Abstract B045: ATX-559, a first-in-class, clinical-stage DHX9 inhibitor, as a targeted therapeutic for molecularly defined tumors with genomic instability and replicative stress

Abstract Background: DHX9, a multi-functional RNA helicase, plays important roles in maintaining genome stability by unwinding various nucleic acid secondary structures that may lead to replication stress and DNA damage if left unresolved. DHX9 is overexpressed in multiple cancers, with selective vulnerability to DHX9 inhibition noted in tumors characterized by genomic instability and high replicative stress. ATX-559 is an orally bioavailable, small-molecule inhibitor of DHX9 helicase activity currently in Phase 1 clinical development. ATX-559 induces robust anti-tumor activity in a variety of preclinical models with genomic instability, including those with microsatellite instability-high (MSI-H) and/or deficient mismatch repair (dMMR), BRCA alterations, and homologous recombination repair deficiency (HRD). Materials and Methods: ATX-559 anti-proliferative activity was tested in a multi-indication cell panel screen. Triple negative breast cancer (TNBC) and colorectal cancer (CRC) cells were used to evaluate ATX-559 mechanistic activity using immunofluorescence imaging, dot blot, and western blot assays. ATX-559 was dosed orally BID to evaluate its anti-tumor activity in CRC and TNBC cell line-derived xenograft (CDX) models, as well as a panel of 64 patient-derived xenograft (PDX) models including TNBC, Ovarian, CRC, endometrial, and gastric cancers. qPCR was used to evaluate the target engagement PD biomarker, circBRIP1. Results: ATX-559 treatment leads to increased accumulation of R-loops and G-quadruplexes resulting in increased replicative stress, subsequent DNA damage, and cell death selectively in cancer models with genomic instability and replicative stress. ATX-559 sensitivity was enriched in dMMR/MSI-H cell lines including CRC. Sensitivity was also enriched in BRCA altered TNBC and HRD ovarian cancer cell lines. ATX-559 is well tolerated in vivo, resulting in robust dose-dependent tumor growth inhibition and regression selectively observed in CRC dMMR/MSI-H and BRCA altered TNBC CDX models, along with a well correlated PK/PD/efficacy relationship. Additionally, ATX-559 demonstrated enriched sensitivity in a large panel of BRCA altered TNBC (75%), dMMR/MSI-H (68%), and HRD ovarian (55%) PDX models. Conclusions: Together, these findings represent preclinical validation of DHX9 as a selective therapeutic in cancers with genomic instability and replication stress. ATX-559 is currently in a first-in-human, Phase 1/2, open-label, dose-escalation and expansion study to evaluate the safety profile of ATX-559 and to determine the recommended phase 2 dose (RP2D) and preliminary antitumor activity in patients with locally advanced or metastatic solid tumors, and molecularly defined cancers (NCT06625515). Citation Format: Sunaina Nayak, Jennifer Castro, Monique Laidlaw, Priya Rajaratnam, Maureen Lynes, Stuart Ince, Jason A. Sager, Serena J. Silver. ATX-559, a first-in-class, clinical-stage DHX9 inhibitor, as a targeted therapeutic for molecularly defined tumors with genomic instability and replicative stress [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2025 Oct 22-26; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2025;24(10 Suppl):Abstract nr B045.