Breast cancer brain metastasis (BCBM) affects 10–38% of metastatic patients, particularly those with HER2-positive and triple-negative subtypes. BCBM is highly aggressive, with a poor prognosis and an average survival rate of less than two years. BCBM diverge from their primary breast tumours both genomically and clinically and decoding mechanisms allowing drug-tolerant metastatic tumour cells to persist therapy and proliferate in the brain remains a challenge.

In this study, we performed DNA exome sequencing (N=38), RNA sequencing (N=63), and DNA methylation analysis (N=18) of patient-matched primary and BCBM sample pairs to identify genomic and transcriptomic vulnerabilities. This approach in combination with a high-throughput drug screening in five BCBM cell lines (LY2-MET [ER+], T347 [ER+HER2+], SUM190-BR [HER2+], MDA-MB-231-BR [TNBC], and JIMT1-BR [HER2+]) revealed significant sensitivity to AURKA pathway inhibitors.

Our analyses identified aberrant activation of AURKA in BCBM patient samples, with high AURKA mRNA levels correlating with poorer overall and post-metastasis survival. Both genetic and pharmacological inhibition of AURKA yielded significant anti-tumor effects across cell lines, patient-derived organoids, and brain organotypic cultures. In vivo, alisertib substantially reduced brain metastasis growth. Furthermore, transcriptomic and phosphoproteomic analysis revealed that targeting AURKA modulated Notch signaling, which appears to enhance tumor proliferation. Elevated expression levels of AURKA and MAML1 were linked to worse post BCBM survival outcomes in patient samples.

Our findings establish AURKA as a critical vulnerability in BCBM. Targeting both its kinase-dependent and kinase-independent functions may offer new therapeutic strategies to improve patient outcomes.