In Silico Analysis of RNA-Seq Data Identifies IORT-Induced Downregulation of Neuroactive Signaling and Glycosylation Pathways in Breast Cancer

Background: Intraoperative radiation therapy (IORT) delivers a single, high-dose radiation dose to the tumor bed during breast-conserving surgery. While clinically effective, its molecular impact remains unclear. This study aimed to characterize gene expression changes induced by IORT in hormone receptor–positive, HER2-negative breast cancer. Methods: RNA-seq data from GSE253650, including samples from patients with and without IORT (n = 11 per group), were analyzed using GEO2R. Differentially expressed genes were identified (adjusted p < 0.05, |log2FC| ≥ 1). Downregulated genes were evaluated using GO and KEGG enrichment via cluster Profiler in R. Results: We identified 1,662 differentially expressed genes, including 787 downregulated in IORT-treated tissues. Enrichment analyses revealed suppression of neuroactive ligand-receptor signaling, ion channel activity, glycosylation, and RNA processing. Affected GO terms included sialylation, synaptic membrane organization, and spliceosomal complex components. These molecular changes align with histologic and immune features observed in IORT-treated samples. Conclusion: IORT induces transcriptomic suppression of pathways critical for signaling and RNA regulation. These changes may promote a less permissive and more immunogenic tumor microenvironment, offering insight into IORT’s therapeutic mechanisms.