Abstract IA021: Neogenes induced by oncogenic chimeric transcription factors as potential targets for therapy

Abstract We recently showed that oncogenic chiemeric transcription factors (OCTF) of various pediatric cancers induce the expression of highly tumor-specific long intergenic non coding RNAs which are not expressed in normal tissues and which we called neogenes. Since recent reports indicate that such LincRNA may not be as non-coding as initially thought we sought for potential peptides encoded by these neogenes. Using the EWSR1::FLI1 chimera of Ewing sarcoma as a paradigm of such chimeras and through Riboseq profiling and whole cell proteomics we indeed show that some of these neogenes encode peptides. Immunopeptidomic experiments were performed on a series of Ewing sarcoma cell lines and PDX and further showed that peptides encoded by Ewing-specific neogenes are associated with MHC-Class I molecules at the surface of Ewing cells. Ewing peptide-specific CD8 T-cells were isolated from healthy donors. We show that these cytotoxic T-cells can be activated by Ewing cells to secrete cytokins, They can also kill Ewing cells. This killing is specific for the MHC-Class I types, specific for Ewing sarcoma cells as compared to other tumor types and is strictly deendent upon the expression of EWSR1::FLI1 that regulates the neogenes and of the expression of the neogene encoding the peptide. These data support the idea that OCTF-specific neogenes may constitute an interesting resource for various immunotherapy approaches including vaccination, BiTE or TCR-T-cell therapy. Citation Format: Floriane Petit, Ana Lalanne, Céline Collin, Joshua Waterfall, Olivier Lantz, Olivier Delattre. Neogenes induced by oncogenic chimeric transcription factors as potential targets for therapy [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pediatric Cancer Research; 2024 Sep 5-8; Toronto, Ontario, Canada. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl):Abstract nr IA021.