Prostate cancer (PCa) which has relapsed after first line androgen deprivation therapy (ADT), known as castration resistant prostate cancer (CRPC), is incurable and frequently lethal. Resistance is also observed with second generation antiandrogens, such as enzalutamide and apalutamide. PCa progression and the acquisition of therapy resistance is associated with changes in binding of the androgen receptor (AR, the key therapy target in PCa) to different collections of cis-regulatory enhancer elements. Recently, enhancers have been found to be transcribed, producing non-coding enhancer RNAs (eRNAs), which are increasingly being recognized for their role in contributing to enhancer function. While eRNAs have been shown to be transcribed from several critical AR-bound active enhancers, their role in AR-regulated gene expression and progression to CRPC remains largely unknown.
In this project, we aim to identify potentially oncogenic roles for such eRNAs in selective disruption of AR enhancer interactions thereby altering target gene expression in CRPC. To this end, we performed Global Run On (GRO) sequencing (GRO-Seq) to capture nascent RNA transcriptomes from isogenic pairs of therapy-sensitive and -resistant PCa cell lines (C42Parental, C42EnzR, V16D, MR49FEnzR), with and without DHT stimulation. GRO-seq datasets identified differentially expressed de-novo novel (unannotated) non-coding RNA transcripts in resistant versus sensitive cell lines. Integration of these data with publicly available genomic enhancer annotations, ChIP-seq, and ChIA-PET datasets was used to identify transcripts that are linked to AR regulated enhancers and thus potentially represent resistance associated eRNAs. Several of the differentially expressed eRNAs encoding enhancers are associated with genes linked to PCa progression, including transcription factors such as Grainy Head Like Transcription Factor 2 (GRHL2) as well as transcriptional regulators such as the corepressor REST corepressor 1 (RCOR1). Significantly, differentially expressed non-coding RNA transcripts also included previously characterized long non-coding (lncRNA) associated with PCa, (e.g. SCHLAP1, PCAT1) and novel lncRNA, several of which are transcribed from regions encoding super-enhancers. Ongoing studies are testing the functional implications of these novel enhancer associated RNAs on AR signalling and downstream effects in CRPC.
In conclusion, we have identified several eRNAs and lncRNAs that are dysregulated in CRPC and are exploring their role in enhancer functioning and potential utility as therapeutic targets in this disease.