Bulk transcriptomic analysis of two models of zebrafish beta-catenin-driven HCC

Up to 41% of hepatocellular carcinomas (HCCs) result from activating mutations in the CTNNB1 gene encoding ß-catenin. ß-catenin has dual cellular functions as a component of the Wnt signaling pathway and adherens junctions. HCC-associated CTNNB1 mutations stabilize the ß-catenin protein, leading to nuclear and/or cytoplasmic localization of ß-catenin and downstream activation of Wnt target genes. In patient HCC samples, ß-catenin nuclear and cytoplasmic localization are typically patchy, even among HCC with highly active CTNNB1 mutations. The functional and clinical relevance of this heterogeneity in ß-catenin activation are not well understood. To define mechanisms of ß-catenin-driven HCC initiation, we generated a Cre-lox system that enabled switching on activated ß-catenin in 1) a small number of hepatocytes in early development; or 2) the majority of hepatocytes in later development or adulthood. We discovered that switching on activated ß-catenin in a subset of larval hepatocytes was sufficient to drive HCC initiation. To determine the role of Wnt/ß-catenin signaling heterogeneity later in hepatocarcinogenesis, we performed RNA-seq analysis of zebrafish ß-catenin-driven HCC. Ingenuity Pathway Analysis of differentially expressed genes in the Cre-lox HCC model revealed that “Cancer” and “Liver Tumor” categories were significantly altered, indicating transcriptional similarities with human HCC and other vertebrate HCC models. At the single-cell level, 2.9% to 15.2% of hepatocytes from zebrafish ß-catenin-driven HCC expressed two or more of the Wnt target genes axin2, mtor, glula, myca, and wif1, indicating focal activation of Wnt signaling in established tumors. Thus, heterogeneous ß-catenin activation drives HCC initiation and persists throughout hepatocarcinogenesis. Overall design: Examination of HCC and nonHCC liver samples from two different models of zebrafish, compared to wildtype/nonHCC siblings.