A first-in-class polymerase theta inhibitor selectively targets homologous-recombination-deficient tumors

Abstract

DNA polymerase theta (POLθ) is synthetic lethal with Homologous Recombination (HR) deficiency and thus a candidate target for HR-deficient cancers. Through high-throughput small molecule screens we identified the antibiotic Novobiocin (NVB) as a specific POLθ inhibitor that selectively kills HR-deficient tumor cells in vitro and in vivo . NVB directly binds to the POLθ ATPase domain, inhibits its ATPase activity, and phenocopies POLθ depletion. NVB kills HR-deficient breast and ovarian tumors in GEMM, xenograft and PDX models. Increased POLθ levels predict NVB sensitivity, and BRCA-deficient tumor cells with acquired resistance to PARP inhibitors (PARPi) are sensitive to NVB in vitro and in vivo. Mechanistically, NVB-mediated cell death in PARPi-resistant cells arises from increased double-strand break end resection, leading to accumulation of single-strand DNA intermediates and non-functional RAD51 foci. Our results demonstrate that NVB may be useful alone or in combination with PARPi in treating HR-deficient tumors, including those with acquired PARPi resistance. (151/150)

DNA Polymerase θ: A Cancer Drug Target with Reverse Transcriptase Activity

“…Consistent with this, small-molecule inhibition of either domain causes the preferential killing of BRCA-deficient cells [54,57]. For example, in addition to the synthetic lethal effects observed for Artios Pharma's Polθ-pol inhibitor, a recent paper indicates that small-molecule inhibition of Polθ-hel also induces synthetic lethality in BRCA-deficient cells [57]. On the other hand, simultaneous inactivation of both domains may have the largest therapeutic index in BRCAdeficient cells and potentially other DNA repair defective cells, such as those deficient in non-homologous end-joining (NHEJ).…”

“…Taken together, multiple lines of evidence demonstrate that both Polθ enzymatic domains contribute to MMEJ and the survival of HR-deficient cells. Consistent with this small-molecule inhibition of either domain causes the preferential killing of BRCA-deficient cells [54,57]. For example, in addition to the synthetic lethal effects observed for Artios Pharma's Polθ-pol inhibitor, a recent paper indicates that small-molecule inhibition of Polθ-hel also induces synthetic lethality in BRCA-deficient cells [57].…”

“…In support of this, all of the reported synthetic lethal studies on Polθ used either CRISPR/Cas9 or shRNA to respectively knockout or strongly suppress the expression of Polθ, which is equivalent to simultaneous inactivation of both enzymatic domains (https://depmap.org/portal/ccle/ accessed on 1 May 2021) [ Taken together, multiple lines of evidence demonstrate that both Polθ enzymatic domains contribute to MMEJ and the survival of HR-deficient cells. Consistent with this, small-molecule inhibition of either domain causes the preferential killing of BRCA-deficient cells [54,57]. For example, in addition to the synthetic lethal effects observed for Artios Pharma's Polθ-pol inhibitor, a recent paper indicates that small-molecule inhibition of Polθ-hel also induces synthetic lethality in BRCA-deficient cells [57].…”

Approaches to Enhance Precise CRISPR/Cas9-Mediated Genome Editing

“…The synergistic effect of genetic depletion of polymerase theta, combined with M3814 mediated inhibition of DNA-PK enhances HDR [33], suggesting that simultaneous small-molecule inhibition of NHEJ and MMEJ could further bias repair towards HDR. It will be interesting to determine whether a first-in-class polymerase theta inhibitor, novobiocin (which was recently shown to exhibit synthetic lethality with HDR deficiency in tumor cells [58]) phenocopies polymerase theta knockdown in gene editing applications.…”

Polymerase θ Coordinates Multiple Intrinsic Enzymatic Activities during DNA Repair

“…Nevertheless, NVB reduces the mass of tumors in both a genetically engineered mouse model (GEMM) of BRCA1 deficiency, and in human ovarian cancer xenographs (FANCF-deficient TOV21G cells) as monotherapy. NVB has been the subject of prior clinical cancer research, but not extensively in the context of HR-deficiency [26]. The biotech Ideaya Bioscience (San Francisco, CA) has announced that Polθ-i Investigational New Drug (IND) trials will begin soon (https://www.ideayabio.com/pipeline/, accessed on 23 August 2021) [72], in which compounds potentially related to NVB will be tested specifically in human HR-deficient cancer patients for the first time.…”