MicroRNA expression data from brainstem gliomas
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ABSTRACT:
ORGANISM(S): synthetic construct Homo sapiens
PROVIDER: GSE112009 | GEO | 2018/03/20
REPOSITORIES: GEO
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Project description:Gliomas arising in the brainstem and thalamus are devastating tumors that are difficult to surgically resect due to their proximity to eloquent brain structures. Here, we performed a comprehesive genomic and epigenomic study, using gene expression and methylation microarrays, to research on th different genomic and epigenetic signatures between brainstem, thalamic, and supratentorial gliomas. Comparison of brainstem, thalamic and supratentorial gliomas
2014-05-27 | E-GEOD-50774 | biostudies-arrayexpress
Project description:Gliomas arising in the brainstem and thalamus are devastating tumors that are difficult to surgically resect due to their proximity to eloquent brain structures. Here, we performed a comprehesive genomic and epigenomic study, using gene expression and methylation microarrays, to research on th different genomic and epigenetic signatures between brainstem, thalamic, and supratentorial gliomas.
2014-05-27 | GSE50774 | GEO
Project description:Purpose: More than 90% of children with diffuse intrinsic pontine glioma (DIPG) die within 2 years of diagnosis. There is a dire need to identify therapeutic targets, however lack of patient material for research has limited progress. We evaluated a large cohort of diffuse intrinsic pontine gliomas (DIPGs) to identify recurrent genomic abnormalities and gene expression signatures underlying DIPG. Patients and Methods: We used single nucleotide polymorphism arrays to evaluate genomic copy number imbalances in 43 DIPGs from 40 patients and in 8 low-grade exophytic brainstem gliomas. Gene expression arrays were used to evaluate expression signatures from 27 DIPGs, 6 low-grade exophytic brainstem gliomas and 66 low-grade gliomas arising outside the brainstem. Results: Frequencies of specific large-scale and focal imbalances varied significantly between DIPGs and pediatric glioblastomas outside the brainstem. Focal amplifications of genes within the receptor tyrosine kinase-Ras-PI3-kinase signaling pathway were found in 47% of DIPG, with PDGFRA and MET showing the highest frequency. 30% of DIPG contained focal amplifications of cell-cycle regulatory genes controlling RB phosphorylation, and 21% had concurrent amplification of genes from both pathways. Some tumors showed heterogeneity in amplification patterns. DIPGs showed distinct gene expression signatures relating to developmental processes compared to pediatric glioblastomas arising outside the brainstem, while expression signatures of low-grade exophytic brainstem gliomas were similar to low-grade gliomas outside the brainstem. Copy number analaysis: 43 DIPG samples, 8 Low Grade Gliomas using SNP6.0. Available matched normals are also profiled with SNP6.0. Expression analysis: 29 DIPG samples, 6 Low grade samples Please contact Suzanne Baker at Suzanne.Baker@stjude.org for CEL files and genotype calls.
2011-09-20 | E-GEOD-26576 | biostudies-arrayexpress
Project description:MicroRNA expression data from brainstem gliomas
| PRJNA438947 | ENA
Project description:We have used Illumina Infinium HumanMethylation450 BeadChip array profiling to profile paediatric high grade gliomas within the HERBY clinical trial. The HERBY trial was a phase-II open-label, randomised, multicentre trial evaluating bevacizumab in patients with newly-diagnosed non-brainstem HGG between the ages of 3-18yrs. The 450K methylation array was used to separate brain tumour samples on the basis of their methylation profiles which represent the cell of origin the time and place in which tumours arise. Methylation arrays provide data for an integrated molecular diagnosis of brain tumours and define specific molecular subgroups and subtypes of high grade gliomas carrying distinct driver mutations and patterns of somatic alterations.
2018-05-11 | E-MTAB-5552 | biostudies-arrayexpress
Project description:Purpose: More than 90% of children with diffuse intrinsic pontine glioma (DIPG) die within 2 years of diagnosis. There is a dire need to identify therapeutic targets, however lack of patient material for research has limited progress. We evaluated a large cohort of diffuse intrinsic pontine gliomas (DIPGs) to identify recurrent genomic abnormalities and gene expression signatures underlying DIPG. Patients and Methods: We used single nucleotide polymorphism arrays to evaluate genomic copy number imbalances in 43 DIPGs from 40 patients and in 8 low-grade exophytic brainstem gliomas. Gene expression arrays were used to evaluate expression signatures from 27 DIPGs, 6 low-grade exophytic brainstem gliomas and 66 low-grade gliomas arising outside the brainstem. Results: Frequencies of specific large-scale and focal imbalances varied significantly between DIPGs and pediatric glioblastomas outside the brainstem. Focal amplifications of genes within the receptor tyrosine kinase-Ras-PI3-kinase signaling pathway were found in 47% of DIPG, with PDGFRA and MET showing the highest frequency. 30% of DIPG contained focal amplifications of cell-cycle regulatory genes controlling RB phosphorylation, and 21% had concurrent amplification of genes from both pathways. Some tumors showed heterogeneity in amplification patterns. DIPGs showed distinct gene expression signatures relating to developmental processes compared to pediatric glioblastomas arising outside the brainstem, while expression signatures of low-grade exophytic brainstem gliomas were similar to low-grade gliomas outside the brainstem.
