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. 2020 Jun 4;30(10):833–853. doi: 10.1038/s41422-020-0338-1

Fig. 4. Addition of macrophages activates extracellular matrix and invasiveness signatures.

Fig. 4

a UMAP analysis of RNA-seq data from GSCs grown in (1) sphere culture, (2) tri-culture, (3) tetra-culture with THP1-derived macrophage, and (4) tetra-culture with hiPSC-derived macrophages. b Heatmap displaying mRNA expression of differentially expressed genes between conditions. c Upset plot showing the number of differentially expressed genes between conditions. For conditions containing sphere cultured cells, genes were considered differentially expressed if the log2 fold change of mRNA expression was greater than 0.5 (or < −0.5) with an adjusted P value of 1e−0. For other conditions, genes were considered differentially expressed if the log2 fold change of mRNA expression was greater than 0.5 (or < −0.5) with an adjusted P value of 1e−5. d Volcano plot of transcriptional landscapes profiled by RNA-seq comparing the CW468 GSC grown in tetra-culture containing THP1-derived macrophages vs GSCs in the tri-culture model. The x-axis depicts the log transformed fold change, while the y-axis shows the log transformed P value adjusted for multiple test correction. n = 2 technical replicates per condition. e Pathway gene set enrichment connectivity diagram displaying pathways enriched among gene sets upregulated (red) and downregulated (orange) in GSCs in the 3D tetra-culture system vs tri-culture system. f GSEA of the extracellular matrix structural constituent pathway between tetra-culture and tri-culture models. FDR q value = 0.008. g GSEA of the Anastassiou multicancer invasiveness pathway between tetra-culture and tri-culture models. FDR q value = 0.02. h Gene set enrichment analysis (GSEA) of the collagen degradation pathway between tetra-culture and tri-culture models. FDR q value = 0.02.