Figure 3 from A Compendium of Syngeneic, Transplantable Pediatric High-Grade Glioma Models Reveals Subtype-Specific Therapeutic Vulnerabilities
Year: 2023
Type: other
Abstract: A, Uniform manifold approximation and projection (UMAP) of KNF and KPP integration colored by cell type annotation summarized in Supplementary Table S5 (left) and by replicate (right). Cells that did not meet quality control thresholds, as determined from individual sample analysis, and cells with no cell type consensus are not plotted. OL, oligodendrocyte. B, Distribution of ssGSEA scores per cell for human tumor signatures in OPC-projected cells of KNF samples (top) and KPP samples (bottom). Signatures were derived from differential expression of bulk RNA-seq data for tumor subtypes (see Methods). N = 34,326 cells in KNF; N = 3,892 cells in KPP. C, UMAP as in A with cells colored by cluster. D, Predominant cell types per cluster of KNF and KPP integration (left), corresponding proportion of each genotype within the cluster (middle), and number of cells per cluster (right). Only cells passing QC and with a cell type consensus are considered. Cell types comprising at least 30% of the cluster are shown. ASTR, astrocyte. E, Proportion of cells per replicate annotated as OPC (left), microglia (middle), and macrophages (right). F, Proportion of cells with detected Mag (left) and Pdgfra (right). G, UMAPs of each replicate from individual sample analysis with cells colored by normalized expression of Myrf (left) and Cspg4 (right). H, Mean inferred TF activity scores (scaled) and percent of cells with activity of TF shown for clusters 0, 7, 10, and 2, with predominant cell types of OPC, proliferating OPC (P-OPC), newly forming oligodendrocytes (NFOL), and mature oligodendrocytes, respectively; cluster number is indicated in parenthesis. Representative TFs with differing activity patterns between genotypes are shown. I, Proportion of cells with detected Ptprc (left) and Ly86 (right). J, Mean expression of DAM signature genes in immune cluster 5, with cells grouped by genotype. P < 2.2e-16.
Language: English
Subfield: Genetics
Field: Medicine
Domain: Health Sciences
Open Access status: gold
OpenAlex ID: W4383495952