Abstract 520: circBRIP1 RNA as a non-invasive target engagement pharmacodynamic biomarker for DHX9 inhibition
Authors: Brennan David , Castro Jennifer , Daniels Matthew H. , Laidlaw Monique , Lu Chuang , Blakemore Stephen J. , Silver Serena J. , Boriack-Sjodin P. Ann , Duncan Kenneth W. , Sager Jason A. , Copeland Robert A. 
Published: March 2024

DHX9 is a multifunctional DEAH-box ATP-independent RNA helicase which has been reported to play important roles in replication, transcription, translation, RNA splicing and RNA processing which contribute to DHX9’s role in maintenance of genomic stability. DHX9 can bind specifically to inverted repeat Alu elements, preventing back-splicing events that lead to circular RNA and exon skipping of the linear transcript. Upon DHX9 inhibition, a robust induction of Alu-mediated circular RNA is observed. For example, circBRIP1 is an Alu-mediated circular RNA that is robustly elevated upon DHX9 loss, with no observed change to levels of linear BRIP1. Here we describe data demonstrating circBRIP1 as a DHX9 specific target engagement pharmacodynamic (PD) biomarker and its potential utility as a non-invasive clinical PD biomarker. We have previously demonstrated that DHX9 inhibition by novel small molecule inhibitors is efficacious in microsatellite instable (MSI) colorectal cancer (CRC) with defective mismatch repair (dMMR), both in vitro and in vivo. DHX9 inhibition in the HCT116 dMMR CRC cell line results in a robust dose dependent induction of the Alu-mediated circular RNA, circBRIP1, as early as 6 hours after compound treatment. The development of lead series DHX9 inhibitors exhibited a positive correlation between circBRIP1 EC50 and DHX9 biochemical activity, as well as proliferation inhibition in a dMMR CRC cell line. However, dose dependent induction of circBRIP1 following DHX9 inhibition occurs with similar potencies across DHX9i sensitive and insensitive CRC cell lines. This suggests that elevation of circBRIP1 is a unique proximal target engagement PD biomarker of DHX9 inhibition, but not a predictor of DHX9 sensitivity. Importantly, induction of circBRIP1 is observed intratumorally in human xenograft in vivo efficacy studies in mice. Induction in each individual tumor correlates with observed tool compound exposure, providing evidence of a predictable PK/PD relationship. We also observe dose dependent circBRIP1 induction in mouse peripheral blood mononuclear cells (PBMC). We have extended these studies to primary human whole blood, where we see robust dose dependent induction of circBRIP1 after ex vivo treatment with DHX9 inhibitor for 24 hours. Altogether, these studies show evidence for the utility of circBRIP1 as a non-invasive target engagement biomarker for DHX9 inhibitors in the clinic.

Citation Format: David Brennan, Jennifer Castro, Matthew H. Daniels, Monique Laidlaw, Chuang Lu, Stephen J. Blakemore, Serena J. Silver, P. Ann Boriack-Sjodin, Kenneth W. Duncan, Jason A. Sager, Robert A. Copeland. circBRIP1 RNA as a non-invasive target engagement pharmacodynamic biomarker for DHX9 inhibition [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 520.