Fig. 5

Fibroblast contexture within the tumor microenvironment of Esophageal Adenocarcinoma and gene expression profile changes following NACT. A UMAP embedding overlaid with cluster cell type annotations, UMAP embeddings split by treatment and tissue type and Automated per-cell annotations of cell type using SingleR with the hpca coarse reference dataset. B UMAP embeddings overlaid with selected canonical Fibroblast sub-type marker genes. C Average expression profile of top cluster marker genes. Dot size indicates the percentage of the cluster showing expression. D Breakdown of cluster proportions by sample, chemotherapy treatment and tissue type. E 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 sample Fibroblast cells and p values determined by Mann-Whitney test. F Summary of genes identified as differentially expressed in post vs pre NACT EAC tumor sample data. DEG count noted alongside cluster: (pre expresn=2654sed, post expressed). G Summary of genes identified as differentially expressed in EAC Tumor (T) vs Adjacent Normal (AN) sample data. DEG count noted alongside cluster: (AN expressed, T expressed). Coloured points indicate DEGs (BH adjusted p < 0.001 and absolute average log2FC > 0.5)