Diffuse intrinsic pontine glioma (DIPG) is the most aggressive brain tumour found in children with a peak incidence of 5-7 years of age, and a median survival of less than one year. In more than 60% of DIPG cases, there is a driving somatic mutation of the H3F3A gene, that leads to a lysine 27 to methionine mutation at the histone variant H3.3 (H3.3K27M). Physiologically, histone variants H3.3 and H2A.Z are frequently found in the same nucleosome and cooperate to regulate transcription. We have identified that acetylation of H2A.Z (H2A.Zac) can be an oncogenic driver in adult cancer through the mislocalization of H2A.Z at promoters and enhancers of cancer-associated genes. However, the role of H2A.Z in DIPG has never been studied. Here we aim to unravel the molecular relationship between H2A.Zac and H3.3K27M in DIPG and their link to oncogenesis.
We have profiled H2A.Zac by mass spectrometry and ChIP-seq in patient-derived DIPG cell lines. In addition, ChIP-seq of the different histone marks and H3K27M to identify chromatin regulatory regions and its association with H3K27M and H2A.Zac.
Histone mass spectrometry revealed the level of H2A.Zac is significantly higher in samples with H3K27M compared to H3.3WT. In addition, the comparison between H2A.Zac with H3.3K27M ChIP-seq data in several DIPG cell lines, showed that around 30% of H3.3K27M peaks overlapped with H2A.Zac marked regions, a similar proportion found between H3.3 and H2A.Z under physiological conditions. Interestingly, active enhancers are the most enriched regulatory regions for H3.3K27M/H2A.Zac overlapping regions and those enhancers are associated with genes involved in pathways commonly altered in H3.3K27M gliomas.
These data suggest H2A.Zac levels are altered in DIPG and H2A.Zac may be involved in aberrant enhancer activation in DIPG and thus constitute a novel therapeutic target for H3.3K27M+ DIPG.