Fig. 2: Earliest biological response to RNAi-mediated β-catenin inhibition is observed 3-days following LNP treatment.
From: Precision targeting of β-catenin induces tumor reprogramming and immunity in hepatocellular cancers
a LNP treatment scheme in β-catenin-Nrf2 (β-N) model. b (Left) Representative gross liver images and (Right) liver weight/body weight (LW/BW) comparing LNP-CTRL (n = 4) and LNP-CTNNB1 (n = 4; 1 mg/kg) β-N treated animals 3-days post 1st LNP treatment. c qPCR RNA expression levels of Ctnnb1 and β-catenin target genes (Glul, Ccnd1, Lect2, Rgn) between LNP-CTRL (n = 3) and LNP-CTNNB1 (n = 3) β-N treated animals. d, e Representative immunohistochemistry (IHC) images for glutamine synthetase (GS), Ki67, and TUNEL comparing LNP-CTRL and LNP-CTNNB1 treated β-N animals 3-days post 1st LNP treatment. Scale bar represents 100 μm. f Quantification of number of Ki67- and TUNEL-positive cells across multiple high-power fields (HPF) between LNP-CTRL (n = 3) and LNP-CTNNB1 (n = 3) treated β-N animals 3-days post 1st LNP treatment (p = 0.0006). g Principal component analysis of bulk RNA-sequencing transcriptomic profiles of β-N and β-M model treated with LNP-CTRL or LNP-CTNNB1 and harvested 3-days post-LNP treatment, using all genes (n = 3–4 per condition and model). h Venn diagram highlighting number of common downregulated differentially expressed genes (DEGs) (n = 230) between β-N and β-M models treated with LNP-CTRL or LNP-CTNNB1 3-days post-LNP treatment. i Venn diagram highlighting number of common upregulated DEGs (n = 73) between β-N and β-M models treated with LNP-CTRL or LNP-CTNNB1 3-days post-LNP treatment. DEGs defined by FDR = 0.05 and fold change >1.5. j Heatmap of selected common downregulated and upregulated genes demonstrating normalized z-score expression value in each model with each LNP treatment condition from (h) and (i). k Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway gene set enrichment analysis (GSEA) in β-N model comparing LNP-CTRL and LNP-CTNNB1 treated animals. l KEGG pathway GSEA in β-M model comparing LNP-CTRL and LNP-CTNNB1 treated animals. For (k, l), normalized enrichment score (NES) was normalized from ES, which was calculated by Kolmogorov–Smirnov-like statistic and the p-value was calculated using the one-tailed empirical permutation test procedure. Created in BioRender. Lehrich (2025) https://BioRender.com/kymtir0. For (b), (c), and (f), data are presented as mean values ± standard deviation (SD) and P-values calculated by unpaired two-tailed Student’s t-test. Source data are provided as a Source Data File. *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001.
