Fig. 4: Neoadjuvant treatment leads to profound changes in gene and pathway expression in EAC.
a, PCA of single sample gene set enrichment analysis of cancer hallmark gene sets. Background shading represents a visual highlight. PC, principal component. b, Principal-component feature loadings (magnitude and direction) from PCA in a. Vectors are colored according to their biological classification of cancer hallmark gene sets. c, 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. d, Enrichment analyses in KEGG pathways in REPs between timepoint A and C. Samples from REPs: n = 19 at timepoint A and n = 19 at timepoint C. e, Enrichment analyses in KEGG pathways in NRPs between timepoint A and C. Samples from NRPs: n = 8 at timepoint A and n = 10 at timepoint C. f, Enrichment analyses in KEGG pathways during chemotherapy (all samples at timepoint B versus REPs at timepoint C). Samples at timepoint B: n = 24 and REPs at timepoint C: n = 19. Dotted lines in d–f indicate significance level of Padj < 0.05 (false discovery rate (FDR)-adjusted P values). g, Plot shows immune cell composition based on CIBERSORT analysis in REPs and NRPs during neoadjuvant treatment. Samples from NRPs: n = 8 at timepoint A, n = 8 at timepoint B, n = 10 at timepoint C; Samples from REPs: n = 19 at timepoint A, n = 16 at timepoint B, n = 19 at timepoint C. sig., significant; diff., differentiation.
