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Transcription profiling of 20 human primary high grade glioma cell cultures

ABSTRACT: Gene expression profiling of 20 primary high grade glioma cell cultures

ORGANISM(S): Homo sapiens

SUBMITTER: Hägerstrand Daniel

PROVIDER: S-ECPF-MEXP-1063 | biostudies-other |

REPOSITORIES: biostudies-other

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Transcription profiling of 20 human primary high grade glioma cell cultures

Project description:Gene expression profiling of 20 primary high grade glioma cell cultures

2007-05-31 | E-MEXP-1063 | biostudies-arrayexpress

Transcription profiling by array of low- and high-grade resected tumors from glioma patients

Project description:Samples of resected tumor from patients with low- and high-grade gliomas

| S-ECPF-MTAB-1928 | biostudies-other

Comparative single-cell RNA-sequencing profiling of BMP4-treated primary glioma cultures reveals therapeutic markers.

Project description:BackgroundGlioblastoma (GBM) is the most aggressive primary brain tumor. Its cellular composition is very heterogeneous, with cells exhibiting stem-cell characteristics (GSCs) that co-determine therapy resistance and tumor recurrence. Bone Morphogenetic Protein (BMP)-4 promotes astroglial and suppresses oligodendrocyte differentiation in GSCs, processes associated with superior patient prognosis. We characterized variability in cell viability of patient-derived GBM cultures in response to BMP4 and, based on single-cell transcriptome profiling, propose predictive positive and early-response markers for sensitivity to BMP4.MethodsCell viability was assessed in 17 BMP4-treated patient-derived GBM cultures. In two cultures, one highly-sensitive to BMP4 (high therapeutic efficacy) and one with low-sensitivity, response to treatment with BMP4 was characterized. We applied single-cell RNA-sequencing, analyzed the relative abundance of cell clusters, searched for and identified the aforementioned two marker types, and validated these results in all 17 cultures.ResultsHigh variation in cell viability was observed after treatment with BMP4. In three cultures with highest sensitivity for BMP4, a substantial new cell subpopulation formed. These cells displayed decreased cell proliferation and increased apoptosis. Neuronal differentiation was reduced most in cultures with little sensitivity for BMP4. OLIG1/2 levels were found predictive for high sensitivity to BMP4. Activation of ribosomal translation (RPL27A, RPS27) was up-regulated within one day in cultures that were very sensitive to BMP4.ConclusionThe changes in composition of patient-derived GBM cultures obtained after treatment with BMP4 correlate with treatment efficacy. OLIG1/2 expression can predict this efficacy, and upregulation of RPL27A and RPS27 are useful early-response markers.

| S-EPMC9713526 | biostudies-literature

Transcription profiling of human high-grade astrocytomas reveals prognostic subgroups

Project description: Not available

| S-ECPF-GEOD-4271 | biostudies-other

Inhibition of cell growth by EGR-1 in human primary cultures from malignant glioma.

Project description:BACKGROUND: The aim of this work was to investigate in vitro the putative role of EGR-1 in the growth of glioma cells. EGR-1 expression was examined during the early passages in vitro of 17 primary cell lines grown from 3 grade III and from 14 grade IV malignant astrocytoma explants. The explanted tumors were genetically characterized at the p53, MDM2 and INK4a/ARF loci, and fibronectin expression and growth characteristics were examined. A recombinant adenovirus overexpressing EGR-1 was tested in the primary cell lines. RESULTS: Low levels of EGR-1 protein were found in all primary cultures examined, with lower values present in grade IV tumors and in cultures carrying wild-type copies of p53 gene. The levels of EGR-1 protein were significantly correlated to the amount of intracellular fibronectin, but only in tumors carrying wild-type copies of the p53 gene (R = 0,78, p = 0.0082). Duplication time, plating efficiency, colony formation in agarose, and contact inhibition were also altered in the p53 mutated tumor cultures compared to those carrying wild-type p53. Growth arrest was achieved in both types of tumor within 1-2 weeks following infection with a recombinant adenovirus overexpressing EGR-1 but not with the control adenovirus. CONCLUSIONS: Suppression of EGR-1 is a common event in gliomas and in most cases this is achieved through down-regulation of gene expression. Expression of EGR-1 by recombinant adenovirus infection almost completely abolishes the growth of tumor cells in vitro, regardless of the mutational status of the p53 gene.

