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Series GSE2787 Query DataSets for GSE2787
Status Public on Oct 25, 2005
Title Gene expression profiling of children affected by Alveolar Rhabdomyosarcoma (ARMS)
Organism Homo sapiens
Experiment type Expression profiling by array
Summary We analyzed the expression signatures of 10 tumor biopsies from children affected by alveolar rhabdomyosarcoma (ARMS) to identify genes correlating to biological features of this tumor. Five of these patients were positive for the PAX3-FKHR fusion gene and five were negative. We used a cDNA platform containing a large majority of probes derived for muscle tissues.
The comparison of transcription profiles of tumor samples with normal fetal skeletal muscle identified 171 differentially expressed genes common to all ARMS patients. The functional analysis of altered genes led to the identification of a group of transcripts (BCOR, DDX5, LGALS1, BIN1) that may be relevant for the tumorigenic processes leading a normal muscle cell to become a malignant rhabdomyoblast.
The muscle-specific platform was able to distinguish PAX3-FKHR positive and negative ARMS through the expression pattern of a limited number of genes (RAC1, CFL1, CCND1) that might be biologically relevant for the different clinical behavior and aggressiveness of the two ARMS subtypes. Expression levels for selected candidate genes were validated by quantitative real-time reverse-transcription PCR.
Keywords: human fetal skeletal muscle, alveolar rhabdomyiosarcoma, gene expression profiling, PAX3-FKHR
 
Overall design We compared the transcription profiles of ARMS samples by microarray competitive hybridization against an arbitrary total RNA reference prepared from a pool of 5 human fetal skeletal muscles. Two replicates of each experiment were performed using different microarray slides, in which sample and reference RNAs, labeled either with Cy3 or Cy5 fluorochromes, were crossed in both combinations (dye-swapping procedure).
 
Contributor(s) De Pitta C, Tombolan L, Albiero G, Sartori F, Romualdi C, Jurman G, Carli M, Furlanello C, Lanfranchi G, Rosolen A
Citation(s) 16381018
Submission date Jun 09, 2005
Last update date Jul 26, 2013
Contact name Gerolamo Lanfranchi
E-mail(s) stefano.cagnin@unipd.it
Phone +39-0498276219
Organization name University of Padova
Department CRIBI - Biotechnology Center and Biology Department
Lab Functional Genomics Lab
Street address Via U. Bassi, 58/B
City Padova
ZIP/Postal code 35131
Country Italy
 
Platforms (1)
GPL2011 Human Array 2.0
Samples (28)
GSM60462 Gene expression profiling of ARMS No. 1 (A)
GSM60463 Gene expression profiling of ARMS No. 1 (B)
GSM60465 Gene expression profiling of ARMS No. 2 (A)
Relations
BioProject PRJNA92485

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