Decitabine Induces Subtype-Specific Epigenomic Remodeling and Perturbs Age-Associated Regulatory CpGs in Breast Cancer

Objectives: Breast cancer (BC) subtypes such as HR+, HER2+, and triple-negative (TNBC) show distinct molecular features, treatment responses, and outcomes. DNA methylation is a key, targetable epigenetic regulator in BC. This study examined whether the DNA methyltransferase inhibitor decitabine (DAC) produces subtype-specific epigenomic and transcriptional effects in breast cancer cell lines representing distinct molecular subtypes. Methods: Gene expression and DNA methylation data from DAC-treated and untreated T-47D (Luminal-A) and JIMT-1 (HER2-amplified, trastuzumab-resistant with a TNBC-like phenotype) breast cancer cell lines were obtained from a published dataset. Differential expressions were assessed using limma , and methylation changes were defined using β-value thresholds. Integrated epigenomic–transcriptional analysis, functional enrichment, Horvath clock CpG evaluation, and survival analysis were performed in the METABRIC and TCGA cohorts. Results: In JIMT-1, DAC caused hypomethylation at 1195 CpG sites and upregulation of 187 genes, including TFAP2E , an age-associated locus selectively hypomethylated after DAC. In T-47D, DAC induced hypomethylation at 1937 CpGs and upregulated 248 genes. Amongst these, KRT20 was upregulated despite promoter hypermethylation, indicating a subtype-specific regulatory architecture. DAC-responsive genes in JIMT-1 were enriched for cytokine signaling and piRNA-mediated epigenetic silencing, whereas T-47D showed enrichment for extracellular matrix organization, collagen dynamics, and piRNA processing pathways. Horvath clock CpG analysis showed selective perturbation of age-associated sites. Survival analysis identified 114 DAC-responsive genes associated with overall survival in ER/PR-positive BC and 8 in the JIMT-1-derived gene set. Conclusion: DAC induces subtype-dependent epigenomic and transcriptional remodeling, selectively disrupts age-associated regulatory programs, and underscores the need for subtype-stratified evaluation of epigenetic therapies in breast cancer.