeleted oligodendroglioma. Replacing Cdkn2a with Trp53 loss in this mouse model shifted tumor histology towards high grade astrocytoma. OligoCdkn2a tumors displayed metabolic and transcriptional changes associated with IDH and CIC mutations, and single cell sequencing identified a bias towards oligodendrocyte differentiation compared to an IDH wild-type glioblastoma mouse model. OligoCdkn2a tumors represent the first mouse model system to recapitulate the genetic, histological and transcriptional features of human IDH-mutant 1p/19q-codeleted oligodendrogliomas, offering a platform to further dissect tumor biology and test new therapeutic strategies.
2026-04-15 | GSE326763 | GEO
Project description:Oligodendroglioma is a primary central nervous system tumor classified by the presence of isocitrate dehydrogenase (IDH) mutations and codeletion of 1p/19q. Here we describe the generation of an IDH-mutant 1p/19q-codeleted oligodendroglioma mouse model using in utero electroporation. We identified IDH1R132H, PIK3CAE545K, CicKO, Fubp1KO and Cdkn2aKO as the optimal combination (termed OligoCdkn2a) to drive fully penetrant tumors that histologically resemble human grade II/III IDH-mutant, 1p/19q-codeleted oligodendroglioma. Replacing Cdkn2a with Trp53 loss in this mouse model shifted tumor histology towards high grade astrocytoma. OligoCdkn2a tumors displayed metabolic and transcriptional changes associated with IDH and CIC mutations, and single cell sequencing identified a bias towards oligodendrocyte differentiation compared to an IDH wild-type glioblastoma mouse model. OligoCdkn2a tumors represent the first mouse model system to recapitulate the genetic, histological and transcriptional features of human IDH-mutant 1p/19q-codeleted oligodendrogliomas, offering a platform to further dissect tumor biology and test new therapeutic strategies.
2026-04-15 | GSE326991 | GEO
Project description:Oligodendroglioma is a primary central nervous system tumor classified by the presence of isocitrate dehydrogenase (IDH) mutations and codeletion of 1p/19q. Here we describe the generation of an IDH-mutant 1p/19q-codeleted oligodendroglioma mouse model using in utero electroporation. We identified IDH1R132H, PIK3CAE545K, CicKO, Fubp1KO and Cdkn2aKO as the optimal combination (termed OligoCdkn2a) to drive fully penetrant tumors that histologically resemble human grade II/III IDH-mutant, 1p/19q-codeleted oligodendroglioma. Replacing Cdkn2a with Trp53 loss in this mouse model shifted tumor histology towards high grade astrocytoma. OligoCdkn2a tumors displayed metabolic and transcriptional changes associated with IDH and CIC mutations, and single cell sequencing identified a bias towards oligodendrocyte differentiation compared to an IDH wild-type glioblastoma mouse model. OligoCdkn2a tumors represent the first mouse model system to recapitulate the genetic, histological and transcriptional features of human IDH-mutant 1p/19q-codeleted oligodendrogliomas, offering a platform to further dissect tumor biology and test new therapeutic strategies.
2026-04-15 | GSE326990 | GEO
Project description:High-grade gliomas are malignant neuroepithelial tumors. The current WHO classification for adult-type diffuse gliomas is based on IDH1/2 mutational and 1p/19q-codeletion status, which can be refined by emerging genomics, transcriptomics, and methylomics approaches. Nevertheless, therapy has been dominated by radiochemotherapy for about 15 years and progressed little in efficacy or precision through advanced molecular patient stratification. Glioma proteome alterations remain undercharacterized despite their promise for a better stratification and, in particular, the identification of therapeutic targets. Here, we used mass spectrometry (MS) to characterize 42 formalin-fixed, paraffin-embedded (FFPE) samples from IDH-wildtype (IDHwt), IDH-mutant (IDHmut) gliomas with and without 1p/19q-codeletion, and non-neoplastic brain tissue controls. Based on more than 5500 quantified proteins and 5000 phospho-sites, gliomas separated according to IDH1/2 mutational status and reflected loss of proteins encoded on 1p/19q in IDHmut, gains on chromosome 7 and losses on chromosome 10 in IDHwt. Unexpectedly, the 1p/19q-codeletion resulted in minor proteome changes. Instead, two proteomic subtypes of IDHmut gliomas showed major perturbations of mitochondrial DNA-encoded proteins, aerobic/anaerobic energy metabolism, RNA metabolism, chromatin dynamics, the extracellular matrix as well as tumor suppressor and oncoproteins. Reanalysis of three glioma proteomics studies independently validate the observed hallmarks and associate these proteomic subtypes with the well-established proneural and classic/mesenchymal IDHwt glioma subtypes. These results suggest an alternative stratification of IDHmut gliomas as part of common phenotypic subtypes independent of the IDH status, with broad therapeutic implications for patients with IDHmut gliomas in the future. Altogether, our study provides a rich protein and phospho-site resource restratifying glioma subtypes and supporting future mechanism of action and target discovery investigations.
2023-02-07 | GSE212838 | GEO
Project description:A Cartes d'Identite des Tumeurs (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net: Oligodendroglial tumours (OT) are a heterogeneous group of gliomas. Three molecular subgroups are currently distinguished based on the IDH mutation and the 1p/19q co-deletion. Here we performed an integrated analysis of the transcriptome, genome and methylome of 156 OT. Beyond the 3 well-known molecular classes, our multi-omics classification revealed 3 subgroups within 1p/19q co-deleted tumours, associated with different expression patterns of oligodendroglial progenitor cell (OPC), astrocytic, oligodendrocytic and neuronal lineage genes. The validity of these 3 subgroups was confirmed on public datasets. The OPC-like group was associated with a more aggressive histological and genomic profile and with MYC activation that occurred through various alterations including MYC locus genomic gain, MYC exon 3 hypo-methylation and down-regulation of microRNA-34b/c. In the lower grade glioma TCGA dataset, the OPC-like group was associated with a poorer outcome independently from histological grade. Our study unravels previously unrecognized heterogeneity among 1p/19q co-deleted tumours.
2016-03-11 | E-MTAB-3892 | biostudies-arrayexpress