Heterozygous Kmt2d loss diminishes enhancers to render medulloblastoma cells vulnerable to combinatory inhibition of lysine demethylation and oxidative phosphorylation [ChIP-Seq]

The histone methyltransferase KMT2D (alias MLL4) is frequently mutated in medulloblastoma (MB). Heterozygous loss of KMT2D is prevalent in MB. However, the role of heterozygous KMT2D loss remains unknown. Here, we show that heterozygous Kmt2d loss highly promotes Ptch+/–-driven MB genesis in mice. Heterozygous Kmt2d loss upregulated tumor-promoting programs, including oxidative phosphorylation (OXPHOS), in Ptch+/–-driven MB genesis. Heterozygous Kmt2d loss extensively diminished enhancer signals and H3K4me3 signature, including those for transcription-repressive tumor suppressor genes (e.g., Ncor2). NCOR2 repressed the expression of tumor-promoting genes. Combinatory pharmacological inhibition of OXPHOS and the enhancer-decommissioning demethylase LSD1 drastically reduced the tumorigenicity of MB cells bearing heterozygous Kmt2d loss. These findings reveal the mechanistic basis underlying the MB-promoting effect of heterozygous KMT2D loss. Overall design: ChIP assay was performed using a modified version of the previously described method (Dhar et al., 2016; Dhar et al., 2012). Cerebellar tissues were processed for ChIP using Ren lab's protocol from Roadmap Epigenome (https://www.encodeproject.org). The ChIP-seq libraries were prepared using NEB adapters as described earlier (Alam et al., 2020). Libraries were multiplexed together, and sequencing was performed in Hiseq2000 or HiSeq4000 (Illumina). CUT&RUN assays were performed using CUTANA ChIC/ CUT&RUN Kit. Analysis was performed with Pluto (https://pluto.bio) software.