Single-cell multi-omics uncovers CPS1 as a breast cancer immune evasion therapeutic target

Despite significant advances in early detection and therapeutic interventions, breast cancer persists as the most frequently diagnosed malignancy and the leading cause of cancer-related deaths among women globally. Although multiple prognostic signatures have been proposed, their predictive power and clinical applicability remain limited. In this study, we utilized an integrated approach combining single-cell multi-omics analysis with machine learning to comprehensively examine the clinical relevance of mitochondrial-related gene sets in TCGA-BRCA and developed a mitochondrial gene set scoring system, termed MitoScore. Based on the median of MitoScore, BRCA patients were classified into high-risk and low-risk groups. Our multi-omics analysis revealed that BRCA patients with higher Mitoscore exhibited poorer prognoses compared to those with lower MitoScore. The predictive ability of the model was successfully validated using an external GEO dataset. Immune infiltration analysis further indicated that high-risk group contributed to an immunosuppressive tumor microenvironment, marked by a decrease in CD8⁺ T cells. This finding was corroborated by cell-cell communication analysis, which revealed abnormal activation of the MIF-CXCR4 signaling axis. Notably, carbamoyl-phosphate synthetase 1 (CPS1) emerged as the most critical factor in the MitoScore model. CPS1 was significantly upregulated in malignant BRCA cells and was closely associated with tumor aggressiveness and poor prognosis. Both in vitro and in vivo experiments confirmed the role of CPS1 in BRCA. In this study, CPS1 was identified as a metabolism-related oncogene, suggesting its involvement in enhancing glycolysis and mediating immune evasion in breast cancer cells. Knockdown of CPS1 markedly improved the efficacy of anti-PD-1 therapy in immunocompetent mice, prolonged survival, and ameliorated the immunosuppressive tumor microenvironment. In summary, this study underscores the clinical significance of mitochondrial genes in BRCA, proposes Mitoscore for precise patient stratification and personalized treatment, and highlights the therapeutic potential of targeting CPS1 to simultaneously modulate glycolysis and immune evasion mechanisms.