Project description:Glioma stem cells (GSCs) have been identified in glioma tissues and suggested to play important roles in the tumorigenesis of glioblastoma multiform (GBM). We established a novel cellular bioinformative pipeline that consisted of principal component analysis (PCA) with factor loading, intracellular pathway analysis, and immunopathway analysis and attempted to clarify the differences in gene expression profiles comprehensively among GSCs, a glioma cell line (U251), and a human GBM tissue (hGBM). To this end, we extracted total RNAs from the GSCs, U251, and the hGBM, performed microarray, and applied the data to the bioinformatics analyses described above. As the results, PCA clearly distinguished the three groups. Moreover, the second principal component (PC2) distinguished the GSCs from the hGBM and U251; it reflected the characteristics of stemness. The factor loading for PC2 suggested MYCN, DPP4, and, MIF as contributing factors to the stemness of GSCs. We clarify the similarities and differences among samples such as the GSCs, U251, and hGBM.

2019-07-01 | GSE124145 | GEO

Modulation of gene expression in U251 glioblastoma cells by binding of mutant p53 to intronic and intergenic sequences

Project description:Missense point mutations in the TP53 gene are frequent genetic alterations in human tumor tissue and cell lines derived thereof. Mutant p53 (mutp53) proteins have lost sequence-specific DNA binding, but have retained the ability to interact in a structure-selective manner with non-B DNA and to act as regulators of transcription. To identify functional binding sites of mutp53, we established a small library of genomic sequences bound by p53R273H in U251 human glioblastoma cells using chromatin immunoprecipitation (ChIP). Mutp53 binding to isolated DNA fragments confirmed the specificity of the ChIP. The mutp53 bound DNA sequences are rich in repetitive DNA elements, which are dispersed over non-coding DNA regions. Stable down-regulation of mutp53 expression strongly suggested that mutp53 binding to genomic DNA is functional. We identified the PPARGC1A and FRMD5 genes as p53R273H targets regulated by binding to intronic and intra-genic sequences. We propose a model that attributes the oncogenic functions of mutp53 to its ability to interact with intronic and intergenic non-B DNA sequences and modulate gene transcription via re-organization of chromatin. For the study of the consequences of mutant p53 (R273H) knockdown on gene expression, total RNA from parental U251 glioblastoma cells and UsiA12 clone was prepared from two independent cell culture experiments (biological replicates) and processed for microarray-based profiling of gene expression. UsiA12 clone was derived from the U251 cells transfected with the pSuper-p53 and pCI-neo vectors.

2010-06-24 | E-GEOD-13991 | biostudies-arrayexpress

Gene expression profiling of glioblastoma cell lines transfected with FGFR3-TACC3

Project description:Gene expression profiling of SNB19 and U251 glioblastoma cell lines transfected with the FGFR3-TACC3 fusion, FGFR3 wildtype and TACC3 wildtype constructs.

2012-12-01 | GSE42401 | GEO

Gene expression profiling of glioblastoma cell lines transfected with FGFR3-TACC3

Project description:Gene expression profiling of SNB19 and U251 glioblastoma cell lines transfected with the FGFR3-TACC3 fusion, FGFR3 wildtype and TACC3 wildtype constructs. SNB19 and U251 cells were transfected with different clones of the FGFR3-TACC3 fusion and with wildtype FGFR3 and TACC3 constructs. Total RNA was extracted and hybridized onto Agilent dual channel gene expression microarrays. In each hybridization, empty vector transfected SNB19 or U251 cells were hybridized into the reference channel.

2012-12-01 | E-GEOD-42401 | biostudies-arrayexpress