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

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.PHDMolecular & Cellular PathologyUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/107221/1/prensner_1.pd

The long non-coding RNA PCAT-1 promotes prostate cancer cell proliferation through cMyc.

Long non-coding RNAs (lncRNAs) represent an emerging layer of cancer biology, contributing to tumor proliferation, invasion, and metastasis. Here, we describe a role for the oncogenic lncRNA PCAT-1 in prostate cancer proliferation through cMyc. We find that PCAT-1-mediated proliferation is dependent on cMyc protein stabilization, and using expression profiling, we observed that cMyc is required for a subset of PCAT-1-induced expression changes. The PCAT-1-cMyc relationship is mediated through the post-transcriptional activity of the MYC 3\u27 untranslated region, and we characterize a role for PCAT-1 in the disruption of MYC-targeting microRNAs. To further elucidate a role for post-transcriptional regulation, we demonstrate that targeting PCAT-1 with miR-3667-3p, which does not target MYC, is able to reverse the stabilization of cMyc by PCAT-1. This work establishes a basis for the oncogenic role of PCAT-1 in cancer cell proliferation and is the first study to implicate lncRNAs in the regulation of cMyc in prostate cancer

The lncRNA landscape of breast cancer reveals a role for DSCAM-AS1 in breast cancer progression.

Molecular classification of cancers into subtypes has resulted in an advance in our understanding of tumour biology and treatment response across multiple tumour types. However, to date, cancer profiling has largely focused on protein-coding genes, which comprise <1% of the genome. Here we leverage a compendium of 58,648 long noncoding RNAs (lncRNAs) to subtype 947 breast cancer samples. We show that lncRNA-based profiling categorizes breast tumours by their known molecular subtypes in breast cancer. We identify a cohort of breast cancer-associated and oestrogen-regulated lncRNAs, and investigate the role of the top prioritized oestrogen receptor (ER)-regulated lncRNA, DSCAM-AS1. We demonstrate that DSCAM-AS1 mediates tumour progression and tamoxifen resistance and identify hnRNPL as an interacting protein involved in the mechanism of DSCAM-AS1 action. By highlighting the role of DSCAM-AS1 in breast cancer biology and treatment resistance, this study provides insight into the potential clinical implications of lncRNAs in breast cancer

The landscape of somatic copy-number alteration across human cancers

available in PMC 2010 August 18.A powerful way to discover key genes with causal roles in oncogenesis is to identify genomic regions that undergo frequent alteration in human cancers. Here we present high-resolution analyses of somatic copy-number alterations (SCNAs) from 3,131 cancer specimens, belonging largely to 26 histological types. We identify 158 regions of focal SCNA that are altered at significant frequency across several cancer types, of which 122 cannot be explained by the presence of a known cancer target gene located within these regions. Several gene families are enriched among these regions of focal SCNA, including the BCL2 family of apoptosis regulators and the NF-κΒ pathway. We show that cancer cells containing amplifications surrounding the MCL1 and BCL2L1 anti-apoptotic genes depend on the expression of these genes for survival. Finally, we demonstrate that a large majority of SCNAs identified in individual cancer types are present in several cancer types.National Institutes of Health (U.S.) (Dana-Farber/Harvard Cancer Center and Pacific Northwest Prostate Cancer SPOREs, P50CA90578)National Institutes of Health (U.S.) (Dana-Farber/Harvard Cancer Center and Pacific Northwest Prostate Cancer SPOREs, R01CA109038))National Institutes of Health (U.S.) (Dana-Farber/Harvard Cancer Center and Pacific Northwest Prostate Cancer SPOREs, R01CA109467)National Institutes of Health (U.S.) (Dana-Farber/Harvard Cancer Center and Pacific Northwest Prostate Cancer SPOREs, P01CA085859)National Institutes of Health (U.S.) (Dana-Farber/Harvard Cancer Center and Pacific Northwest Prostate Cancer SPOREs, P01CA 098101)National Institutes of Health (U.S.) (Dana-Farber/Harvard Cancer Center and Pacific Northwest Prostate Cancer SPOREs, K08CA122833

Tumour genomic and microenvironmental heterogeneity as integrated predictors for prostate cancer recurrence: a retrospective study

Clinical prognostic groupings for localised prostate cancers are imprecise, with 30–50% of patients recurring after image-guided radiotherapy or radical prostatectomy. We aimed to test combined genomic and microenvironmental indices in prostate cancer to improve risk stratification and complement clinical prognostic factors