Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

12 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Epigenetic determinants of self-renewal in glioblastoma

ABSTRACT: We over-expressed an epigenetic regulator in a glioblastoma (GBM) primary culture from an adult patient. These GBM cells have cancer stem cell phenotypes, as they have self-renewal properties and tumor initiation potential when transplanted in immunocompromised mice. An epigenetic regulator (ER) was over-expressed in the GBM primary culture G514NS. EGFP was expressed from the same vector backbone as a control. N = 3 biological replicates for each of EGFP- and ER-overexpressing cells. Please note that complete data output (with 74,342 data rows) from Partek analysis contains several identifiers which are not represented in the GPL17586, and therefore is linked as Series supplementary file.

ORGANISM(S): Homo sapiens

SUBMITTER: Marco Gallo

PROVIDER: E-GEOD-63296 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Epigenetic determinants of self-renewal in glioblastoma

Project description:We over-expressed an epigenetic regulator in a glioblastoma (GBM) primary culture from an adult patient. These GBM cells have cancer stem cell phenotypes, as they have self-renewal properties and tumor initiation potential when transplanted in immunocompromised mice. ATAC-seq was performed on cells over-expressing the epigenetic regulator and control cells expressing EGFP. ATAC-Seq on glioblastoma cells that over-express EGFP or an epigenetic regulator.

2015-12-08 | E-GEOD-67633 | biostudies-arrayexpress

Identification and molecular characterization of distinct glioblastoma cancer stem cell populations

Project description:Malignant glioblastoma (GBM) is a highly aggressive brain tumor with a dismal prognosis and limited therapeutic options. Genomic profiling of GBM samples in the TCGA database has identified four molecular subtypes (Proneural, Neural, Classical and Mesenchymal), which may arise from different glioblastoma stem-like cell (GSC) populations. In the present study, we identify two GSC populations that produce GBM tumors by subcutaneous and intracranial injection with identical histological features. Gene expression analysis revealed that xenografts of GSCs grown as spheroid cultures had a Classical molecular subtype similar to that of bulk tumor cells. In contrast xenografts of GSCs grown as adherent cultures on laminin-coated plates expressed a Mesenchymal gene signature. Adherent GSC-derived xenografts had high STAT3 and ANGPTL4 expression as well as enrichment for stem cell markers, transcriptional networks and pro-angiogenic markers characteristic of the Mesenchymal subtype. Examination of clinical samples from GBM patients showed that STAT3 expression was directly correlated with ANGPTL4 expression, and that increased expression of these genes correlated with poor patient survival and performance. A pharmacological STAT3 inhibitor abrogated STAT3 binding to the ANGPTL4 promoter and exhibited anticancer activity in vivo. Taken together, we identified two distinct GSC populations that produce histologically identical tumors but with very different gene expression patterns, and a STAT3/ ANGPTL4 pathway in glioblastoma that may serve as a target for therapeutic intervention. 2 samples of each variable were analyzed. Cells were cultured under normal adherent conditon (Bulk tumor cells), non-adherent plates with stem cell medium (Sp-GSC) or laminin-coated plates with stem cell medium (Ad-GSC). Xenografts were generated in NSG mice by subcutaneous inoculation.

2015-07-01 | E-GEOD-65576 | biostudies-arrayexpress

Validation of EZH2 targets in GSCs treated with shNT (control), shMELK, shFOXM1, and EZH2 overexpression

Project description:We demonstrate that the catalytic subunit of Polycomb Repressive Complex 2, EZH2, is targeted by the MELK-FOXM1 complex, which in turn promotes resistance to radiation in GSCs. Clinically, EZH2 and MELK are co-expressed in GBM and significantly induced in post-irradiation recurrent tumors whose expression inversely correlated with patient prognosis. Through gain-and loss-of-function study, our data show that MELK or FOXM1 contributes on GSC radioresistance by regulation of EZH2. We used microarrays to validate EZH2 target gene expression. GSCs were treated with shNT (control), shMELK, shFOXM1, and EZH2 overexpression. Total RNA was isolated using the Qiagen RNeasy kit (Qiagen).

