Exploratory Transcriptomic Profiling of Triple-Negative Breast Cancer Patient-Derived Organoids Following Treatment with Radiation Alone and in Combination with Polo-like Kinase 4 Inhibition

Identification of novel biomarkers in triple-negative breast cancer (TNBC), one of the most aggressive breast cancer subtypes, is of critical clinical importance. Although radiation treatment (RT) is a cornerstone of TNBC treatment, resistance to RT compromises its therapeutic efficacy. Combining RT with radiosensitizing drugs may help overcome treatment resistance. The Polo-like kinase 4 (PLK4) inhibitor, CFI-400945, has been shown to exert anticancer effect when combined with RT, likely through perturbations in centriole and cell cycle regulation, and DNA-damage response pathways. We aimed to gain insight into the molecular mechanisms underlying the anticancer effects of these treatment modalities in TNBC. We performed exploratory bulk RNA-sequencing on a TNBC patient-derived organoid model treated with CFI-400945, RT or a combination of the two treatments. We found that RT alone and its combination with CFI-400945 led to gene expression changes and the enrichment of various pathways, such as cell division and DNA replication. Compared to RT alone, combination treatment resulted in a substantially greater number of differentially expressed genes and perturbed pathways. Validation of selected differentially expressed genes using RT-qPCR in TNBC patient-derived organoids and immortalized cell lines identified that melanoma cell adhesion molecule (MCAM) gene expression is upregulated upon combination treatment compared to control. Our findings provide insights regarding bulk gene expression changes following treatment of TNBC patient-derived organoids with radiation and its combination with PLK4 inhibitor CFI-400945. They also set a foundation for future studies into the identification of novel treatment-response biomarkers and therapeutic targets in TNBC.