Fig. 4

Single-cell RNA-seq analysis reveals interaction between representative TAM subsets and exhausted T cells. a, b UMAP projection of 122,626 single cells isolated from 17 glioma patients (six grade2/3 LGG and 11 grade 4 GBM samples), coloured by LGG/GBM (a) and normal/malignant cells (b). c–e UMAP plot coloured by expression pattern of PTPRC (c), CD68 (d) and CD3D (e). f Chord plot showing the significantly interacting pathways between TAMs and lymphocytes in the glioma TME. g UMAP plot and violin plot showing SPP1’s expression pattern and levels in LGG and GBM. h UMAP projection of the three clusters of TAMs in the 17 glioma patients. i Dot plot indicating the expression of CCL3, CCL4L2, IL1B, AIF1, C1QA, C1QB, SPP1, S100A11 and LGALS1 in each cluster of the TAM subsets. j Box plot showing the proportion of AIF1⁺TAM and SPP1⁺TAM in total cells between LGG and GBM. k UMAP projection of six clusters of lymphocytes in the 17 glioma patients. l Dot plot indicating the expression of marker genes in each cluster of the lymphocytes. m Heatmap revealing the intensity of outgoing and incoming signals for TAM and lymphocyte subsets. Statistical significance was determined by unpaired two-tailed Student’s t-test for (j). *p < 0.05