Fig. 2

Modulation of T cell contexture, functional signatures and key cell subtype ratios within the tumor microenvironment of Esophageal Adenocarcinoma following NACT. A UMAP embedding overlaid with cluster cell type annotations and UMAP embeddings split by treatment and tissue type. B Average expression profile of top cluster marker genes. C UMAP embeddings overlaid with selected canonical T cell type marker genes. D Scaled enrichment score calculated by GSVA for selected MSigDB Hallmark gene sets. E UMAP embeddings overlaid with selected signature module scores and distributions of module scores stratified by chemotherapy treatment. F Breakdown of cluster proportions by sample, chemotherapy treatment and tissue type. G Comparison of Adjacent Normal (AN) vs Tumor (T), pre vs post chemotherapy and Mandard score cluster proportions. Points represent within-sample cluster proportion of total T cells. H CD4:CD8, CD4:Treg and CD8:Treg ratios stratified by tissue type and chemotherapy. P values determined by Mann-Whitney test