Dysregulation of alternative splicing in glioma cells: unraveling splice variants across cell-states, invasiveness, and quiescence in SmartSeq-2 single cell RNA sequencing data of glioma patients

Abstract

Glioblastoma (GBM), the most aggressive form of glioma, is characterized by intratumor heterogeneity, which drives treatment resistance and recurrence. Single-cell RNA sequencing (scRNA-seq) has identified multiple cellular states within GBM, including invasive and quiescent cells that contribute to tumor malignancy. However, previous studies investigating GBM heterogeneity have primarily focused on gene expression, overlooking the complexity introduced by alternative splicing events. In this study, we conduct an in-depth analysis of cell-state-specific alternative splicing in 37 glioma tumors using SmartSeq-2 scRNA-seq data. We found that no single isoform driving invasion and quiescence was differentially expressed across all tumors, emphasizing the complexity and intertumoral differences of glioma. However, functional enrichment analysis of genes with cell-state-specific exons revealed that alternative splicing predominantly affects the regulation of mRNA splicing via the spliceosome. With alternative splicing events significantly more prevalent in malignant cells than in healthy tissue, our results suggest that dysregulation of the splicing machinery is a fundamental driver of isoform variability in GBM. This highlights the role of spliceosome dysfunction as a key contributor to glioma progression and treatment resistance. We propose that targeting the spliceosome and splicing-related pathways may offer novel therapeutic avenues in gliomas. Addressing the tumor-specific splicing landscape could ultimately help overcome the challenges posed by intratumor heterogeneity and improve patient outcomes.