Fig. 7.

Gene expression analysis of qGBM cells from different GBM subtype confirms mesenchymal shift in quiescent GBM cells of 3D organoids.

a) Heatmaps of gene expression changes of qGBM relative to pGBM cells in 3D organoids as measured by NanoString and RNA-Seq verified reliability of Nanostring platform as compared to RNA-Seq approach to measure gene expression changes. Selected common DEGs are labeled.

b) Principal component analysis (PCA) of NanoString gene expression profiles from SD2- and SD3-iH2B-GFP GFP^high or GFP^low populations after 2 or 4 week -Dox chases (three independent experiments per paradigm).

c) Heatmap of gene expression changes of qGBM relative to pGBM cells in SD2 and SD3 organoids shows largely common patterns, with some differences between the two cell lines (note: SD2 cells are classified as mesenchymal GBM subtype, SD3 cells as proneural GBM subtype).

d) NanoString pathway score analysis of gene expression changes in SD2 and SD3 qGBM relative to pGBM cells reveals a common pattern of increased pathway scores for pathways associated with ECM, EMT, hypoxia, and TGFβ signaling. Each data point represents an independent experiment with 10–12 pooled organoids.