Leveraging the IDH2 Dependencies for Enhanced Therapeutic in Triple Negative Breast Cancer

Triple-negative breast cancer (TNBC) is an aggressive subtype with limited targeted treatment options and pronounced metabolic flexibility. In this study, we identify a synthetic vulnerability in TNBC through concurrent inhibition of wild-type isocitrate dehydrogenase 2 (IDH2) and the ubiquitin–proteasome system. Pharmacological inhibition of IDH2 using AGI-6780 synergizes with the proteasome inhibitors, carfilzomib and the E1 enzyme inhibitor TAK-243, leading to pronounced apoptosis, suppression of colony formation, and loss of viability across multiple TNBC models. Mechanistically, Reverse Phase Protein Array (RPPA) analysis revealed marked suppression of pro-survival signaling networks (including NF-κB, PI3K, and BCL-2), without activation of DNA damage markers, suggesting a non-genotoxic mode of action. Genome-wide CRISPR-Cas9 screening in AGI-6780-treated MDA-MB-231 cells identified components of mitochondrial oxidative phosphorylation, notably ATP5O and NDUFS1, as critical sensitizers, implicating mitochondrial energy metabolism as a key determinant of therapeutic response. Functional validation confirmed that perturbation of mitochondrial ATP production enhances the cytotoxic effects of IDH2 inhibition. Importantly, IDH2 knockout rendered cells resistant to AGI- 6780, suggesting the compound’s off-target effect. While IDH2 depletion alone had minimal impact on proliferation, it revealed a conditional essentiality under stress, supporting the concept of “non-oncogene addiction”. Furthermore, loss of the chromatin factor STAG2 increased sensitivity to IDH2 inhibition, suggesting that chromatin remodeling contributes to adaptation under metabolic constraint. Together, these results uncover a critical metabolic–proteostatic axis in TNBC and provide strong preclinical rationale for dual inhibition of IDH2 and the proteasome machinery. This approach offers a promising strategy to target metabolic resilience and overcome therapeutic resistance in mesenchymal breast cancer.