Fig 1: Perturbed immune cell transcriptomes and cellular interactions in prostate tumor(A) Violin plot of gene module score of GO term corresponding to antigen processing and presentation in tumor versus normal in myeloid cells. Kruskal-Wallis test was performed between normal and tumor for each cluster and p < 0.05 was considered statistically significant.(B) Pie chart of co-activating and co-inhibitory DEGs between normal (light colored sections) and tumor (dark colored sections) in myeloid clusters. Darker sections indicate genes that were that were upregulated in tumor versus normal and lighter section indicate upregulation is in normal versus tumor (> = 1.25 log2 fold change). Grey sections indicate < 1.25 log2 fold change.(C) Mean expression dot plot of costimulatory/coinhibitory molecules. Increasing expression corresponds with increasing gradient from white to red (MNP/B cell/epithelial/stromal) or white to blue (T/NK/B cell) corresponding to increasing expression value. Size of circles indicate the percentage of cells expression the gene.(D) Violin plot of gene set test (AUCell) results in CD8 cytotoxic T cell cluster for murine CD8 T cell exhaustion gene set curated from (Doering et al., 2012). Significance is denoted by ∗p < 0.05 (Mann-Whitney test).(E) GSEA of KEGG pathways for NK CD16neg tumor versus normal. Statistically significant pathways are colored and labeled.(F) Mean expression dot plot of leading edge genes in cytokine-cytokine receptor interaction as in (E). Only genes that are expressed by at least 20% of cells are plotted.(G) (Top) Expression of CCL5 and prediction/label transfer score of NK CD16neg cells in visium data of normal and tumor prostate sections. (Bottom) Spatial correlation of CCL5 with NK CD16neg cells in prostate cancer visium data. Only positive correlations are plotted; increasing value of correlation is shown as a gradient from white to red.(H) CellPhoneDB receptor-ligand interaction analysis between B cell and myeloid clusters.(I) Representative immunofluorescence confocal microscopy of BAFF and HLA-DR in human prostate tumor section. Scale bars, 20 μm.(J–L) (J) Expression of TNFSF13B and prediction/label transfer score of MAC-MT cells, and correlation of TNFSF13B with MAC-MT cells in prostate cancer visium data. Only positive correlations are plotted; increasing value of correlation is shown as a gradient from white to red. CellPhoneDB receptor-ligand interaction analysis between (K) fibroblasts and T cell clusters, and fibroblast and myeloid clusters and (L) myeloid clusters with LE clusters split by group (N = normal; T = tumor). The order of the receptor-ligand interactions corresponds to the order of the cell-types i.e., cell type A expressing molecule A interacts with cell type B expressing molecule B. Size of circles and color gradient corresponds to the receptor-ligand interaction score, which purple, blue, green to yellow for increasing values. Significant interactions (p < 0.05) are highlighted in red. See also Figure S7.