Fig. 8

Tie2 responsive single cell gene expression data derived modules translate to clinical output of HNSCC patients.(A) (i) UMAP plot showing colour coded clustering of cancer cells co-cultured with UT-CAF, TGF-CAF and TGF > > Tie2i-CAF. (ii) Violin plot showing EMT and stemness AUC score generated by R tool ‘AUCell’. (iii) Table depicting gene expression based classified molecular subtypes of HNSCC signatures (from [47]) (iv) Pseudo-bulk analysis of AUCell scores over cancer cells co cultured with distinct CAF subtypes for the given molecular subtype gene signatures. (B) Heatmap showing trajectory variable gene expressions from early to late pseudotime. (C) Expression heatmap of co-regulatory gene modules for each cluster of merged cancer cell subset. Marked green box indicates similar expression pattern of module 2, module 5; and module 4, module 8 on exclusive Tie2 responsive cancer cell clusters. (D) AUC scoring of cancer cells from the aforementioned patient groups from Puram et al. and Quah et al. HNSCC datasets shows significant enrichment of modules 4 & 8 in High BMP4 group (C1-like CAF high tumors) in both datasets, and modules 2 & 5 in High ITGA3 group (C2-like CAF high tumors) in Puram et al. and Quah et. al. dataset. (E) Prediction of survival probability of TCGA HNSCC patients. Kaplan Meier plot showing survival probability of HNSCC patients harbouring gene signatures of (i)Top 30 upregulated or (ii)Top 30 downregulated genes of TGF-CAF cocultured cancer cells form bulk RNAseq data (iii) Survival probability of patients harbouring gene expression signature obtained from scRNAseq analysis of unique subset of cancer cells co-cultured with TGF-CAF, as mentioned