Fig. 4: NR2F2-Iso2 controls an expression signature enriched in metastasis promoting gene sets.
a Ridge and Bubble plots showing transcriptomic changes after NR2F2-Iso2 loss in 4L cells are significantly associated with reduced angiogenesis and EMT gene sets. p.adj indicates FDR. b Heatmap showing Log2 fold changes of 500 NR2F2-Iso2 signature genes that were significantly down-regulated in 4L and 12-273BM cells upon NR2F2-Iso2 knockdown. Most of these genes are up-regulated in MeWo cells upon ectopic NR2F2-Iso2 expression. Scatter plots and Spearman tests (p < 0.001) correlate average NR2F2-Iso2 signature gene expression directly with NR2F2-Iso2 expression (c) and indirectly with NR2F2-Iso2 CpG methylation (d) in human melanoma samples from TCGA. Scatter plots showing the NR2F2-Iso2 signature gene score is significantly higher in unmethylated compared to methylated (e) and metastatic compared to primary (f) melanoma samples from TCGA (two-tailed Mann–Whitney test, bar represents median). g Heatmap showing Log2 fold-change expression of selected EMT genes between shNR2F2-Iso2 and shSCR expressing 4L or 12-273BM cells. h qRT-PCR and i western blotting show significantly reduced SNAI1 expression in shNR2F2-Iso2 compared to shSCR expressing 4L or 12-273BM cells. (N = 3, two-way ANOVA, data shown from one representative experiment; bars represent SD; tubulin served as western blot loading control). j–m tSNE and Violin plots showing scRNA-seq data from the Tyr-CreER; BRAFCA/+/ PtenFL/FL;R26-LSL-tdTomato mouse model [ref. 31.]. j Dimensionality plot identifies neural crest-like (NC), melanocytic (Mc), intermediate (I), EMT-like, and proliferative (P) melanoma cells. Feature plots show enrichment of (k) Nr2f2 expression and (l) NR2F2-Iso2 signature score in melanoma cell states. m Violin plots show Nr2f2-Iso2 signature gene enrichment in EMT-like cells (two-way unpaired Mann-Whitney test). Source data are provided as a Source Data file.
