GEO DataSets

(Submitter supplied) As a first step towards identifying the target genes of EGFR activity in glioma cells, genome-wide expression analyses were performed using the Affymetrix GeneChip Human Genome U133A array. To accomplish this, mRNA expression levels of these genes were measured in the glioblastoma cell lines, U87 and U178, engineered with EGFR by retrovirus transduction (termed U87-EGFR and U178-EGFR respectively), with or without 20 ng/mL EGF treatment for 3 h.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL96

8 Samples

Download data: CEL

(Submitter supplied) To gain insight into the molecular mechanisms underlying TRIP13-mediated oncogenic activity in GBM, we performed RNA-seq on spheres derived from U87MG-shTRIP13 and control cells .This analysis identified 1094 genes whose expression was markedly reduced by TRIP13 knockdown in U87MG-derived spheres (fold change >2, p < 0.05; Supplementary ). These downregulated genes were highly overrepresented in gene ontologies (GO) that are associated with growth factor activity, angiogenesis and chemotaxis. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20795

2 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24676 GPL16791

8 Samples

Download data

(Submitter supplied) Epidermal growth factor receptor (EGFR) signaling is constitutively activated in majority of GBM and is associated with a worse prognosis. Here we show that EGFR is responsible for overexpression of the m6A "reader" YTHDF2 in GBM through the EGFR/Src/ERK signaling pathway. YTHDF2 overexpression clinically correlates with poor glioma patient prognosis. EGFR signaling stabilizes YTHDF2 protein through phosphorylation of YTHDF2 serine 39 and threonine 381 by ERK1/2. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

4 Samples

Download data: XLSX

(Submitter supplied) Epidermal growth factor receptor (EGFR) signaling is constitutively activated in majority of GBM and is associated with a worse prognosis. Here we show that EGFR is responsible for overexpression of the m6A "reader" YTHDF2 in GBM through the EGFR/Src/ERK signaling pathway. YTHDF2 overexpression clinically correlates with poor glioma patient prognosis. EGFR signaling stabilizes YTHDF2 protein through phosphorylation of YTHDF2 serine 39 and threonine 381 by ERK1/2. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

4 Samples

Download data: XLSX

(Submitter supplied) Analysis of rat tumor xenografts revealed genes that are upregulated in tumors expressing EGFRvIII

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Platform:

GPL6101

12 Samples

Download data: TXT

(Submitter supplied) Analysis of human glioblastoma multiforme tumors revealed genes that are upregulated in tumors expressing EGFRvIII compared to those expressing wild-type EGFR

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

52 Samples

Download data: CEL

(Submitter supplied) We have previously established two sibling glioma subclones, J3T-1 and J3T-2, showing distinct invasive and angiogenic phenotypes. J3T-1, expressing high annexin A2, demonstrates robust angiogenesis and tumor invasion around neovasculature. J3T-2, expressing low annexin A2, demonstrates diffuse invasion along white matter tracts. Knockdown of annexin A2 in J3T-1 (J3T-1shA) resulted in diffuse invasion pattern, and overexpression of annexin A2 in J3T-2 (J3T-2A) showed prominent angiogenesis. more...

Organism:

Canis lupus familiaris

Type:

Expression profiling by array

Platform:

GPL3738

4 Samples

Download data: CEL

(Submitter supplied) The diffuse invasion of glioblastoma (GBM) cells into healthy brain tissue is a main contributor for the high lethality of this most frequent form of malignant brain tumor. Plexins are cell surface receptors for semaphorins and control cell adhesion and cytoskeletal dynamics in development and in adult physiology. Gene expression of Plexin-B2 is upregulated in GBM and correlates with its lethality. We show here that Plexin-B2 activity can reduce the cohesiveness of GBM cells, which facilitates their invasive capacity. Targeted deletion of Plexin-B2 in GBM cells increased their cohesion to each other, revealing that a major function of Plexin-B2 activity is to downregulate cell-cell adhesion, possibly by downregulating other cell adhesion systems. In an in vivo intracranial transplant model, invasion of Plexin-B2 mutant GBM cells was impaired, with cells invading shorter distances. Interestingly, the loss of Plexin-B2 also changed the migration mode of cells, with the balance of cells in brain stroma vs. capillary space shifted: Plexin-B2 mutant cells were more likely to adhere to the vasculature. Our structure-function analyses revealed that the Ras-GAP domain of Plexin-B2 that is the main functional output responsible for the cohesion regulating function of Plexin-B2. Transcriptomic analyses of Plexin-B2 KO cells suggests that Plexin-B2 loss in different GBM cell lines has no direct transcriptional target genes, however, consistently, cell adhesion molecules were changed in expression, suggesting that cells compensate for loss of Plexin-B2. Thus, Plexin-B2 acts as a key regulator of the cohesiveness of GBM cells, thereby facilitating their invasiveness.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

