Mis-splicing-derived neoantigens and cognate TCRs in splicing factor mutant leukemias

  • Cell. 2025 Jun 26;188(13):3422-3440.e24. doi: 10.1016/j.cell.2025.03.047.
Won Jun Kim  1 ,  Edie I Crosse  2 ,  Emma De Neef  3 ,  Inaki Etxeberria  4 ,  Erich Y Sabio  1 ,  Eric Wang  5 ,  Jan Philipp Bewersdorf  1 ,  Kuan-Ting Lin  6 ,  Sydney X Lu  7 ,  Andrea Belleville  2 ,  Nina Fox  1 ,  Cynthia Castro  1 ,  Pu Zhang  1 ,  Takeshi Fujino  1 ,  Jennifer Lewis  1 ,  Jahan Rahman  1 ,  Beatrice Zhang  1 ,  Jacob H Winick  1 ,  Alexander M Lewis  1 ,  Robert F Stanley  1 ,  Susan DeWolf  1 ,  Brigita Meškauskaitė Urben  8 ,  Meril Takizawa  8 ,  Tobias Krause  8 ,  Henrik Molina  9 ,  Ronan Chaligne  8 ,  Priya Koppikar  10 ,  Jeffrey Molldrem  10 ,  Mathieu Gigoux  11 ,  Taha Merghoub  11 ,  Anthony Daniyan  1 ,  Smita S Chandran  4 ,  Benjamin D Greenbaum  12 ,  Christopher A Klebanoff  13 ,  Robert K Bradley  14 ,  Omar Abdel-Wahab  15
Affiliations
  • 1. Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center (MSK), New York, NY, USA.
  • 2. Public Health Sciences and Basic Sciences Divisions, Fred Hutchinson Cancer Center, Seattle, WA, USA.
  • 3. Public Health Sciences and Basic Sciences Divisions, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA.
  • 4. Human Oncology and Pathogenesis Program, MSK, New York, NY, USA.
  • 5. The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
  • 6. Codify Therapeutics, Cambridge, MA, USA.
  • 7. Department of Medicine, Division of Hematology, Stanford University, Palo Alto, CA, USA.
  • 8. Single-cell Analytics Innovation Laboratory, MSK, New York, NY, USA.
  • 9. Proteomics Resource Center, Rockefeller University, New York, NY, USA.
  • 10. Department of Hematopoietic Biology and Malignancy, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
  • 11. Swim Across America and Ludwig Collaborative Laboratory, Department of Pharmacology, Sandra and Edward Meyer Cancer Center, Weill Cornell Medical Center, New York, NY, USA.
  • 12. Computational Oncology, Department of Epidemiology and Biostatistics, MSK, New York, NY, USA.
  • 13. Human Oncology and Pathogenesis Program, MSK, New York, NY, USA; Parker Institute for Cancer Immunotherapy, New York, NY, USA. Electronic address: [email protected].
  • 14. Public Health Sciences and Basic Sciences Divisions, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA. Electronic address: [email protected].
  • 15. Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center (MSK), New York, NY, USA. Electronic address: [email protected].
PMID: 40273911 DOI: 10.1016/j.cell.2025.03.047
Abstract

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+ 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 CLK3 and RHOT2 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.

Keywords
RNA splicing; SF3B1; SRSF2; T cell receptor; U2AF1; ZRSR2; acute myeloid leukemia; immunotherapy; myelodysplastic syndromes; neoantigen.
Products