Targeting the splicing factor RBM39 reduces mitotic fidelity and enhances taxane cytotoxicity in triple negative breast cancer cells

Abstract Background Triple-negative breast cancer (TNBC) accounts for 15% of breast cancers (BCs) and includes heterogeneous tumors lacking expression of estrogen, progesterone, and HER2 receptors. Unlike other BC subtypes, no targeted therapies are available for TNBC patients, leading to poorer outcomes and shorter survival. Thus, the identification of new therapeutic strategies is an urgent clinical need of TNBC. Mounting evidence points to splicing dysregulation as a hallmark of TNBC and to pharmacologic inhibition of the splicing process as a promising treatment option. Methods By using representative TNBC cell lines and patient-derived organoids, we tested the biological activity of indisulam, a splicing inhibitor inducing degradation of the splicing factor RBM39. RNA-sequencing analysis was then employed to uncover the genome-wide transcriptomic effects of the treatment. Biological pathways altered by indisulam were annotated by gene ontology analyses and validated by functional experiments in cell models. Results Treatment with indisulam strongly impaired proliferation and viability of TNBC cells. Transcriptomic analyses revealed that mitotic genes are highly susceptible to splicing deregulation caused by indisulam-mediated depletion of the splicing factor RBM39. The splicing defects of genes encoding for key regulators of mitotic spindle assembly and dynamics, such as AURKB, BORA and CHEK1, was associated with reduced expression of the corresponding proteins. Coherently, these splicing defects were associated with disruption of mitotic fidelity and increased cell death. Time-lapse microscopy showed that RBM39 depletion leads to aberrant mitotic spindle dynamics, causing defective chromosome alignment and cytokinesis. The mitotic alterations induced by indisulam increase the susceptibility of TNBC cells to taxanes used in first-line chemotherapy for these tumors, by inducing unsurmountable cytotoxic and cytostatic effects that persisted after drug removal. Conclusions Our study uncovers mitosis as a vulnerability unmasked by inhibition of RBM39 splicing activity, highlighting a novel strategy to increase the efficacy of antimitotic chemotherapy in TNBC.