High-Resolution Analysis of Paraffin-Embedded and Formalin-Fixed Prostate Tumors Using Comparative Genomic Hybridization to Genomic Microarrays

Abstract

We have used prostate cancer, the most commonly diagnosed noncutaneous neoplasm among men, to investigate the feasibility of performing genomic array analyses of archival tissue. Prostate-specific antigen and a biopsy Gleason grade have not proven to be accurate in predicting clinical outcome, yet they remain the only accepted biomarkers for prostate cancer. It is likely that distinct spectra of genomic alterations underlie these phenotypic differences, and that once identified, may be used to differentiate between indolent and aggressive tumors. Array comparative genomic hybridization allows quantitative detection and mapping of copy number aberrations in tumors and subsequent associations to be made with clinical outcome. Archived tissues are needed to have patients with sufficient clinical follow-up. In this report, 20 formalin-fixed and paraffin-embedded prostate cancer samples originating from 1986 to 1996 were studied. We present a straightforward protocol and demonstrate the utility of archived tissue for array comparative genomic hybridization with a 2400 element BAC array that provides high-resolution detection of both deletions and amplifications. Array comparative genomic hybridization (aCGH) affords high-resolution quantitative information regarding DNA copy number changes within tumor genomes. Recurrent deletions and amplifications reveal loci encoding tumor suppressor genes and oncogenes, respectively, and their identification is now facilitated by completion of the human genome sequence. Moreover, it is increasingly evident that differing clinical behavior of histologically similar tumors is because of distinct and recurrent patterns of genomic alterations and that these may define distinct subsets of disease and thus be prognostic.

Expression analysis of imbalanced genes in prostate carcinoma using tissue microarrays

“…Both are involved in signal transduction, apoptosis, protein synthesis and intracellular transport, RNA splicing, and cell-cycle regulation (Janssens and Goris, 2001;Garcia et al, 2003). The catalytic subunit of PP1a is located on chromosomal band 11q13 that showed frequent gain in array CGH analysis (Paris et al, 2003). Accordingly, we found enhanced cytoplasmic PP1a immunostaining in tumours vs BPH.…”

“…To reveal the most abundant chromosomal imbalances detected in prostate carcinoma, we performed an exhaustive search of six CGH studies, including a total of 145 primary prostate cancers (Sattler et al, 1999;Alers et al, 2001;Verdorfer et al, 2001;Zitzelsberger et al, 2001;Steiner et al, 2002;Wolter et al, 2002;Paris et al, 2003) as well as one array CGH study of 16 primary prostate cancers (Paris et al, 2003). In order to identify candidate genes that may be directly affected by these chromosomal imbalances, we screened a list of the top 250 most up-regulated and down-regulated genes as revealed by a recent meta-analysis of four independent expression microarrays including 61 prostate cancer samples (Rhodes et al, 2002).…”

“…First, an exhaustive search for imbalanced chromosomal regions from seven CGH and array CGH studies was performed (Sattler et al, 1999;Alers et al, 2001;Verdorfer et al, 2001;Zitzelsberger et al, 2001;Steiner et al, 2002;Wolter et al, 2002;Paris et al, 2003). Next, the results were compared to a recent meta-analysis of four independent expression array data sets (Rhodes et al, 2002) in order to define candidate genes located within regions recurrently changed in copy number.…”

Overexpression of LRP12, a gene contained within an 8q22 amplicon identified by high-resolution array CGH analysis of oral squamous cell carcinomas

“…Array CGH technology has been applied to several different tumor types in order to identify copy number gains and losses (Martinez-Climent et al, 2003;Paris et al, 2003;Veltman et al, 2003;Weiss et al, 2003). In this study, a minimal overlapping tiling set of 165 RPCI-11 BAC clones representing 8q21-24 (B52 Mbp) was selected from the FPC database and the map location of sequenced clones was verified using the UCSC Human Genome Browser (Karolchik et al, 2003).…”

High-resolution analysis of chromosome rearrangements on 8p in breast, colon and pancreatic cancer reveals a complex pattern of loss, gain and translocation

“…Davidson et al, 2000;AbdelRahman et al, 2001;Karan et al, 2003;Hurst et al, 2004;Hwang et al, 2004), and more recently array CGH has begun to provide more detail of these losses (e.g. Paris et al, 2003;Douglas et al, 2004;Hurst et al, 2004;Nakao et al, 2004;Garcia et al, 2005). Distal 8p also frequently shows loss of heterozygosity (LOH), which would often reflect loss through unbalanced translocation (for references see Adams et al, 2005).…”