Extended Data Fig. 8: Reanalyzes of immune related results excluding post-treatment samples from patients with complete remission.
(a) Hierarchical clustering with heatmap showing the significantly differentially expressed pathways between the two clusters (right cluster is predominantly samples from timepoint A/B and left cluster is predominantly timepoint C). Sample IDs and timepoints are annotated at the bottom of the heatmap. (b) Enrichment in KEGG pathways in Responders between Timepoint A and C (left) and in NonResponder between Timepoint A and C (right). Dotted lines indicate significance level of padj < 0.05. FDR-adjusted P values. Samples from NonResponder: n = 8 at timepoint A, n = 8 at timepoint B, n = 8 at timepoint C; Samples from Responder: n = 19 at timepoint A, n = 16 at timepoint B, n = 18 at timepoint C. (c) Plot shows immune cell composition based on CIBERSORT analysis in Responders and NonResponders during neoadjuvant treatment. Samples from NonResponder: n = 8 at timepoint A, n = 8 at timepoint B, n = 8 at timepoint C; Samples from Responder: n = 19 at timepoint A, n = 16 at timepoint B, n = 18 at timepoint C. (d) Absolute CD4 and CD8 cell counts per mm2 during treatment. (e) T cell phenotypes in EAC patients during treatment were analyzed for markers of T cell activation and exhaustion. Fractions of CD8 cells (top row) and CD4 cells (bottom row) were compared among patient groups and visualized by violin plots. (f) Ratio of activated and exhausted CD8 cells (left) and CD4 cells (right) during treatment including both single and multi-region IMC datasets. (g) Ratio of activated and exhausted CD8 cells (left) and CD4 cells (right) stratified by treatment type. P values in all panels are calculated by the two-sided Wilcoxon test, unless other stated.
