Abstract 1758: ATX-559, a first in class DHX9 inhibitor, and targeted therapeutic for molecularly defined tumors with genomic instability and replicative stress
Authors: Jennifer Castro, Matthew H. Daniels, Sunaina Nayak, David Brennan, Cindy Collins, Sophie A. Shen, Monique Laidlaw, Jie Wu, Anugraha Raman, Deepali Gotur, Kevin Knockenhauer, Shihua Yao, Simina Grigoriu, Gordon J. Lockbaum, Kate Newberry, Stephen J. Blakemore, P. Ann Boriack-Sjodin, Kenneth W. Duncan, Stuart Ince, Jason A. Sager, Robert A. Copeland, Serena J. Silver
Journal: Cancer Research (2025)

Abstract DHX9, a multi-functional RNA helicase, contributes to genome stability by unwinding nucleic acid secondary structures, including DNA/RNA hybrids (R-loops), circular RNA and G-quadruplexes. Multiple cancer types exhibit increased expression of DHX9, and selective dependance to DHX9 has been observed in molecular defined tumors that exhibit genomic instability. These tumors often have elevated replicative stress due to rapid unregulated proliferation and defective DNA damage repair (DDRD) pathways; DHX9 inhibition in these tumors further increases replicative stress and DNA damage to catastrophic levels. We previously demonstrated that DHX9 genetic loss or inhibition by the DHX9 tool compound ATX968 was efficacious in tumor types that exhibit DDRD and/or genomic instability; these include tumors with defective mismatch repair and/or high microsatellite instability (dMMR/MSI-H) or alterations in the DDR genes BRCA1 and/or BRCA2 (BRCA). Here we describe ATX-559, a potent, selective, orally bioavailable, small-molecule inhibitor of DHX9 helicase activity that is currently in clinical development. In preclinical studies, ATX-559 treatment leads to increased accumulation of R-loops and G-quadruplexes resulting in increased replicative stress and stalling, subsequent DNA damage, and cell death selectively in cancer models with high genomic instability. In a panel of 36 colorectal (CRC) and endometrial cancer (EC) cell lines, approximately 55% were sensitive (IC50 ≤ 1 μM) to ATX-559 treatment, with enriched antiproliferation activity (80%) in dMMR/MSI-H cells. ATX-559 sensitivity was also enriched in breast cancer cell lines, including 76% of BRCA altered triple negative breast cancer (TNBC) models. ATX-559 is well tolerated in vivo across multiple cell line-derived xenograft (CDX) and patient-derived xenograft (PDX) models, when dosed orally BID for periods out to 28 days or more. Robust dose-dependent tumor growth inhibition (TGI) and regression are selectively observed in CRC and EC dMMR/MSI-H and BRCA altered TNBC CDX models. TGI is correlative with plasma and tumor drug exposure, as well as with induction of the target engagement PD biomarker, circBRIP1, in both tumors and mouse PBMCs. ATX-559 was also profiled in a PDX mouse clinical trial design in vivo study of 46 models including TNBC, CRC, EC, and gastric cancers. Oral treatment of 45 mg/kg BID demonstrated enriched sensitivity in BRCA altered TNBC (75%) and dMMR/MSI-H (68%) PDX models. Together, these findings represent preclinical pharmacological validation of DHX9 as a selective therapeutic target in cancers that exhibit genomic instability and replication stress. ATX-559 is currently in a first-in-human, Phase 1, open-label, dose-escalation and expansion study in patients with locally advanced or metastatic solid tumors and molecularly defined cancers (NCT06625515). Citation Format: Jennifer Castro, Matthew H. Daniels, Sunaina Nayak, David Brennan, Cindy Collins, Sophie A. Shen, Monique Laidlaw, Jie Wu, Anugraha Raman, Deepali Gotur, Kevin Knockenhauer, Shihua Yao, Simina Grigoriu, Gordon J. Lockbaum, Kate Newberry, Stephen J. Blakemore, P. Ann Boriack-Sjodin, Kenneth W. Duncan, Stuart Ince, Jason A. Sager, Robert A. Copeland, Serena J. Silver. ATX-559, a first in class DHX9 inhibitor, and targeted therapeutic for molecularly defined tumors with genomic instability and replicative stress [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 1758.