Metabolic-Pathway-Based Subtyping of Triple-Negative Breast Cancer Reveals Potential Therapeutic Targets

Triple-negative breast cancer (TNBC) remains an unmet medical challenge. We investigated metabolic dysregulation in TNBCs by using our multi-omics database (n = 465, the largest to date). TNBC samples were classified into three heterogeneous metabolic-pathway-based subtypes (MPSs) with distinct metabolic features: MPS1, the lipogenic subtype with upregulated lipid metabolism; MPS2, the glycolytic subtype with upregulated carbohydrate and nucleotide metabolism; and MPS3, the mixed subtype with partial pathway dysregulation. These subtypes were validated by metabolomic profiling of 72 samples. These three subtypes had distinct prognoses, molecular subtype distributions, and genomic alterations. Moreover, MPS1 TNBCs were more sensitive to metabolic inhibitors targeting fatty acid synthesis, whereas MPS2 TNBCs showed higher sensitivity to inhibitors targeting glycolysis. Importantly, inhibition of lactate dehydrogenase could enhance tumor response to anti-PD-1 immunotherapy in MPS2 TNBCs. Collectively, our analysis demonstrated the metabolic heterogeneity of TNBCs and enabled the development of personalized therapies targeting unique tumor metabolic profiles. [Display omitted] •The metabolic reprogramming and heterogeneity of TNBC is systematically characterized•TNBCs are classified into three subtypes on the basis of metabolic pathways•Three subtypes show distinct sensitivities to various metabolic inhibitors•Inhibition of LDH enhances tumor response to anti-PD-1 immunotherapy in MPS2 TNBCs Gong et al. reveal the metabolic heterogeneity of triple-negative breast cancer and identify three metabolic-pathway-based subtypes with distinct molecular features and sensitivities to various metabolic inhibitors. They find that inhibition of lactate dehydrogenase could enhance the anti-PD-1 immunotherapy response in a certain subtype of triple-negative breast cancer.