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Specific killing of Ewing sarcoma by TCR-T cells targeting public neogene-encoded antigens

Lalanne, A. I.; Collin, C.; Petit, F.; Lacaud, M.; Arribas, Y. A.; Darbois Delahousse, A.; Leruste, A.; Koshkina, M. K.; Raymond, K. A.; Klein, P.; Vibert, J.; Zaidi, S.; Grossetete, S.; Pilet, J.; Laud-Duval, K.; Aflaki, S.; Jamet, C.; Faigle, W.; Maggi, J.; Carrascal, M.; Menegatti, S.; Fuentealba, J.; Alcantara, M.; Waterfall, J. J.; Lantz, O.; Delattre, O.

2026-06-25 immunology
10.64898/2026.06.20.733160 bioRxiv
Show abstract

EWSR1::FLI1, the oncogenic chimeric transcription factor driving Ewing sarcoma (EwS)induces expression of exquisitely EwS-specific neogenes (Ew_NGs) through neomorphic binding and transcription activation at GGAA microsatellites in genomic regions that are silent in normal tissues. We show that peptides encoded by Ew_NGs are presented on HLA-I complexes on EwS cells. The cytokine secretion of CD8+ T cells specific for Ew_NG-encoded HLA-I-bound peptides is activated by all HLA-I-matched EwS cells but not by non-EwS cells. These T cells kill EwS cells in an HLA-I restricted manner. This cytotoxicity is dependent on the expression of EWSR1::FLI1 and of the corresponding Ew_NG. It can be reproduced by transduction of the TCR into donor T cells (TCR-T) which kill EwS cells in vivo. Moreover, we show that neither off target nor allogeneic activation are observed with TCR-T thus paving the way for cell therapy in relapsed/resistant EwS patients for which therapeutic options are very limited. Statement of significanceThe chimeric transcription factor EWSR1::FLI1 generates tumor-specific neogenes encoding neoantigen presented by the HLA-I molecules of Ewing cells. Neoantigen-specific CD8+ T-cell clones and engineered TCR-T cells can selectively recognize and kill EwS tumor cells in vitro and in vivo.

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