Detection of differentially expressed genes in prostate cancer by combining suppression subtractive hybridization and cDNA library array

The molecular mechanisms underlying the development and progression of pros tate cancer have remained poorly understood. The identification of differen tially expressed genes has been used as a tool to recognize genes that are involved in disease processes. In this study me combined suppression subtra ctive hybridization (SSH) and cDNA array hybridization to identify genes wh ose expression is decreased in prostate cancer. cDNA from benign prostatic hyperplasia (BPH) was subtracted with cDNA from the prostate cancer cell li ne PC-3 and 386 of the subtracted clones were arrayed onto a nylon filter m embrane. The differential gene expression was then verified by hybridizing the filter with radioactively labelled first-strand cDNA preparations from BPH, PC-3, four other cancer cell lines, and a normal prostate epithelial c ell line (PrEC), In order to validate SSH and cDNA array hybridization, the enrichment of clones in the subtraction, as well as the sensitivity and li nearity of array hybridization, was first evaluated. The array hydridizatio n results were confirmed by northern analysis and selected clones were sequ enced. Altogether, several known genes, such as prostate-specific antigen ( PSA), human glandular kallikrein 2 (hK2), phosphatidic acid phosphatase typ e 2a (PAP2a), alpha -tropomyosin, and insulin-like growth factor binding pr otein 7 (IGFBP-7), as well as an anonymous transcript (EST), were found to be expressed less in PC-3 than in BPH. Further studies on the significance of these genes in the development of prostate cancer are now warranted. Cop yright (C) 2000 John Wiley & Sons, Ltd.