Long Reads RNAseq reveals an isoform switching pattern in healthy microglial cell lines exposed to radiotherapy.

Background/Objectives: Radiotherapy (RT) is a fundamental treatment for brain tumors but often leads to long-term neurotoxicity, partly caused by microglial dysfunction. In this study, we used long-read RNA sequencing (LR-RNA-seq) to map the isoform-specific transcriptome of human microglial HMC3 cells after RT exposure Methods: HMC3 Microglial cell line was treated with standard radiotherapy and, after RNA extraction and library preparation, long reads RNAseq has been carried out. Further bioinformatic analyses allowed to investigate on the isoform switching pattern after radiation therapy exposure. Results: Gene-level analysis found 591 differentially expressed genes, with increased activity in PI3K/AKT signaling pathways and decreased translation-related processes. Isoform-level analysis uncovered 827 significant isoform switching events across 420 genes, often involving shifts from protein-coding transcripts to non-coding variants. Functional annotation showed that most isoform switches resulted in the loss of open reading frames and protein domains, especially in ribosomal proteins and translation machinery components