Extended Data Fig. 7: Macrophage diversity in the TME of T-VEC-treated BCCs.
a, UMAP presenting post-treatment myeloid cells with a total of four cluster (FCN1 + , C1QC + , SPP1+ and one triple negative cluster). b, Bubble plot indicating the average expression of selected marker genes in each cluster (FCN1 + , C1QC + , SPP1 + ). c, Bar plots presenting the composition of myeloid cells, split by pathological and clinical response. The colors reflect the ones of the immune cell clusters of panel a). d-f, Functional enrichment analysis of FCN1 + (yellow), C1QC+ (green), SPP1 + (pink) macrophages with (d) the Gene Ontology Biological Processes (GOBP) (e) MSigDB Hallmarks and (f) BioPlanet gene sets, using enricher one-sided hypergeometric test with false discovery rate correction (Benjamini & Hochberg) [111]. Adjusted p-values are shown. The universe is defined by all detected genes in the macrophage subset. g, Violin plots showing inflammatory tumor-associated macrophages (TAMs) (IFN_TAM1), pro-angiogenic macrophages (Anigo_TAM1), classical tumor-infiltrating monocytes (Classical_TIM1), resident tissue macrophages (RTM_TAM1) and immune regulatory TAMs (Reg_TAM1) signatures in relation to FCN1 + , C1QC + , SPP1+ and triple negative cell clusters. h, Feature plot presenting the gene expression of FCGR3A (CD16). i, Box plots displaying the proximity analysis of CD68+ macrophages surrounding CD20 + B cells (p = 0.0052) and CD4 + T cells (p = 0.1754) within 10 µm, pre- versus post-treatment from patients with paired tumor tissue samples (n = 16) (two-sided Wilcoxon signed-rank test, statistical significance determined with p < 0.05). The box plots display the distribution of cell counts for each immune cell population based on response categories. Data are presented as mean values +/- SEM. Each box extends from the 25th (Q1, lower bound of box) to the 75th (Q3, upper bound of box) percentile, the horizontal line in the center of the box represents the median value (Q2). The whiskers extend to the 5th (min, lower bound) and the 95th percentile (max, upper bound). Dots represent individual patient data points.
