Sustained YAP1 activation induces DNA demethylation that promotes the development of hepatocellular carcinomas lacking driver gene mutations

Recent advances in next-generation nucleotide sequencing have led to the identification of driver gene mutations (DGMs) in human cancers. However, a significant percentage of human malignancies without DGMs has been reported, and the mechanism of their tumorigenesis remains unclear. Here we show that sustained YAP1-TEAD activation induces the formation of DGM-negative hepatocellular carcinomas (HCCs). Whole exome sequencing of six independent YAP1-TEAD-induced HCCs identified three of them to be DGM-negative. Reduced representation bisulfite sequencing of these six HCCs pinpointed shared DNA sites whose demethylation led to oncogene expression. Single-cell spatial transcriptomics of a DGM-negative HCC revealed multiple constituent hepatocyte subsets, including a subpopulation expressing the demethylation-promoting enzyme TET1. Our study implicates the YAP1–TEAD–TET1 axis as a cause of DGM-negative HCC formation, and documents a fundamental molecular mechanism that may be applicable to a broad range of human cancers. *Misaki Kosaka, Yoshimi Okamoto-Uchida1, & Haruka Hirose contributed equally as first authors.