Fig. 3

Characterization of CD8 + effector T cells within the ESCC TME. A The CellPhoneDB-generated heatmap shows the count of cell–cell interactions in baseline tumors obtained from pCR, MPR, and IPR patients. B UMAP embedding of T cells overlaid with cluster cell type annotations (left), sample label (middle), and proportional sample contributions to each cell type cluster (right). C Dot plots of canonical T cell marker gene expression in each T cell lineage. Dot size and color indicate the fraction of expressing cells and normalized expression levels, respectively. D Volcano plots show the differentially expressed genes (DEGs) in subgroup analysis. E Gene Ontology (GO) pathway enrichment analysis of the top 10 enriched biological processes (BP) for baseline ESCC tumor in pCR patients compared to IPR patients. F Box plots show the mRNA expression of MT2A in baseline ESCC tumors of pCR and IPR patients at the single-cell level. G The Venn diagram shows the intersections of three gene sets. Gene sets were based on DEG analysis comparing baseline tumors of patients with different pathological responses to neoadjuvant chemo-immunotherapy. H, I Dot plots show the top 30 (based on the expression level) ligand-receptor interactions from CD8 + effector T cells obtained from baseline ESCC tumors of IPR (H) and pCR patients (I). The size of the circle represents the P values, and the color of the circle indicates the average expression level of interacting pairs. The cell clusters labeled in blue and red on the x-axis indicate that CD8 + effector T cells act as ligands and receptors in the interaction pairs, respectively. J, K Dot plots illustrate a range of immune checkpoint interaction pairs involving CD8 + effector T cells and various other cell types obtained from pre-treatment ESCC tumors of IPR (J) and pCR patients (K)