Extended Data Fig. 10: NPM1 is overexpressed in HCC and required for WNT-driven hepatocyte proliferation.
From: Nucleophosmin supports WNT-driven hyperproliferation and tumor initiation
a, Npm1 expression in murine livers of indicated genotypes and timepoints normalised to wild-type (GEO data: GSE230137) (wild-type(d10), R26lsl-MYC/lsl-MYC(d4), Ctnnb1+/(Dex3)(d10), Ctnnb1+/(Dex3)R26lsl-MYC/lsl-MYC(d10), n = 3; Ctnnb1+/(Dex3)(d4), Apcfl/fl(d10), R26lsl-MYC/lsl-MYC(d10), n = 4; Ctnnb1+/(Dex3)R26lsl-MYC/lsl-MYC(d4), Apcfl/flR26lsl-MYC/lsl-MYC(d10), n = 5). One-way ANOVA with Tukey’s test. b, c, NPM1 expression in TCGA-LIHC tumours stratified by MYC amplification or CTNNB1 mutation status. d, e, WNT signatures GSVA scores in wild-type and mutant CTTNB1 TCGA-LIHC tumours. f, g, NPM1 expression and WNT signatures GSVA scores correlation scatterplots in TCGA-LIHC tumours. Two-sided Pearson correlation. h, HCC patient survival with high/low NPM1 (n = 249 low, n = 115 high). Log-rank test; tick marks: censored subjects. i, H&E, NPM1, glutamine synthetase (GS) and BrdU staining in Npm1+/+ (n = 3) and Npm1fl/fl (n = 5) livers 120 days post high dose AAV8.TBG.Cre. Scale bars, 50 μm. j-l, Liver-to-body weight ratios, BrdU+ cells (9-13 10X fields of view (FOV)) and blood alanine transaminase (ALT) levels from groups in (i). m-o, GS staining, GS+ cells and H-score quantification in Ctnnb1+/(Dex3)R26lsl-MYC/lsl-MYC±Npm1fl/fl livers ten days post high dose AAV8.TBG.Cre (n = 5/group). Scale bars, 1 mm. p, q, BrdU staining and quantification (six 10X FOV) in Apcfl/fl and Apcfl/flNpm1fl/fl livers ten days post high dose AAV8.TBG.Cre (n = 3/group). Scale bars, 100 μm. r, s, BrdU and NPM1 staining, and BrdU+ cell quantification (ten 10X FOV) in BrafLSL-V637E/+ (n = 5) and BrafLSL-V637E/+Npm1fl/fl (n = 4) livers four days post high dose AAV8.TBG.Cre. Scale bars, 100 μm. t, BrdU, NPM1 and p21 staining in BrafLSL-V637E/+ and BrafLSL-V637E/+Npm1fl/fl livers (n = 4/group) eight days post high dose AAV8.TBG.Cre. Scale bars, 100 μm. u, BrdU+ (ten 10X FOV) and v, p21+ hepatocytes from groups in (t). Unpaired two-tailed Mann Whitney test. w, RNAseq comparing Ctnnb1+/(Dex3)R26lsl-MYC/lsl-MYC±Npm1fl/fl livers ten days post-induction (n = 4/group). Two-sided Wald test, Benjamini–Hochberg correction. Significant (adj p.value < 0.05, log2FC < -1 or >1) transcripts in red. x, y, Shallow NPM1 deletion frequency and/or TP53 mutations in TCGA-LIHC (n = 351). Two-sided Fisher’s exact test. Data (bar charts), mean ± SEM. Boxplots boxes extend from 25th-75th percentiles, whiskers from minimum to maximum values; the line denotes the median. Statistics in (b-e), (j-l), (n-o), (q), (s), (u): unpaired two-tailed t tests. Significant p-values in red.
