Background
Breast cancer exhibits extensive molecular heterogeneity across intrinsic subtypes, yet convergent metabolic reprogramming may represent an obligate feature of tumour initiation. We hypothesised that suppression of nuclear-encoded mitochondrial fatty acid oxidation (FAO) constitutes such a convergence point, defining a shared metabolic phenotype independent of subtype.
Methods
RNA-seq data from 1,106 primary breast tumours and 113 normal-adjacent tissues (TCGA-BRCA) were intersected with 1,079 nuclear-encoded mitochondrial genes from MitoCarta 3.0. Differential expression was assessed using Welch t-test with Benjamini–Hochberg correction at all tumour stages, at Stage I specifically, and stratified across PAM50 subtypes. A 55-gene core FAO signature was derived by three-way intersection. Ten candidate genes were selected by pre-specified objective scoring, locked before any clinical testing. Gene set enrichment analysis (GSEA) was performed using MitoCarta 3.0 pathway annotations. Diagnostic performance, clinical associations, survival, and mutation independence were characterised. External validation used two independent GEO cohorts (GSE42568, n = 121; GSE109169, n = 50); prognostic validation used METABRIC (Molecular Taxonomy of Breast Cancer International Consortium; n = 1,980). DESeq2 was applied as methodological cross-validation.
Results
Among 126 differentially expressed mitochondrial genes, fatty acid oxidation was the most significantly depleted pathway (normalised enrichment score −2.130; false discovery rate 0.001). The 55-gene core signature replicated in both external cohorts with 100% directional concordance (hypergeometric p < 10⁻¹⁵). All 10 candidate genes discriminated tumour from normal tissue (area under the curve 0.915–0.979) and demonstrated broad clinical associations. The composite FAO suppression score predicted overall survival in METABRIC (log-rank p = 7.82 × 10⁻⁷) and MAOA achieved independent prognostic significance in multivariable Cox regression (hazard ratio 0.890; adjusted p = 0.009). DESeq2 cross-validation confirmed Spearman ρ = 0.980 concordance.
Conclusions
Nuclear-encoded FAO suppression is a robust, pan-subtype feature of breast cancer detectable at Stage I and validated across independent platforms and cohorts. These 10 candidate genes constitute a consistent initiation-phase mitochondrial signature, implicating FAO suppression as a potential convergence point in breast cancer oncogenesis and motivating targeted functional investigation.