Fig. 7

Neutrophil remodeling after therapy. A UMAP plot of neutrophils colored by clusters. B Heatmap of normalized expression of neutrophil marker genes among clusters. NETs, neutrophil extracellular traps; ISGs, interferon-stimulated genes. C The developmental trajectory of neutrophils inferred by Monocle2. The Neu_S100A12 cells were the roots of trajectory, and differentiated into Neu_CCL3 or Neu_IFIT3 cells. D Two-dimensional plots showing the dynamic expression of CXCR2 and CXCR4 during the neutrophils aging along the pseudo-time. E Boxplot of average expression of CXCL8 (IL8) in Neu_CCL3 cells in TN (n = 3), MPR (n = 4), and NMPR (n = 7, one sample with less than 10 Neu_CCL3 cells was removed) patients. One-sided t-test was used. F Boxplot showing cellular fractions of each neutrophil cluster in TN (n = 3), MPR (n = 4), and NMPR (n = 8) patients. Center line indicates the median, lower, and upper hinges represent the 25th and 75th percentiles, respectively, and whiskers denote 1.5× interquartile range. All differences with adjusted P < 0.05 are indicated. One-sided unpaired Wilcoxon test was used, and the P values were adjusted by the FDR method. G Heatmap showing potential ligands driving the phenotype of Neu_CCL3 neutrophils. H Summary of selected ligand-receptor interactions from CellPhoneDB between Neu_CCL3 neutrophils and Macro_SPP1 macrophages. I Scatter diagram showing a significantly positive correlation between the Neu_CCL3 signature and Macro_SPP1 signature in TCGA-LUAD patients. P values were determined by two-sided Pearson correlation test. J Inferred regulation network between Neu_CCL3 neutrophils and Macro_SPP1 macrophages