Construction of a novel zinc homeostasis-related gene signature to predict breast cancer prognosis by integrating single-cell and bulk RNA-seq data

This study was conducted to explore the role of zinc homeostasis in breast cancer (BC). We identified a gene signature in BC comprising nine key zinc homeostasis-related genes ( CCDC74B , ELOVL2 , FAM234B , FUT3 , KCNJ11 , NXPH4 , RIBC1 , UPK2 , and WNK4 ), from which we constructed a risk score model. Cox regression analyses confirmed the independent prognostic value of the risk score. BC patients with low-risk scores had significantly higher overall survival rates. The high-risk group exhibited lower immune cell infiltration but significantly decreased tumor immune dysfunction and exclusion (TIDE) scores, suggesting a greater likelihood of benefiting from immunotherapy. Significant differences were observed between the high- and low-risk groups in terms of biological pathways and the carcinogenic process. A single-cell analysis identified CD8 + T cells as the most abundant cell population in the tumor tissue. A methylation analysis revealed that methylation levels of eight genes differed significantly between the disease and control groups. Quantitative real-time PCR and western blotting analyses confirmed significant increases in the mRNA and protein levels of the genes CCDC74B , ELOVL2 , FAM234B , RIBC1 , and UPK2 . In summary, we established a novel zinc homeostasis-related gene signature for BC that robustly stratifies patients into distinct risk groups with different characteristics and survival outcomes.