Extended Data Fig. 7: Characterization and mapping of ATRT patient samples.
From: Stalled developmental programs at the root of pediatric brain tumors
a, Deconvolution analysis (CIBERSORT) of bulk ATRT patient samples (n = 11), using mouse developmental populations. b, Top 25 leading edge genes driving ssGSEA enrichment of F-e15 Dorsal RGC signature in bulk ATRT samples (n = 11), and other tumor types of focus (ETMR: n = 14, WNT-MB: n = 10, HGG: n = 12). Genes which are specific to the leading edge of ATRT are indicated with boxes; all other genes appear in the leading edge for this signature in other tumors. Boxplots: center line, median; box limits, upper and lower quartiles; whiskers, 1.5x interquartile range. c, Best matching developmental populations for bulk tumors by ssGSEA, when the true lineage of origin (glial populations for HGG, and neuronal populations for WNT MB and ETMR) is removed, indicating that most tumors map non-specifically to RGCs in the absence of the lineage of origin. d-e, scRNA-seq profiling of two additional patient ATRT samples as in Fig. 7. Left: t-SNE visualization and clustering, with non-malignant clusters labeled, and number of cells indicated in parentheses. Right panels: mean expression of inferred ATRT subtype, microglia, and cytotoxic T-cell gene signatures, and expression of VIM, represented in t-SNE embedding (top) and violin plots generated as in Fig. 7 (bottom). Expression of each gene set was normalized to a [0, 1] scale for visualization in t-SNE embeddings. f-g, snRNA-seq profiling of two additional patient ATRT samples as in (d-e).
