Identification and functional validation of EPS15L1 as a key driver of triple-negative breast cancer

Triple-negative breast cancer (TNBC) is a heterogeneous and aggressive subtype with no effective targeted therapies. To identify novel therapeutic targets, we conducted transcriptome-wide association studies (TWAS) integrating genome-wide association studies (GWAS) summary statistics from the Breast Cancer Association Consortium (BCAC) and UK Biobank with expression quantitative trait loci (eQTL) summary statistics from breast mammary tissues via the Genotype-Tissue Expression (GTEx) study. Our approach identified novel candidate genes positively or negatively associated with TNBC based on their TWAS effect size. We validated these candidates by confirming their differential expression between TNBC and normal tissues using The Cancer Genome Atlas (TCGA) breast cancer cohort. Among these, Epidermal Growth Factor Receptor Pathway Substrate 15 Like 1 (EPS15L1) emerged as a top candidate significantly associated with TNBC. EPS15L1 was found to be overexpressed in basal-like and claudin-low TNBC tumors and cell lines, with its high expression correlating with poor prognosis. Functional studies demonstrated that EPS15L1 enhances TNBC cell growth, as evidenced by increased metabolic activity in high-density conditions, enhanced clonogenic ability in low-density settings, and improved 3D spheroid formation. Additionally, knockdown of EPS15L1 suppressed the formation and stellate morphology of single-cell-initiated spheroids within the 3D microenvironment. Collectively, these findings establish EPS15L1 as a driver of TNBC initiation, implying its potential as a biomarker for early detection and a target for prevention.