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Series GSE17601 Query DataSets for GSE17601
Status Public on Sep 30, 2009
Title Affymetrix Gene Expression array data for Sézary Syndrome (SS) samples
Organism Homo sapiens
Experiment type Expression profiling by array
Summary This study used tumour and paired normal samples from 28 Sézary Syndrome (SS) patients to define recurrent regions of chromosomal aberrations. Our data identified recurrent losses of 17p13.2-p11.2 and 10p12.1-q26.3 occurring in 71 and 68% of cases respectively; common gains were detected for 17p11.2-q25.3 (64%) and chromosome 8/8q (50%). Moreover, we identified novel genomic lesions recurring in more than 30% of tumours: loss of 9q13-q21.33 and gain of 10p15.3-10p12.2. In the Sézary Syndrome cases analysed, we could find several small and few large Uniparental Disomies involving interstitial or telomeric regions of LOH occurring mainly for chromosome 10 and to a lesser extent for chromosome 9 and 17. In the attempt to correlate Copy Number data and clinical parameters we find a relationship between complex pattern of chromosomal aberrations, involving at least three recurrent Copy Number alterations, and shorter survival. Integrating mapping and transcriptional data we were able to identify a total of 113 deregulated transcripts in aberrant chromosomal regions that included cancer related genes such as members of the NF-kB pathway (BAG4, BTRC, NKIRAS2, PSMD3, TRAF2) that might explain its constitutive activation in CTCL. Matching this list of genes with those discriminating patients with different survival times we identify several common candidates that might exert critical roles in Sézary Syndrome, like BUB3 and PIP5K1B.
 
Overall design Affymetrix Gene Expression arrays were performed, according to the manufacturer's directions, on RNA extracted from cryopreserved lymphomonocytes purified by Ficoll density gradient centrifugation and positive selection using anti-human CD3-conjugated dynabeads (tumour samples). Gene expression analyses of Affymetrix HG-U133 A arrays were performed for 32 tumour samples.
 
Contributor(s) Arcelli D, Caprini E
Citation(s) 19843862, 30518749
Submission date Aug 11, 2009
Last update date Dec 10, 2018
Contact name Elisabetta Caprini
E-mail(s) e.caprini@idi.it
Organization name IDI-IRCCS
Street address Via dei Monti di Creta 104
City Roma
State/province Italy
ZIP/Postal code 00167
Country Italy
 
Platforms (1)
GPL96 [HG-U133A] Affymetrix Human Genome U133A Array
Samples (32)
GSM439390 SS patient number 44; diagnostic sample; expression
GSM439391 SS patient number 30; diagnostic sample; expression
GSM439392 SS patient number 32; diagnostic sample; expression
This SubSeries is part of SuperSeries:
GSE17602 Identification of regions and genes important in Sézary syndrome pathogenesis using genomic and expression microarrays
Relations
BioProject PRJNA123363

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
GSE17601_RAW.tar 68.3 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table
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