29 Samples

Download data: TXT

(Submitter supplied) Insulin-like growth factor-binding protein 2 (IGFBP2) is increasingly recognized as a glioma oncogene, emerging as a target for therapeutic intervention. In this study, we used an integrative approach to characterizing the IGFBP2 network, combining transcriptional profiling of human glioma with validation in glial cells and the replication competent ASLV long terminal repeat with a splice acceptor/tv-a glioma mouse system. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL1708

4 Samples

Download data: TXT

(Submitter supplied) We have found that cyclophilin B (CypB) expression is important for malignant glioblastoma multiforme (GBM) cell proliferation. To identify molecular mechanisms that could explain CypB-dependent survival in human GBM cells, a microarray analysis was performed using RNA prepared from U251MG GBM cells transduced with lentiviral CypB shRNA. These data revealed that about 130 genes were more than 2-fold affected by CypB depletion. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS4828

Platform:

GPL10558

6 Samples

Download data: TXT

Analysis of U251 glioblastoma multiforme (GBM) cells depleted for cyclophilin B (CypB), a prolyl isomerase in the endoplasmic reticulum. CypB depletion reduces GBM cell survival. Results provide insight into the role of CypB in the survival of GBM cells.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 2 protocol sets

Platform:

GPL10558

Series:

GSE50756

6 Samples

Download data

(Submitter supplied) Most patients affected by Glioblastoma multiforme (GBM) experience a recurrence of the disease because of the spreading of tumor-initiating cells (TICs) beyond surgical boundary. Unveiling and targeting molecular mechanisms causing this process is a logic goal to impair GBM killing ability. In an orthotopic xenograph model, we have noticed that GBM TICs isolated from several patients may fall into two classes of invasive behavior: nodular or diffuse. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

6 Samples

Download data: CEL

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20301

30 Samples

Download data: BED, BW, TDF

(Submitter supplied) Here, we performed ChIP-seq and ATAC-seq and identified two novel super enhancers (SE1 and SE2) responsible for EGFR transcription present within the first intron of the EGFR gene in HNSCC and GBM. SE1 and SE2 span 37kb and 33kb respectively, contain H3K27Ac enhancer histone marks and open chromatin, functionally enhance transcription in reporter assays, interact with the EGFR promoter, and negatively impact EGFR transcript levels and anchorage-independent growth when perturbed by CRISPR/Cas9-deletion and dCas9-KRAB-silencing. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20301

20 Samples

Download data: BED, TDF

(Submitter supplied) Here, we performed ChIP-seq and ATAC-seq and identified two novel super enhancers (SE1 and SE2) responsible for EGFR transcription present within the first intron of the EGFR gene in HNSCC and GBM. SE1 and SE2 span 37kb and 33kb respectively, contain H3K27Ac enhancer histone marks and open chromatin, functionally enhance transcription in reporter assays, interact with the EGFR promoter, and negatively impact EGFR transcript levels and anchorage-independent growth when perturbed by CRISPR/Cas9-deletion and dCas9-KRAB-silencing. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20301

10 Samples

Download data: BED, BW

(Submitter supplied) Many current cellular models aimed to elucidate cancer biology do not recapitulate pathobiology including tumor heterogeneity, an inherent feature of cancer that underlies treatment resistance. Here we introduce a new cancer modeling paradigm using genetically engineered human pluripotent stem cells (hiPSCs) that capture authentic cancer pathobiology. Orthotopic engraftment of the neural progenitor cells derived from hiPSCs introduced with tumor-associated genetic driver mutations revealed by The Cancer Genome Atlas project for glioblastoma (GBM) results in formation of brain tumors. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

14 Samples

Download data: H5, HTML

(Submitter supplied) Many current cellular models aimed to elucidate cancer biology do not recapitulate pathobiology including tumor heterogeneity, an inherent feature of cancer that underlies treatment resistance. Here we introduce a new cancer modeling paradigm using genetically engineered human pluripotent stem cells (hiPSCs) that capture authentic cancer pathobiology. Orthotopic engraftment of the neural progenitor cells derived from hiPSCs introduced with tumor-associated genetic driver mutations revealed by The Cancer Genome Atlas project for glioblastoma (GBM) results in formation of brain tumors. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

6 Samples

Download data: TSV

(Submitter supplied) Glioblastoma cell lines were xenografted onto mice and resulting tumors were profiled by microarray. Xenograft recipient mice were NOD/SCID/gamma (NSG) male mice 3 months old.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL8119

6 Samples

Download data: CEL

(Submitter supplied) To investigate the functional role of EGFR in the formation of large vessels, we established a mesenchymal glioma stem cell line (GSC83) with intact EGFR and knocked down EGFR by Crispr-Cas9. We then performed single cells gene expression profiling analysis using data obtained from RNA-seq of 2 different tumours, derived by injection of GSC83 WT or GSC83 KO in NSG mice. In addition, GSC83 WT or GSC83 KO tumours in NSG mice were subjected to spatial gene expression profiling in situ using GeoMX platform. more...

Organism:

Homo sapiens; Mus musculus; synthetic construct

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL24247 GPL26526 GPL25431

45 Samples

Download data: DCC, PKC, RDS, TAR, XLSX