Fig. 3

Changes in gene expression, tumor-infiltrating immune and stromal cell composition following NAC. A Volcano plots showing differentially expressed genes (DEGs) between the matched pre- and post-treatment tumors. Significant DEGs are shown as red (upregulated) and blue (downregulated) dots (fold change > 2, FDR < 0.05). B Significantly down­ and up-regulated pathways following NAC (FDR < 0.01). C, D The fractions of B cell, M2 macrophage, activated dendritic cell (aDC), endothelial cell, and gamma delta T (γδT) cell in the pre- and post-treatment tumors. P values are calculated based on the Wilcoxon signed-rank test. E–G The expression of DEGs was significantly related to positive regulations of γδT cell activation (E), antigen processing and presentation (F), and angiogenesis (G) between the pre- and post-treatment tumors. Values are presented as paired fold changes of post-/pre-treatment. P values were calculated by the Wilcoxon signed-rank test. ***P < 0.001, **P < 0.01, *P < 0.05