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Comparative analyses of gene copy number and mRNA expression in GBM tumors and GBM xenografts

ABSTRACT: Comparative analyses of gene copy number and mRNA expression in GBM tumors and GBM xenografts

OTHER RELATED OMICS DATASETS IN: GSE14806

PROVIDER: PRJNA112037 | ENA |

REPOSITORIES: ENA

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SNP copy number data from glioblastoma subcutaneous xenografts

Project description:Development of model systems that recapitulate the molecular heterogeneity observed amongst GBM tumors will expedite the testing of targeted molecular therapeutic strategies for GBM treatment. In this study, we profiled DNA copy number and mRNA expression in 21 independent GBM tumor lines maintained as subcutaneous xenografts (GBMX), and compared GBMX molecular signatures to those observed in GBM clinical specimens derived from The Cancer Genome Atlas (TCGA). The predominant copy number signature in both tumor groups was defined by chromosome-7-gain/chromosome-10-loss, a poor prognosis genetic signature. We also observed, at frequencies similar to that detected in TCGA GBMs genomic amplification and overexpression of known GBM oncogenes such as EGFR, MDM2, CDK6 and MYCN, and novel genes including NUP107, SLC35E3, MMP1, MMP13 and DDX1. The transcriptional signature of GBMX tumors, which was stable over multiple subcutaneous passages, was defined by overexpression of genes involved in M-phase, DNA Replication, and Chromosome organization (MRC) and was highly similar to the poor-prognosis mitosis-and-cell-cycle-module (MCM) in GBM. Assessment of gene expression in TCGA-derived GBMs revealed overexpression of MRC cancer genes AURKB, BIRC5, CCNB1, CCNB2, CDC2, CDK2, and FOXM1, which form a transcriptional network important for G2/M- progression and/or -checkpoint activation. In conclusion, our study supports propagation of GBM tumors as subcutaneous xenografts as a useful approach for sustaining key molecular characteristics of patient tumors, and highlights therapeutic opportunities conferred by this GBMX tumor panel for testing targeted therapeutic strategies for GBM treatment. Disease state analysis

2009-03-07 | GSE14804 | GEO

Comparative analyses of gene copy number and mRNA expression in GBM tumors and GBM xenografts

Project description:This SuperSeries is composed of the SubSeries listed below.

2009-03-07 | GSE14806 | GEO

Genomic copy number number characterisation of glioblastoma (GBM) cell lines.

Project description:Early passages (< 10) of frequently used GBM cell lines A172, LN18, LN229, T98G, U87-MG, U138-MG and U251-MG were characterised for genomic copy number by array CGH.

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Comparative analyses of gene copy number and mRNA expression in glioblastoma multiforme tumors and xenografts.

Project description: Not available

| S-EPMC2765338 | biostudies-literature

Genomic copy number number characterisation of glioblastoma (GBM) cell lines.

Project description:Genomic copy number number characterisation of glioblastoma (GBM) cell lines.

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Gene expression analysis reveals close resemblance between Glioblastoma (GBM) patient tumors and corresponding patient-derived orthotopic xenografts (PDOXs)

Project description:Glioblastoma (GBM) patient-derived orthotopic xenografts (PDOXs) were derived from organotypic spheroids obtained from patient tumor samples. To detect whether gene expression profiles of GBM patient tumors are retained in PDOXs, we performed genome-wide transcript analysis by human-specific microarrays . In parallel, we analyzed GBM cell cultures and corresponding intracranial xenografts from stem-like (NCH421k, NCH644) and adherent GBM cell lines (U87, U251). PDOXs show a better transcriptomic resemblance with patient tumors than other preclinical models. The major difference is largely explained by the depletion of human-derived non-malignant cells.

2020-07-01 | GSE134470 | GEO

Copy number variation comparison between control and CC214-2 resistant GBM39 xenografts

Project description:Here we present genome-wide copy number variation data on two vehicle treated and two CC214-2 (an mTOR kinase inhibitor) resistant GlioBlastoma Multiforme 39 (GBM39) xenografts, showing the absence of significant differences between the two groups, demonstrating that resistance to CC214-2 is due to adaptation rather than gene mutations.

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Copy number variation comparison between control and CC214-2 resistant GBM39 xenografts

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Comparative genomic hybridization of 5 human prostate cancer cell lines and 13 prostate cancer xenografts to create genomic profiles of copy number alterations

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2005-12-31 | E-MEXP-335 | biostudies-arrayexpress

Copy number analysis of human glioblastoma multiforme

Project description:Copy number analysis of human GBM samples were performed, and a high frequency of deletions of the PTPRD gene on chromosome 9p23-24.1 were identified. Keywords: SNP microarray, glioblastoma multiforme, copy number, amplification, deletion Genomic DNA from 58 GBM tumor samples were hybridized to Affymetrix 250K NspI Gene Chip Arrays and analyzed by dChip using the hg17 genome assembly.

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