Extended Data Fig. 1: The association between the IL-17A signaling and MAPK pathways.
(a) Gene set enrichment analysis in the discovery cohort showing (left) the normalized enrichment scores in pathways according to significance level and the corresponding enrichment plot for IL-17 signaling pathway (right). (b) Volcano plot showing the difference in MAPK wt (n = 36 triple wt tumors) and MAPK mt (n = 120 tumors with BRAF/NRAS hotspot and NF1 mutated tumors) associated gene expression (log2 values) and q-values (-log10 adjusted p-values from multiple unpaired t-test with Benjamini, Krieger and Yekutieli test correction) in the discovery cohort. Each dot represents a gene; significant DEGs (q < 0.05) are shown in a color-coded manner (left). Bar plot showing the enrichment scores (-log10 adjusted p-values, Benjamini–Hochberg corrected FDR) of functional pathways as defined by the Wiki, Reactome, and KEGG pathway databases (right). (c) Box and whiskers plots for gene expression of Th17/IL-17-inducing genes in the TCGA-SKCM cohort grouped according to BRAF status (n = 197 wt and n = 166 mt biologically independent tumors). Boxplot show the median (line) and interquartile ranges (Tukey whiskers that extend to 1.5 × IQR); p-values represent Mann-Whitney U test. (d) Scatter dot plots for gene expression of Th17/IL-17-inducing genes in the MAPKi dataset (Long et al, Rizos et al, and Kakavand et al datasets: GSE61992, GSE50509, GSE99898 series combined) grouped according to sample collection time point (PRE: before, ON: during therapy). Dots represent biologically independent tissues (n = 47 ON, n = 11 PRE) and are color-coded according to dataset; shown is mean ± 95% CI; p – values are from unpaired t-test. (e) qPCR analysis of BRAF mt (WM9, WM983B, 451Lu) melanoma cells treated with 1 nM dabrafenib/0.2 nM trametinib vs. DMSO for 7 days. Bar plot shows mean ± SEM where single dots represent biologically independent cell lines; p-values are from unpaired t-test. Shown is one representative out of three independently performed experiments. All p-values are two-tailed. mt: mutant, wt: wild-type, GSEA: gene set enrichment analysis, FDR: false discovery rate, NES: normalized enrichment score, TCGA: The Cancer Genome Atlas, SKCM: Skin cutaneous melanoma, MAPKi: mitogen-activated protein kinase inhibitor, IQR: interquartile range.
