Satellite repeat RNA expression in epithelial ovarian cancer is linked to a tumor immunosuppressive phenotype

Repeatome profiling across ovarian, pancreatic, and colorectal cell lines identifies distinct clustering that is independent of tissue of origin highlighting differences in repeat co-expression patterns. Deeper analysis of ovarian cancer cell lines demonstrated that HSATII satellite repeat expression was highly associated with epithelial mesenchymal transition (EMT) and anti-correlated with interferon (IFN) response genes indicative of a more aggressive phenotype. Different cell lines and extracellular vesicles were subjected to total RNA-seq using the Clontech-Takara Smarter Stranded Total RNA-Seq kit v2 (Cat No#634413). RNA-seq across a panel of cell lines and extracellular vesicles was done as a single sample. When cell lines were treated, the cell lines were collected at different time points after treatment (HSATII LNA, HDAC inhibitor, DNMT inhibitor).