A mitochondrial quality regulation gene signature for prognosis and tumor microenvironment characterization in breast cancer: an integrative analysis with experimental validation

Background: Breast cancer (BC) remains a leading cause of female cancer mortality, necessitating the identification of novel biomarkers for precise prognostic stratification. Mitochondrial quality-related genes (MQRGs) are critical players in tumorigenesis; however, their specific role in BC remains insufficiently characterized. Methods: We integrated transcriptomic and clinical datasets from TCGA, GTEx, and GEO to identify differentially expressed MQRGs. A 7-gene prognostic signature, comprising SLC45A1 , HPN , CHAD , CXCL9 , GLYATL2 , KRT14 , and IGLV6-57 , was developed using LASSO and multivariate Cox regression. Its predictive robustness was rigorously assessed via Kaplan-Meier and time-dependent ROC analyses.We further characterized the tumor microenvironment (TME) and validated our findings through quantitative real-time PCR（qRT-PCR） and multiplex immunohistochemistry (mIHC). Results: Unsupervised consensus clustering identified two distinct molecular subtypes related to MQRG (Clusters A and B), which exhibited significantly different clinical outcomes and tumor microenvironment (TME) characteristics. Utilizing subtype-specific differentially expressed genes, we developed a 7-gene prognostic signature (including SLC45A1 , HPN , CHAD , CXCL9 , GLYATL2 , KRT14 , and IGLV6-57 ) through LASSO-Cox regression. The signature demonstrated robust prognostic reliability across cohorts. High-risk group were distinguished by an immunosuppressive TME architecture, augmented TMB, and divergent therapeutic sensitivities, contrasting sharply with the low-risk group.Experimental validation via qRT-PCR confirmed the dysregulation of these critical genes in breast cancer cells. Notably, mIHC revealed the spatial distribution of CXCL9 , highlighting its predominant expression in tumor-associated macrophages and its significant positive correlation with M1 (iNOS+) rather than M2 (CD206+) polarization, indicating its role in modulating anti-tumor immunity. Conclusion: This study establishes a robust Mitochondrial Quality Regulation Gene Signature as an independent prognostic biomarker for BC. By elucidating the spatial dynamics of CXCL9 in promoting M1 macrophage recruitment, our findings provide an integrative framework for risk stratification and personalized therapeutic interventions, particularly for immunotherapy.