Fig. 4: TME analysis reveals cell-cell interaction between tumor cells and myeloid cells in longitudinal meningioma.

a tSNE visualization of 21,800 cells from macrophages and monocytes colored according to corresponding cell types. Detailed cell counts are available in the Source Data file. b Heatmap for expression of representative marker genes in myeloid cell types of meningioma (n = 21,800 cells)(top) and tSNE visualization of each marker genes (bottom). c Cell type proportion of myeloid cell (n = 21,800) by per-sample basis. Detailed cell counts are available in the Source Data file. d The pathway enrichment analysis between primary (n = 10,776) and recurrent (n = 11,024) myeloid cells. p-values are from two-sided Fisher’s exact test. e Beeswarm plot showing the distribution of log₂ fold change in abundance between conditions in neighborhoods from different cell type clusters (n = 21,341 cells). Each dot represents a neighborhood, a group of cells clustered based on shared gene expression profiles. f Comparison of integral signal with input and output signals between myeloid (n = 21,800) and tumor cells (n = 37,460). Statistical significance was assessed by permutation in CellChat. g Circle plots showing the interactions and strengths among different cell types in primary (left) (n = 10,776) and recurrent (n = 11,024) myeloid cells (right). h IHC staining images of COL6A3, C1QA, and CD163 in matched primary (MEN10) and recurrent (MEN10) meningiomas. Representative images are shown; IHC performed on 36 tumor samples (18 primary meningioma and 18 recurrent meningioma samples). Scale bar, 300 μm. i Scatter plot showing correlation between COL6A3 and C1QA expression scores in primary (n = 18) and recurrent (n = 18) meningiomas. p-values were calculated by Spearman correlation tests. Source data are provided as a Source Data file.