KMT2A is a prerequisite of malignant transformation during IDH-mutant gliomagenesis [RNA-Seq]

Rationale: IDH1R132H is the defining mutation of low-grade gliomas (LGGs), inflicting broad epigenetic rewiring that leads to malignant transformation. Recent studies demonstrated that cell fate change from astrocyte to LGG is accompanied by redistribution of H3K4 methylation. By modulating H3K4-methyltransferase KMT2A in a conditionally IDH1R132H-expressing human astrocyte model system, we sought to define requirements of IDH1R132H dependent gliomagenesis and identify novel therapeutic targets. Methods: Using KMT2A inhibitor MM-102, we targeted H3K4me3 in IDH1R132H -expressing astrocytes. Flow cytometry for LGG-associated marker L1CAM served as primary read-out. Transcriptional and translational changes were determined with RNA-Seq and Mass spectrometry. Phenotypic profiling included spherogenic, clonogenic, invasion and migration assays; key findings were assessed in patient-derived IDH1R132H glioma lines and validated with an shRNA-mediated knockdown. Epigenetic transformation was characterized with CUT&Tag and the MethylationEPIC array. Downstream targets were assessed utilizing siRNAs. Results: KMT2A inhibition significantly decreased L1CAM expression and led to broad transcriptional downregulation, including LGG marker genes. Analyses of intersected transcriptomics and proteomics pointed to altered lipid metabolism and migratory capacity. Phenotypic characterization showed impaired invasion, migration, clonal proliferation and sphere formation. Epigenetically, we observed significantly reduced deposition of H3K4me3 at promoters of DEGs and enhanced global DNA methylation. PDGFRA and SCD were identified as KMT2A-dependent downstream targets. Conclusion: Disruption of H3K4me3 methylation by KMT2A inhibition is associated with extensive epigenetic reshaping, resulting in reduced expression of LGG-relevant programs, manifesting phenotypically in decreased tumorigenic potential. Our results suggest that H3K4me3 methylation by KMT2A is essential for low-grade gliomagenesis and maintenance, highlighting KMT2A as a potential therapeutic target.