It has been shown that PRMT5 inhibition by small molecules can selectively kill cancer cells with homozygous deletion of the MTAP gene if the inhibitors can leverage the consequence of MTAP deletion, namely, accumulation of the MTAP substrate MTA. Herein, we describe the discovery of TNG908, a potent inhibitor that binds the PRMT5·MTA complex, leading to 15-fold-selective killing of MTAP-deleted (MTAP-null) cells compared to MTAPintact (MTAP WT) cells. TNG908 shows selective antitumor activity when dosed orally in mouse xenograft models, and its physicochemical properties are amenable for crossing the blood–brain barrier (BBB), supporting clinical study for the treatment of both CNS and non-CNS tumors with MTAP loss.
Abstract Background: DHX9 is a DEAH-box RNA helicase which has been reported to play important roles in replication, transcription, translation and RNA splicing/processing, all of which contribute to DHX9’s role in the maintenance of genomic stability. Functionally, DHX9 unwinds and/or resolves regions of double-stranded DNA and RNA helices but has a greater propensity for secondary structures such as DNA/RNA hybrids (R-loops), circular RNA (circRNA) and DNA/RNA G-quadraplexes. Overexpression of DHX9 is evident in multiple cancer types, including colorectal cancer (CRC) and lung cancer. In particular, microsatellite instable (MSI) tumors exhibiting defective mismatch repair (dMMR) show a strong dependence on DHX9, making this helicase an attractive target for oncology drug discovery. Here, we will demonstrate validation of DHX9 as a novel target for CRC-MSI, and the identification of potent and selective in vitro and in vivo small molecule inhibitors of DHX9. Materials and Methods: DHX9 targeted siRNA or DHX9 small molecule inhibitors were used to assess anti-proliferative activity in multiple different CRC-MSI and CRC-MSS cell lines through either CellTiter-Glo proliferation or colony formation assays. Downstream biological consequences of DHX9 knockdown or inhibition in vitro were determined using immuno-fluorescent imaging, western blot, flow cytometry to measure RNA/DNA secondary structure, cell cycle changes, apoptosis, and qPCR to measure circBRIP1 induction. CRC-MSI and CRC-MSS tumor xenografts were treated with DHX9 inhibitor ATX968 BID orally for 21-28 days. Tumor and plasma samples were collected for pharmacokinetics (PK) and pharmacodynamic (PD) (circBRIP1) measurement. Results: We demonstrate that DHX9 inhibition in CRC-MSI leads to an increase in RNA/DNA secondary structures such as R-loops, G-quadruplexes and Alu mediated circRNA such as circBRIP1, leads to subsequent DNA damage and increased replication stress. Cell lines that exhibit defective DNA repair pathways such as dMMR are unable to resolve this replication stress and demonstrate S-G2 phase cell cycle arrest prior to onset of apoptosis. We confirmed this selective dependency in a panel of cancer cell lines, where anti-proliferative effects mediated by DHX9 inhibition were associated with dMMR status. Furthermore, DHX9 tool compound ATX968 was well tolerated in vivo across a 28-day treatment period with robust and durable tumor regression observed in the MSI CRC tumor xenograft model. Following cessation of treatment, minimal tumor regrowth was observed in a 28-day post treatment window. Tumor and plasma concentrations of ATX968 and changes in PD markers of DHX9 inhibition were measured and resulting PK, PD and efficacy data were highly correlated. Conclusions: Together, these preclinical data validate DHX9 as a tractable new target with potential utility as a novel treatment for patients with CRC-MSI. Conflict of Interests: All authors are current or former employees and shareholders of Accent Therapeutics, Inc. Citation Format: Jennifer Castro, Matthew H Daniels, David Brennan, Brian T Johnston, Rishabh Bansal, Monique Laidlaw, Chuang Lu, Deepali Gotur, Young-Tae Lee, Kevin Knockenhauer, April Case, Jie Wu, Anugraha Raman, Jae Eun Cheong, Julie Liu, Shane M Buker, E. Allen Sickmier, Stephen J Blakemore, P. Ann Boriack-Sjodin, Kenneth W Duncan, Serena J Silver, Scott Ribich, Robert A Copeland. DHX9 inhibition as a novel therapeutic modality in microsatellite instable colorectal cancer [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr C087.
