EPCO-08. EPIGENETIC THERAPY POTENTIATES TRANSPOSABLE ELEMENT TRANSCRIPTION TO CREATE TUMOR-ENRICHED ANTIGENS IN GLIOBLASTOMA

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Abstract Epigenetic treatment has been studied as a means to augment anti-tumor immune cell activity by increasing the expression of antiviral response genes. Previous studies, including our own, have revealed an additional consequence of epigenetic treatment: reactivation of transposable elements (TEs). Normally, most TEs are epigenetically repressed in healthy somatic tissues. However, epigenetic treatment can reactivate TEs as previously unannotated promoters, particularly in rapidly proliferating cells. These reactivated TEs could generate unique proteins that may act as novel antigens for immunotherapy. To study epigenetic treatment as a novel method to augment immunotherapy in cancers with a low number of somatic mutation-derived antigens, we chose glioblastoma as a model. Specifically, we investigated if drug-induced TE expression increases the antigen repertoire upon combinatorial treatment with DNMT inhibitor (Decitabine) and HDAC inhibitor (Panobinostat), agents currently being tested for clinical use in cancers, including CNS tumors. Using patient-derived primary glioblastoma stem cell (GSC) lines and control cell lines (astrocytes and fibroblasts), we first profiled treatment-induced changes in the epigenetic landscape using WGBS-seq and ATAC-seq. Then, using nanoCAGE-seq, both short-read and long-read RNA-seq, we identified treatment-induced, TE-derived transcripts that are predominantly expressed in glioblastoma cells along with upregulation of antiviral gene programs. Finally, using LC-MS/MS, we validated that tumor-enriched reactivated TEs, which mostly originate from the LTR class, encode HLA-I presented antigens in primary GSCs. Notably, epigenetic therapy also reactivated many TEs in proliferating control cell lines, and thus we provide evidence that targeted approaches like CRISPRa might reduce the side effects of activating nonspecific TE loci. Overall, our findings suggest that the therapeutic utilization of epigenetic treatment-induced, TE-derived antigens holds great promise but also provides a cautionary tale regarding the careful selection of tumor-enriched antigen targets.

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