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Background  The prostate cancer antigen 3 ( PCA3/DD3)  gene is a highly specific biomarker upregulated in prostate cancer (PCa). In order to understand the importance of  PCA3  in PCa we investigated the organization and evolution of the  PCA3  gene locus.    Methods/Principal Findings  We have employed cDNA synthesis, RTPCR and DNA sequencing to identify 4 new transcription start sites, 4 polyadenylation sites and 2 new differentially spliced exons in an extended form of  PCA3 . Primers designed from these novel  PCA3  exons greatly improve RT-PCR based discrimination between PCa, PCa metastases and BPH specimens. Comparative genomic analyses demonstrated that  PCA3  has only recently evolved in an anti-sense orientation within a second gene,  BMCC1/PRUNE2 . BMCC1 has been shown previously to interact with RhoA and RhoC, determinants of cellular transformation and metastasis, respectively. Using RT-PCR we demonstrated that the longer  BMCC1-1  isoform - like  PCA3  – is upregulated in PCa tissues and metastases and in PCa cell lines. Furthermore  PCA3  and  BMCC1-1  levels are responsive to dihydrotestosterone treatment.    Conclusions/Significance  Upregulation of two new PCA3 isoforms in PCa tissues improves discrimination between PCa and BPH. The functional relevance of this specificity is now of particular interest given  PCA3's  overlapping association with a second gene  BMCC1 , a regulator of Rho signalling. Upregulation of  PCA3  and  BMCC1  in PCa has potential for improved diagnosis.

New Genomic Structure for Prostate Cancer Specific Gene PCA3 within BMCC1: Implications for Prostate Cancer Detection and Progression