Coordinated Promoter Methylation and METTL3–YTHDF2 m6A-Dependent Decay Define a Tumor-Suppressive ZNF677 Program with Independent Prognostic Value in Oral Squamous Cell Carcinoma

Abstract Oral squamous cell carcinoma (OSCC) is an aggressive malignancy driven partly by epigenetic and epitranscriptomic dysregulation. ZNF677 is a candidate tumor suppressor, but its regulation by DNA methylation and N6-methyladenosine (m6A), and its prognostic significance, remain unclear.We integrated clinical, RNA-sequencing and DNA-methylation data from a TCGA-derived OSCC cohort (n = 25). Associations were assessed using Spearman correlation, false-discovery rate control, and bootstrap confidence intervals. Prognostic value was evaluated using Kaplan–Meier and multivariable Cox regression. Mechanistic effects were examined using MeRIP-qPCR, YTHDF2 RIP-qPCR, actinomycin-D decay assays, luciferase reporters, functional assays, and xenograft models. ZNF677 expression inversely correlated with YTHDF2 (ρ=−0.35) and promoter methylation (ρ=−0.36). Although median-dichotomized survival was not significant, continuous ZNF677 independently predicted better survival (HR = 0.10, 95% CI 0.02–0.67; p = 0.017; C-index = 0.85). METTL3 knockdown reduced ZNF677 m6A enrichment and prolonged transcript half-life, whereas METTL3 overexpression shortened it. Restoring ZNF677 suppressed pro-tumorigenic phenotypes (Hedges’ g = − 0.90; p = 0.003) and cancer-stemness markers (g = − 1.59; p = 0.016). ZNF677, METTL3, or YTHDF2 knockdown reduced xenograft tumor volume, whereas METTL3 overexpression increased tumor growth (all Tukey p < 0.001). ZNF677 undergoes coordinated DNA methylation- and METTL3–YTHDF2-dependent repression in OSCC. Higher ZNF677 is associated with improved survival and tumor-suppressive activity, supporting the ZNF677–m6A axis as a potential prognostic and therapeutic target.