DUSP12 Regulates NAT10-Mediated RNA Acetylation to Modulate DNA Repair and Therapeutic Response in Hepatocellular Carcinoma.

Hepatocellular carcinoma (HCC), an aggressive type of liver cancer, has limited treatment options, and chemotherapy remains an important clinical approach. This study investigates the role of dual-specificity phosphatase 12 (DUSP12) and its interaction with the nucleolar protein N-acetyltransferase 10 (NAT10) in HCC models under genotoxic stress. We demonstrate that doxorubicin (DX) induces greater cytotoxicity than cisplatin, correlating with a stronger DNA damage response (DDR), nucleolar stress, and NAT10 relocalization. CRISPR-Cas9-mediated DUSP12 knockout sensitized cells to DX, increasing markers of DNA damage (γH2AX, p53) and delaying DNA break repair. This was accompanied by redistribution of nucleolar proteins NAT10 and TCOF1. Remodelin treatment enhanced DX sensitivity in DUSP12 knockout cells, suggesting a context-dependent interaction between DUSP12 loss and the NAT10 inhibition. Protein interaction assays confirmed that DUSP12 binds NAT10, corroborating a regulatory interaction. DUSP12 deletion increased NAT10 phosphotyrosine levels and reduced N4-acetylcytidine (ac4C) RNA modification, consistent with altered NAT10-dependent RNA acetylation. Analysis of patient data revealed frequent DUSP12 amplification in HCC, whereas elevated DUSP12 expression was associated with poor survival and enrichment of DDR- and ribosome biogenesis-related transcriptional programs. Our findings identify the DUSP12-NAT10-ac4C axis as a novel molecular link between DDR and nucleolar stress, unveiling a potential therapeutic vulnerability in HCC.