33: Targeting mis-splicing-derived neoantigens in splicing factor mutant leukemias

Kim WJ et al., Cell - This episode examines a study that identifies recurrent neoantigens produced by SRSF2 and ZRSR2 splicing factor mutations in myeloid leukemias, isolates cognate TCRs, and demonstrates antigen-specific TCR-T cell activity in vitro and in vivo. Key terms: neoantigens, SRSF2, ZRSR2, TCR-T therapy, myeloid leukemia.

Study Highlights:
The authors used large-scale RNA-seq to identify recurrent mis-spliced isoforms from SRSF2- and ZRSR2-mutant myeloid malignancies and predicted HLA-I-binding peptides. They validated peptide presentation by HLA-IP LC-MS/MS and demonstrated immunogenicity with peptide priming and dextramer isolation of reactive CD8+ T cells. Panels of neoantigen-specific TCRs were cloned from donors and patients and TCR-engineered T cells specifically recognized and killed SRSF2-mutant leukemia cells in vitro and reduced tumor burden in NSG xenografts. Single-cell profiling of patient blood showed circulating neoantigen-reactive CD8+ T cells that are clonally expanded but exhibit impaired NF-kB/TNF signaling.

Conclusion:
Recurrent mis-splicing events from splicing factor mutations generate shared, actionable neoantigens in myeloid leukemias and can be targeted by isolated TCRs, supporting TCR-based immunotherapy strategies while noting patient T cell dysfunction and HLA allele scope as limitations.

Music:
Enjoy the music based on this article at the end of the episode.

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

First author:
Kim WJ

Journal:
Cell

DOI:
10.1016/j.cell.2025.03.047

Reference:
Kim WJ, Crosse EI, De Neef E, et al. Mis-splicing-derived neoantigens and cognate TCRs in splicing factor mutant leukemias. Cell. 2025;188:1–19. doi:10.1016/j.cell.2025.03.047

License:
This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/

Support:
Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00

Official website https://basebybase.com

On PaperCast Base by Base you'll discover the latest in genomics, functional genomics, structural genomics, and proteomics.

Episode link: https://basebybase.com/episodes/mis-splicing-neoantigens-tcrs-ep33

QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2025-06-05.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music
- transcript coverage: Substantive audit of the transcript's representation of the article's central scientific narrative: generation of recurrent mis-splicing-derived neoantigens by SRSF2/ZRSR2 mutations, prediction and validation of HLA-I neoepitopes, isolation and characterization of neoantigen-reactive TCRs (CLK3, RHOT2, c16orf70), funct
- transcript topics: AML immunotherapy challenges and targeting; Splicing-factor mutations (SRSF2, ZRSR2) and stereotyped mis-splicing; Neoantigen discovery pipeline (RNA-seq, NetMHCpan, MHCFlurry, HLA-A*02:01); HLA-I binding validation (T2 shift assay) and immunogenicity testing; Dextramer-based isolation of neoantigen-reactive CD8+ T cells; CLK3 neoantigen and exon 4 skipping; NMD involvement

QC Summary:
- factual score: 10/10
- metadata score: 10/10
- supported core claims: 5
- claims flagged for review: 0
- metadata checks passed: 4
- metadata issues found: 0

Metadata Audited:
- article_doi
- article_title
- article_journal
- license

Factual Items Audited:
- Splicing-factor mutations SRSF2 and ZRSR2 generate recurrent mis-splicing-derived neoantigens expressed on HLA-I
- neoantigen discovery used large RNA-seq cohorts and in silico predictions (NetMHCpan/MHCFlurry) for HLA-A*02:01 binding
- CLK3-derived neoantigen results from exon 4 skipping; linked to NMD processing and surface presentation
- RHOT2 and c16orf70 mis-spliced transcripts yield neoantigens validated by HLA-IP LC-MS/MS and dextramer staining
- TCRs recognizing CLK3 neoantigen show high affinity (picomolar EC50 range) and redirect CD8+ T cells to kill SRSF2-mutant leukemia cells
- In vivo NSG xenograft data show CLK3 TCR-T cells reducing tumor burden with specificity and minimal off-target effects

QC result: Pass.