Genome-wide characterization of gene expression variations and DNA copy number changes in prostate cancer cell lines.
BACKGROUND
The aim of this study was to characterize gene expression and DNA copy number profiles in androgen sensitive (AS) and androgen insensitive (AI) prostate cancer cell lines on a genome-wide scale.


METHODS
Gene expression profiles and DNA copy number changes were examined using DNA microarrays in eight commonly used prostate cancer cell lines. Chromosomal regions with DNA copy number changes were identified using cluster along chromosome (CLAC).


RESULTS
There were discrete differences in gene expression patterns between AS and AI cells that were not limited to androgen-responsive genes. AI cells displayed more DNA copy number changes, especially amplifications, than AS cells. The gene expression profiles of cell lines showed limited similarities to prostate tumors harvested at surgery.


CONCLUSIONS
AS and AI cell lines are different in their transcriptional programs and degree of DNA copy number alterations. This dataset provides a context for the use of prostate cancer cell lines as models for clinical cancers.
Department of Urology, Stanford University School of Medicine, Stanford, California, USA.
Hongjuan
H
Zhao
Young
Y
Kim
Pei
P
Wang
Jacques
J
Lapointe
Rob
R
Tibshirani
Jonathan R
JR
Pollack
James D
JD
Brooks
D045744:Cell Line, Tumor; D016000:Cluster Analysis; D004273:DNA, Neoplasm / Q000235:genetics* / Q000378:metabolism; D018628:Gene Dosage; D015972:Gene Expression Regulation, Neoplastic / Q000235:genetics*; D015894:Genome, Human; D006801:Humans; D008297:Male; D020411:Oligonucleotide Array Sequence Analysis; D011471:Prostatic Neoplasms / Q000235:genetics* / Q000378:metabolism; D012334:RNA, Neoplasm / Q000737:chemistry / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction
D004273:DNA, Neoplasm; D012334:RNA, Neoplasm