Extracellular vesicle-derived non-coding RNAs to predict outcome in patients with triple-negative breast cancer (TNBC) with residual disease (RD).

578 Background: TNBC patients with RD after neoadjuvant systemic therapy (NAST) have high risk of recurrence. Biomarkers to risk-stratify patients with RD could individualize adjuvant therapy and inform adjuvant therapy trials. We aim to investigate the impact of circulating extracellular vesicle (EV)-derived non-coding RNAs (exo-ncRNAs) on outcomes in TNBC patients with RD. Methods: The study population included 79 TNBC patients with RD post-NAST and available end-of- treatment plasma samples enrolled in an IRB-approved multisite prospective registry. EVs and their associated exo-ncRNAs were isolated by membrane affinity spin columns (Qiagen exoRNeasy). Exo-ncRNA was subjected to next-generation sequencing (Qiagen QIAseq miRNA library kit). N=47 served as a discovery cohort and N=32 served as validation cohort. With inclusion of transcripts expressed in ≥ 80% of samples, there were 1,123 normalized reads/sample. Hazard ratios and C-statistics for event-free survival (EFS) were computed for each exo-ncRNA. We report exo-ncRNAs that were significantly associated with EFS in both the discovery and validation cohorts. Results: Patient and tumor characteristics were balanced in discovery and validation cohorts. Three exo-ncRNAs were associated with increased recurrence risk in both the discovery dataset ( miR-200a-3p, HR=1.39, 95%CI 1.01-1.89, P=0.04, C-stat=0.55; miR-203a-3p, HR=1.77, 95%CI 1.15-2.73, P=0.01, C-stat=0.59; and miR-7845-5p, HR=1.53, 95%CI 1.15-2.05, P=0.004, C-stat=0.62) and the validation dataset ( miR-200a-3p, HR=1.83, 95%CI 1.24-2.72, P=0.003, C-stat=0.76; miR-203a-3p, HR=1.78, 95%CI 1.10-2.87, P=0.02, C-stat=0.67; and miR-7845-5p, HR=2.06, 95%CI 1.06-4.01, P=0.03, C-stat=0.52). Using the miRNA Target Prediction Database (miRDB), we identified 1,088, 1,352, and 387 predicted targets for miR-200a-3p, miR-203a-3p, and miR-7845-5p, respectively. Amongst 2,827 prediction events there were 2,526 unique target mRNAs. 2,235 mRNAs were targets for one candidate miRNAs, 281 mRNAs were predicted targets for two candidate miRNAs, and 10 mRNAs were predicted as targets for all three candidate miRNAs. Conclusions: The expression of miR-200a-3p, miR-203a-3p, and miR-7845-5p in plasma-derived EVs in TNBC patients with RD after NAST is associated with increased risk of recurrence. We identified ten mRNAs that are predicted targets of all three of these miRNAs. If validated in additional cohorts these exo-ncRNAs could be used in a liquid-biopsy assay to identify high-risk patients with RD who could benefit from adjuvant treatment intensification. [Table: see text]