Extended Data Fig. 4: Gene program changes in response to safusidenib treatment.

a. Comparison of all tumor cells in matched pre- and post-safusidenib samples using GSEA following the methodology described by Spitzer et al¹. Each dot represents a gene-set. X axis shows the GSEA normalized enrichment score (NES), Y axis shows the Adjusted p-value. b. RRHO2 plot comparing GSEA results for all cells to GSEA analysis performed by Spitzer et al. Negative log₁₀ p-values represent the correlation strength, and low p-values in the upper right and lower left quadrants represent concordant up and down regulation, respectively. c. Comparison of AC-like tumor cells in matched pre- and post-safusidenib samples using GSEA via ranked lists according to DEG results. Each dot represents a gene-set and color indicates whether the gene-set belongs to a glioma program and top enriched pathways are annotated. X axis shows the GSEA normalized enrichment score (NES), Y axis shows the adjusted p-value. Line indicates significance threshold (Adjusted p-value 0.05). d. As in (c) for OPC-like tumor cells. e. As in (c) for Progenitor tumor cells. f. Enrichment of the ranked list used for GSEA via ranked lists according to DEG results for AC-like (left), OPC-like (middle) and progenitor cells (right). Dots represent the percentage of genes, in a sliding window of 30 genes at fixed intervals of 0.10 (by -log₁₀ p-value accounting for the direction of logFC), that overlap four main glioma programs. Trend line was computed using LOESS regression. g. Log-fold change in the IFN program compared to log-fold change in STING and HIF-1-alpha programs in AC-like tumor cells pre- relative to post-safusidenib treatment (n = 9 participants, t-test). Participant legend as in (h). h. Log-fold change in the IFN program in AC-like tumor cells compared to proportional change in immune cells pre- relative to post-safusidenib treatment (n = 9 participants, t-test). i. Spatial maps of the average log expression of genes in “Inflammation Response” pathway (left) and cells annotated as immune cells (right) with cell density indicated by contour plots for participant O-01. Pathway inferred by CytoSPACE integration of spatial transcriptomics and snRNA-seq and summarized as hex bins. Scale, 1 mm.