Hepatocellular carcinoma-linked AXIN1 mutations drive low Wnt/β-catenin activity enabling niche-independent growth and YAP/TAZ signaling

AXIN1 organizes assembly of a destruction complex that degrades the transcriptional co-activator β-catenin, thereby preventing inappropriate Wnt/β-catenin signaling. In hepatocellular carcinoma (HCC), <i>AXIN1</i> mutations associate with a poor-prognosis subtype distinct from β-catenin-mutant HCC (<i>CTNNB1</i>). To assess how <i>AXIN1</i>-deficiency drives HCC, we introduced HCC-associated <i>AXIN1</i> and <i>CTNNB1</i> mutations in human liver cancer cells and liver-derived organoids. We show that <i>AXIN1</i> mutations activate Wnt/β-catenin signaling to varying but generally lower levels than <i>CTNNB1</i> mutations. Strikingly, premature 5'-end stop codons do not yield knockout mutations but drive alternative translation of N-terminally truncated AXIN1 variants with partial suppressor activity. All <i>AXIN1</i> variants enable liver progenitor organoids to grow without Wnt and R-spondin, indicating downstream Wnt/β-catenin activation. Additionally, Wnt/β-catenin signaling inversely correlates with YAP/TAZ-mediated signaling, leaving higher YAP/TAZ activity in <i>AXIN1</i>-mutant versus <i>CTNNB1</i>-mutant cells. Thus, <i>AXIN1</i> mutations drive physiologically relevant Wnt/β-catenin activation, providing a permissive environment for YAP/TAZ signaling, thereby distinguishing them from <i>CTNNB1</i> mutations.