1. ¹Department of Genitourinary Pathology, Armed Forces Institute of Pathology, Washington, DC, USA
2. ²Center for Prostate Disease Research, Department of Surgery Uniformed Services, University of the Health Sciences, Rockville, MD, USA
3. ³Genomatix Software GmbH, Munich, Germany
4. ⁴Division of Retrovirology, Walter Reed Army Institute of Research, Rockville, MD, USA
5. ⁵Urology Service, Walter Reed Army Medical Center, Washington, DC, USA

Correspondence: Dr IA Sesterhenn, Department of Genitourinary Pathology, Armed Forces Institute of Pathology, 6825 16th Street NW, Building 54, PB13, Washington, DC 20306-6000, USA. E-mail: sesterhe@afip.osd.mil

⁶These authors have contributed equally to this work.

Received 9 July 2007; Revised 26 July 2007; Accepted 26 July 2007; Published online 4 September 2007.

Abstract

Formalin-fixed paraffin-embedded (FFPE) prostate specimens are rich sources of molecular pathological information. However, FFPE-based microarray analysis of tissue samples may be hampered by the degradation and chemical alteration of RNA molecules due to the preservation procedure. In this report, we employed a probe analyses of Affymetrix oligonucleotide arrays at individual probe level to compensate for the potential loss of gene identifications associated with compromised mRNA quality in FFPE preparations. Furthermore, to increase the sample quality, we utilized laser capture microdissection of prostate tumor and benign epithelial cells. Remarkably, combination of these approaches recapitulated the common prostate cancer-associated gene expression alteration. Identification of prostate cancer associated-gene expression alterations such as AMACR, Kallikrein gene family and genes associated with androgen signaling such as PDEF and STEAP were consistent with previous findings reported in prostate cancer. These data suggest that combination of laser capture dissection with computational enhancement of microarray data may be useful for the assessment of gene expression changes in FFPE prostate cancer specimens.