ESRP1 deficiency promotes doxorubicin resistance by modulating alternative splicing of SEPTIN9 and SPTBN1-mediated cytoskeleton organization in breast cancer

Background Breast cancer remains one of the most prevalent malignancies among women, with doxorubicin resistance posing a significant challenge that undermines treatment success and survival outcomes. Aberrant alternative splicing (AS), driven by dysregulation or mutations in splicing factors (SFs), is implicated in cancer initiation, progression, and drug resistance. This study aims to investigate the role of the epithelial cell-specific splicing factor ESRP1 in regulating doxorubicin resistance in breast cancer, focusing on how ESRP1 deficiency contributes to AS changes that promote chemoresistance. Methods We analyzed RNA-sequencing (RNA-seq) data from doxorubicin-resistant (MCF7-DR) and parental (MCF7) breast cancer cell lines to identify enhanced AS events (ASEs) and changes in ESRP1 expression. An integrative analysis combining crosslinking immunoprecipitation (CLIP-seq) data and The Cancer Genome Atlas (TCGA) database was performed to validate ESRP1 binding targets and assess the impact of ESRP1-mediated splicing on cytoskeleton organization and small GTPase-mediated signaling. Results We observed extensive AS changes and downregulated ESRP1 expression in doxorubicin-resistant cells. Integrative analysis revealed that ESRP1 directly regulates the splicing of SEPTIN9 and SPTBN1, two genes involved in cytoskeletal remodeling and small GTPase-mediated signaling. ESRP1 deficiency was associated with increased doxorubicin resistance, in part by driving critical ASEs linked to cytoskeletal organization. Conclusions Our findings suggest that ESRP1 plays a crucial role in modulating doxorubicin resistance through its regulation of ASEs in breast cancer cells. Targeting the ESRP1-dependent splicing network may offer new strategies to overcome chemoresistance and improve patient outcomes.