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肿瘤全基因组RNA剪接异常产生可靶向的公共新抗原。

Tumour-wide RNA splicing aberrations generate actionable public neoantigens.

作者信息

Kwok Darwin W, Stevers Nicholas O, Etxeberria Iñaki, Nejo Takahide, Colton Cove Maggie, Chen Lee H, Jung Jangham, Okada Kaori, Lakshmanachetty Senthilnath, Gallus Marco, Barpanda Abhilash, Hong Chibo, Chan Gary K L, Liu Jerry, Wu Samuel H, Ramos Emilio, Yamamichi Akane, Watchmaker Payal B, Ogino Hirokazu, Saijo Atsuro, Du Aidan, Grishanina Nadia R, Woo James, Diaz Aaron, Hervey-Jumper Shawn L, Chang Susan M, Phillips Joanna J, Wiita Arun P, Klebanoff Christopher A, Costello Joseph F, Okada Hideho

机构信息

Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA.

Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.

出版信息

Nature. 2025 Mar;639(8054):463-473. doi: 10.1038/s41586-024-08552-0. Epub 2025 Feb 19.


DOI:10.1038/s41586-024-08552-0
PMID:39972144
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11903331/
Abstract

T cell-based immunotherapies hold promise in treating cancer by leveraging the immune system's recognition of cancer-specific antigens. However, their efficacy is limited in tumours with few somatic mutations and substantial intratumoural heterogeneity. 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.

摘要

基于T细胞的免疫疗法有望通过利用免疫系统对癌症特异性抗原的识别来治疗癌症。然而,在体细胞突变少且肿瘤内异质性大的肿瘤中,其疗效有限。在此,我们介绍了一类以前未被描述的全肿瘤共有新抗原,它们源自多种癌症类型中的RNA剪接异常。我们鉴定出了能够识别和靶向源自GNAS和RPL22异常剪接的新抗原的T细胞受体克隆。在进行多点活检的病例中,我们在神经胶质瘤、间皮瘤、前列腺癌和肝癌中检测到了GNAS新连接在全肿瘤中的表达。这些新抗原在生理条件下由肿瘤细胞内源性产生并呈递,足以触发新抗原特异性CD8 T细胞对癌细胞的清除。此外,我们的研究突出了特定癌症类型中剪接因子表达失调的作用,导致新连接上调的反复出现模式。这些发现为基于T细胞的免疫疗法应对肿瘤内异质性挑战奠定了分子基础。

相似文献

[1]
Tumour-wide RNA splicing aberrations generate actionable public neoantigens.

Nature. 2025-3

[2]
Tumor-wide RNA splicing aberrations generate immunogenic public neoantigens.

bioRxiv. 2023-10-20

[3]
Discovery of U2AF1 neoantigens in myeloid neoplasms.

J Immunother Cancer. 2023-12-12

[4]
Comprehensive profiling of cancer neoantigens from aberrant RNA splicing.

J Immunother Cancer. 2024-5-15

[5]
Enhanced detection of neoantigen-reactive T cells targeting unique and shared oncogenes for personalized cancer immunotherapy.

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[6]
TCR-mimicking STAR conveys superior sensitivity over CAR in targeting tumors with low-density neoantigens.

Cell Rep. 2024-11-26

[7]
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[8]
Generation of tumor neoantigens by RNA splicing perturbation.

Trends Cancer. 2025-1

[9]
Isolation of T cell receptors targeting recurrent neoantigens in hematological malignancies.

J Immunother Cancer. 2018-7-13

[10]
An effective mouse model for adoptive cancer immunotherapy targeting neoantigens.

JCI Insight. 2019-5-16

引用本文的文献

[1]
Functional tumor-reactive CD8 + T cells in pancreatic cancer.

J Exp Clin Cancer Res. 2025-8-25

[2]
Targeting the roots of myeloid malignancies with T cell receptors.

Nat Rev Cancer. 2025-8-21

[3]
Exploiting TCR Repertoire Analysis to Select Therapeutic TCRs for Cancer Immunotherapy.

Cells. 2025-8-7

[4]
Comprehensive tumor-immune profiling reveals mediators of paradoxical immune sensitivity in sarcomatoid renal cell carcinoma.

Cancer Cell. 2025-7-23

[5]
Vaccine therapies for glioma: clinical frontiers and potential breakthrough.

Front Oncol. 2025-6-25

[6]
Computation strategies and clinical applications in neoantigen discovery towards precision cancer immunotherapy.

Biomark Res. 2025-7-9

[7]
Alternative Splicing in Tumorigenesis and Cancer Therapy.

Biomolecules. 2025-5-29

[8]
Neo-antigen specific cancer vaccines for acute lymphoblastic leukemia-challenges, opportunities, and future directions.

Cancer Immunol Immunother. 2025-6-23

[9]
Peptide-MHC I regulatory mechanisms and intervention strategies in anti-tumor T cell immunity.

Acta Pharmacol Sin. 2025-5-16

[10]
Strategies for neoantigen screening and immunogenicity validation in cancer immunotherapy (Review).

Int J Oncol. 2025-6

本文引用的文献

[1]
Challenges in the discovery of tumor-specific alternative splicing-derived cell-surface antigens in glioma.

Sci Rep. 2024-3-16

[2]
Glioblastoma evolution and heterogeneity from a 3D whole-tumor perspective.

Cell. 2024-1-18

[3]
Whole tumor analysis reveals early origin of the TERT promoter mutation and intercellular heterogeneity in TERT expression.

Neuro Oncol. 2024-4-5

[4]
MAJIQlopedia: an encyclopedia of RNA splicing variations in human tissues and cancer.

Nucleic Acids Res. 2024-1-5

[5]
Proteogenomic analysis reveals RNA as a source for tumor-agnostic neoantigen identification.

Nat Commun. 2023-8-2

[6]
IRIS: Discovery of cancer immunotherapy targets arising from pre-mRNA alternative splicing.

Proc Natl Acad Sci U S A. 2023-5-23

[7]
An HLA map of the world: A comparison of HLA frequencies in 200 worldwide populations reveals diverse patterns for class I and class II.

Front Genet. 2023-3-23

[8]
Late-Stage Metastatic Melanoma Emerges through a Diversity of Evolutionary Pathways.

Cancer Discov. 2023-6-2

[9]
Multi-region sampling with paired sample sequencing analyses reveals sub-groups of patients with novel patient-specific dysregulation in Hepatocellular Carcinoma.

BMC Cancer. 2023-2-3

[10]
Proteomics separates adult-type diffuse high-grade gliomas in metabolic subgroups independent of 1p/19q codeletion and across IDH mutational status.

Cell Rep Med. 2023-1-17

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