Integrative sequencing reveals alterations in untreated and castration-resistant prostate cancer. Homo sapiens

We conducted an integrative sequencing of genomic, transcriptomic and DNA methylation changes in 28 untreated (PC) and 13 castration-resistant prostate cancers (CRPC). We wanted to search for previously unannotated transcripts from the RNA-sequencing data. Transcriptome assembly uncovered 128 previously unannotated prostate cancer-associated transcripts. Trans-acting correlation analysis associated the expression of several TPCATs with prostate cancer-associated transcriptional regulators, such as ERG or AR. The strongest positive correlation was observed between ERG and transcript TPCAT-10-36067 that was expressed in a subset of PCs and CRPCs as well as ETV4-positive PC-3 and ERG-positive VCaP cells. We suppressed the expression of TPCAT-10-36067 with three different siRNAs in PC-3 cells, and studied the changes in the genome-wide expression patterns of the cell line using expression arrays. Gene Ontology enrichment analysis indicated that cell cycle, mitosis and Aurora signaling were the most extensively affected processes. Experimental assay showed that the siRNA suppression of TPCAT-10-36067 had a dramatic effect on the growth, invasiveness, and rate of apoptosis of prostate cancer cells. Overall design: Two different siRNAs targeting TPCAT-10-36067 were chosen for the expression array experiments. We transfected the siRNAs to the PC-3 prostate cancer cell line which expresses TPCAT-10-36067. Gene expression arrays were made for both experiments in two replicates with dye swap comparing the RNA from transfected cell line with a non-transfected cell line.