Extended Data Fig. 1: BMP signaling is downregulated and CHRDL1 is highly expressed in H3.3K27M and ACVR1 WT DIPG subtype.
(a) Heatmap to show single sample GSEA (ssGSEA) scores of hallmark gene sets in control group and the drug (JQ1, Panobinostat, THZ1, or Corin) treatments group in SU-DIPG6 or SU-DIPG13 cells (GEO: GSE94259, GSE1105722). Each column represents a sample with or without drug. Each row represents the specific gene signature of the pathway and the normalized z-score of the ssGSEA score corresponding to the sample is displayed in the heatmap where the colors correspond to the normalized z-score. (b) GSEA analysis using the “BMP signaling signature” gene set to compare PPCs and the H3.3K27M and ACVR1 WT DIPG cells (SU-DIPG6 and SU-DIPG13). (c, d) GSEA analysis using the “BMP signaling signature” gene set to compare PPCs and the H3.1K27M and ACVR1 mutant DIPG cell (SU-DIPG4)23 (c); or to compare 10 normal tissues and 18 H3.3K27M and ACVR1 WT DIPG tissues (d). (e) FPKM (Fragments Per Kilobase of exon model per Million mapped fragments) values of CHRDL1 in RNA-seq data of TT150630, TT150714, and PPCs (n = 2 independent experiments). (f) FPKM values of CHRDL1 in RNA-seq data of pons and a group of H3K27M DIPG tissues. Genotype of H3 and ACVR1 in each sample is marked10. (g) Unsupervised clustering of single-cell H3K27M DIPG RNA-seq data using the most variable genes9. (h-k) Gene expression of OLIG2, ASCL1, SOX2 and CHRDL1 in (g). Expression of each gene was scaled to [0, 2] for visualization. (l) Among the CHRDL1-expressing cells in (g), boxplots representing CHRDL1 gene expression differences between ACVR1 mutant (MUT, blue, n = 286 tumor single cells) and wild-type (WT, red, n = 136 tumor single cells) (left). Boxplots representing CHRDL1 gene expression differences between H3.3K27M (red, n = 406 tumor single cells) and H3.1K27M (blue, n = 16 tumor single cells) (right). Boxplots define the interquartile range (IQR) split by the median, with whiskers extending to the most extreme values within 1.5 × IQR beyond the box, statistical significance was calculated by two-tailed unpaired Student’s t-test.
