Fig. 3: KAT5-dependent cell state changes across 9 different GBM isolates.

Single cell gene expression was used to assess changes in cell states in response cells after KAT5 inhibition in vitro. GSCs were collected for analysis post nucleofection of sgCD8 (control) and sgKAT5 RNPs after 5 days of growth in NSC self-renewal media. a Scheme for comparing KAT5 versus CD8 KO populations in scRNA-seq data. For each isolate, we co-embedded scRNA-seq data from KAT5 KO and control CD8 KO cells into a single merged scRNA-seq object. Then, de novo clustering was applied to each GSC line, and each cluster was examined for admixtures of KAT5 and CD8 KO cells. For assessment of gene expression changes, for clusters mainly composed of control CD8 KO cells (CD8 KO:KAT5 KO cell ratios of ≳3) or KAT5 KO cells (CD8 KO: KAT5 KO cell ratios of ≲.33), cluster marker gene enrichment (or “method 2”) was used. For clusters composed of mixed populations of CD8 and KAT5 KO cells (cell ratios between 3 and. 33), DESeq2 was used to compare gene expression changes between CD8 KO to KAT5 KO cells within that cluster (or “method 1”). For both methods cutoffs were log2 fold change of 0.321 and adjusted pvalue for 0.05. The example in (a) highlights three clusters from each category. UMAPs for all 9 GSC isolates can be found in Supplementary Fig. 6. The full results from this analysis can be found in Supplementary Data S6. b Comparisons of KAT5 KO dependent changes in cell states for 9 GSC isolate. The genes found significantly changed for each GSC cluster by either method 1 or 2 were compared using the Fisher’s exact hypergeometric enrichment test and the -log10 p value and the overlapping marker genes were recorded for each pairwise comparison. Call out clusters from a are shown as filled circle, square, and triangle. *denotes novel KAT5 KO clusters from Fig. 2. c Gene set enrichment analysis for gene enriched in CD8 KO. Comparisons of 272 genes enriched in CD8 KO clusters with S, S/G2, and G2/M phase genes form the ccAF cell cycle classifier. d Comparisons of 718 gene enriched in KAT5 KO clusters with Neural G0 genes and outer radial glial genes (from human fetal brain development). Genes were required to overlap with ≥50% of clusters to be considered for (c, d).