Background

Currently, lowering hormone levels through androgen deprivation therapy (ADT) is the initial treatment for men with metastatic prostate cancer. However, despite initial response rates of 80 to 90 percent, nearly all men eventually develop progressive disease following ADT, referred to as castrate-resistant prostate cancer (CRPC). To date prostate cancer research has primarily focused on the deregulation of protein-coding genes to identify potential diagnostic and therapeutic targets. However, long non-coding RNAs (lncRNAs) represent an emerging class of transcripts that have a significant role in human cancers. Recently, we found 131 novel lncRNAs to be involved in prostate tumorigenesis and CRPC. Due to their tissue-enriched expression many lncRNAs can serve as valuable biomarkers to stratify patients with aggressive prostate carcinomas. We are now faced with the critical challenge of therapeutically targeting each patient population. This represents a critical gap in our ability to translate these findings into the clinic. Although originally regarded as noise, several well-described examples indicate that lncRNAs may be master regulators in cancer biology. However, our understanding of how lncRNAs function in cancer is still in its infancy. Therefore, we hypothesize that a subset of lncRNAs altered in prostate cancer bind directly with a specific protein complex, alter its normal function, and cause aggressive disease. To address this, over the last year we have optimized a high-throughput assay to identify the subset of lncRNAs altered in prostate cancer that associate with the Polycomb Repressive Complex 2 (PRC2), which is known to promote aggressive disease. Overall, a better understanding of how lncRNAs enable primary tumors to invade and metastasize could lead to the development of more specific treatments to improve patient outcomes.

Progress Year 1

Over the last year we have focused on the global detection of Polycomb associated lncRNAs associated with prostate tumor progression. In order to accomplish this we have focused on optimizing RNA immunoprecipitation coupled with RNA-Seq, or RIP-Seq, to capture PRC2-bound lncRNAs. We have optimized different aspects from previously published methods resulting in our optimized method identifying RNAs directly binding to a protein. Next, we performed deep sequencing of the RNA generated from our RIP method followed by integrative analysis using multiple published RIP-Seq analysis tools to maximize our confidence in identifying PRC2 associated lncRNAs Through this approach we discovered >20% of lncRNAs were interacting with the Polycomb Repressive Complex 2 (PRC2). Of these, we were able to validate the association of prostate cancer associated transcript 1 (PCAT-1) which we had previously reported to interact with the PRC2 complex and define a subgroup of patients with aggressive prostate cancer. Based on our hypothesis that a lncRNA modulates chromatin remodeling via PRC2 to promote metastasis, we expect that altering a lncRNA interacting with PRC2 will confer metastatic phenotypes similar to what has been observed when silencing PRC2 components. Therefore, we have begun initial in vitro experiments confirming whether these lncRNA promote cell migration or invasion.

Goals for Year 2

In the upcoming year we intend to focus on understanding how altered lncRNAs control PRC2 regulation and determine the regulatory mechanism by which lncRNAs promote CRPC. This will enable us to decipher the regulatory network of aberrant lncRNAs that may reveal novel targets for cancer diagnosis and therapy. Given the sensitivity of lncRNAs as prognostic markers, and the ability to detect them in urine, we envision monitoring the expression of lncRNAs found in this study to identify patients that may respond to treatments targeting the lncRNA or lncRNA-guided PRC2 target genes promoting aggressive disease.