Fig. 3: Spatial analysis of C19MC expression across malignant cell types.
a, Schematic illustrating the genomic location of 46 miRNA members of C19MC, grouped into 17 miRNA families. b, t-SNE representation of n = 2,520 malignant ETMR cells highlighting the normalized expression of the C19MC pri-miRNA, as determined using scRNA-seq. c, t-SNE representation of n = 2,520 malignant ETMR cells colored for the relative expression of the C19MC fusion partner TTYH1. d, Microscopy images of RNA ISH analysis of the ETMR sample MUV3N stained for miR-512 (C19MC marker) and miR-124 (marker for neuron-like cells) on two consecutive tumor slices. Three tumor regions of the same slides are shown. The dashed outline indicates regions that are shown at higher magnification. Images show representative regions of one sample with a total of n = 3 patient tumors. e, Microscopy images of H&E (left) and DNA FISH (right) analysis of the C19MC-amplified sample MUV45 on consecutive tumor slices. The dashed outline indicates regions that are shown at higher magnification. The red and green boundaries in the rightmost image show automated segmentation of nuclei and subcellular C19MC foci, respectively. DNA FISH was performed and quantified on three individual ETMR samples. Images shown are representative of the three samples. f, Pseudo images showing systematic analysis of cell density and the number of distinct C19MC foci per nucleus derived from the DNA FISH images shown in e. A total of n = 35,585 nuclei were analyzed. The bar plot summarizes the numbers of C19MC foci per nucleus grouped according to cell density. e, Scale bars, 250 µm (H&E and DNA FISH, left) and 25 µm (DNA FISH, right).
