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Series GSE49324 Query DataSets for GSE49324
Status Public on Jul 30, 2013
Title Identification of neural stem cell gene expression signatures associated with disease progression in alveolar soft part sarcoma by integrated molecular profiling [aCGH]
Organism Homo sapiens
Experiment type Genome variation profiling by genome tiling array
Summary Alveolar soft part sarcoma (ASPS) is a soft tissue sarcoma with poor prognosis. Apart from the recurrent, non-reciprocal t(X,17)(p11.2;q25) translocation, there is little molecular evidence for the origin, initiation and progression of this cancer. We analysed 16 primary and metastatic ASPS samples to elucidate candidate molecular pathways involved in tumor pathogenesis. FISH analysis identified the ASPL-TFE3 fusion in all cases. High-resolution aCGH revealed a higher number of numerical aberrations in metastatic tumors relative to primaries, but failed to identify any consistent alterations in either group. Gene expression analysis highlighted 1,063 genes which were differentially expressed between primary and metastatic tumors. Gene set enrichment analysis identified 16 enriched genesets (p < 0.1) associated with differentially expressed genes. Notable among these were several stem cell gene expression signatures and pathways related to differentiation. In particular, the paired box transcription factor PAX6 was up-regulated in the primary tumors, along with several genes whose mouse orthologs have previously been implicated in Pax6-DNA binding during neural stem cell differentiation. In addition to suggesting a neural origin for ASPS, these results implicate transcriptional deregulation from fusion genes in the pathogenesis of ASPS, rather than extensive chromosomal instability.
 
Overall design 15 different tumor and normal paired samples were analysed
 
Contributor(s) Selvarajah S, Saumyadipta P, Chen E, Ligon A, Nielsen P, Dranoff G, Stack E, Loda M, Flavin R
Citation(s) 24493828
Submission date Jul 29, 2013
Last update date Mar 21, 2017
Contact name Ramakrishna Sompallae
E-mail(s) ramakrishnas@gmail.com
Phone 319 353 5548
Organization name University of Iowa
Department Iowa Institute of Human Genetics
Lab Bioinformatics
Street address 285 Newton Road, 5292 CBRB
City Iowa City
State/province IA
ZIP/Postal code 52240
Country USA
 
Platforms (1)
GPL9777 Agilent-021850 SurePrint G3 Human CGH Microarray (Feature Number version)
Samples (15)
GSM1197409 1M [aCGH]
GSM1197410 2M [aCGH]
GSM1197411 4M [aCGH]
This SubSeries is part of SuperSeries:
GSE49327 Identification of neural stem cell gene expression signatures associated with disease progression in alveolar soft part sarcoma by integrated molecular profiling
Relations
BioProject PRJNA213634

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Supplementary data files not provided
Processed data included within Sample table

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