2015-04-16 | E-GEOD-63963 | biostudies-arrayexpress

Regulation of transcription by HIPPI and its molecular partner HIP1

Project description:This SuperSeries is composed of the following subset Series: GSE26115: Regulation of transcription by HIP1 protein interactor (HIPPI) in HeLa cells GSE26116: Role of HIP1 in HIPPI mediated transcription regulation in HeLa cells Refer to individual Series

2011-09-20 | E-GEOD-26117 | biostudies-arrayexpress

Role of HIP1 in HIPPI mediated transcription regulation in HeLa cells

Project description:Nuclear entry of transcription factor HIPPI is mediated by its interacting partner Huntingtin Interacting Protein 1 (HIP1), a nuclear localization signal containing nucleo-cytoplasmic shuttling protein. In oredr to investigate the role of HIP1 in HIPPI mediated transcriptional regulation in cell, here we performed microarray experiments using stable HIP1 knocked down HeLa cells (Hip1Si) exogenously expressing Green fluorescent protein tagged HIPPI. Total RNA extracted from HIP1 knocked down HeLa cells (Hip1Si) transfected with empty GFP vector served as control and Total RNA extracted from Hip1Si cells transfected with GFP-Hippi construct served as test. Biological replicates: 4

2011-09-20 | E-GEOD-26116 | biostudies-arrayexpress

Regulation of transcription by HIP1 protein interactor (HIPPI) in HeLa cells

Project description:HIPPI is a novel transcription factor that regulates caspase1 gene expression. To find out new transcriptional targets of HIPPI and to investigate the effect of HIPPI on cellular transcriptome, microarray study is performed using HeLa cells exogenously transfected with Green Fluorescent Protein tagged HIPPI (GFP-Hippi) construct Total RNA extracted from HeLa cells transfected with empty GFP vector served as control and Total RNA extracted from HeLa cells transfected with GFP-Hippi construct served as test. Biological replicates: 4

2011-09-20 | E-GEOD-26115 | biostudies-arrayexpress

CD44 promotes stemness by enhancing hypoxia-inducible factor activity in the glioma perivascular niche

Project description:T98G cells treated (or not) with Doxycycline to induce expression of EGFP-CD44ICD in cells transfected with control or HIF2A siRNA.

2014-05-24 | E-MEXP-3914 | biostudies-arrayexpress

Functional genomics of glioblastoma: from epigenetics to proteomic investigation of tumor-initiating cell secretome

Project description:The main objectives of the project are as follows: 1) Deciphering the TIC specific secretome signature. The secretome collected from four different TICs and their corresponding differentiated cell cultures will be subjected to label-free quantitative proteomic analysis to identify a TIC specific secretome signature. 2) Validation and functional characterization of selected molecules from TIC specific secretome signature. Selected molecules based on the level of regulation and literature information will be validated at the level of transcript and protein. The importance of a set of validated proteins will be studied both in vitro using neurosphere cultures and angiogenesis assays, and in vivo using an intracranial glioma model in nude mice 3) Characterizing of GBM specific serum proteome signature. Using label-free quantitative proteomics, we will compare the serum proteome of tumor bearing mice (xenotransplantated with TICs), early after tumor establisment and after the tumor has reached its maximum size.We will also explore by targeted quantitative proteomics whether the level of “specific” TIC-secreted proteins is increased in the serum of TIC initiated GBM bearing mice and verify, using the same strategy, proteins found to be differentially expressed in serum in both mice groups. These studies will reveal whether TIC-secreted proteins (and/or other GBM-derived proteins) can be retrieved in serum and thus be considered as candidate biomarkers of GBM.

2022-06-07 | PXD032958 | Pride

Epigenomic profiling of patient-derived GBM cell lines obtained from GBM patient surgical samples (HGCC resource)

Project description:The recent incorporation of molecular features into the diagnosis of Glioblastoma Multiforme patients has led to an improved categorisation into different tumour subtypes with different prognosis and disease management. In this work, we have exploited the benefits of genome-wide multiomic approaches to identify potential molecular vulnerabilities existing on GBM patients. We used the Illumina MethylationEPIC Beadchip platform to describe the genome-wide 5mC and 5hmC DNA methylation landscape of a total of 9 patient-derived Glioblastoma Multiforme Cell lines obtained from the human glioblastoma cell culture resource (HGCC) and 4 brain samples obtained from non-tumoral controls

2023-06-01 | E-MTAB-12473 | biostudies-arrayexpress

Transcription profiling of human foetal neural stem (NS) cell lines and human glioma neural stem (GNS) cell lines

Project description:Gliomas have been proposed to be driven by a population of neural stem-like cells. We isolated a panel of novel human glioma cell lines using adherent neural stem cell conditions. The normal human foetal (hf) NS cells and the tumorigenic glioma NS cell lines were expanded using growth factors EGF and FGF in adherent culture conditions. In these conditions apoptosis and differentiation are suppressed resulting in more homogeneous populations of stem cells than has been reported previously. We included parallel primary biopsies of non-malignant brain tissue ('Normal Brain'). Experiment Overall Design: Cell lines were expanded until 70-90% confluent and then harvested for RNA extraction. All cell lines were gorwn in identical culture media. We also include 'Normal Brain' samples which are regions of the adult human cortex.

2009-03-21 | E-GEOD-15209 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data