Abstract A66: Repeatome profiling in high-grade serous ovarian cancer reveals abundant repeat noncoding RNA expression

Abstract

Abstract The lack of consensus on clinically relevant molecular subtypes by gene expression in high-grade serous ovarian carcinoma (HGSOC) creates a barrier to subtype-based clinical investigation for the development of targeted therapies. We previously discovered aberrant expression of noncoding repeat RNAs across epithelial cancers including ovarian (Ting, Science 2011), which can invoke innate immune responses in tumors (Chiappinelli, Cell 2015). Epigenetic alterations and loss of tumor suppressor function, especially p53, can derepress endogenous repetitive elements in cancer. Further, BRCA1 deficiency induces satellite repeat RNAs, which promote genomic instability via interacting with the BRCA1 complex (Zhu, Mol Cell 2018), highlighting their potential significance in HGSOC. Here we aim to comprehensively define the as yet uncharacterized “repeatome” in HGSOC to refine molecular subtypes and identify novel biomarkers and therapeutic targets. We developed a Total RNASeq platform and novel computational pipelines to quantify the repeatome (Solovyov, Cell Rep 2018). Results from RNASeq are validated in cell lines and human tumors with RNA in situ hybridization (RNA-ISH) using probes to specific repeat RNAs, and combined IHC is performed to quantify intratumoral immune subpopulations. Whole-exome sequencing is performed to link the repeatome with somatic mutations. To obtain a global landscape of the ovarian cancer repeatome, Total RNASeq was performed on 32 patient-derived ovarian cancer cell lines, 11 HGSOC PDX, and 11 additional ovarian cancer cell lines. We detect abundant repeat RNA expression from all major subclasses including retrotransposons, endogenous retroviruses, and satellites. HGSOC are enriched for satellite repeats compared with other cancers, most notably in BRCA-mutant HGSOC. Human satellite II (HSATII), a cancer-specific satellite, is strongly upregulated in HGSOC compared with fallopian tube epithelial cells and displays highly variable expression across different models. RNA-ISH for HSATII on human ovarian cancer tissue microarrays confirms the abundance and variation of HSATII. Additionally, the repeatome is altered in HGSOC following exposure to in vitro chemotherapy and epigenetic agents with distinct patterns of expression linked to specific agents. Additional RNAseq analysis using hierarchical clustering and principal component analysis are being used to understand the relationship of repeatome expression patterns with coding gene expression, somatic mutations, in vitro drug sensitivity, and clinical outcomes. Digital image analysis of repeat RNA-ISH expression and immune cell infiltrate quantitation will determine the link between tumor cell repeat RNA levels and the responding immune tumor microenvironment. Overall, these studies will define the undiscovered repeatome in HGSOC and provide a foundation for discovery of novel biomarkers and potential therapeutic strategies, particularly those to increase efficacy of immunotherapies. Citation Format: Rebecca L. Porter, Anna Szabolcs, Niyati Desai, Vishal Thapar, Raghav Mohan, Alexander Solovyov, David Pepin, Joyce Liu, Benjamin Greenbaum, David T. Ting. Repeatome profiling in high-grade serous ovarian cancer reveals abundant repeat noncoding RNA expression [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research; 2019 Sep 13-16, 2019; Atlanta, GA. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(13_Suppl):Abstract nr A66.