The Landscape of Ferroptosis-Related Gene Signatures as Molecular Stratification in Triple-Negative Breast Cancer

Background: Triple-negative breast cancer (TNBC) represents the most aggressive breast cancer subtype, characterized by high genomic instability, metabolic stress, and limited therapeutic options. Ferroptosis, an iron-dependent form of regulated cell death, has emerged as a promising vulnerability in TNBC, yet its subtype-specific regulatory landscape remains insufficiently defined. Methods: Using transcriptomic (METABRIC, TCGA, GEO) and proteomic (CPTAC) datasets, ferroptosis-related genes were profiled across PAM50 breast cancer subtypes. Differential expression, univariate Cox regression, LASSO modeling, survival analyses, GSEA, and dimensionality reduction (PCA, t-SNE) were applied. A Ferroptosis Index (FI) was calculated using β-coefficients from the Cox/LASSO regression model. Single-cell RNA-seq data was used to map ferroptosis-associated signature across tumor and microenvironmental compartments. Results: Basal-like tumors exhibited the strongest ferroptosis-associated transcriptional shift, characterized by upregulation of ACSL4 and EZH2 and downregulation of AR, GPX4, and CIRBP. Sixteen ferroptosis-related genes were associated with overall survival, forming a ferroptosis-associated signature. The FI was significantly higher in Basal-like tumors, indicating elevated ferroptosis-associated transcriptional state. GSEA revealed enrichment of cell cycle, mitotic, cytoskeletal, and metabolic stress pathways. Single-cell analysis demonstrated expression of ferroptosis markers across cancer epithelial, stromal, and myeloid populations. Conclusions: Basal-like tumors harbor a distinct ferroptosis-associated transcriptional state linked to tumor aggressiveness and poor prognosis. These findings provide a biologically grounded framework for ferroptosis-related stratification and support future functional and translational studies targeting ferroptosis vulnerabilities in aggressive breast cancer.