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

Won Jun Kim¹, Edie I Crosse², Emma De Neef³, Inaki Etxeberria⁴, Erich Y Sabio¹, Eric Wang⁵, Jan Philipp Bewersdorf¹, Kuan-Ting Lin⁶, Sydney X Lu⁷, Andrea Belleville², Nina Fox¹, Cynthia Castro¹, Pu Zhang¹, Takeshi Fujino¹, Jennifer Lewis¹, Jahan Rahman¹, Beatrice Zhang¹, Jacob H Winick¹, Alexander M Lewis¹, Robert F Stanley¹, Susan DeWolf¹, Brigita Meškauskaitė Urben⁸, Meril Takizawa⁸, Tobias Krause⁸, Henrik Molina⁹, Ronan Chaligne⁸, Priya Koppikar¹⁰, Jeffrey Molldrem¹⁰, Mathieu Gigoux¹¹, Taha Merghoub¹¹, Anthony Daniyan¹, Smita S Chandran⁴, Benjamin D Greenbaum¹², Christopher A Klebanoff¹³, Robert K Bradley¹⁴, Omar Abdel-Wahab¹⁵

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: klebanoc@mskcc.org.
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: rbradley@fredhutch.org.
¹⁵ Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center (MSK), New York, NY, USA. Electronic address: abdelwao@mskcc.org.

PMID: 40273911
PMCID: PMC12204805 (available on 2026-06-26)
DOI: 10.1016/j.cell.2025.03.047

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

Won Jun Kim et al. Cell. 2025.

. 2025 Jun 26;188(13):3422-3440.e24.

doi: 10.1016/j.cell.2025.03.047. Epub 2025 Apr 23.

Authors

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: klebanoc@mskcc.org.
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: rbradley@fredhutch.org.
¹⁵ Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center (MSK), New York, NY, USA. Electronic address: abdelwao@mskcc.org.

PMID: 40273911
PMCID: PMC12204805 (available on 2026-06-26)
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.

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Conflict of interest statement

Declaration of interests R.K.B. and O.A.-W. are founders and scientific advisors of Codify Therapeutics; they hold equity and receive research funding from this company. K.T.-L. is an employee of Codify Therapeutics. W.J.K., E.I.C., R.K.B., and O.A.-W. are inventors on a patent related to this study. C.A.K. and I.E. are inventors on TCR patents unrelated to this study and are recipients of licensing revenue shared according to MSK institutional policies. C.A.K. has consulted for or is on scientific advisory boards for Achilles Therapeutics, Affini-T Therapeutics, Aleta BioTherapeutics, Bellicum Pharmaceuticals, Bristol Myers Squibb, Catamaran Bio, Cell Design Labs, Decheng Capital, G1 Therapeutics, Klus Pharma, Obsidian Therapeutics, PACT Pharma, Roche/Genentech, and Royalty Pharma. C.A.K. is a scientific co-founder and equity holder in Affini-T Therapeutics. R.K.B. is a founder and scientific advisor of Synthesize Bio and holds equity in this company. O.A.-W. has served as a consultant for Amphista Therapeutics and MagnetBio and is on scientific advisory boards of Envisagenics Inc. and Harmonic Discovery Inc.; O.A.-W. received research funding from Nurix Therapeutics, Minovia Therapeutics, and LOXO Oncology unrelated to this study.

References

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

Affiliations

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

Authors

Affiliations

Abstract

Conflict of interest statement

References

MeSH terms

Substances

Grants and funding

LinkOut - more resources

Full Text Sources

Medical

Molecular Biology Databases

Research Materials