TME subtype identification and verification
TCGA
Because we observed differential enrichment of hallmarks between well and poor responders, we further calculated the single-sample GSEA score of 13 cancer-associated hallmarks and performed half-supervised cluster analysis. To explore the correlation between inflamed TME-related signatures and clinical benefits, we defined ‘TME subtype’, and patients were clustered and labeled as IE, tumor-proliferation and fibroblast-enriched subtypes according to the half-supervised results of 13 cancer-associated hallmarks. To confirm the observed TME subtype pattern, we applied the TME subtype in the TCGA ESCC cohorts and several published pan-cancer immunotherapy datasets. Hierarchical clustering was then performed on these samples with heatmap v.1.0.12 using row-scaling, Euclidean distance and ward.D2 clustering.