Laser-capture microdissection and transcriptional profiling in archival FFPE tissue in prostate cancer

Abstract

Prognostic markers can improve prediction of the behaviour of a cancer at the point of diagnosis. A key value of any prognostic marker is at the point of tumour diagnosis. In the context of prostate cancer, this implies profiling in the diagnostic formalin-fixed, paraffin-embedded (FFPE) transrectal ultrasound-guided (TRUS) needle biopsy. TRUS needle biopsies commonly contain both stromal and epithelial cells, and malignant glands are found as isolated foci within this tissue. Using the entire biopsy for genetic analysis inevitably results in a significant contamination of malignant cells with benign tissue. This combination of minimal tumour yields and tissue heterogeneity have so far prohibited prognostic transcript and microarray molecular studies in needle biopsies. Laser-capture microdissection (LCM) allows enriched cell populations to be accurately isolated from heterogeneous tissue, hence facilitating analysis of different components from a single tissue sample. Here, we describe its use in isolating tumour cells in archival FFPE prostate needle biopsies and subsequent application for RNA extraction and quantitative real-time PCR (QPCR).