Mutant IDH1 inhibition induces dsDNA sensing to activate tumor immunity [ChIP-Seq]

Isocitrate Dehydrogenase 1 (IDH1) is the most commonly mutated metabolic gene across human cancers. Mutant IDH1 (mIDH1) generates the oncometabolite (R)-2-hydroxyglutarate, disrupting enzymes involved in epigenetics and other processes. A hallmark of IDH1-mutant solid tumors is T cell exclusion, whereas mIDH1 inhibition in preclinical models restores anti-tumor immunity. Here, we define a cell-autonomous mechanism of mIDH1-driven immune evasion. IDH1-mutant solid tumors show striking, selective hypermethylation and silencing of the cytoplasmic dsDNA sensor, CGAS, compromising innate immune signaling. mIDH1 inhibition restores DNA demethylation, derepressing CGAS and transposable element (TE) subclasses. dsDNA produced by TE-reverse transcriptase activates cGAS, triggering viral mimicry and stimulating anti-tumor immunity. Thus, we demonstrate that mIDH1 epigenetically suppresses innate immunity and link endogenous reverse transcriptase activity to the mechanism of action of an FDA-approved oncology drug. This study used the mIDH inhibitor, AG120 (Servier Pharmaceuticals). Murine ICC (2205) cells were treated for 10 days with either DMSO or 1 μM mIDH inhibitor (AG120). Where indicated, 20ng/mL IFNγ was added for the final two days of culturing. 20 million cells per replicate for each condition (DMSO, AG120, IFNγ, AG120 + IFNγ) were cross-linked using 1% formaldehyde for 10 minutes at room temperature and quenched using glycine for 5 minutes. ChIP experiments were performed using SimpleChIP Enzymatic Chromatin IP Kit based on manufacturer's protocol. Sequencing libraries were prepared using the NEBNext Ultra II DNA library preparation kit (New England Biolabs) and were sequenced using NovaSeq 6000 (Illumina) with paired-end 150 bp reads.