2-hydroxyglutarate inhibits transcription factor mediated differentiation by preventing H3K9 demethylation

ATAC-seq associates impairment of myogenic differentiation in cells with an IDH2 mutation with differences in chromatin accessibility. Differences are especially apparent in regions flanking binding sites for myogenic regulatory factors and key myogenesis noncoding RNA linc-MD1. Oncogenic IDH1/2 mutations produce 2-hydroxyglutarate (2HG), resulting in competitive inhibition of DNA and protein demethylation. IDH-mutant cancer cells show an inability to differentiate but whether 2HG accumulation is sufficient to perturb differentiation directed by lineage-specifying transcription factors is unknown. A MyoD-driven model was used to study the role of IDH mutations in the differentiation of mesenchymal cells. The presence of 2HG produced by oncogenic IDH2 blocks the ability of MyoD to drive differentiation into myotubes. DNA 5mC hypermethylation is dispensable while H3K9 hypermethylation is required for this differentiation block. IDH2-R172K mutation results in H3K9 hypermethylation and impaired accessibility at myogenic chromatin regions but does not result in genome-wide decrease in accessibility. The results demonstrate the ability of the oncometabolite to 2HG block transcription factor-mediated differentiation in a molecularly defined system. Overall design: ATAC-seq of mouse 10T1/2 cells, WT for IDH2 vs. R172K mutation of IDH2, with tamoxifen-inducible differentiation via activation of MyoD-ER. ChIP-seq of mouse 10T1/2 cells, WT for IDH2 vs. R172K mutation of IDH2, with tamoxifen-inducible differentiation via activation of MyoD-ER, with and without UNC0638, a G9a/GLP inhibitor.