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E-GEOD-20196 - Gene expression profile of poorly differentiated synovial sarcoma

Status
Released on 1 September 2010, last updated on 10 June 2011
Organism
Homo sapiens
Samples (34)
Array (1)
Protocols (7)
Description
Poorly differentiated type synovial sarcoma (PDSS) is a variant of synovial sarcoma characterized by predominantly round or short-spindled cells. Although accumulating evidence from clinicopathological studies suggests a strong association between this variant of synovial sarcoma and poor prognosis, little has been reported on the molecular basis of PDSS. To gain insight into the mechanism(s) that underlie the emergence of PDSS, we analyzed the gene expression profiles of 34 synovial sarcoma clinical samples, including 5 cases of PDSS, using an oligonucleotide microarray. In an unsupervised analysis, the 34 samples fell into 3 groups that correlated highly with histological subtype, namely, monophasic, biphasic, and poorly differentiated types. PDSS was characterized by down-regulation of genes associated with neuronal and skeletal development and cell adhesion, and up-regulation of genes on a specific chromosomal locus, 8q21.11. This locus-specific transcriptional activation in PDSS was confirmed by reverse transcriptase (RT)-PCR analysis of 9 additional synovial sarcoma samples. Our results indicate that PDSS tumors constitute a distinct genetic group based on expression profiles. 34 SYT-SSX fusion transcript-positive SS samples, consisting of 21 MSS, 8 BSS and 5 PDSS cases, were analyzed using an oligonucleotide microarray using a GeneChip Human Genome U133 plus 2.0 array (Affymetrix).
Experiment type
transcription profiling by array 
Contacts
Hitoshi Ichikawa, Robert Nakayama
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-20196.idf.txt
Sample and data relationshipE-GEOD-20196.sdrf.txt
Raw data (1)E-GEOD-20196.raw.1.zip
Processed data (1)E-GEOD-20196.processed.1.zip
Array designA-AFFY-44.adf.txt
R ExpressionSetE-GEOD-20196.eSet.r
Links