Extended Data Fig. 2: Ctnnb1ex3/WT;R26LSL-MYC Tumours express Igfbp2.
From: Hepatic zonation determines tumorigenic potential of mutant β-catenin
End point Ctnnb1ex3/WT;R26LSL-MYC liver tumours. a and b, Images of IGFBP2 immunohistochemistry and images of in situ hybridisation for Igfbp2, n = 3. Scale bars, 100 μm. c, Tumor scoring for Igfbp2 positive and negative tumours, Biological replicates n = 5. d-f, GSEA of Hoshida22 subtypes, comparing single clones to lesions in day-60 spatial transcriptomic data. For all GSEA plots the NES was calculated by normalising to the mean enrichment of random samples, and two-sided permutation testing was applied to determine statistical significance. Benjamini-Hochberg multiple test correction was applied to the resulting, p-adj = p adjusted value. g, Gene set variation analysis (GSVA) on TCGA-LIHC samples stratified by CTNNB1 activating mutation status and MYC copy gain status. Samples with Genomic identification of significant targets in cancer (GISTIC) copy number 1 (gain) or 2 (high level amplification) are considered to have copy gains. Mean GSVA scores for samples within each group are shown. h, Heatmap showing differential gene expression of factors that regulate CTNNB1 activity at a protein and transcriptional level from the spatial transcriptomics assay. Selected regions of interest: n = 34 clonal; n = 49 lesions. Significantly changed genes highlighted in bold text. Biological replicates: n = 4 mouse livers. Black scale bars, 100 μm. Red scale bars, 20 μm. NES = normalised enrichment score, p-adj = p adjusted value.
