Prostate cancer-associated gene expression alterations determined from needle biopsies.
OBJECTIVE
To accurately identify gene expression alterations that differentiate neoplastic from normal prostate epithelium using an approach that avoids contamination by unwanted cellular components and is not compromised by acute gene expression changes associated with tumor devascularization and resulting ischemia.


METHODS
Approximately 3,000 neoplastic and benign prostate epithelial cells were isolated using laser capture microdissection from snap-frozen prostate biopsy specimens provided by 31 patients who subsequently participated in a clinical trial of preoperative chemotherapy. cDNA synthesized from amplified total RNA was hybridized to custom-made microarrays composed of 6,200 clones derived from the Prostate Expression Database. Expression differences for selected genes were verified using quantitative reverse transcription-PCR.


RESULTS
Comparative analyses identified 954 transcript alterations associated with cancer (q < 0.01%), including 149 differentially expressed genes with no known functional roles. Gene expression changes associated with ischemia and surgical removal of the prostate gland were absent. Genes up-regulated in prostate cancer were statistically enriched in categories related to cellular metabolism, energy use, signal transduction, and molecular transport. Genes down-regulated in prostate cancers were enriched in categories related to immune response, cellular responses to pathogens, and apoptosis. A heterogeneous pattern of androgen receptor expression changes was noted. In exploratory analyses, androgen receptor down-regulation was associated with a lower probability of cancer relapse after neoadjuvant chemotherapy followed by radical prostatectomy.


CONCLUSIONS
Assessments of tumor phenotypes based on gene expression for treatment stratification and drug targeting of oncogenic alterations may best be ascertained using biopsy-based analyses where the effects of ischemia do not complicate interpretation.
Division of Hematology and Medical Oncology, Oregon Health and Science University, OR, USA.
David Z
DZ
Qian
Chung-Ying
CY
Huang
Catherine A
CA
O'Brien
Ilsa M
IM
Coleman
Mark
M
Garzotto
Lawrence D
LD
True
Celestia S
CS
Higano
Robert
R
Vessella
Paul H
PH
Lange
Peter S
PS
Nelson
Tomasz M
TM
Beer
D014408:Biomarkers, Tumor / Q000235:genetics* / Q000378:metabolism; D001707:Biopsy, Needle; D020869:Gene Expression Profiling; D006801:Humans; D007834:Lasers; D008297:Male; D042282:Microdissection; D020411:Oligonucleotide Array Sequence Analysis; D011470:Prostatic Hyperplasia / Q000235:genetics / Q000378:metabolism / Q000473:pathology; D011471:Prostatic Neoplasms / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction
D014408:Biomarkers, Tumor; D012333:RNA, Messenger