Fig. 5

Patient-derived spheroid show distinct transcriptomic changes compared to monolayer cultures. a 3D Principal component analysis plot showing the variance between transcriptomes of patient tissues (blue triangles), 2D cultures (red squares), and 3D cultures (green circles) of matched patient material. b Heatmap of hierarchical clustering analysis of the logarithmic transformation of gene expression values. Samples are clustered into tissue (red) and cell culture, which splits into a 3D (green) and 2D (blue) cluster. c Scatter plot of GSEA analysis showing the top 10 most enriched gene ontology (GO) biological processes in tissues compared to 2D cultures (red) and 3D cultures (blue). Nominal enrichment score (NES) is represented on the x-axis. Dot size represents nominal p-value. d Volcano plot of differentially expressed genes in 3D compared to 2D cultures. 869 genes are upregulated (red) and 1010 genes are downregulated (blue) (adjusted p-value (padj) < 0.05, log2FC > 1), not significantly deregulated genes are indicated in grey. e Scatter plot of GSEA analysis showing the 15 top and bottom enriched GO biological processes in 3D cultures compared to 2D cultures. Nominal enrichment score (NES) is represented on the x-axis. Dot size represents the gene ratio and colour represents nominal p-value