Epigenetic therapies in ovarian cancer alter repetitive element expression in a TP53-dependent manner: Isogenic TP53 Cell Line RNA-seq

Abstract: Epithelial ovarian carcinomas (OC) are particularly deadly due to intratumoral heterogeneity, resistance to standard-of-care therapies, and poor response to alternative treatments such as immunotherapy. Targeting the OC epigenome with DNA methyltransferase inhibitors (DNMTi) or histone deacetylase inhibitors (HDACi) increases immune signaling and recruits CD8+ T cells and NK cells to fight OC in murine models. This increased immune activity is caused by increased transcription of repetitive elements (RE) that form double-stranded RNA (dsRNA) and trigger an interferon response. To understand which REs are affected by epigenetic therapies in OC, we assessed the effect of DNMTi and HDACi on OC cell lines and patient samples. Subfamily-level (TEtranscripts) and individual locus-level (Telescope) analysis of REs showed that DNMTi treatment upregulated more REs than HDACi treatment. Upregulated REs were predominantly LTR and SINE subfamilies, and SINEs exhibited the greatest loss of DNA methylation upon DNMTi treatment. Cell lines with TP53 mutations exhibited significantly fewer upregulated REs with epigenetic therapy than wild type TP53 cell lines. This observation was validated using isogenic cell lines; the TP53 mutant cell line had significantly higher baseline expression of REs but upregulated fewer upon epigenetic treatment. In addition, p53 activation increased expression of REs in wild type but not mutant cell lines. These data give a comprehensive, genome-wide picture of RE chromatin and transcription-related changes in OC after epigenetic treatment and implicate p53 in RE transcriptional regulation. The data in this data series represent the analysis of triplicate RNAseq libraries generated from two isogenic lines derived from the Hey ovarian carcinoma cell line. HC2 is TP53 wild type as is the parent Hey line. HH23 was edited to express TP53 with the R175H mutation. Each line was treated with 5-azacytidine, Nutlin-3A, or a combination of both. RNA-seq libraries were sequenced, trimmed, aligned, and analyzed with TEtranscripts and Telescope software. Note that because the core facility did not reach our target number of reads after the first run, a second run was performed on the same library sample. These two runs were treated as one sample in the analysis. Three biological replicates of RNA-seq were performed in isogenic Hey-derived cell lines designated HC2 (TP53 WT) and HH23 (TP53 Mutant R175H) given mock, Nutlin-3A (N3A), 5-azacytidine (AZA), or combined N3A/AZA.