Fig. 1: scRNA-seq and multiplexed imaging of ETMR tumors.
a, Overview of clinical and molecular characteristics of the ETMR scRNA-seq cohort (n = 11 tumor samples). Sex, age at sample collection, tumor type, location and C19MC activation status are indicated. Samples indicated with X originated from the same patient at different disease stages. b, t-SNE visualization of high-quality malignant cells (n = 2,520 cells) from six samples of the fresh cohort, integrated using Harmony. Cells are colored according to the sample of origin. c, t-distributed stochastic neighbor embedding (t-SNE) visualization of n = 2,520 cells colored according to two major malignant cell clusters, identified using hierarchical clustering. d, Heatmap showing the relative expression of 100 genes specific to malignant clusters 1 (stem-like signature) and 2 (differentiated signature). Single cells (n = 2,520 cells) are ranked according to the difference in signature scores. The percentages of cells belonging to malignant clusters 1 and 2 are indicated above. Selected genes of interest are indicated on the right. e, Heatmap showing the relative expression of signature genes in n = 26 ETMR samples profiled using bulk expression arrays. Samples are ranked according to the difference in signature scores, shown above the heatmap. Red indicates the primary lesion (ET1) and two recurrences (ET1R1, ET1R2) collected from the same patient. Correlations to clinical and molecular annotations are indicated below the heatmap. Age at diagnosis is given in years. A two-sided Student’s t-test was used to determine the statistical significance between scores for malignant cluster 1 in primary and recurrent ETMR. PNET, primitive neuroectodermal tumor. f, t-SNE visualization of n = 2,520 cells colored according to the expression of the marker genes LIN28A (red) and STMN2 (green). g, Representative hematoxylin and eosin (H&E) and IF staining for LIN28A (red), STMN2 (green), and 4′,6-diamidino-2-phenylindole (DAPI) (blue) across the histological subtypes ETANTR, MEPL and EBL. Staining was performed on at least n = 3 different tumor samples for each subtype. EBL, ependymoblastoma; ETANTR, embryonal tumor with abundant neuropil and true rosettes; MEPL, medulloepithelioma. h, GSEA of malignant gene signatures in transcriptional profiles generated from microdissected rosette-like and neuropil-abundant tumor regions. NES, normalized enrichment score; Padj, adjusted P value. GSEA P values were calculated using a permutation test and adjusted for multiple comparisons using the Benjamini–Hochberg procedure. g, Scale bars, 300 µm.