Nuclear segmentation is a hallmark feature of mammalian neutrophil differentiation, but the mechanisms that control this process are poorly understood. Gene expression in maturing neutrophils requires combinatorial actions of lineage-restricted and more widely expressed transcriptional regulators. Examples include interactions of the widely expressed ETS transcription factor, GA-binding protein (GABP), with the relatively lineage-restricted E-twenty-six (ETS) factor, PU.1, and with CCAAT enhancer binding proteins, C/EBPα and C/EBPε. Whether such cooperative interactions between these transcription factors also regulate the expression of genes encoding proteins that control nuclear segmentation is unclear. We investigated the roles of ETS and C/EBP family transcription factors in regulating the gene encoding the lamin B receptor (LBR), an inner nuclear membrane protein whose expression is required for neutrophil nuclear segmentation. Although C/EBPε was previously shown to bind the Lbr promoter, surprisingly, we found that neutrophils derived from Cebpe null mice exhibited normal Lbr gene and protein expression. Instead, GABP provided transcriptional activation through the Lbr promoter in the absence of C/EBPε, and activities supported by GABP were greatly enhanced by either C/EBPε or PU.1. Both GABP and PU.1 bound Ets sites in the Lbr promoter in vitro, and in vivo within both early myeloid progenitors and differentiating neutrophils. These findings demonstrate that GABP, PU.1, and C/EBPε cooperate to control transcription of the gene encoding LBR, a nuclear envelope protein that is required for the characteristic lobulated morphology of mature neutrophils.
Abstract CRISPR-based functional genomic screening is a powerful approach for identifying novel classes of synthetic lethal drug targets. Here, we define the deubiquitinase USP1 as a synthetic lethal target in cancers with underlying DNA repair vulnerabilities. A highly potent and selective small molecule USP1 inhibitor conferred a viability defect in BRCA1-mutant, but not WT cell lines by activating replication stress. Genome-wide CRISPR screening uncovered RAD18 and UBE2K, which promote PCNA mono- and poly-ubiquitination respectively, as key mediators of USP1-BRCA1 dependency. Increased cellular mono- and poly-ubiquitination reduced PCNA protein levels, and restoration of PCNA protein expression rescued USP1 inhibitor sensitivity. USP1 dependency is associated with upregulated RAD18 and UBE2K expression, suggesting that elevated PCNA ubiquitination in the context of BRCA1 deficiency mediates USP1 synthetic lethality. Interestingly, USP1, but not PARP1 inhibition, elicited a viability defect in a subset of BRCA1/2 WT lung cancer cell lines, indicative of novel synthetic lethal interactions unique to USP1. Moreover, dual inhibition of PARP1 and USP1 are strongly synergistic in PARP1 inhibitor-responsive cell line models. Strong in vivo anti-tumor activity across multiple tumor models was demonstrated with USP1 inhibition alone and in combination with the PARP1 inhibitor olaparib. Our studies suggest that USP1 and PARP1 inhibitors target BRCA1-mutant cancer though distinct yet synergistic mechanisms. As such, USP1 inhibitors may provide novel treatment strategies for PARP1 inhibitor-resistant and -naïve BRCA1-mutant cancer. Citation Format: Justin Engel, Madhavi Bandi, Antione Simoneau, Katherine Lazarides, Deepali Gotur, Truc Pham, Shangtao Liu, Samuel Meier, Ashley Choi, Hongxiang Zhang, Binzhang Shen, Fang Li, Douglas Whittington, Shanzhong Gong, Xuewen Pan, Yi Yu, Lina Gu, Scott Throner, John Maxwell, Yingnan Chen, Alan Huang, Jannik Andersen, Tianshu Feng. USP1 inhibitor synthetic lethality in BRCA1-mutant cancer is driven by PCNA ubiquitination [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2603.
