Integrating single-cell and bulk RNA sequencing data establishes a cuproptosis-related gene predictive signature in breast cancer

Breast cancer (BRCA) remains the most common malignancy and the leading cause of cancer-related death among women worldwide. Recent studies have highlighted dysregulated copper homeostasis as a contributor to tumorigenesis, with cuproptosis-a copper-dependent form of regulated cell death-emerging as a potential therapeutic target. In this study, we systematically evaluated the prognostic significance of cuproptosis-related genes (CRGs) in BRCA by integrating multi-omics data from TCGA and GEO cohorts. Through weighted gene co-expression network analysis (WGCNA), we identified four key CRGs (CCDC24, TMEM65, XPOT, and NUDCD1) to construct a prognostic signature. The resulting risk score effectively stratified patients into high- and low-risk groups, with the high-risk group showing significantly worse overall survival, higher TP53 mutation frequency, and features of an immunosuppressive tumor microenvironment (TME). Functional enrichment analyses further implicated these genes in immune evasion and metabolic reprogramming pathways. Single-cell RNA sequencing (scRNAseq) confirmed heterogeneous expression of the signature genes across distinct cell populations, supporting their involvement in both tumor biology and immune modulation. Clinically, this CRG-based model provides a promising tool for individualized risk assessment and treatment planning. High-risk patients may benefit from intensified therapies or immunomodulatory strategies, while low-risk individuals could be considered for treatment de-escalation. In summary, our findings suggest that cuproptosis may play a regulatory role in BRCA progression and offer a novel, clinically actionable framework for prognostic stratification.