Mapping glioblastoma's isoform diversity using long-read single-cell analysis

Area of Science:

• Genomics
• Oncology
• Molecular Biology

Background:

• Glioblastoma (GBM) is an aggressive brain tumor characterized by significant intratumoral heterogeneity and dysregulated RNA splicing.
• Alternative splicing significantly impacts cellular identity, function, tumor progression, and treatment resistance in GBM.
• Existing short-read sequencing methods limit the comprehensive analysis of full-length RNA isoforms in GBM.

Purpose of the Study:

• To create an isoform-level atlas of glioblastoma using single-cell long-read RNA sequencing.
• To identify novel, tumor-specific RNA isoforms and potential therapeutic targets within glioblastoma.
• To explore the potential of newly discovered isoforms as neoantigens for cancer immunotherapy.

Main Methods:

• Application of single-cell long-read RNA sequencing to capture full-length transcripts in glioblastoma cells.
• Development of a framework to identify and prioritize tumor-restricted isoforms.
• Analysis of differential transcript usage across distinct glioblastoma cell populations.
• Prediction of peptide binding to MHC class I molecules for neoantigen identification.

Main Results:

• Hundreds of isoforms with differential transcript usage were identified across diverse glioblastoma cell populations.
• A framework successfully prioritized tumor-restricted isoforms, identifying potential surface-intracellular target pairs in seven patients.
• 6,524 novel isoforms were discovered, including 179 that are specific to glioblastoma.
• Peptides derived from tumor-specific isoforms demonstrated strong predicted binding to MHC class I molecules.

Conclusions:

• Single-cell long-read RNA sequencing provides unprecedented resolution for characterizing glioblastoma isoform complexity.
• The identified tumor-specific isoforms and target pairs offer potential avenues for developing novel dual-specific ligand-based therapies.
• Newly discovered tumor-specific isoforms represent a promising source of potential neoantigens for glioblastoma immunotherapy.