Abstract Background: Metastasis is the leading cause of breast cancer-related mortality. Current classification is based mainly on immunohistochemical markers and fails to reliably predict metastatic potentials. In recent decades, microRNAs (miRNAs) have emerged as promising clinical biomarkers due to their capacity to regulate key molecules involved in cancer progression and metastatic spread. Methods: To identify novel miRNA-based biomarkers, we analyzed three retrospective cohorts. A miRNA Affymetrix Gene Chip 4.0 array was used to identify relevant miRNAs in the discovery cohort (n=40). Next, RT-qPCR analysis was performed to evaluate the accuracy of selected miRNAs in identifying patients who developed distant metastases in the extended cohort (n=223). A stepwise logistic regression model was used to construct a prognostic tool for metastases, including miRNA levels and clinicopathological features. The effects that both miRNAs may exert on tumor cell phenotype was preliminary assessed in a panel of breast cancer cell lines in terms of cell viability. Following ectopic modulation of candidate miRNAs by miRVANA miRNA mimics, cell viability was measured by PrestoBlue viability reagent. Results: Global expression analysis of the discovery cohort identified eight miRNAs with differential expression between metastatic and non metastatic tumors. In the extended cohort, miR-3916 and miR-3613-5p were the best miRNAs for identifying patients who developed distant metastases. Increased expression levels of miR-3916 were associated with a reduced risk of developing distant metastases (OR=0.42, 95% CI: 0.23-0.70, p=0.002), while increased expression levels of miR-3613-5p were associated with an elevated risk (OR=2.06, 95% CI: 1.27-3.50, p=0.005). Importantly, by including the expression levels of miR-3916 and miR-3613-5p in a model with clinicopathological covariates, the discriminatory power reached an AUC of 0.85 (95% CI: 0.79-0.91), outperforming a model with clinicopathological covariates only (AUC=0.76, 95% CI: 0.68-0.84) (delta-AUC p=0.001). As expected, the evaluation of the effects of miR-3613-5p and miR-3916 transfection in vitro showed that both miRNAs were able to impair cell viability in breast cancer cell lines. Conclusions: In this study, we identified miR-3613-5p and miR-3916 as putative metastases associated miRNAs. A logistic regression model including both miRNAs and clinicopathological characteristics were able to predict the risk of metastases development supporting their potential utility in the clinical setting. Moreover, our initial in vitro studies suggest both miRNAs may affect tumor cell phenotype. Further in vitro and in vivo are currently ongoing to characterize miR-3613-5p and miR-3916 role in the mechanisms underlying metastases development in breast cancer. Citation Format: Andrea Fontana, Raffaela Barbano, Barbara Pasculli, Tommaso Mazza, Orazio Palumbo, Elena Binda, Tommaso Biagini, Michelina Rendina, Antonio lo Mele, Giuseppina Prencipe, Sara Bravaccini, Roberto Murgo, Luigi Ciuffreda, Maria Morritti, Vanna Maria Valori, Francesca Sofia Di Lisa, Patrizia Vici, Marina Castelvetere, Massimo Carella, Paolo Graziano, Evaristo Maiello, Massimiliano Copetti, Paola Parrella. A miRNA expression profiling of breast cancer to develop a metastases predictor model and identify new molecular players of metastatic outgrowth [abstract]. In: Proceedings of the San Antonio Breast Cancer Symposium 2024; 2024 Dec 10-13; San Antonio, TX. Philadelphia (PA): AACR; Clin Cancer Res 2025;31(12 Suppl):Abstract nr P3-07-22.
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