Transcriptomic profiling of breast cancer subtypes identifies “FANCE” as universal and subtype-specific biomarkers

Breast cancer’s molecular heterogeneity demands precise biomarkers to differentiate subtypes and guide personalized therapies. In this study, transcriptomic profiling combined with multi-omics approaches was employed to identify novel genes associated with triple-negative breast cancer (TNBC) and luminal subtypes using GEO datasets, based on subtype-specific reciprocal expression patterns. Functional enrichment analysis indicated that the identified genes are primarily involved in antigen processing and immune regulation, underscoring the pivotal role of immune modulation in breast cancer progression. Protein–protein interaction network analysis revealed 143 hub genes, among which CADM1, FANCE, and GNB4 emerged as key regulators. Subsequent validation through the UALCAN database and Kaplan–Meier survival analysis confirmed their prognostic significance, with expression levels showing strong correlations with patient survival across subtypes. Genetic alteration and immune infiltration analyses further demonstrated that FANCE exhibits significant associations with copy number variations and enhanced immune cell infiltration. Unlike CADM1 and GNB4, which have been previously reported in breast cancer, FANCE represents a novel universal and subtype-specific biomarker, offering critical insights into immune-linked molecular mechanisms and providing potential targets for precision therapy in breast cancer.