| S-EPMC324562 | biostudies-literature

Proteomic Profiling of mouse High Grade Glioma

Project description:High throughput proteomics profiling provide an unprecedented opportunity for dissecting molecular mechanisms in cancer biology. Here we present deep profiling of whole proteome and phosphoproteome in two high-grade glioma mouse models driven by mutated receptor tyrosine kinase (RTK) oncogenes. Using multiplex isobaric labeling (10-plex TMT) coupled with extensive liquid chromatography and mass spectrometry, we analyzed ~ 12K genes and > 30K phosphosites by extensive mass spectrometry. Systematical reprogramming of the proteome and phosphoproteome were observed in HGG tumors compare to normal cortex.

2019-06-24 | PXD005360 | Pride

Transcription profiling of human astrocytomas classified as low or high grade and glioma cell line controls (glioblastoma) to to identify genetic differences between the two types

Project description:Summary: Astrocytomas can be categorized as either low grade or high grade (glioblastoma). Low grade astrocytomas are not generally aggressive tumors whereas glioblastomas are and in turn have a high mortality rate. The purpose of this experiment is to identify genetic differences between the two types. Hypothesis: There will be a difference in RNA expression between high grade and low grade tumors. Specific Aim: To identify genes which make a tumor high grade or low grade Experiment Overall Design: Comparison of 8 high grade and 12 low grade tumors

| S-ECPF-GEOD-3185 | biostudies-other

Transcription profiling of human primary breast tumors and matched short-term epithelial cultures

Project description:Background To identify the spectrum of malignant attributes maintained outside the host environment, we have compared global gene expression in primary breast tumors and matched short-term epithelial cultures. Results In contrast to immortal cell lines, a characteristic 'limited proliferation' phenotype was observed, which included over expressed genes associated with the TGFbeta signal transduction pathway, such as SPARC, LOXL1, RUNX1, and DAPK1. Underlying this profile was the conspicuous absence of hTERT expression and telomerase activity, a significant increase in TGFbeta receptor2, its cognate ligand, and the CDK inhibitor, p21CIP1/WAF1. Concurrently, tumor tissue and primary cultures displayed low transcript levels of proliferation-related genes, such as, TOP2A, ANKT, RAD51, UBE2C, CENPA, RRM2, and PLK. Conclusions Our data demonstrate that commonly used immortal cell lines do not reflect some aspects of tumor biology as closely as primary tumor cell cultures. The gene expression profile of malignant tissue, which is uniquely retained by cells cultured on solid substrates, could facilitate the development and testing of novel molecular targets for breast cancer.

| S-ECPF-SMDB-2888 | biostudies-other

Patient-derived primary cultures of paediatric high grade glioma and DIPG - molecular profiling by methylation array (Infinium HumanMethylationEPIC)

Project description:Molecular profiling by methylation array (Illumina Infinium HumanMethylationEPIC) in a panel of models generated under 2D (laminin matrix) and/or 3D (neurospheres) conditions fully credentialed by phenotypic and molecular comparison to the original tumour sample. Patient-derived in vitro primary cell cultures represent potentially useful tools for mechanistic and preclinical investigation based upon their retention of key features of tumour subgroups under experimental conditions amenable to high-throughput approaches.

2020-08-31 | E-MTAB-9297 | biostudies-arrayexpress

Patient-derived primary cultures of paediatric high grade glioma and DIPG - molecular profiling by methylation array (Infinium HumanMethylation450)

Project description:Molecular profiling by methylation array (Illumina Infinium HumanMethylation450K) in a panel of models generated under 2D (laminin matrix) and/or 3D (neurospheres) conditions fully credentialed by phenotypic and molecular comparison to the original tumour sample. Patient-derived in vitro primary cell cultures represent potentially useful tools for mechanistic and preclinical investigation based upon their retention of key features of tumour subgroups under experimental conditions amenable to high-throughput approaches.

2020-08-31 | E-MTAB-9298 | biostudies-arrayexpress

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