Profiling of transcriptomic changes in androgen-dependent prostate cancer cells in response to anrogen deprivation.

Castration-resistant prostate cancer (CRPC) emerges in response to androgen deprivation therapies and exhibits high cellular plasticity eventually progressing into neuroendocrine prostate cancer (NEPC). In this study, we took advantage of the dynamic prostate cancer cell system recapitulating the CRPC onset to identify lncRNAs induced early in response to androgen deprivation. In this system, first, adenocarcinoma LNCaP cells are grown in the presence of dihydrotestosterone (DHT) mimicking primary epithelial androgen-dependent luminal tumors (NE_0j). Then, they are subjected to androgen deprivation which induces immediate growth arrest, progressive change in cell morphology and properties towards the neuroendocrine-like phenotype (NE-like cells, NE_15j, 1m, 3m) and finally lead to acquisition of androgen independence (NE_6m). Total RNA-sequencing followed by differential expression analysis of scallop-assembled transcripts and multiple filtering isolated gencode annotated protein-coding and long noncoding RNA genes but also 15 novel lncRNAs highly upregulated upon androgen deprivation. Overall design: Cells were cultured and treated in triplicates for each condition to extract RNA. RNA samples were treated with Dnase, quality controlled (RIN above 9) and used for the library preparation). To perform differential expression analysis a condition of growth in the presence of androgen NE_0j) was considered as a reference to define up- and down-regulated genes in cells grown in the absence of androgen.