Fig. 1: The EMT signature inversely correlates with PI3K pathway activation in basal and mesenchymal HNC patient subtypes.
A Stratification of patient HNC based on the single-sample Gene Set Enrichment Analysis (ssGSEA) score of hallmark EMT genes using TCGA-HNC mRNA-seq data identified EMTLo (n = 127) and EMTHi (n = 84) patient groups. The comparison between the two groups was performed using an unpaired t test (**** two-tailed p-value < 0.0001). Data are shown as mean ± SEM. B Hazard ratio (HR) and adjusted Kaplan-Meier curve analyses of EMT for overall survival of n = 337 patients from the TCGA-HNC cohort. HRs were estimated using multivariate Cox proportional hazard models. Asterisks indicate statistical significance per clinically-relevant factor. HR estimates are shown as dots at the centre of error bars and error bars represent 95% confidence intervals of hazard ratios by two-sided Wald test. C The EMT ssGSEA score was significantly higher in mesenchymal (n = 34) compared to basal (n = 38) HNC subtype. The results are presented as mean ± SEM with **** two-tailed p-value < 0.0001. The comparison between the two groups was performed using an unpaired t test. D Significantly negative correlation between ssGSEA scores of the EMT and PI3K/AKT/mTOR gene sets from the basal and mesenchymal HNC (n = 72, Spearman’s correlation, R = –0.3631, two-sided p-value=0.0017). 95% confidence bands of the best-fit line are shown in pink. E Volcano plot of differentially expressed proteins between basal and mesenchymal HNC samples using the TCGA-HNC reverse-phase protein array (RPPA) data. Labelled proteins associated with EMT were upregulated in the mesenchymal subtype and those associated with PI3K/AKT/mTOR were upregulated in the basal subtype. Significant differentially expressed proteins with two-sided q-value < 0.05 are highlighted in pink, NS (not significant). The comparison between the two groups was performed using an unpaired t test. F Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) terms enrichment for significant DEGs using DAVID functional annotation bioinformatics microarray analysis. Basal HNC showed enrichment for PI3K/mTOR signalling and mitotic activation while mesenchymal samples were enriched for migratory activation. Statistical values were considered significant at a false discovery rate (FDR) with two-sided p-value < 0.01. Source data are provided as a Source Data file.
