Please note that we have stopped the regular imports of Gene Expression Omnibus (GEO) data into ArrayExpress. This may not be the latest version of this experiment.

E-GEOD-60740 - Expression profiles of Ewing family of tumors authenticate distinct molecular entities

Status
Released on 30 June 2015, last updated on 19 August 2015
Organism
Homo sapiens
Samples (31)
Array (1)
Protocols (5)
Description
The concept of Ewing family of tumors (EFT), characterized by FET-ETS fusions, has been recently challenged by the description of Ewing-like tumors with different gene fusions. Here we investigate the similarities and differences of FET-ETS, BCOR-CCNB3, CIC-DUX4 and EWSR1-NFATc2 tumors samples with a number of other sarcomas. Unsupervised clustering of gene expression profiles fully discriminates these four molecular entities. Specific gene signatures and pathways were further validated in model cell lines. While a clear inflammatory signature characterizes EWSR1-NFATc2 tumors, BCOR-CCNB3 and CIC-DUX4 exhibit high expression of homeobox and ETS protein families, respectively. We strongly suggest that abnormalities of chromatin remodeling may gather CIC-DUX4 and BCOR-CCNB3 tumors with rhabdoid tumors and synovial sarcomas. This dataset conains 14 CIC-DUX4 and 7 EWSR1-NFATc2 tumor samples as well as Human mesenchymal cell line expressing EWSR1-NFATc2 (duplicates) or mock treated (duplicates) and IB120 CIC-DUX4 cell line expressing an shRNA directed against CIC-DUX4 (4 replicates) or mock treated (duplicates).
Experiment type
transcription profiling by array 
Contacts
Franck Tirode <geo@ncbi.nlm.nih.gov>, Karoly Szuhai, Olivier Delattre, Pancras C Hogendoorn, Sarah Watson, Virginie Perrin
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-60740.idf.txt
Sample and data relationshipE-GEOD-60740.sdrf.txt
Raw data (1)E-GEOD-60740.raw.1.zip
Processed data (1)E-GEOD-60740.processed.1.zip
Array designA-GEOD-17811.adf.txt
Links