SAGA/ATAC complexes sustain aberrant chromatin regulation and metabolic programs in diffuse midline glioma

Diffuse midline gliomas (DMG) are aggressive pediatric brain tumors characterized by chromatin and transcriptional dysregulation induced by H3K27M mutations. Strategies for overcoming epigenetic dysfunction to reduce DMG tumorigenesis remain limited. We identified multiple components of the SAGA and ATAC chromatin regulatory complexes as DMG genetic dependencies and found that genetic or pharmacological inhibition of the SAGA/ATAC-associated chromatin reader, SGF29, reduces DMG proliferation. Small molecules targeting SAGA/ATAC-associated histone acetylation, ubiquitination, and methylation similarly suppressed DMG growth. Further chromatin profiling and RNAseq analyses reveal that SGF29 controls H3K9ac and H3K4me3 dynamics at both H3K27M-bound and H3K27M-independent target genes linked to proliferation, differentiation, and metabolism. Finally, we find that SAGA/ATAC inhibition may reduce DMG viability by repressing cholesterol metabolism gene expression and show that combinations of cholesterol- and SAGA/ATAC-targeting drugs synergistically reduce DMG growth. These findings reveal a functional link between SAGA/ATAC-dependent chromatin regulation and both transcriptional and metabolic dysregulation underlying DMG malignancy. Overall design: In one experiment, SU-DIPGXIII+Cas9 cells were transduced with control or SGF29-targeting sgRNAs and selected with 250 ug/mL hygromycin for 7 days 48 hours later. Equal live cell numbers were collected for RNAseq analysis at day 16 following the start of hygromycin selection and processed for bulk RNAseq of polyA transcripts. In another experiment, SU-DIPGXIII cells were treated with small molecules targeting either the bromodomains of KAT2A/2B (GSK4027) or the acetyltransferase activity of KAT2A/2B (CPTH2), with DMSO serving as a vehicle control. Equal live cell numbers were collected for RNAseq analysis 25 hours after starting treatment with these inhibitors.