Fig. 4

Phenotypic differences between ATRX knockout and wildtype gliomas in an IDH-mutant background. A A schematic overview of the murine studies. B An enzymatic cleavage assay, indicating homozygous knockout in ATRX exon 9 (Top), a Western blot showing complete loss of ATRX protein (bottom). C Fluorometric 2-HG detection assay, comparing wildtype IDH1 and IDH1R132H overexpression in ATRX-KO SB28 cells, *t test p<0.05. D Representative BLI images of ATRX-KO and wildtype intercranial tumors. E BLI timeseries. F Percentages of tumor-infiltrating monocytic-lineage cells expressing the given markers in ATRX-KO vs. wildtype, in an IDH1R132H background. G (Top) Differential expression test of snRNA-seq data via MAST, comparing tumor-infiltrating monocytic-lineage cells between ATRX-KO and wildtype tumors in an IDH1R132H background. (Bottom) Differential expression test of snRNA-seq data via MAST, comparing neoplastic cells between ATRX-KO and ATRX-wildtype tumors in an IDH1R132H background. H Differential peaks from scATAC-seq data called between neoplastic cells from ATRX-KO and ATRX-wildtype tumors with an IDH1R132H background. Peaks are called via MACS at p<0.05 and represented as a heatmap (bottom) and moving average (top) of reads per 10 bp, in a 2 Kbp window around the transposase cut site. I ScATAC-seq motif enrichment in differential peaks between ATRX-KO and ATRX-wildtype neoplastic cells. Motif frequency relative to a genome-wide background was scored via HOMER. J) Extracellular-matrix invasion assay, comparing ATRX-KO and wildtype cells with an IDH1R132H background