Tumour-wide RNA splicing aberrations generate actionable public neoantigens

Our plain-English summary of Tumour-wide RNA splicing aberrations generate actionable public neoantigens, by D.W. Kwok, N.O. Stevers, I. Etxeberria, et al (Nature, 2025).

The study

• Authors: D.W. Kwok, N.O. Stevers, I. Etxeberria, T. Nejo, M. Colton Cove, L.H. Chen, J. Jung, K. Okada, S. Lakshmanachetty, M. Gallus, A. Barpanda, C. Hong, G.K.L. Chan, J. Liu, S.H. Wu, E. Ramos, A. Yamamichi, P.B. Watchmaker, H. Ogino, A. Saijo, A. Du, N.R. Grishanina, J. Woo, A. Diaz, S.L. Hervey-Jumper, S.M. Chang, J.J. Phillips, A.P. Wiita, C.A. Klebanoff, J.F. Costello, H. Okada
• Journal: Nature
• Published: 2025;639(8054):463-473
• Cited by: 80 articles, as counted by NIH iCite
• Read it: PubMed · Publisher · Free full text

Abstract

T cell-based immunotherapies hold promise in treating cancer by leveraging the immune system's recognition of cancer-specific antigens1. However, their efficacy is limited in tumours with few somatic mutations and substantial intratumoural heterogeneity2-4. Here we introduce a previously uncharacterized class of tumour-wide public neoantigens originating from RNA splicing aberrations in diverse cancer types. We identified T cell receptor clones capable of recognizing and targeting neoantigens derived from aberrant splicing in GNAS and RPL22. In cases with multi-site biopsies, we detected the tumour-wide expression of the GNAS neojunction in glioma, mesothelioma, prostate cancer and liver cancer. These neoantigens are endogenously generated and presented by tumour cells under physiologic conditions and are sufficient to trigger cancer cell eradication by neoantigen-specific CD8+ T cells. Moreover, our study highlights a role for dysregulated splicing factor expression in specific cancer types, leading to recurrent patterns of neojunction upregulation. These findings establish a molecular basis for T cell-based immunotherapies addressing the challenges of intratumoural heterogeneity.

© 2025. The Author(s).

In plain English

This laboratory and computational study looked for cancer-specific RNA splicing events (called neojunctions) that are shared between patients and present throughout a tumour. The authors analysed RNA-sequencing data from 12 cancer types in The Cancer Genome Atlas, compared them with 9,166 normal GTEx tissue samples, and reported an average of 94 'public' neojunctions per tumour type. Using multi-region biopsies, including about ten spatially mapped biopsies from each of 51 glioma cases, they found at least one tumour-wide neojunction in 45 (88.2%) of those patients. Mass spectrometry of glioma datasets detected neopeptides mapping to 302 (38.3%) unique public neojunctions. From healthy-donor T cells the authors isolated seven T cell receptors reactive to an RPL22-derived neoantigen and one to a GNAS-derived neoantigen; transduced CD8+ T cells killed tumour cell lines in an HLA-dependent way. The authors reported the GNAS neojunction as expressed tumour-wide in glioma, mesothelioma, prostate cancer and hepatocellular carcinoma.

We wrote this plain-English summary from the full article with the help of AI, and a second AI model checked each sentence against the article. It is not the authors' wording; the abstract and the article are their own account.

What the study did and found

• Design: Laboratory study combining computational analysis of public tumour RNA-sequencing and proteomic datasets with in vitro cell and T cell experiments
• Who was studied: RNA-sequencing data from 12 TCGA cancer types (including mesothelioma, n = 516 samples), 9,166 GTEx normal tissue samples, multi-region biopsy datasets from several cancers, 51 spatially mapped glioma cases, glioma mass spectrometry datasets (n = 447 patients), healthy-donor PBMCs and tumour cell lines
• Exposure: Not an exposure study; the subject was tumour-specific RNA splicing aberrations (neojunctions) and the neoantigens they encode, notably in GNAS and RPL22
• Main results:
  • Across TCGA tumour types, an average of 94 public neojunctions were identified per tumour type
  • In the 51 spatially mapped glioma cases, at least one tumour-wide neojunction was found in 45 (88.2%) patients, and 13 (25.5%) expressed more than 50
  • Of TCGA-characterized LGG and GBM neojunctions, 774 (98.1%) were detectable in more than one tumour region, but only 37 (4.7%) were present across all samples in more than 10% of the cohort
  • Mass spectrometry data from glioma patients (n = 447) yielded neopeptides mapping to 302 (38.3%) unique public neojunctions
  • In vitro sensitization of healthy-donor CD8+ T cells identified seven T cell receptors reactive to the RPL22 neoantigen and one to the GNAS neoantigen
  • TCR-transduced CD8+ T cells killed GBM115 cells at a 1:1 effector/target ratio, and an HLA-I blocking antibody partially blocked killing
  • Circulating neoantigen-reactive CD8+ T cells were detected in one of three patients with glioma after short-term in vitro sensitization
  • The GNAS neojunction was reported as tumour-wide in several tumour types, including mesothelioma
  • CRISPRi knockdown of CELF2 in a patient-derived IDHmut cell line reduced expression of the NJACAP2 neojunction
  • Knockdown of SNRPD2 or SF3A3 in the GBM115 cell line increased NJACAP2 or NJPEA15 levels, respectively
• The authors' conclusion: The authors concluded that RNA splicing aberrations are a source of intratumourally conserved public tumour-specific antigens that the immune system can recognize and that could be targeted with engineered T cells.
• Limitations the authors state:
  • HLA class II-restricted neoepitopes and CD4+ T cell responses could not be assessed because of current prediction limitations
  • Only neopeptides binding HLA-A*02:01 were pursued, as proof of concept
  • More intratumoural sampling sites per patient would be needed to validate neojunctions as tumour-wide in cancers other than glioma
  • The contribution of the studied neoantigen-encoding junctions to tumour biology was not assessed
  • Surface-bound neojunction-derived neoantigens were not investigated

Topics

Medical terms in this study, explained in our Lexicon: Somatic Mutation, Mesothelioma.

Related studies

• Splicing modulation as novel therapeutic strategy against diffuse malignant peritoneal mesothelioma — R. Sciarrillo, A. Wojtuszkiewicz, et al. (2019)
• BAP1 missense mutation c.2054 A>T (p.E685V) completely disrupts normal splicing through creation of a novel 5' splice site in a human mesothelioma cell line — A. Morrison, Y. Chekaluk, et al. (2015)
• Identification of a CD8+ T-cell response to a predicted neoantigen in malignant mesothelioma — S. Sneddon, C.M. Rive, et al. (2020)
• Mesothelin Immunotherapy for Cancer: Ready for Prime Time? — R. Hassan, A. Thomas, et al. (2016)
• Serologic responses in patients with malignant mesothelioma: evidence for both public and private specificities — C. Robinson, M. Callow, et al. (2000)
• A regional approach for CAR T-cell therapy for mesothelioma: from mouse models to clinical trial — M. Mayor, M. Zeltsman, et al. (2016)

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