Therapeutic Synergy Overcomes Carboplatin Resistance in Triple-Negative Breast Cancer [bulk RNA-seq]

Background: Triple-negative breast cancer (TNBC) is an aggressive subtype lacking targeted therapeutic options, where platinum-based chemotherapy such as carboplatin serves as a cornerstone of treatment. Despite initial responses, the rapid emergence of acquired resistance remains a major clinical barrier. Understanding the molecular adaptations that drive platinum resistance is essential to develop strategies to restore sensitivity and identify alternative vulnerabilities. Methods: We generated four isogenic patient-derived xenograft (PDX) pairs (WHIM30, BCM‑2147, BCM‑3887, BCM‑7482) through serial carboplatin exposure to model acquired resistance in TNBC. Bulk RNA sequencing, immunohistochemistry, and histopathological analyses were performed to define transcriptomic and phenotypic changes associated with resistance. Synergistic therapeutic combinations were identified using high-throughput drug screening in carboplatin-resistant (CR) PDX-derived models, followed by in vivo validation in NSG mice. Tumor growth and survival were assessed using mixed-effects modeling, two-way ANOVA, and Welch’s student t-test. Results: The resulting isogenic PDX pairs captured both convergent and model-specific adaptations to carboplatin. CR tumors demonstrated heterogeneous activation of DNA damage repair pathways, including restoration of BRCA1-dependent homologous recombination (BCM‑2147, WHIM30) and compensatory upregulation of mismatch repair (BCM‑3887). In the BRCA1-mutant BCM‑7482 model, resistance correlated with HORMAD1 upregulation, suggesting an alternative HRD-associated mechanism. Morphologically, BCM‑7482CR tumors exhibited a significant increase in nuclear size compared to their sensitive counterpart (p < 0.0001). Drug screening identified mTOR pathway inhibition as a recurrent vulnerability across CR models. Sacituzumab govitecan (SG) combined with Everolimus produced robust synergy in vitro and superior tumor control in vivo compared to single agents in both WHIM30CR and BCM‑2147CR. A second combination, Everolimus + Selinexor (KPT‑330), also reduced tumor burden, achieving statistical significance in an expanded WHIM30CR cohort and suppressing metastatic progression in the intrinsically resistant WHIM2 model. Conclusions: Isogenic PDX models of TNBC provide a powerful platform to define molecular mechanisms of acquired carboplatin resistance and uncover actionable therapeutic strategies. Our findings reveal multiple adaptive routes to platinum resistance, including restoration of homologous recombination and activation of alternative DNA repair programs. Synergistic interactions between SG and mTOR inhibition offer a promising avenue for overcoming resistance, supporting further clinical investigation of these combinations in TNBC.