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Series GSE25771 Query DataSets for GSE25771
Status Public on Jan 01, 2012
Title High-resolution, genome-wide analysis of human metastatic neuroblastoma samples by array-Comparative Genomic Hybridization (aCGH)
Organism Homo sapiens
Experiment type Genome variation profiling by array
Summary Neuroblastoma (NB) is an aggressive tumor that affects both infants and children. The disease outcome is greatly influenced by age of patient, stage, chromosome copy number aberrations (CNAs) and gene expression abnormalities. We analyzed, by microarray technology, genome and transcriptome of 3 groups of tumors of patients with metastatic disease: G1, stage 4S and MYCN single copy; G2, stage 4 younger than 18 months of age, MYCN single copy with no disease progression and G3, stage 4, older than 19 months, with unfavorable outcome. We found an accumulation of structural copy number aberrations (CNAs) in G3 whereas G1 tumors had mostly numerical (N) CNAs and G2 showed an intermediate behavior. Pair wise comparisons demonstrated that the average of N CNAs significantly decreased from G1 to G2 to G3 (9.6 G1 < 7.2 G2 < 3.6 G3); in contrast S CNAs significantly increased in G3 (0.7 G1 < 3.7 G2 < 7.0 G3). Interestingly, we observed several intra-chromosomal rearrangements in G3 tumors on chromosomes not usually involved in NB. Excluding MYCN amplified tumors by G3 we found a high frequency of S CNAs in this group. Gene expression analysis showed a deregulation of downstream genes of Ras and Rho signaling pathway among the 3 groups. It has been also observed a progressive switch off of development and adhesion genes and a switch on of cell cycle genes from G1 to G2 to G3. Moreover, the telemorase genes were significantly expressed in G3 with respect to remaining groups. Present data show an accumulation of S CNAs from stage 4S to 4. The deregulation of genes Rho/Ras pathway may explain the increase of tumor aggressiveness from G1 to G2 to G3. The increase of cell cycle and telomerase genes expression associated with G3 would provide unlimited replicative potential for these tumors and may be responsible for accumulation of S CNAs. Finally, we can argue that accumulation of structural aberrations and gene deregulation is age-dependent and it is associated with a more aggressive tumor phenotype.
 
Overall design We analyzed 133 samples of metastatic neuroblastoma from patients divided into three groups: G1 49 patients stage 4S and MYCN single copy; G2 37 patients stage 4 younger than 18 months of age at diagnosis, MYCN single copy with no disease progression; G3 47 patients stage 4 older than 19 months of age at diagnosis, with unfavorable outcome.
 
Contributor(s) Coco S, Theissen J, Scaruffi P, Stigliani S, Valdora F
Citation(s) 22234802, 24737690
Submission date Dec 02, 2010
Last update date Sep 18, 2014
Contact name simona coco
E-mail(s) simona.coco@hsanmartino.it, coco.simona@gmail.com
Phone +390105558316
Organization name IRCCS Ospedale Policlinico San Martino
Lab Lung Cancer Unit
Street address L.go R. Benzi, 10
City Genova
ZIP/Postal code 16132
Country Italy
 
Platforms (4)
GPL2873 Agilent-012750 Human Genome CGH Microarray 44A (Feature number version)
GPL2879 Agilent-013282 Human Genome CGH Microarray 44B (Feature number version)
GPL4093 Agilent-014698 Human Genome CGH Microarray 105A (G4412A)
Samples (133)
GSM634058 G1_Cologne_251469812732_1_1.txt
GSM634059 G1_Cologne_251328220491.txt
GSM634060 G1_Cologne_251275011615.txt
Relations
BioProject PRJNA135823

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE25771_RAW.tar 1.8 Gb (http)(custom) TAR (of TXT)
Processed data included within Sample table
Processed data provided as supplementary file

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