Extended Data Fig. 7: DC and monocyte/macrophage subclustering.
From: A single-cell map of intratumoral changes during anti-PD1 treatment of patients with breast cancer
a, Heatmap showing 3 marker genes for each DC phenotype. b, UMAP of DCs color-coded for one marker gene per DC phenotype. c, Heatmap of genes specific for cDC2 and pDC showing that ASDCs share characteristics of cDC2s and pDCs. d, UMAP of DCs color-coded for PD-L1/L2 and CCL19. e, Heatmap showing expression of the mregDC signature described by Maier and colleagues26 across DC phenotypes. f, Relative contribution of each DC phenotype (in %) to all cells pre-treatment, comparing Es (n = 9) versus NEs (n = 20). P>0.05 for all by two-sided Mann-Whitney test. Box, median ± interquartile range; whiskers, minimum and maximum. g, Volcano plot showing DEGs in DCs comparing Es versus NEs pre-treatment. Black dots: P=ns; gray: P < 0.05; red: P < 0.05 and absolute log2FC ≥ 0.5. P values by MAST test and Bonferroni-corrected (Seurat). Genes in bold are discussed in the manuscript. h, Heatmap showing marker genes for each myeloid cell phenotype. i, UMAP of myeloid cells color-coded for one marker gene per myeloid cell phenotype. j, Heatmap showing expression of functional genes in the 10 myeloid cell phenotypes. k, Boxplot showing relative percentage of DCs and macrophages detected in each patient (n = 31) by scRNA-seq. Box, median ± interquartile range; whiskers, minimum and maximum. FC: fold change. l, GSEA (hypeR) based on REACTOME for DEGs in macrophages comparing Es versus NEs pre-treatment.
