Tumor suppressor syntaxin binding protein 1 regulates alternative splicing of DNA repair genes related to radiation sensitivity in breast cancer cells

Abstract

As the most aggressive subtype of breast cancer, triple-negative breast cancer (TNBC) is frequently treated with radiotherapy. Downregulation of syntaxin binding protein 1 (STXBP1) gene expression is notably associated with poor prognosis in patients with breast cancer and its protein expression level is associated with tumor radioresistance. However, the precise molecular mechanisms by which STXBP1 regulates breast cancer pathogenesis and radiotherapy resistance remain to be elucidated. In the present study, STXBP1 was overexpressed in MDA-MB-231 cells to investigate its effects on cell proliferation and apoptosis. Transcriptomic sequencing (RNA-sequencing; RNA-seq) was performed to identify differentially expressed genes and alternative splicing events regulated by STXBP1. Additionally, a publicly available RNA-seq dataset (GSE189495) associated with breast cancer radiotherapy, including three fractionally irradiated 20 Gy and three age-matched control MCF-7 cell samples were analyzed to identify radiotherapy-associated alternative splicing alterations. Integrated analysis of these two datasets was conducted to explore the potential mechanisms underlying STXBP1-mediated radiotherapy response in breast cancer. Key gene expression changes and alternative splicing events were validated using reverse transcription-quantitative (RT-q) PCR. In MDA-MB-231 cells, the overexpression of STXBP1 notably inhibited cell proliferation and enhanced levels of apoptosis. Through an analysis of RNA-seq data, the present study discovered that STXBP1 regulates global gene expression and alternative splicing profiles in MDA-MB-231 cells by modulating 111 differentially expressed genes and 1,161 regulated alternative splicing events. STXBP1 plays a key role in regulating the splicing patterns of numerous DNA repair-related genes, including USP48 and PLEC. In addition, the present study conducted an overlap analysis on the transcriptome data from radiotherapy-treated MCF-7 cells alongside the dataset generated in the present study, which revealed 21 alternative splicing events associated with radiotherapy. Notably, these include the DNA repair-related gene UBE2I, and its expression pattern has been confirmed through RT-qPCR. The present study systematically delineated the downstream targets and functional mechanisms of STXBP1 in breast cancer cells, revealing its antitumor molecular role. Moreover, STXBP1 may be associated with radiation sensitivity by regulating the alternative splicing of genes associated with DNA repair. These molecular targets, such as UBE2I, hold potential as novel therapeutic avenues for breast cancer treatment, particularly for TNBC.