Nucleolar METTL16 drives ccRCC tumorigenesis and pazopanib resistance via translational activation of JAG1/Notch signaling pathway.

Resistance to tyrosine kinase inhibitors (TKIs), particularly pazopanib, is the primary driver of treatment failure in patients with advanced clear cell renal cell carcinoma (ccRCC). However, the epitranscriptomic mechanisms underlying TKI resistance, especially the regulatory role of N6-methyladenosine (m6A) modification, remain poorly understood. We integrated multi-omics analyses with in vitro and in vivo functional assays, multi-cohort clinical validation, and development of targeted small-molecule inhibitors to dissect the role of methyltransferase-like 16 (METTL16) in ccRCC resistance to pazopanib. METTL16, an independent catalytically active m6A writer, was significantly upregulated in pazopanib-resistant ccRCC cells and in clinical tumor tissues. High METTL16 expression was strongly associated with advanced nuclear grade, pazopanib non-response, and unfavorable clinical prognosis in ccRCC patients. Functionally, METTL16 promoted ccRCC proliferation, metastasis, stemness, and pazopanib resistance in both in vitro and in vivo settings. Mechanistically, METTL16 bound and stabilized the small nucleolar RNA SNORA80B in an m6A-dependent manner, which was associated with enhanced translational output and activation of the JAG1/Notch signaling axis. A novel small-molecule inhibitor targeting the METTL16 methyltransferase activity pocket, METTL16-IN, markedly suppressed resistant tumor growth and synergized with pazopanib to reverse TKI resistance. Our findings support a model in which METTL16-mediated m6A remodeling contributes to pazopanib resistance through altered ribosome biogenesis and translational reprogramming.