Drug Repurposing Identifies Proteasome Inhibitors as Antiproliferative Agents Counteracting Inflammation-Driven Chemoresistance in Triple-Negative Breast Cancer Organoids
Background: Triple-negative breast cancer (TNBC) is an aggressive subtype with limited treatment options, characterized by high relapse rates and poor survival outcomes due to chemoresistance. This study aimed to repurpose FDA-approved drugs for TNBC and investigate their mechanisms of action in inhibiting cancer cells and counteracting  chemoresistance. Methods: Patient-derived TNBC organoids were generated from residual tumors of patients  with disease progression despite receiving standard-of-care chemotherapy. A high throughput screen of 133 FDA-approved anticancer drugs was performed on the organoids to identify potent cytotoxic agents using image-based analysis and drug-sensitivity assays. Drug response dynamics were analyzed to evaluate the efficacy of these agents in counteracting clinical drug resistance. The molecular and functional effects of the identified agents were investigated through proteomic and transcriptomic analyses, as well as translation and cell cycle assays. Results: Proteasome inhibitors bortezomib (BTZ) and carfilzomib (CFZ) were identified as potent candidates for inhibiting TNBC organoids. These drugs significantly downregulated ribosomal protein expression, suppressing translation and disrupting cell cycle progression. While TNBC organoids exhibited resistance to conventional chemotherapeutics, they were susceptible to proteasome inhibitors. Transcriptomic profiling revealed that proteasome inhibitors counteracted inflammation-driven resistance to doxorubicin (DXR) by exerting dual anti-inflammatory and anti-proliferative effects. Conclusions: This study identifies proteasome inhibition as a promising therapeutic strategy for TNBC, offering a novel approach to address unmet clinical needs. Using patient-derived organoids, this work highlights inflammation as a driver of DXR resistance and establishes it as a therapeutic target effectively counteracted by proteasome inhibitors. Overall design: RNA-seq profile of FDA-approved anticancer drugs was performed on TNBC organoids reveals drug resistance mechanisms.