CDK13 drives clear cell renal carcinoma through METTL16-mediated m⁶A modification of ACLY mRNA

Cyclin-dependent kinase 13 (CDK13) has emerged as a critical regulator of oncogenic metabolism, but its role in rewiring lipid metabolism in clear cell renal cell carcinoma (ccRCC) remains undefined. Here we identify CDK13 as a master orchestrator of lipid dysregulation in ccRCC, demonstrating that it drives de novo lipogenesis through a phosphorylation-dependent RNA N⁶-methyladenosine (m⁶A) modification axis. Clinically, CDK13 overexpression correlates with advanced tumor stage, poor prognosis and aberrant lipid accumulation in patient-derived ccRCC tissues. Mechanistically, CDK13 directly phosphorylates the methyltransferase-like protein 16 (METTL16) at Ser329, augmenting its catalytic activity to install m⁶A modifications on ATP-citrate synthase (ACLY) messenger RNA. These m⁶A marks are selectively recognized by the YTHDC2 reader protein, leading to mRNA stabilization and increased acetyl-CoA production, which fuels lipogenesis and sustains ccRCC aggressiveness. Genetic or pharmacological disruption of the CDK13-METTL16-ACLY axis synergistically suppresses lipid deposition, tumor growth and metastasis in vitro and in vivo. Notably, targeting CDK13 with the small-molecule inhibitor 1NM-PP1 potentiates METTL16 depletion-mediated anticancer effects. Our findings establish a kinase-RNA modifier axis that links CDK13 to epitranscriptomic control of lipid metabolism, positioning the CDK13-METTL16-ACLY pathway as a promising target for precision therapies against ccRCC.