Figure 3

LHFPL3-AS2 knockdown reduced expression of genes, known to regulate epithelial morphology, including CTNNB1. (A) PCA using 11,489 protein-coding genes that passed expression filtering and colored by LHFPL3-AS2 knockdown (g1 and g2 in red) and gCtl (blue). (B) Heatmap of 584 genes that were differentially expressed between LHFPL3-AS2 knockdown cells (g1 and g2) compared to controls (gCtl, fold change >  = 1.5 and FDR corrected p <  = 0.05). (C) ToppGene³² functional annotation enrichment of 462/584 downregulated gene protein-coding genes with the associated − log10(FDR P value). (D) STRING⁴³ predicted interaction network with visualization using Cytoscape³⁴ of the downregulated genes. (E) qPCR validation of genes that were reduced in the mRNAseq dataset, normalized to GAPDH. The two-sided t-test is shown. *P ≤ 0.05, **P ≤ 0.01, ***P ≤ 0.001, ****P ≤ 0.0001. (F) Schematic representation of Wnt signaling activation by LiCl. (G) Western blots (representative experiment out of 3 replications) of LHFPL3-AS2 knockdown cells (g1 and g2) and controls (gCtl) with and without LiCl to activate the Wnt pathway showing reduction of CTNNB1 and TCF4 at baseline and after LiCl in LHFPL3-AS2 knockdown cells, and of CDH1 with LiCl.