KMT2A is a prerequisite of malignant transformation during IDH-mutant gliomagenesis

IDH1R132H is the defining mutation of low-grade gliomas (LGGs), driving broad epigenetic rewiring that leads to malignant transformation. Recent studies have demonstrated that cell fate change from astrocyte to LGG is accompanied by redistribution of H3K4 methylation. By modulating the 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.

Using the KMT2A inhibitor MM-102, we targeted H3K4me3 in IDH1R132H-expressing astrocytes and profiled L1CAM expression, proliferation, clonogenicity, invasion, migration, transcriptional and translational changes. Findings were validated in patient-derived IDH1R132H glioma lines using shRNA-mediated knockdown. Epigenetic transformation was characterized with CUT&Tag and MethylationEPIC, and downstream targets were assessed using siRNAs.

KMT2A inhibition significantly decreased L1CAM expression and led to broad transcriptional downregulation, including that of LGG marker genes. Transcriptomic and proteomic analyses pointed to altered lipid metabolism and migratory capacity. Phenotypic characterization revealed impaired invasion, migration, and proliferation. We observed significantly reduced H3K4me3 deposition at the promoters of DEGs and increased DNA methylation at subsets of CpGs associated with H3K4me3 loss and downregulated genes. We identified SCD as a 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.

Disrupting KMT2A-mediated H3K4me3 deposition reshapes the epigenome and attenuates LGG-relevant programs and phenotypes in vitro, supporting a strong role in tumor initiation. In vivo, the survival results in the TS603 model highlight context-dependent effects on tumor maintenance and prompt cautious, microenvironment-aware therapeutic exploration of the KMT2A axis and its downstream targets, such as SCD.