<i>TET2</i> and <i>DNMT3A</i> Mutations Exert Divergent Effects on DNA Repair and Sensitivity of Leukemia Cells to PARP Inhibitors

Abstract

Somatic variants in <i>TET2</i> and <i>DNMT3A</i> are founding mutations in hematological malignancies that affect the epigenetic regulation of DNA methylation. Mutations in both genes often co-occur with activating mutations in genes encoding oncogenic tyrosine kinases such as <i>FLT3^ITD, BCR-ABL1, JAK2^V617F</i> , and <i>MPL^W515L</i> , or with mutations affecting related signaling pathways such as <i>NRAS^G12D</i> and <i>CALR^del52</i> . Here, we show that <i>TET2</i> and <i>DNMT3A</i> mutations exert divergent roles in regulating DNA repair activities in leukemia cells expressing these oncogenes. Malignant TET2-deficient cells displayed downregulation of BRCA1 and LIG4, resulting in reduced activity of BRCA1/2-mediated homologous recombination (HR) and DNA-PK-mediated non-homologous end-joining (D-NHEJ), respectively. TET2-deficient cells relied on PARP1-mediated alternative NHEJ (Alt-NHEJ) for protection from the toxic effects of spontaneous and drug-induced DNA double-strand breaks. Conversely, DNMT3A-deficient cells favored HR/D-NHEJ owing to downregulation of PARP1 and reduction of Alt-NHEJ. Consequently, malignant TET2-deficient cells were sensitive to PARP inhibitor (PARPi) treatment <i>in vitro</i> and <i>in vivo</i>, whereas DNMT3A-deficient cells were resistant. Disruption of TET2 dioxygenase activity or TET2-Wilms' tumor 1 (WT1)-binding ability was responsible for DNA repair defects and sensitivity to PARPi associated with TET2 deficiency. Moreover, mutation or deletion of <i>WT1</i> mimicked the effect of <i>TET2</i> mutation on DSB repair activity and sensitivity to PARPi. Collectively, these findings reveal that <i>TET2</i> and <i>WT1</i> mutations may serve as biomarkers of synthetic lethality triggered by PARPi, which should be explored therapeutically. SIGNIFICANCE: <i>TET2</i> and <i>DNMT3A</i> mutations affect distinct DNA repair mechanisms and govern the differential sensitivities of oncogenic tyrosine kinase-positive malignant hematopoietic cells to PARP inhibitors.