DUSP12 regulates NAT10-mediated RNA acetylation to modulate DNA repair and therapeutic response in hepatocellular carcinoma

Hepatocellular carcinoma (HCC), the most common type of primary liver cancer arising from hepatocytes, is an aggressive hepatic malignancy with limited therapeutic options and poor prognosis. Chemotherapy remains an important treatment for advanced disease, though the mechanisms influencing drug sensitivity remain elusive. This study investigates the role of dual-specificity phosphatase 12 (DUSP12) and its interaction with the nucleolar protein NAT10 in the hepatic cellular response to genotoxic stress. We demonstrate that doxorubicin (DX) induces superior cytotoxicity over cisplatin in hepatocellular carcinoma models, associated with a stronger DNA damage response (DDR), nucleolar stress, and delocalization of NAT10 from the nucleolus to the nucleoplasm, where it colocalized with DUSP12. Genetic ablation of DUSP12 sensitized cells to DX, increasing DNA damage markers (p53, p-p53(Ser15), {gamma}H2AX(Ser139)) and delaying the repair of DNA strand breaks. DUSP12 knockout also caused redistribution of nucleolar proteins NAT10 and TCOF1. Pharmacological inhibition of NAT10 in DUSP12-deficient cells further enhanced DX sensitivity, revealing a synthetic-lethal interaction. We identified a direct association between NAT10 and DUSP12s functional domains, with evidence indicating NAT10 is a DUSP12 substrate. Consequently, DUSP12 knockout elevated NAT10 phosphotyrosine levels and reduced ac4C RNA acetylation, indicating functional impairment of NAT10. Corroborating these findings, patient data showed frequent DUSP12 amplification in HCC, correlating with poor survival and enrichment in DDR and ribosome biogenesis pathways. Our results establish the DUSP12-NAT10-ac4C axis as a molecular link between the DDR and nucleolar stress, highlighting previously unrecognized therapeutic vulnerability in HCC.