2011-09-21 | GSE26576 | GEO
Project description:Using the RCAS/tv-a system, we induced murine brainstem gliomas (PDGF-B; p53 loss using RCAS-Cre with and without H3.3K27M) in Nestin tv-a; p53 floxed mice
2017-05-11 | GSE98765 | GEO
Project description:We have used Illumina Infinium HumanMethylation450 BeadChip array profiling to profile paediatric high grade gliomas and diffuse intrinsic pontine gliomas. The 450K methylation array is being used to separate brain tumour samples on the basis of their methylation profiles which represent the cell of origin the time and place in which tumours arise. Methylation arrays provide data for an integrated molecular diagnosis of brain tumours and define specific molecular subgroups and subtypes of high grade gliomas carrying distinct driver mutations and patterns of somatic alterations. These data form part of an integrated meta-analysis of high grade gliomas in children combining DNA copy number, methylation and high throughput sequencing datasets.
2017-09-28 | E-MTAB-5528 | biostudies-arrayexpress
Project description:Diffuse intrinsic pontine gliomas (DIPGs) are highly lethal childhood brain tumors. Their unique genetic makeup, pathological heterogeneity, and brainstem location all present challenges to treatment. Developing mouse models that accurately reflect each of these distinct features will be critical to advance our understanding of DIPG development, progression, and therapeutic resistance. The aim of this study was to generate new mouse models of DIPG, and characterize the role of specific oncogenic combinations in DIPG pathogenesis. We used in utero electroporation (IUE) to transfect neural stem cells in the developing brainstem with PiggyBac DNA transposon plasmids. Combinations of PDGFB or PdgfraD842V, dominant negative Trp53 (DNp53), and H3.3K27M expression induced fully penetrant brainstem gliomas. IUE enabled the targeted transfection of brainstem neural stem cells. PDGFB + DNp53 induced the rapid development of grade-IV gliomas. PdgfraD842V + DNp53 produced slower forming grade-III gliomas. Addition of H3.3K27M only significantly accelerated PdgfraD842V DIPG development. Glioma subgroup molecular signatures were associated with differences in bulk PDGFB and PdgfraD842V tumor composition. H3.3K27M induced both overlapping and unique gene expression changes in PDGFB and PdgfraD842V tumors. Paracrine effects of PDGFB promote disruption of pericyte-endothelial interactions and angiogenesis in PDGFB DIPG mouse models. Brainstem targeted in utero electroporation provides a rapid and flexible system to generate diverse DIPG mouse models. Using IUE to investigate mutation and pathohistological heterogeneity of DIPG will provide a valuable tool for future genetic and preclinical studies.
2019-11-14 | GSE128807 | GEO
Project description:The different clinical behavior of low and high grade gliomas and the chance to develop novel selective agents that specifically target tumor-associated proteins in gliomas stimulate the research of molecules playing a role in glioma progression. Gene expression profiling using microarrays allows the study at the same time of the expression patterns of thousands of genes in tumor cells. In the present study microarrays with about 20,000 genes have been employed to discover the gene expression profile in 39 glial neoplasias (28 glioblastomas (GBM) and 11 low grade gliomas, namely 4 oligodendrogliomas, 5 pilocytic astrocytomas (PA), 2 fibrillary astrocytomas (FA)). Unsupervised classification through hierarchical cluster analysis identified 2 groups of tumours: one group mainly composed of low grade malignant tumours (10 low grade gliomas and 3 GBM), the other one constituted by GBM, with the exception of one low grade case. The nearest shrunken centroid classification method was used to identify genes useful to classify and best characterize high and low grade gliomas. [Tibshirani et al. 2002]; This procedure selected 9 genes as most informative for the classification task: ; Among them 7 genes were overexpressed in low grade gliomas, but underexpressed in GBM; on the contrary 2 genes were overexpressed in GBM, but underexpressed in low grade tumours; Forty five tumors were immunostained for IGFBP-2 . 81,5% GBM resulted immunopositive. On the contrary only one low grade glioma was positive. Gene expression profiling and immunohistochemistry suggest that IGFBP-2 may play a role in glioma progression. IGFBP-2 appears to be a novel immunohistochemical marker of malignancy in glial tumours and probably is the basis for targeted chemotherapy. Experiment Overall Design: We retrieved for this study 185 randomly selected cases of gliomas. All the cases had been received unfixed. A sample of neoplastic tissue had been flash frozen over liquid nitrogen and stored at -80°C into the frozen tissue bank of the Section of Pathology of Bellaria Hospital between 1990 and 2002. The remaining (specular) tissues were formalin fixed and paraffin embedded for routine histologic diagnosis. Experiment Overall Design: In the present investigation, only samples with rRNA 28S/18S ratio > 1.0 measured by Bioanalyzer 2100 (Agilent)and no evidence of ribosomal degradation were included. Some cases were excluded as the tissue samples were composed only by necrosis; other cases did not show neoplastic proliferation. Therefore only 39 glial neoplasias were suitable for the study: i.e. 28 GBMs and 11 low grade CNS tumors, namely 4 oligodendrogliomas (OL), 5 pilocytic astrocytomas (PA), 2 fibrillary astrocytoma (FA) showed a good quality of RNA. Experiment Overall Design: All the tumors were re-staged and graded according to 2000 WHO criteria at time of gene expression analysis by two pathologists (GM and VE). Experiment Overall Design: 39 glial neoplasias were labeled by Cy5. Common reference pool consisted of a mixture of total RNA from the low grade CNS tumor group (4 OL, 5 PA, 2 FA) labeled by Cy3. A series of the most informative genes were confirmed by RT-qPCR. Experiment Overall Design:
2008-06-17 | E-GEOD-9885 | biostudies-arrayexpress