Combinatorial screening reveals novel gene-drug synergies in breast cancer cells

Background: Breast cancer is the most common malignancy among women in the United States. It is a molecularly heterogeneous disease with diverse therapeutic responses. Our previous transcriptome-wide association (TWAS) and fine-mapping studies identified candidate genes potentially involved in breast cancer susceptibility. To advance personalized chemo-preventive and therapeutic strategies, we conducted a gene-drug synergy study on selected candidate susceptibility genes. Methods: Based on our previous multi-omics analyses, TWAS, and fine-mapping, we conducted a high-throughput siRNA screen to assess cell proliferation and prioritized 25 candidate genes for combinatorial screening. Using reverse transfection with ON-TARGETplus SMARTpool siRNAs (Dharmacon), these genes were silenced in three breast cancer cell lines (MCF-7, T47D, and MDA-MB-231). Following knockdown, cells were treated for 72 h with 18 clinically relevant agents for cancer therapy, including PARP inhibitors, CDK4/6 inhibitors, endocrine therapies, and chemotherapeutics, at clinically relevant concentrations. Cell viability and cytotoxicity were assessed by Hoechst 33342 and propidium iodide staining with automated image analysis. Gene-drug combinations showing >2-fold increase in cell death versus siRNA-silenced DMSO controls were considered synergistic. Statistical significance was determined using Student's t-test. Results: This combinatorial screening approach revealed multiple gene-drug synergies. In MCF-7 cells, silencing R3HDM2 markedly increased sensitivity to CDK4/6 inhibitors, with fold-changes >8 for abemaciclib and >4 for palbociclib, implicating a critical role in cell cycle regulation. SUGP1 knockdown enhanced responsiveness to docetaxel (3.81-fold) and everolimus (3.37-fold). In T47D cells, knockdown of SLC25A12 , DNAJC27 , and DYNC1I2 genes sensitized cells to everolimus, docetaxel, and lapatinib (fold-change >14, >6, and >5). In MDA-MB-231 cells, knockdown of CEP192 and SLC25A12 genes significantly enhanced sensitivity to anastrozole and docetaxel (fold-change >7 and >4). Conclusions: Knockdown of several newly identified putative breast cancer susceptibility genes profoundly altered drug sensitivity in breast cancer cells, revealing mechanistic insights and potential drug targets for breast cancer. Genes such as R3HDM2, SUGP1, CEP192 , and SLC25A12 exhibited strong synergy with CDK4/6 inhibitors, taxanes, and mTOR-targeted agents, implicating roles in cell cycle regulation, microtubule dynamics, and metabolic signaling. These findings support using genetic information to guide treatment and personalized approaches in breast cancer care.