Fig. 4

Single-cell analysis of cells grown in myxoid liposarcoma scaffolds and as cell-derived xenografts. A Experimental single-cell analysis workflow. B Uniform manifold approximation and projection (UMAP) analysis of individual HT1080 cells with and without FUS::DDIT3-eGFP expression grown in myxoid liposarcoma (MLS) scaffolds or as xenografts, n = 1387 (scaffold HT1080 wild-type (WT)), 894 (scaffold HT1080 FUS::DDIT3-eGFP), 1315 (xenograft HT1080 WT), 819 (xenograft HT1080 FUS::DDIT3-eGFP). C Bar chart illustrating the percentage of cells in each cell-cycle phase, G1, S and G2/M, based on known cell-cycle-associated genes, for each sample. D–G Pseudo-time trajectory analysis performed with Monocle 2 using DDR-Tree for dimensional reduction. D Distribution of cells along the pseudo-time trajectory is shown. E Pseudo-time trajectory with marked sample group. F Expression of FUS::DDIT3-eGFP across the pseudo-time trajectory (estimated by measuring eGFP expression). G Significantly differentially expressed genes across pseudo-time are clustered based on co-expression into four modules. The color schemes for pseudo-time and sample group from subplots D and E are used. H Functional enrichment analysis using the Reactome gene set collection for the genes in module 1. Top 5 categories are shown based on q-value. Size of dots indicate gene count. I–L Expression of selected genes across the pseudo-time trajectory, I HLA-DRA, J PGK1, K FN1 and L MKI67