Identification of androgen-regulated genes in the prostate cancer cell line LNCaP by serial analysis of gene expression and proteomic analysis

Abstract

A common therapy for nonorgan-confined prostate cancer involves androgen deprivation. To develop a better understanding of the effect of androgen on prostatic cells, we have analyzed gene expression changes induced by dihydrotestosterone (DHT) in the androgen responsive prostate cancer line LNCaP, at both RNA and protein levels. Changes at the RNA level induced by DHT were determined by means of serial analysis of gene expression (SAGE), and protein profiling was done by means of quantitative two-dimensional polyacrylamide gel electrophoresis. Among 123,371 transcripts analyzed, a total of 28,844 distinct SAGE tags were identified representing 16,570 genes. Some 351 genes were significantly affected by DHT treatment at the RNA level (p < 0.05), of which 147 were induced and 204 repressed by androgen. In two independent experiments, the integrated intensity of 32 protein spots increased and 12 decreased at least two-fold in response to androgen, out of a total of 1031 protein spots analyzed. The change in intensity for most of the affected proteins identified could not be predicted based on the level of their corresponding RNA. Our study provides a global assessment of genes regulated by DHT and suggests a need for profiling at both RNA and protein levels for a comprehensive evaluation of patterns of gene expression.

Profiling, comparison and validation of gene expression in gastric carcinoma and normal stomach

“…This correlation is at least as good as previous SAGE papers in which between 7 and 50% of differentially expressed tags were not corroborated (Zhang et al, 1997;Hibi et al, 1998;de Waard et al, 1999;Waghray et al, 2001). Moreover, although mRNA abundance can be a poor indicator of protein levels (Pradet-Balade et al, 2001), we found that, for a given gene, the relative level of mRNA in different samples correlated well with the relative protein level as gauged by immunohistochemical staining (Figure 2).…”

“…These numbers are slightly smaller than those in other recent SAGE publications, with upwards of 20 000 tags (Zhang et al, 1997;Hibi et al, 1998;Nacht et al, 1999;Velculescu et al, 1999;Hough et al, 2000;Waghray et al, 2001). However, the global distribution of genes in our gastric libraries is Figure 1 Northern blotting for selected genes identified by SAGE.…”

“…As SAGE is labour-intensive and hence limited to small numbers of specimens, resulting candidate genes are usually validated in a larger sample set. SAGE has already been applied to the other common adenocarcinomas, of colon, pancreas, breast, ovary and prostate, and to squamous lung carcinoma and other cancers (Velculescu et al, 1995;Zhang et al, 1997;Hibi et al, 1998;Lal et al, 1999;Nacht et al, 1999;Velculescu et al, 1999;Hough et al, 2000;Waghray et al, 2001) but, to our knowledge, no SAGE data for gastric carcinoma have yet been published in the literature.…”

Nuclear LYRIC/AEG-1 interacts with PLZF and relieves PLZF-mediated repression

“…Prostate cancer is dependent on the action of androgens, and PLZF has been shown to be an androgen-responsive gene (Jiang and Wang, 2004). LYRIC/AEG-1 is upregulated in response to androgens (Waghray et al, 2001).…”

Proteome analysis of prostate cancer

“…We consider the discrepancies were caused by the following reason: several reports told that correlation between mRNA and protein levels was insufficient to predict protein expression levels from quantitative mRNA data. 40,41 The proteomic approach is considered to have a capability of finding biomarkers other than those found by genomic approach. We stratified the cancer-related proteins into seven functional categories based on the prostate expression database (PEDB).…”