Extended Data Fig. 6: Spatial associations of myeloid cells and glioma niches.

a) Schematic illustrates the analysis approach for spatial transcriptomics samples: cNMF was applied to spatial transcriptomic data from Ravi et al. to define broad transcriptomic tumor niche programs; in parallel, the cell content of each spot was inferred based on scRNA-seq signatures (RCTD demultiplexing; see Methods). Spatial Pie plot (middle) of a representative 10X Visium section depicts tumor niche programs. Each pie represents a spot and is colored by expression of the indicated tumor niche programs. Spatial plot (right) of the same section depicts relative expression of the indicated cell type programs (gray scale indicates RCTD-predicted spot proportions). b) Heatmap shows expression of genes (rows) grouped by niche program across all spots (columns) in the cohort of spatial transcriptomic samples. Top 40 genes of each niche program are shown. Gene expression data is column normalized, then log normalized and scaled by variance. c) Spatial plots show relative expression of cellular programs in the 10X Visium section shown in Fig. 2a (gray scale indicates RCTD-predicted spot proportions). d) Dotplot displays the spatial proximity enrichment score between niche programs, calculated independently per sample (p-value ordinary least squares, see Methods). Dot size denotes the proportion of samples showing a significant correlation (p-adj <0.01), while color signifies a positive (red) or negative (blue) correlation. e) Dotplot displays the spatial proximity enrichment score between cell programs, calculated independently per sample (p-value ordinary least squares, see Methods). f) Network graph illustrates recurrent spatial relationships of cell types in tumor microenvironment across spatial transcriptomic samples. Nodes denote cell types, with edges marking significantly enriched proximities between cell types, observed in at least 40% of samples with an average enrichment score >0.1. Edge width reflects this average score. g) Scatter plot exhibits the mean Scavenger Immunosuppressive program score (x-axis) versus the MES2 or MES1 cancer program score (y-axis) across glioma samples in the scRNA-seq dataset. Ordinary least square results are shown (line, and p-value).