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

Area of Science:

• Oncology
• Molecular Biology
• Immunology

Background:

• Alternative RNA splicing (AS) is implicated in tumor biology and the generation of tumor antigens.
• Understanding AS heterogeneity within the tumor microenvironment is crucial for developing targeted therapies.

Purpose of the Study:

• To develop a method for detecting AS in single-cell 5'-RNA-sequencing data.
• To characterize AS heterogeneity and dynamic changes in individual cell types within tumors.
• To identify potential mediators of AS and their role in cancer and immune responses.

Main Methods:

• Single-cell 5'-RNA-sequencing data analysis.
• Identification of cell-type-specific splicing events.
• Correlation of splicing events with splicing regulator expression.
• Functional validation of splicing regulators like ESRP1.
• Prioritization of splicing events as potential tumor antigens.

Main Results:

• Numerous AS events were identified specific to cancer cells, stromal cells, or different breast cancer subtypes (TNBC vs. ER+).
• The splicing regulator ESRP1 was identified and validated as a driver of AS in breast cancers responding to immune checkpoint blockade (ICB).
• Aggregated tumor antigen load from AS events correlates with immune activity and predicts T cell expansion and improved survival in patients receiving ICB.

Conclusions:

• A novel framework for analyzing AS in single-cell data was established.
• AS plays a significant role in the response to ICB therapy.
• AS-derived tumor antigens represent a promising avenue for cancer immunotherapy.