A novel histone H3K27 reader, CBFA2T2, inhibits H3K27me3 demethylation and tumor growth by regulating metabolic genes and metabolite levels [RNA-seq]

Histone H3.1/3.2K27M and H3.3K27M mutation are driver mutations frequently identified in diffuse midline glioma (DMG). However, the precise mechanism by which H3K27M mediates tumorigenesis remains incompletely understood. By carrying out bait Protein-Protein Interaction followed by genome-wide screening (bPPI-seq) in H3.3WT and H3.3K27M mouse NSC models, we identified a novel histone reader CBFA2T2, which recognizes non-mutated or un-modified histone H3K27. Importantly, CBFA2T2 binding to H3K27, mediated by the NHR2 domain, is abrogated by the H3K27M oncogenic mutation. In H3.3 wildtype cells, CBFA2T2 represses transcription of genes involved in carbon metabolism and TCA cycle through its binding to H3K27. This alters the α-KG/Succinate (alpha-ketoglutarate/ Succinate) ratio and indirectly impacts H3K27me3 level, possibly through affecting the H3K27me3 demethylases. CBFA2T2 does not bind the H3.3K27M decorated chromatin in vivo, thus the K to M mutation, partially compromises the CBFA2T2 repressive function. However, over-expressing CBFA2T2 rescues the low H3K27me3 level in H3.3K27M mNSC and H3.3K27M DIPG cells, thus suppressing the H3.3K27M tumor growth. Our findings suggest a new mechanism, which may contribute to the low H3K27me3 level observed in the H3K27M cells, and provide a new strategy for H3K27M therapy through manipulation of CBFA2T2.