Fig. 3

A gene signature to separate TAMs by ontogeny in mouse and human gliomas. a PCA of human TAMs in the space of genes that are ontogeny-specific in murine gliomas. The density curves of a Gaussian mixture model are in gray. b Consensus clustering of TAMs in the space of genes that are ontogeny-specific in murine gliomas. PCA-based cluster assignments from (a) are indicated by color. c Heatmap of the average expression (z-score) of indicated genes in windows of ten cells, sorted according to their PC1 score. d Log2 ratios of gene expression in murine blood-derived TAMs over murine microglial TAMs, averaged over the mouse models of Bowman et al. * = adjusted p value < 0.05 in both mouse models. Error bars indicate standard error of the mean. e Pearson correlation coefficients, computed via RNA-seq of LGGs and GBMs from TCGA (n = 558 cases). Genes are ordered by hierarchical clustering, boxes indicate a dendogram cut obtaining two clusters. f Top left: Flow cytometric analysis of TAMs gated on live CD11b + myeloid cells from a primary GBM (SF10941) stained for P2RY12 and CX3CR1. Top right: Flow cytometric analysis of TAMs gated on live CD11b + myeloid cells from a primary GBM (SF10941) stained for P2RY12 and HLA-DR. Bottom: Flow cytometric analysis of TAMs gated on live CD11b + myeloid cells from a primary GBM (SF11425) stained for P2RY12 and CD49D (encoded by ITGA4). g Gene expression from the Ivy Glioblastoma Atlas Project. Each column annotates expression in RNA‐seq of an anatomically defined tumor compartment. h In situ hybridization for BIN1 and TGFBI in anatomically annotated regions (indicated by color) for two primary GBMs