Fig. 1

The identification and molecular characterization of EIC. A The heatmap of gene expression clusters for 250 late-stage (IIA-IV) LUSC samples by unsupervised NMF illustrates 4 distinct expression patterns. B Stromal and immune enrichment analysis defined the cluster 2 of four expression patterns as an immune-stromal cluster. High and low gene enrichment scores are delineated in red and grey, respectively. C The enrichment scores of gene signatures identified the immune cells for the immune-stromal and other clusters. D The comparison of the absolute fractions of TME cells inferred by CIBERSORT between two classes. E,F Box plots show the differences of leukocyte fraction and TIL percentage between two classes. G Box plots show different expression levels of multiple inhibitory receptors in the immune-stromal cluster compared to the other clusters. H The consensus-clustered heatmap of 250 LUSC samples defined the immune-stromal cluster as exhausted immune class (EIC). High and low gene enrichment scores are represented in red and grey, respectively. I GSEA analysis indicated the EIC showed significant enrichments of hallmark gene sets and KEGG pathways related to cytokine, T cell receptor, epithelial mesenchymal transition, and apoptosis. J The functionally grouped network of KEGG pathways by ClueGO/CluePedia for the interpretation of metagene-specific genes’ biological roles. Colourless and colour nodes represent metagene-specific genes and KEGG pathway terms, respectively. Node colours represent distinct functional groups. Node size represents the significance of KEGG pathways. The more significant KEGG pathways are, the larger highlighted nodes. All statistical differences of two classes were compared by Wilcoxon rank-sum test; *, P < 0.05; **, P < 0.01; ***, P < 0.001; ****, P < 0.0001