ID #674 Unmasking Epigenomic Vulnerabilities in Diffuse Midline Glioma to Guide Epigenetic Therapy

Abstract

Diffuse midline glioma (DMG) is the most aggressive brain tumour in children, with a median survival of less than one year and with no cure. Molecularly, DMG is an epigenetically driven cancer, characterised by a global loss of the repressive epigenetic mark, histone 3 trimethylation at the lysine 27 (H3K27me3). This is caused by a single somatic mutation in the histone H3, called H3K27M, or by the expression of the developmental gene EZHIP, a natural mimic of H3K27M, and subclassifies these DMGs as “H3K27-altered”. Despite the research efforts to study epigenomic alterations in DMG, a full integration of multiple epigenomic landscapes of key histone marks, like H3K27me3, H3K4me3 and H3K27ac, together with the chromatin accessibility landscape of H3K27-altered DMG is still lacking. Understanding this complex multilayer chromatin landscapes is key to rationalize which epigenetic drugs would effectively reverse such aberrations. Our group’s mission is to complete the multilayered epigenomic landscapes of H3K27-altered DMGs for precision epigenetic therapy. Using epigenomic and proteomic approaches, including ChIP-seq of histone marks, ATAC-seq and mass spectrometry, where we compared normal cells and different subtypes of DIPG cell lines, our group has defined the global epigenomic re-arrangements that are specific of DMG malignancy. The chromatin landscape in H3K27-altered DMG is chromatin permissive with global histone hyperacetylation and epigenetic erosion. We also identified specific changes in enhancer activation for neural differentiation and stemness. Functional in vitro studies using DMG H3K27KM knock out cells, revealed the dependency of some of these epigenetic changes with the presence of H3K27M. Finally, a combinatorial epigenetic therapy focused on targeting epigenetic erosion and chromatin plasticity, results in significant reduction of cancer growth both in in vitro and in ex vivo DMG models. In conclusion, a combinatory epigenetic therapy that makes chromatin plasticity irreversible provides a promising therapeutic strategy in DMG.