Fig. 2: MAPK-pathway mediates inflammatory signaling and immune escape.

a Fold-changes by RNAseq expression analysis following 3 days kinase inhibitor treatment in oncogene-driven cancer cell lines. b Fold-changes in BRAF^mut melanoma patients sequenced before (Pre) or during (On) kinase inhibition or after resistance (Resist) to BRAF or BRAF + MEK inhibition. c Fold-changes in primary cells derived from a KRAS^mut PDAC GEMM after 48 h treatment with trametinib compared to controls. d Left: Immunoblot of key inflammatory signaling nodes in EGFR^mut PC9 cells treated for 12 or 24 h with osimertinib (osi, 300 nM) or trametinib (tram, 100 nM). Right: Immunoblot of treated KRAS^mut A549 (trametinib, 100 nM) and BRAF^mut A375 (vemurafenib, 1 µM) for 3 days. Each representative blot of n = 3 independent experiments. e FACS estimation of surface expression in EGFR^mut cells following 3 days treatment with osimertinib (300 nM) or trametinib (100 nM). mean fluorescent intensity (MFI) as fold-change normalized to DMSO controls. Bars display mean ± SEM of independent biological replicates (PC9 B2M/HLA: osi n = 10, tram n = 5; VTCN1: osi n = 5, tram n = 8; HCC827 B2M/HLA: osi/tram n = 4, VTCN1 osi n = 3, tram n = 4; HCC4006 HLA/B2M osi n = 6, tram n = 3, VTCN1 osi/tram n = 3); P-values adjusted by Benjamini–Hochberg. f Combined GSEA of RNA-seq from PC9, HCC827 and HCC4006 cells treated with trametinib (100 nM, 72 h). (Significance as FDR-corrected q-values). g Pairwise correlations of single-sample (ss) GSEA scores for key gene sets in RNA-seq of untreated BRAF^mut melanoma patients (n = 14, top) or TCGA lung adenocarcinoma patients (LUAD, n = 515, bottom). Color indicates Pearson correlation coefficients. h Left: Correlation of RNA-seq inferred CD8 T cell infiltration with an expression of the negative MAPK feedback regulator DUSP6 in untreated BRAF^mut melanoma patients (n = 11) (TPM = transcripts per million). Right: Distribution of individual correlations of CD8 T cell proportion with an extended set of MAPK activity genes⁴⁵ in patients from (b and Fig. 1k). Distribution of the n = 10 genes’ correlation coefficients with CD8 T cell proportion was tested for significance using one-sample t tests adjusted with Bonferroni–Holm. i Left: Correlation of RNA-seq-based CD8 T cell infiltration with DUSP6 in untreated TCGA lung adenocarcinoma patients (n = 350) grouped as n = 10 patients per bin and normalized expression/CD8 T cell proportion as median per bin. Right: Correlation of CD8 T cell proportion with genes of the extended n = 10 MAPK genes in unbinned patients (n = 350). Significance was calculated with two-sided paired t tests for log fold-changes (e) and one-sample t tests in (h, right) and (i, right). Spearman correlation was used in (h, i). Boxplots display median (center line), 25th/75th percentile (lower/upper box hinges), whiskers extend to the most extreme value within 1.5× interquartile range (IQR) of the hinges. Data points beyond the whiskers are displayed individually. Source data are provided as a Source Data file.