DNA Hypomethylation is Not Cell Intrinsically Toxic to Polycomb Repressive Complex 2 Deficient Malignant Peripheral Nerve Sheath Tumors

Malignant peripheral nerve sheath tumors (MPNSTs) are aggressive soft tissue sarcomas and the most common cause of disease-associated death for Neurofibromatosis Type 1 (NF1) patients. In the context of NF1, MPNSTs develop from benign premalignant precursors. In the majority of cases, the transition to malignancy is accompanied by loss of the Polycomb repressive complex 2 (PRC2), which results in aberrant upregulation of over 1200 genes due to global depletion of histone H3 lysine 27 trimethylation (H3K27me3). Studies have suggested that cells compensate for the loss of this repressive histone mark by increasing DNA methylation throughout the genome. This study used a Nanopore-based genome skimming method to analyze genome-wide DNA methylation and the transcriptome in MPNST cell lines and isogenic PRC2-deficient and -proficient CRISPR-engineered immortalized human Schwann cells. In addition to effects of PRC2 status, we also measured the effects of two DNA methyltransferase inhibitors (DNMTi), decitabine and azacitidine. We found that PRC2 status does not affect global DNA methylation state and that decitabine and azacitidine have differential effects on MPNSTs. While both DNMTis greatly decrease global DNA methylation, they upregulate different targets. Azacitidine upregulates genes involved in RNA processing pathways and can kill MPNST cells directly, while decitabine upregulates genes involved in the immune response and is only able to reduce tumor growth via indirect effects on the tumor microenvironment in vivo. We show that DNA hypomethylation alone is insufficient to kill MPNST cells, regardless of PRC2 status. However, DNMTi could be useful in combination with other therapies for MPNST patients.