CTNNB1 Mutations and Overexpression of Wnt/β-Catenin Target Genes in WT1-Mutant Wilms’ Tumors

Gain-of-function mutations in exon 3 of β-catenin (CTNNB1) are specific for Wilms’ tumors that have lost WT1, but 50% of WT1-mutant cases lack such “hot spot” mutations. To ask whether stabilization of β-catenin might be essential after WT1 loss, and to identify downstream target genes, we compared expression profiles in WT1-mutant versus WT1 wild-type Wilms’ tumors. Supervised and nonsupervised hierarchical clustering of the expression data separated these two classes of Wilms’ tumor. The WT1-mutant tumors overexpressed genes encoding myogenic and other transcription factors (MOX2, LBX1, SIM2), signaling molecules (TGFB2, FST, BMP2A), extracellular Wnt inhibitors (WIF1, SFRP4), and known β-catenin/TCF targets (FST, CSPG2, CMYC). β-Catenin/TCF target genes were overexpressed in the WT1-mutant tumors even in the absence of CTNNB1 exon 3 mutations, and complete sequencing revealed gain-of-function mutations elsewhere in the CTNNB1 gene in some of these tumors, increasing the overall mutation frequency to 75%. Lastly, we identified and validated a novel direct β-catenin target gene, GAD1, among the WT1-mutant signature genes. These data highlight two molecular classes of Wilms’ tumor, and indicate strong selection for stabilization of β-catenin in the WT1-mutant class. β-Catenin stabilization can initiate tumorigenesis in other systems, and this mechanism is likely critical in tumor formation after loss of WT1.