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IntroductionSOX2, a key pluripotency gene, plays a central role in breast cancer stem cell (BCSC) biology, driving tumor aggressiveness. Although SOX2 dysregulation has been widely studied across various cancers, its specific regulatory mechanisms in breast cancer (BC) remain incompletely elucidated. This study examined the regulatory axis of the SOX2 gene and associated molecular mechanisms underlying BCSC maintenance and prognosis.MethodsThis retrospective cross-sectional study analyzed breast tumor tissues and adjacent normal controls collected consecutively from two tertiary hospitals. SOX2 promoter methylation was assessed using methylation-Specific PCR, and expression of SOX2, DNMT3b, TET3, miR-200b-3p, and TGFβ1 was quantified by qPCR.ResultsAberrant methylation of the SOX2 promoter, linked to increased expression, was observed in the BC cohort. Notably, several samples exhibited a poised promoter state, reflecting an epigenetic configuration associated with stemness. Upregulation of DNMT3b in miR-200b-reduced cells was significantly associated with SOX2 promoter methylation, suggesting a feedback loop modulating methylation dynamics. Additionally, a positive association between deregulated TET3 and TGFβ1 highlights a positive feedback loop in the dynamic tumor microenvironment. SOX2 methylation emerged as a strong prognostic marker, characterized by a low hazard ratio and high diagnostic sensitivity. Its combination with DNMT3b improved specificity (SE = 90%, SP = 79%). Reduced TET3 and miR200b expression correlated with poor outcomes, and their integration with SOX2 formed a tri-gene signature that enhanced patient stratification. Correlation analyses revealed coordinated expression among SOX2, TET3, and TGFβ1, supporting their role in methylome regulation.ConclusionThe findings underscore the clinical significance of this axis and its embedded feedback circuits in shaping BC progression and therapeutic response.