FTO promotes the progression of triple-negative breast cancer by regulating the m6A methylation of NFKBIE

Epigenetic research, particularly involving m6A RNA methylation-a dynamic and reversible posttranscriptional modification-has increasingly demonstrated its critical involvement in cancer pathogenesis. Although the m6A demethylase FTO is implicated in breast cancer (BC), its specific regulatory mechanisms against triple-negative breast cancer (TNBC) has not been clearly defined. Quantitative PCR (qPCR) was used to compare m6A regulatory enzyme expression in TNBC patient tissues with that in normal breast tissues, identifying FTO as the most differentially expressed enzyme. Two randomly selected TNBC/normal tissue pairs were subjected to methylated RNA immunoprecipitation sequencing (MeRIP-Seq). Integrated analysis utilizing the SRAMP and RMBase databases predicted potential FTO target genes. Transcriptome sequencing of FTO-overexpressing TNBC cell lines identified downstream pathways. Dual-luciferase reporter assays and MeRIP-qPCR validated the functional role of FTO and its target, NFKBIE, and their regulatory interaction in TNBC. Compared with normal samples, clinical samples from TNBC patients presented significantly decreased FTO expression (p < 0.05) and correspondingly elevated global m6A levels. MeRIP-Seq confirmed substantial differences in m6A methylation (R = 0.23, p < 0.05). Bioinformatics and transcriptome analyses identified NFKBIE as the primary FTO target. Dual-luciferase assays demonstrated that FTO overexpression specifically modulated wild-type (WT), but not mutant (MT), NFKBIE promoter activity (p < 0.05). MeRIP-qPCR verified the FTO-mediated reduction in m6A methylation at three specific NFKBIE sites (p < 0.05). Functional assays (CCK-8, Transwell invasion/migration, and scratch wound healing) indicated that FTO overexpression significantly enhanced TNBC cell proliferation and motility; these oncogenic phenotypes were partially rescued by concurrent NFKBIE overexpression. FTO regulates NFKBIE expression via m6A-dependent demethylation, establishing a pivotal FTO-NFKBIE regulatory axis that drives TNBC progression. FTO overexpression promotes TNBC cell proliferation, migration, and invasion, effects that are partially reversible through NFKBIE restoration.