Prostate cancer - Associated gene expression alterations determined from needle biopsies

Zheng (David) Qian, Chung Ying Huang, Catherine A. O'Brien, Ilsa M. Coleman, Mark Garzotto, Lawrence D. True, Celestia S. Higano, Robert Vessella, Paul H. Lange, Peter S. Nelson, Tomasz (Tom) Beer

Research output: Contribution to journalArticle

13 Citations (Scopus)

Abstract

Purpose: 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. Experimental Design: 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.

Original languageEnglish (US)
Pages (from-to)3135-3142
Number of pages8
JournalClinical Cancer Research
Volume15
Issue number9
DOIs
StatePublished - May 1 2009

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Neoplasm Genes
Needle Biopsy
Prostate
Prostatic Neoplasms
Gene Expression
Ischemia
Androgen Receptors
Genes
Neoplasms
Laser Capture Microdissection
Biopsy
Drug Therapy
Drug Delivery Systems
Prostatectomy
Cellular Immunity
Energy Metabolism
Reverse Transcription
Signal Transduction
Research Design
Down-Regulation

ASJC Scopus subject areas

  • Cancer Research
  • Oncology

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Prostate cancer - Associated gene expression alterations determined from needle biopsies. / Qian, Zheng (David); Huang, Chung Ying; O'Brien, Catherine A.; Coleman, Ilsa M.; Garzotto, Mark; True, Lawrence D.; Higano, Celestia S.; Vessella, Robert; Lange, Paul H.; Nelson, Peter S.; Beer, Tomasz (Tom).

In: Clinical Cancer Research, Vol. 15, No. 9, 01.05.2009, p. 3135-3142.

Research output: Contribution to journalArticle

Qian, ZD, Huang, CY, O'Brien, CA, Coleman, IM, Garzotto, M, True, LD, Higano, CS, Vessella, R, Lange, PH, Nelson, PS & Beer, TT 2009, 'Prostate cancer - Associated gene expression alterations determined from needle biopsies', Clinical Cancer Research, vol. 15, no. 9, pp. 3135-3142. https://doi.org/10.1158/1078-0432.CCR-08-1982
Qian, Zheng (David) ; Huang, Chung Ying ; O'Brien, Catherine A. ; Coleman, Ilsa M. ; Garzotto, Mark ; True, Lawrence D. ; Higano, Celestia S. ; Vessella, Robert ; Lange, Paul H. ; Nelson, Peter S. ; Beer, Tomasz (Tom). / Prostate cancer - Associated gene expression alterations determined from needle biopsies. In: Clinical Cancer Research. 2009 ; Vol. 15, No. 9. pp. 3135-3142.
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AU - O'Brien, Catherine A.

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AU - Garzotto, Mark

AU - True, Lawrence D.

AU - Higano, Celestia S.

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AU - Lange, Paul H.

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N2 - Purpose: 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. Experimental Design: 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.

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