Transposable elements as novel therapeutic targets for PARPi-induced synthetic lethality in PcG-mutated blood cancer

Loss-of-function (LoF) mutations frequently found in human cancers are generally intractable by classical small molecule inhibitor approaches. Among them are mutations affecting polycomb-group (PcG) epigenetic regulators, EZH2 and ASXL1 frequently found in haematological malignancies of myeloid or lymphoid lineage, and their concurrent mutations associates with particularly poor prognosis. While there is clear need to develop novel and effective treatments for these patients, the lack of appropriate disease models and mechanistic insights have significantly hindered the progresses. Here we show that genetic inactivation of Asxl1 and Ezh2 in murine haematopoietic stem/progenitor cells results in highly penetrant haematological malignancies as observed in corresponding human diseases. These PcG proteins regulate both coding and non-coding genomes, leading to marked reactivation of transposable elements (TEs) and DNA damage responses in PcG LoF mutated cells, which create a novel vulnerability for PARP inhibitors (PARPi)-induced synthetic lethality. Using both mouse models and primary patient samples, we demonstrate that Asxl1/Ezh2 mutated cells are highly sensitive to PARPi that induce excessive DNA damage and significantly extend disease latency. Intriguingly the observed PARPi-sensitivity can be specifically overridden by reverse transcriptase inhibitors that interrupt target-site primed reverse transcription (TPRT) and life cycle of TEs. This mechanism is contrastingly different from the current concept of BRCAness associated PARPi-induced synthetic lethality, which largely rely on deficient homologous recombination and is independent on reverse transcriptase inhibitors. Together, this study reveals a novel application and mechanism of PARPi-induced synthetic lethal targeting of blood cancers with reactivated TEs such as those carrying PcG epigenetic mutations.