Proteomic Characterization of AS1411 Reveals ATP6AP1 as a Mediator of Triple‐Negative Breast Cancer Progression

Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer characterized by high metastatic potential, poor prognosis, and limited effective therapeutic options. In this study, we investigated the molecular mechanisms underlying the anticancer effects of the nucleolin (NCL)-targeting DNA aptamer AS1411 using label-free quantitative proteomic profiling. AS1411 treatment significantly reduced TNBC cell viability and migration. To uncover the underlying mechanisms, we performed global proteomic analysis of AS1411-treated TNBC cells. Bioinformatic analysis of differentially expressed proteins (DEPs) revealed enrichment of tumor-associated signaling pathways and protein-protein interaction networks regulated by AS1411. Among the DEPs, ATPase H⁺-transporting accessory protein 1 (ATP6AP1) was markedly downregulated in AS1411-treated TNBC cells. Functional studies demonstrated that ATP6AP1 knockdown suppressed TNBC cell proliferation and migration, whereas its overexpression enhanced tumorigenic phenotypes. Importantly, modulation of ATP6AP1 expression showed minimal effects on normal breast epithelial cells. Collectively, these findings identify ATP6AP1 as a key downstream mediator of AS1411 and support its potential as a therapeutic target in TNBC.