KDM6A alternative splicing induced by 25(OH)D inhibits breast cancer cell stemness through repressing TRAP1 transcription.

25-Hydroxyvitamin D (25(OH)D), a metabolite of vitamin D, has demonstrated anticancer properties; however, the role of alternative splicing in mediating these effects remains poorly understood. In this study, we reveal for the first time that 25(OH)D exerts antitumor effects by promoting exon 13 skipping of KDM6A (KDM6A Δexon13), which suppresses the proliferation and stemness of breast cancer cells and lacks H3K27 demethylase activity. Mechanistically, CUT&Tag and RNA-seq analyses demonstrated that KDM6A Δexon13 induces the accumulation of H3K27me3 at the promoter region of TRAP1, thereby inhibiting its transcription. Consequently, the downregulation of TRAP1 reduces Smad2/3 phosphorylation. Furthermore, KHDRBS3 was identified as the splicing factor of KDM6A Δexon13 and was regulated by 25(OH)D. Notably, 25(OH)D exhibited a synergistic effect with GSK-J4, a specific inhibitor of KDM6A, in suppressing breast cancer cell growth. Collectively, our findings uncover a novel anticancer mechanism of 25(OH)D, highlight the critical role of KDM6A Δexon13 in breast cancer progression, and provide further evidence supporting the correction of 25(OH)D deficiency in breast cancer patients.