Identification of Hub Genes, Single-Nucleotide Polymorphisms, and Potential Drug Targets In Breast Cancer Using Transcriptomic Analysis.

HER2-positive (HER2+) breast cancer often develops resistance to therapies like Lapatinib, potentially involving mitochondrial metabolic and redox reprogramming. This study aimed to identify mitochondrial oxidative stress-related genes (MOS-DEGs) as biomarkers of resistance and to characterize their functional nsSNPs and structural impacts. RNA-seq datasets (GSE231524, GSE231525) were analyzed using DESeq2 to identify DEGs, which were intersected with mitochondrial oxidative stress genes to obtain MOS-DEGs. Functional enrichment, PPI analysis, ROC analysis, expression profiling, and survival analysis were performed. nsSNPs were evaluated using multiple predictive tools, and structural impacts were assessed through secondary and 3D modeling. Integrated transcriptomic and clinical analysis identified MTHFD2 and PRDX3 as central MOS-DEGs displaying opposing regulatory roles in mitochondrial redox metabolism. MTHFD2 was significantly upregulated and associated with poor prognosis (HR = 1.53, p = 1.1 × 10⁻16), while PRDX3 exhibited protective expression patterns (HR = 0.73, p = 7.7×10⁻10). ROC analysis suggested their potential as predictors of therapeutic response. nsSNP analysis revealed five deleterious variants in MTHFD2 and four deleterious variants in PRDX3, with rs1471336772 (MTHFD2) and rs747786383 (PRDX3.) identified as the most pathogenic. These variants were predicted to be damaging based on multiple computational scoring systems, including SIFT ≤ 0.05, PolyPhen-2 ≥ 0.85, deleterious CADD scores, and high REVEL scores, and were located within catalytic or redox-active domains. Structural modeling suggested that these substitutions may destabilize conformation, disrupt metal- and cofactor-binding sites, and affect NADPH regeneration or thioredoxin-dependent peroxidase activity. Molecular dynamics predictions indicated potential loss of structural stability and altered flexibility, suggesting possible functional impairment of mitochondrial redox control. This study identifies MTHFD2 and PRDX3 as regulators of mitochondrial oxidative stress in HER2+ breast cancer. Deleterious nsSNPs in these genes may contribute to altered redox balance, potentially influencing metabolic adaptation (MTHFD2) and antioxidant defense (PRDX3).