Variant and cell-context specific H3K27M reprogramming results in distinct enhancer architecture and oncogenic states

Diffuse intrinsic pontine glioma (DIPG) is a fatal malignancy of the childhood pons characterized by a unique lysine-to-methionine substitution in histone-3 at lysine 27 (H3K27M). We show here that the specific Polycomb targets disrupted by H3K27M and resultant oncogenic state is dependent on both the variant of histone-3 and the cell- context in which the mutation occurs. Through primary DIPG tumor characterization and isogenic expression, we show that the same H3K27M mutation displays distinct modes of oncogenic reprogramming and establishes distinct enhancer architecture depending on whether it occurs in genes encoding H3.3 or H3.1. By comparison to non-malignant pediatric pontine tissue, we create a molecular map for DIPG, identifying and functionally validating both shared and subgroup-specific pathophysiology. Directly comparing the earliest events of H3K27M tumor initiation in putative cells-of-origin demonstrates that DIPG arises only from an oligodendrocyte precursor cell state. H3K27Ac profiling of 30 primary DIPG and normal pontine tissue samples. Omni-ATAC profiling of 9 primary samples. RNA-seq profiling of 10 primary samples. ChIP-seq profiling of 12 patient-derived DIPG cultures. Multiple histone and TF ChIP-seq profiling of 5 stages of iPSC differentiation in the presence or absence of H3K27M. There are no restrictions or privacy issues. They were obtained under informed consent under an IRB protocol and have been fully deidentified. Gene expression was quantified in "cnmc842t" primary human DIPG tumor sample and "pons02" primary human non-tumor pontine sample. RNA was sequenced on the Illumina NextSeq 500 and tpm values were quantified using featureCounts (Liao et al, 2014). Due to patient privacy concerns, we are witholding raw sequencing files at this time.