Fig. 5

The EMT profile is altered most strongly and in opposite directions in sensitive versus resistant HNSCC cell models after FGFR inhibition. A Normalized enrichment score (NES) summary of six gene set enrichment analyses (GSEA) for MSigDB hallmark gene sets. Top 20 hallmarks with the highest variance between DEG comparison groups (n = 4; IR, 6 Gy X-ray irradiated; FGFRi, FGFR inhibitor treatment; FGFRi/IR, combined treatment) are depicted. Significance levels (p.adj, adjusted p-value ≤ 0.05) are indicated by triangle size. Triangle direction represents enrichment or suppression in the corresponding DEG comparison group per cell model. B NES summary graph of multiple GSEA of indicated HNSCC-related EMT gene sets (Table S3) in each DEG comparison group of both cell models. Significance levels (adjusted p-value ≤ 0.05) are indicated by triangle size. Triangle direction represents enrichment or suppression in the corresponding DEG comparison group. C Expression heatmap of selected EMT marker genes in both cell models. Genes are annotated by their corresponding HNSCC gene signatures (Table S3). Columns represent individual biological replicates; rows are clustered hierarchically. D Western blot analysis of selected EMT marker proteins from whole cell lysates of 3D lrECM grown cell models upon indicated treatments. β-actin served as loading control. Representative blots are shown. Where indicated, cells were treated with 2 µM FGFRi (DMSO was used as control). E Densitometric analyses of EMT marker expression shown in ‘D’. Mean fold changes (± standard deviation; n = 3) compared to corresponding non-irradiated/irradiated controls are shown. All samples were normalized to their corresponding β-actin loading control (Two-way ANOVA utilizing normalized densitometry data, Tukey multiple comparison test, **p ≤ 0.01; *p ≤ 0.05)