Fig. 5.

Spatial transcriptome reveals the immune microenvironment and CNV landscape after neoadjuvant nivolumab therapy. A Spatial visualization with definitions of the spots in the 16 samples. B Density plot of subtype score of CAF between R and NR groups. C Bar chart showing the proportion of the various cell types (left) and the total number of spots (right) in all samples. D The proportion of the various cell types in the R and NR groups as according to the degree of pathologic tumor necrosis (left panel) and heatmap showing the Odds Ratio (OR) of every spot between the R and NR groups (right panel). E Density plot of M2 polarization and proliferation of TAM between R and NR groups. F Immunohistochemical stains for CD4 and CD8 T cells in representative cases of the R and NR groups. G Correlation between immunohistochemical positivity rate (score) of CD4 and CD8 T cells and the degree of pathologic tumor necrosis. H Heatmap showing the difference in the CNV absolute scores between the R and NR groups. Each row represents a chromosomal arm, and each column represents a cell-type spot. I Boxplot showing the statistical comparison of CNV absolute score in the Tumor/T cell spot between R and NR groups. J Spatial visualization of CNV absolute scores in representative cases of the R and NR groups