Single-cell mapping of alternative splicing linked to checkpoint immunotherapy response

Evidence suggests that alternative RNA splicing (AS) plays a critical role in tumor biology and may contribute to the generation of tumor antigens. Here, we develop a method to detect AS in short-read single-cell 5'-RNA-sequencing data, allowing us to uniquely characterize the heterogeneity and dynamic changes in AS in individual cell types within the tumor microenvironment. We identify numerous splicing events specific to either cancer cells or stromal cell types or for triple-negative versus estrogen receptor-positive breast cancers (BCs). By correlating these splice events with expression of splicing regulators in individual cells, we also identify their potential mediators. For instance, we identify and functionally validate the Epithelial Splicing Regulatory Protein-1 (ESRP1) to drive AS in BCs responding to immune checkpoint blockade (ICB). Prioritization of splicing events based on their likelihood to represent tumor antigens reveals that their aggregated load also correlates with high immune activity in multiple cancers, while also predicting expansion of T cells in BCs receiving ICB and prolonging long-term survival of cancer patients treated with ICB. Collectively, our method provides a framework for analyzing AS in single-cell data and defines a key role for AS in the response to ICB.

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Publication Details

Journal
Nucleic Acids Research
Published
2025-11-13
DOI
https://doi.org/10.1093/nar/gkaf1171
Primary Topic
Single-cell and spatial transcriptomics
Type
article
Field-Weighted Citation Impact
0.00
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article

Single-cell mapping of alternative splicing linked to checkpoint immunotherapy response

Sofie Torfs, Stein Aerts, Jieyi Xiong, Ingrid Arijs et al.
Nucleic Acids Research
Single-cell and spatial transcriptomics
article

Single-cell mapping of alternative splicing linked to checkpoint immunotherapy response

Sofie Torfs, Stein Aerts, Jieyi Xiong, Ingrid Arijs, Oliver Edgar Bechter, Ann Smeets, Jean‐Christophe Marine, Danie Daaboul, Jonas Demeulemeester, Sara Aibar, Gitta Boons, Junbin Qian, Orian Bricard, Joanna Poźniak, Hanne Vos, Lore Van Oudenhove, Diether Lambrechts, Bernard Thienpont, Ayse Bassez, Yong Hou, Qing Lan, Ines Nevelsteen, Chen Gu
article en

Abstract

Evidence suggests that alternative RNA splicing (AS) plays a critical role in tumor biology and may contribute to the generation of tumor antigens. Here, we develop a method to detect AS in short-read single-cell 5'-RNA-sequencing data, allowing us to uniquely characterize the heterogeneity and dynamic changes in AS in individual cell types within the tumor microenvironment. We identify numerous splicing events specific to either cancer cells or stromal cell types or for triple-negative versus estrogen receptor-positive breast cancers (BCs). By correlating these splice events with expression of splicing regulators in individual cells, we also identify their potential mediators. For instance, we identify and functionally validate the Epithelial Splicing Regulatory Protein-1 (ESRP1) to drive AS in BCs responding to immune checkpoint blockade (ICB). Prioritization of splicing events based on their likelihood to represent tumor antigens reveals that their aggregated load also correlates with high immune activity in multiple cancers, while also predicting expansion of T cells in BCs receiving ICB and prolonging long-term survival of cancer patients treated with ICB. Collectively, our method provides a framework for analyzing AS in single-cell data and defines a key role for AS in the response to ICB.

Nucleic Acids ResearchVol. 53(21)
BGI Group (China) (CN), VIB-KU Leuven Center for Cancer Biology (BE), Bone Therapeutics (BE), Center for Human Genetics (US), Women's Hospital, School of Medicine, Zhejiang University (CN), Zhejiang Institute of Mechanical and Electrical Engineering (CN), Io Therapeutics (United States) (US), VIB-KU Leuven Center for Brain & Disease Research (BE), Zhejiang University (CN), KU Leuven (BE)
Openalex Percentile: Top 69%
Single-cell and spatial transcriptomics
DOIOpen Access PDFOpenAlex
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