Fig. 2: Molecular characterization of EwS and CDS tumoroid models.
From: Patient-derived tumoroids from CIC::DUX4 rearranged sarcoma identify MCL1 as a therapeutic target
a Visualization of DNA methylation profiles of CDS and EwS models (n = 9) integrated with methylation profiles of the sarcoma classifier reference cohort30 (n = 1077) using t-SNE dimensionality reduction. Samples are color-coded according to 62 tumor and three control DNA methylation classes. The inset shows a magnification of the dashed-line area and indicates the location of the individual models. For a description of abbreviations, see extended legend in the supplementary section. b Fusion genes and mutational landscape of EwS and CDS tumoroid models. Data from corresponding primary tumors is shown for comparison when available. c Schematic representation of the CIC (NM_001379485.1) and DUX4 gene architectures, with translocation breakpoints in CDS models indicated by red lines. d Unsupervised hierarchical clustering based on RNA-seq gene expression data from EwS and CDS tumoroid models. The 2000 most variably expressed genes were used. e Volcano plot depicting genes differentially expressed between EwS and CDS models. Analysis was performed with DSeq2 using fold change> 2 and FDR < 0.1. The ten most differentially expressed genes, as well as CDS markers ETV4, ETV5 and WT1, are labeled.
