Mis-splicing-derived neoantigens and cognate TCRs in splicing factor mutant leukemias
Won Jun Kim, Edie I. Crosse, Emma De Neef, Iñaki Etxeberría, Erich Sabio, Eric Wang, Jan Philipp Bewersdorf, Kuan‐Ting Lin, Sydney X. Lu, Andrea E. Belleville, Nina Fox, Cynthia Castro, Pu Zhang, Takeshi Fujino, Jennifer Lewis, Jahan Rahman, Beatrice Zhang, Jacob H. Winick, Alexander M. Lewis, Robert F. Stanley, Susan DeWolf, Brigita Meškauskaitė Urben, Meril Takizawa, Tobias Krause, Henrik Molina, Ronan Chaligné, Priya Koppikar, Jeffrey J. Molldrem, Mathieu Gigoux, Taha Merghoub, Anthony F. Daniyan, Smita S. Chandran, Benjamin D. Greenbaum, Christopher A. Klebanoff, Robert K. Bradley, Omar Abdel‐Wahab
Abstract
<h2>Summary</h2> Mutations in RNA splicing factors are prevalent across cancers and generate recurrently mis-spliced mRNA isoforms. Here, we identified a series of bona fide neoantigens translated from highly stereotyped splicing alterations promoted by neomorphic, leukemia-associated somatic splicing machinery mutations. We utilized feature-barcoded peptide-major histocompatibility complex (MHC) dextramers to isolate neoantigen-reactive T cell receptors (TCRs) from healthy donors, patients with active myeloid malignancy, and following curative allogeneic stem cell transplant. Neoantigen-reactive CD8<sup>+</sup> T cells were present in the blood of patients with active cancer and had a distinct phenotype from virus-reactive T cells with evidence of impaired cytotoxic function. T cells engineered with TCRs recognizing SRSF2 mutant-induced neoantigens arising from mis-splicing events in <i>CLK3</i> and <i>RHOT2</i> resulted in specific recognition and cytotoxicity of SRSF2-mutant leukemia. These data identify recurrent RNA mis-splicing events as sources of actionable public neoantigens in myeloid leukemias and provide proof of concept for genetically redirecting T cells to recognize these targets.