DNA Polymerase Theta Protects Leukemia Cells from Metabolic-Induced DNA Damage

Leukemia cells accumulate DNA damage but altered DNA repair mechanisms protect them from apoptosis. We showed here that formaldehyde generated by serine/one-carbon cycle metabolism contributed to accumulation of toxic DNA-protein crosslinks (DPCs) in leukemia cells, especially in driver clones harboring oncogenic tyrosine kinases [OTKs: FLT3(ITD), JAK2(V617F), BCR/ABL1]. To counteract this effect, OTKs enhanced the expression of DNA polymerase theta (POLθ) by ERK1/2 serine/threonine kinase-dependent inhibition of c-CBL E3 ligase-mediated ubiquitination of POLθ and its proteasomal degradation. Overexpression of POLθ in OTK-positive cells resulted in efficient repair of DPC-containing DNA double-strand breaks (DSBs) by POLθ-mediated end-joining (TMEJ). Transforming activity of OTKs and other leukemia-inducing oncogenes, especially of those causing inhibition of BRCA1/2 -mediated homologous recombination (HR) with and without concomitant inhibition of DNA-PK -dependent non-homologous end-joining (D-NHEJ), was abrogated in Polq-/- murine bone marrow cells. Genetic and pharmacological targeting of POLθ polymerase and helicase activities revealed that both activities are promising targets in leukemia cells. Moreover, OTK inhibitor or DPC-inducing drug etoposide enhanced anti-leukemia effect of POLθ inhibitor (POLθi) in vitro and in vivo. POLθ can interplay with PARP1 (alternative NHEJ) and RAD52 (alternative HR) to repair DSBs. Remarkably, transformation potential of the oncogenes inducing HR and NHEJ deficiencies (BCR-ABL1 and AML1-ETO) was severely limited in Polq-/-;Parp1-/- and Polq-/-;Rad52-/- cells when compared to single knockouts. Moreover, simultaneous targeting of POLθ and PARP1 or RAD52 exerted dual synthetic lethality against HR deficient leukemias. In conclusion, we demonstrated that POLθ plays an essential role in protecting leukemia cells from metabolically induced toxic DNA lesions and it can be targeted to achieve therapeutic effect.

Figure 1. POLθ is required to resolve DPCs caused by formaldehyde generated by serine/1C cycle metabolism in OTKs-positive hematological malignancies. A scheme illustrating functional pathway where OTKs - reprogrammed serine/1C cycle - produced formaldehyde induces DPCs which are likely repaired by POLθ-mediated end-joining (TMEJ). OTKs also enhance the expression of POLθ by stimulating ERK1/2 serine/threonine kinases, which inhibit c-CBL E3 ligase-dependent ubiquitination of POLθ and its proteasomal degradation.

Valent:Blueprint Medicines: Honoraria; Celgene: Honoraria, Research Funding; Novartis: Consultancy, Honoraria; Incyte: Honoraria. Pomerantz:Recombination Therapeutics LLC: Current Employment, Research Funding. Levine:Ajax, Abbvie, Constellation, Zenalis, Celgene, Roche, and Prelude: Other: research support; Imago, Mission Bio, Bakx, Zentalis, Ajax, Auron, Prelude, C4 Therapeutics and Isoplexis: Current equity holder in publicly-traded company, Membership on an entity's Board of Directors or advisory committees; Gilead and Novartis: Other: Grant reviews; Syndax, Incyte, Janssen, Astellas, Morphosys and Novartis: Consultancy; Qiagen: Other: supervisory board member; Astra Zeneca and Kura: Other: honoraria for invited lectures . Tallman:AbbVie: Membership on an entity's Board of Directors or advisory committees, Research Funding; Orsenix: Membership on an entity's Board of Directors or advisory committees, Research Funding; Biosight: Membership on an entity's Board of Directors or advisory committees, Research Funding; Glycomimetics: Research Funding; Rafael Pharmaceuticals: Research Funding; Amgen: Research Funding; Daiichi-Sankyo: Membership on an entity's Board of Directors or advisory committees; KAHR-Adv Bd: Membership on an entity's Board of Directors or advisory committees; Oncolyze: Membership on an entity's Board of Directors or advisory committees; Jazz Pharmaceutical: Membership on an entity's Board of Directors or advisory committees; Roche: Membership on an entity's Board of Directors or advisory committees; Novartis: Membership on an entity's Board of Directors or advisory committees; Ipsen Biopharmaceuticals: Membership on an entity's Board of Directors or advisory committees; Innate Pharmaceuticals: Membership on an entity's Board of Directors or advisory committees; Kura: Membership on an entity's Board of Directors or advisory committees; Syros Pharmaceuticals: Membership on an entity's Board of Directors or advisory committees; UpToDate: Patents & Royalties. Fernandez:Incyte: Membership on an entity's Board of Directors or advisory committees; Jazz Pharmaceuticals: Membership on an entity's Board of Directors or advisory committees. Litzow:Abbvie: Research Funding; Amgen: Research Funding; Astellas: Research Funding; Novartis: Research Funding; Syndax: Research Funding; Jazz: Consultancy; Actinium: Research Funding; Pluristem: Research Funding; Biosight: Other: Data Monitoring Board.