Autophagy-Associated Exosomal microRNAs in Triple-Negative Breast Cancer: A Discovery-Phase Study

Triple-negative breast cancer (TNBC) is characterised by aggressive pathobiology and chemoresistance, yet the mechanisms underpinning treatment failure remain incompletely understood. Autophagy, induced by cytotoxic chemotherapy, is increasingly implicated in exosome biogenesis and cargo remodelling; however, whether it systematically reprogrammes the exosomal microRNA (exomiR) landscape in TNBC has not been established. Here, we report that chemotherapy-induced autophagy significantly alters sEV-associated miRNA profiles in two TNBC cell lines (MDA-MB-231, MDA-MB-468) relative to basal and normal mammary epithelial (MCF-10A) controls. Small extracellular vesicles (sEVs), confirmed by TEM, NTA, and CD81/CD63 western blotting, were isolated under doxorubicin induced autophagy conditions. Small RNA sequencing (DESeq; nominal p value < 0.01) identified 10 differentially expressed exomiRs in MDA-MB-231 and 7 in MDA-MB-468. Multi-database in silico target prediction revealed convergent targeting of core autophagy regulators, most prominently Beclin-1 (BECN1), targeted by five independent candidate exomiRs alongside the PI3K/mTOR axis and mitophagy effectors. These discovery-phase findings identify a candidate exomiR panel with mechanistic relevance to autophagy-driven chemoresistance in TNBC and provide a discovery stage transcriptomic foundation for prospective functional validation and clinical biomarker development.