CPDR GENE EXPRESSION DATA

ERG Transcriptome

CPDR tumor-benign 80 genechip dataset
From 40 patients specimens were obtained under an IRB-approved protocol from patients treated with radical prostatectomy (RP) at Walter Reed Army Medical Center (WRAMC). From over 300 patients two groups were selected which had prostate tumors with either well differentiated (WD) or poorly differentiated (PD) after radical RP. The PD group had Gleason score 8-9, seminal vesicle invasion, and poorly differentiated tumor cells; the WD group had Gleason score 6-7, no seminal vesicle invasion, and well to moderately differentiated tumor cells. LCM compatible specimens were selected from age and race (Caucasians) matched PD or WD patients with no family history of CaP.

Note: yearly PSA screening is mandatory for military health care recipients.

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Abstract | Publications | Well Differentiated Normals 1-20 (txt file) | Well Differentiated Tumors 1-20 (txt file)
Poorly Differentiated Normals 21-40 (txt file) | Poorly Differentiated Tumors 21-40 (txt file)

VCaP Cell Response to ERG siRNA
VCaP Human prostate tumor cell line, was obtained from the American Type Culture Collection (ATCC, Rockville, MD) and were maintained in growth medium and under conditions recommended by the supplier. For hormone treatment the R1881 synthetic androgen analogue, was used (New England Nuclear, Boston, MA). Small interference RNA (siRNA) oligo duplex against human ERG (Locus ID: GXL_163565, Accession: NM_004440) was designed as follows: ERG siRNA, 5'-TGATGTTGATAAAGCCTTATT -3' (Dharmacon, Lafayette, CO). Non-target (NT) siRNA duplexes (D-001206-13-20) were from Dharmacon (Lafayette, CO). VCaP cells were seeded into 10 cm tissue culture dishes in the appropriate medium with 10% cFBS for three days. Transfection of siRNA was carried out with Lipofectamine 2000 (Invitrogen, Carlsbad, CA). Twelve hours after transfection of si RNAs, VCaP cells were treated with 100pM R1881, incubated for 24h or 48h and processed for microarray analysis. Total RNA was isolated and five micrograms of RNA from each of the VCaP transfectants were biotin labeled and GeneChip® HG U133 Plus 2.0 chips were hybridized with the labeled probes. Expression data were normalized by Robust Multi-array Averages (RMA) and fold changes in ERGsi/NT (24h) and ERGsi/NT (48h) treatment groups were calculated. A two folds cut-off criterion was applied for subsequent pathway analysis by the Bibliosphere Software using the functional co-citation-based analysis function (Genomatix GmbH, Munich, Germany) (Scherf et al., 2005).

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Publications | CPDR NT 24h (txt file) | CPDR NT 48h (txt file) | CPDR Si1 24h (txt file) | CPDR Si1 48h (txt file)

 

Androgen Regulated Transcriptome in Prostate Cancer Cells

Androgen signaling is extremely important in the life and death of the prostate gland and is believed to play an important role (s) in prostate cancer. Hormonal therapy, the most common treatment strategy for the treatment of metastatic prostate cancer works by inhibiting androgen signaling. Accumulating evidence suggests that alterations of androgen signaling in prostate cancer may involve structural or functional alterations of the critical genes at numerous points in the pathway.
Abstract | Genes Defined by SAGE | Genes Defined by Gene Chip | ARE Data

 

Common Gene Alterations in Prostate Cancer: ERG and Lactoferrin

Transcription factors encoded by the ETS family of genes are central in integrating signals that regulate cell growth and differentiation, stress responses and tumorigenesis. This study, analyzing laser microdissected paired benign and malignant prostate epithelial cells from prostate cancer (CaP) patients (n=114; 228 specimen) by GeneChip and quantitative real time RT-PCR, identifies ERG, a member of the ETS transcription factor family, as the most frequently overexpressed proto-oncogene in the transcriptome of malignant prostate epithelial cells. Combined quantitative expression analysis of ERG with two other genes commonly overexpressed in CaP, AMACR and DD3, revealed overexpression of at least one of these three genes in virtually all CaP specimen (54 of 55). Comprehensive evaluation of quantitative ERG1 expression with clinico-pathological features also suggested that ERG1 expression level in prostate tumor cells relative to benign epithelial cells is indicator of disease free survival after radical prostatectomy.
Publication

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