Discovery and Characterization of Long Non-coding RNAs in Prostate Cancer.

Abstract

The comprehensive delineation of cancer-causing genes is an essential step in understanding the molecular basis of cancer. While much research has interrogated the role of protein-coding genes in cancer, recent discoveries demonstrate that the human genome may additionally contain thousands of non-protein-coding genes, termed non-coding RNAs (ncRNAs). However, the identity and function of these genes is largely unknown.

Here, I describe the systematic discovery and functional characterization of long non-coding RNAs (lncRNAs) in prostate cancer. We used transcriptome sequencing (RNA-Seq) of human prostate cancer samples to identify over 1,800 unannotated, intergenic lncRNAs, of which 121 Prostate Cancer Associated Transcripts (PCATs) demonstrated aberrant expression patterns between benign prostate samples, localized cancers, and metastatic cancers.

To study novel lncRNAs in prostate cancer, we focused on two: PCAT-1 and SChLAP-1 (Second Chromosome Locus Associated with Prostate-1, also referred to as PCAT-114), which are overexpressed in subsets of prostate cancer. We found that upregulation of PCAT-1 mediates increased cellular proliferation in vitro and in vivo through the regulation of genes involved in DNA maintenance, including BRCA2, a tumor suppressor gene essential for DNA break repair by homologous recombination (HR). Mechanistically, PCAT-1 expression repressed BRCA2 in a microRNA-like manner via the BRCA2 3’ untranslated region. BRCA2 repression resulted in defective HR in PCAT-1-expressing prostate cells, leading to increased cell sensitivity to PARP1 inhibitors, which engender synthetic lethality in the context of impaired HR.

By contrast, our investigation of SChLAP-1 revealed a nuclear lncRNA that is involved in prostate cell invasiveness and metastasis in vitro and in vivo. Mechanistically, SChLAP-1 antagonizes the SWI/SNF chromatin remodeling complex, a tumor suppressor complex inactivated in cancer, by directly binding SWI/SNF proteins and impairing their ability to regulate gene expression. Clinically, SChLAP-1 expression defined a subset of prostate cancers associated with aggressive phenotypes and poor outcome.

Taken together, this thesis work represents the first comprehensive assessment of lncRNAs in a major cancer type and describes novel oncogenic lncRNAs in prostate cancer that may further serve as predictive (PCAT-1) or prognostic (SChLAP-1) biomarkers. Broadly, this work suggests that uncharacterized lncRNAs may play critical roles in the pathogenesis of other diseases.