Transcriptional silencing associated with aberrant promoter hypermethylation is a common mechanism of inactivation of tumor suppressor genes in cancer cells. To globally profile the genes silenced by hypermethylation in prostate cancer, we screened a whole genome expression microarray for genes reactivated in the LNCaP, DU-145, PC-3 and MDA2b prostate tumor cell lines after treatment with the demethylating drug 5-aza-2 deoxycytidine and histone deacetylation inhibiting drug trichostatin A. A total of 2997 genes showed at least 2-fold upregulation of expression after drug treatment in at least one prostate tumor cell line. For validation we examined the first 45 genes, ranked by upregulation of expression, that had a typical CpG island and were known to be expressed in the normal cell counterpart. Two important findings were firstly that several genes known to be frequently hypermethylated in prostate cancer were apparent. Secondly, validation studies revealed eight novel genes hypermethylated in the prostate tumor cell lines, four of which were unmethylated in normal prostate cells and hypermethylated in primary prostate tumors (SLC15A3 66%, KRT7 54%, TACSTD2 17%, GADD45b 3%). Thus, we established the utility of our screen for genes hypermethylated in prostate cancer cells. One of the novel genes was TACSTD2/TROP2 a marker of human prostate basal cells with stem cell characteristics. TACSTD2 was unmethylated in prostatic intraepithelial neoplasia and may have utility in emerging methylation-based detection of prostate cancer tests. Further study of the hypermethylome will provide insight into the biology of the disease and facilitate translational studies in prostate cancer.
Keywords: Prostate cancer, promoter hypermethylation, tumor suppressor genes, expression microarray