Fig. 6

Macrophage and dendritic cell remodeling after therapy. A Boxplot showing cellular fractions of each macrophage and DC 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 < 0.10 are indicated. One-sided unpaired Wilcoxon test was used, and the P values were adjusted by the FDR method. B Heatmap of module scores of M0, M1, and M2 signatures among macrophage clusters. C Boxplots of average M0, M1, and M2 signature scores for macrophages in TN (n = 3), MPR (n = 4), and NMPR (n = 8) patients. One-sided t-test was used. D Heatmap of normalized expression of DC marker genes among clusters. E The developmental trajectory of DCs inferred by Monocle2. mregDCs (DC_LAMP3) could derive from cDC1s (DC_XCR1) or cDC2s (DC_CD1C). F Boxplots of average antigen presentation signature scores for DCs in TN (n = 2, one sample with less than 10 DC cells was removed), MPR (n = 4), and NMPR (n = 8) patients. One-sided t-test was used. G Summary of selected ligand-receptor interactions from CellPhoneDB among cancer cells and cDC2s (DC_CD1C) cells