NAT10-mediated N4-acetylcytidine modification promotes intrahepatic cholangiocarcinoma progression by suppressing transposable element expression via regulating chromatin remodeling [CUT&Tag]

Intrahepatic cholangiocarcinoma (ICC) remains a formidable clinical challenge due to its insidious onset, aggressive biological behavior, and propensity for early metastasis, contributing to a dismal 5-year survival rate of less than 10%. Despite advances in understanding the dynamic changes in gene regulatory networks and chromatin landscapes during tumorigenesis, the functional interplay between RNA epitranscriptomic modifications and nuclear events in ICC remains poorly elucidated. Here, we identify N-acetyltransferase 10 (NAT10), the writer for N4-acetylcytidine (ac4C) mRNA modification, as a critical regulator of ICC malignancy. Through integrative multi-omics analysis, we demonstrate that NAT10-mediated ac4C modification enhances the mRNA stability of chromatin assembly factor 1 subunit A (CHAF1A), a key chromatin regulator. Mechanistically, the NAT10-ac4C-CHAF1A axis robustly suppresses the expression of the nuclear transposable element HERV9NC, leading to diminished double-stranded RNA accumulation. This epigenetic silencing not only fuels ICC proliferation and invasion but also attenuates intrinsic innate immune responses, thereby fostering an immunosuppressive tumor microenvironment characterized by reduced cytotoxic T-cell infiltration and impaired tumor surveillance. Strikingly, pharmacological inhibition of NAT10 with Panobinostat achieves significant therapeutic efficacy in patient-derived xenograft (PDX) ICC models. Collectively, our study unveils NAT10 as a master integrator of RNA epitranscriptomic reprogramming and nuclear chromatin dynamics in ICC, providing interesting insights into the molecular basis of ICC progression. We also establish NAT10-ac4C modification as a druggable vulnerability, offering a promising therapeutic strategy for this aggressive malignancy.