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

Background: 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, profiling L1CAM expression, proliferation, clonogenicity, invasion and migration, transcriptional and translational changes. Findings were validated in patient-derived IDH1R132H glioma lines with shRNA-mediated knockdown. Epigenetic transformation was characterized with CUT&Tag and MethylationEPIC. 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 transcriptomics and proteomics pointed to altered lipid metabolism and migratory capacity. Phenotypic characterization showed impaired invasion, migration and proliferation. We observed significantly reduced deposition of H3K4me3 at promoters of DEGs and enhanced global DNA methylation. We identified SCD as putative KMT2A-dependent effector whose knockdown reduced clonogenicity. In patient-derived models, KMT2A suppression impaired viability and spheroid growth in vitro; however, in an orthotopic TS603 model, knockdown shortened survival, indicating stage- and context-dependent effects. Conclusions: Disrupting KMT2A-mediated H3K4me3 reshapes the epigenome and attenuates LGG-relevant programs and phenotypes in vitro, supporting a strong role in tumor initiation. In vivo, the TS603 survival result highlights context-dependent maintenance and motivates cautious, microenvironment-aware therapeutic exploration of the KMT2A axis and downstream targets such as SCD.