Extended Data Fig. 5: Additional profiling of orthotopic xenograft states in H3K27M models.

A. Kaplan-Meier survival analysis (with 95% confidence interval shaded) for xenograft-bearing mice using two other H3K27M cell lines, displaying loss of tumor formation by H3K27M-KO cells in DIPGXIII (n = 17 animals H3K27M group, 15 KO), and substantially greater latency and decreased penetrance of tumor formation by H3K27M-KO cells in HSJ019 (n = 11 H3K27M group, 16 KO group). B. Bubble plots representing fractions of tumor cell populations annotated by cell type classification (bubble size) based on ssGSEA mapping to reference cell types (see Methods). Each bubble is also colored based on the level of cPRC1 looping target gene expression (bubble color), revealing consistent depletion across classified cell types in H3K27M samples, and lower proportions of differentiated cell types. C. In scRNA-seq datasets, the expression levels cPRC1 looping genes are measured on a cell-by-cell level using single sample Gene Set Enrichment Analysis Score (see Methods for more detail). Distributions of scores across population of cells are plotted, with annotations of cell type population on the x axis (see Fig. 5 and Methods for more detail). These scores reveal that cPRC1 looping genes are repressed in a homogenous manner across all cell types in H3K27M pHGG, whereas in WT pHGG, various cell types more highly express these genes.