RNA mis-splicing drives viral mimicry response after DNMTi therapy in SETD2-mutant kidney cancer

Tumors with mutations in chromatin regulators present attractive targets for DNA hypomethylating agent 5-aza-20-deoxycytidine (DAC) therapy, which further disrupts cancer cells' epigenomic fidelity and reactivates transposable element (TE) expression to drive viral mimicry responses. SETD2 encodes a histone methyltransferase (H3K36me3) and is prevalently mutated in advanced kidney cancers. Here, we show that SETD2-mutant kidney cancer cells are especially sensitive in vitro and in vivo to DAC treatment. We find that the viral mimicry response are direct consequences of mis-splicing events, such as exon inclusions or extensions, triggered by DAC treatment in an SETD2-loss context. Comprehensive epigenomic analysis reveals H3K9me3 deposition, rather than DNA methylation dynamics, across intronic TEs might contribute to elevated mis-splicing rates. Through epigenomic and transcriptomic analyses, we show that SETD2-deficient kidney cancers are prone to mis-splicing, which can be therapeutically exacerbated with DAC treatment to increase viral mimicry activation and provide synergy with combinatorial immuno-therapy approaches.

Automated summary

Tumors with mutations in chromatin regulators, such as SETD2, are sensitive to DNA hypomethylating agent DAC therapy, which activates viral mimicry responses through mis-splicing events. Comprehensive epigenomic analysis reveals that H3K9me3 deposition across intronic TEs contributes to increased mis-splicing rates. SETD2-deficient kidney cancers are prone to mis-splicing, and DAC treatment can exacerbate this effect to enhance viral mimicry activation and synergize with immuno-therapy approaches.