Extended Data Fig. 6: APC cell types and states in melanoma clinical samples.
From: Tumour-reactive heterotypic CD8 T cell clusters from clinical samples
a, Dotplot of UCell scores for a set of defined APC types to discriminate APC types in Fig. 3i. Rows labelled by annotated cell states. Colours, average UCell score; dot size, percentage of cells expressing the UCell geneset. b, scRNA-seq UMAP of sequenced DCs and B/plasma cells highlighting the main cell states (left) and average frequencies (right) (n = 5 patients). Each patient was weighted equally (n = 3 for DCs and n = 2 for B/plasma cells). DC and B/plasma cell states were annotated based on marker genes and signatures31,36,37,38,40,41,42. Bonferroni-adjusted P values from generalized linear mixed-effects models; significant increase in cell state frequency of APCs in T cell clusters versus single APCs is indicated. Patients were excluded if <20 cells were detected in the respective APC type from T cell clusters. c, Dotplot showing gene expression of a panel of APC-related genes discriminating different APC cell states. Rows labelled by annotated cell states of Fig. 3j and (b). Colours, average expression of gene; dot size percentage of cells expressing the gene. d, Absolute number of APCs per annotated cell state subdivided by patient (left) or stratified by origin (right): single APCs or APCs from T cell clusters. e, Distribution of single APCs and APCs from T cell clusters on the UMAP of sequenced monocytes and macrophages, DCs and B/plasma cells as provided in Fig. 3j or (b) respectively. f, Frequency of cell states in single APCs or APCs from T cell clusters per patient (n = 5). FDR-adjusted Fisher’s exact test was used. Significantly increased cell state frequencies of APCs in T cell clusters versus single APCs are indicated. Patients were excluded if <20 cells were detected in the respective APC type from T cell clusters. g, Circos plots of top 30 inferred ligands and their receptor interactions focusing on the differential signalling of different APC states towards T cells. Mono/macrophages and DCs were analysed separately. Arrow transparency reflects predicted ligand signalling activity. Ligands or receptors were assigned to specific APC or T cell states respectively based on expression level differences. Ligands for APC states enriched in T cell clusters are highlighted. If the ligand is coloured and bold, it is uniquely associated with that cluster enriched group. Ligands labelled as “other” are not associated with the cluster-enriched groups. Receptors shared between multiple or all T cell states are labelled unspecific. *P < 0.05; **P < 0.01; ***P < 0.001; ****P < 0.0001.
