Abstract 1626: Tumors driven by oncogene amplified extrachromosomal DNA (ecDNA) demonstrate enhanced sensitivity to cell cycle checkpoint kinase 1 (CHK1) inhibition

Abstract Patients whose tumors harbor oncogene amplification on extrachromosomal DNA (ecDNA) fail to respond to targeted or immune therapy and have poor prognosis. ecDNA are cancer-specific circular fragments of genomic DNA engendered with unique properties, including open chromatin architecture associated with hyper transcription and a predilection for structural variation. In addition, ecDNA+ tumors have tremendous copy number heterogeneity mediated through acentric, non-Mendelian segregation. These properties afford ecDNA+ tumors with unparalleled genomic plasticity permitting circumvention of therapeutic pressure. However, these features also confer heightened levels of DNA replication stress (RS), and we have found that ecDNA amplified tumor cells are hyper-reliant on CHK1, a master regulator of the cellular RS response. We identified CHK1 as an ecDNA essential target in a CRISPR genetic screen using a methotrexate-induced ecDNA amplification model in HeLa cancer cells. ecDNA-dependent cell fitness assessment of CHK1 was confirmed using a flow cytometry-based CRISPR competition assay. The target was further validated using a CHK1 inhibitor (CHK1i) tool compound in MYC-amplified COLO320 isogenic cell lines that demonstrated a 10-fold enhanced cytotoxicity in the ecDNA amplified setting.Based on these results, we developed a highly potent, selective, and orally bioavailable CHK1i optimized as an ecDNA-directed therapeutic (ecDTx). An advanced lead, BBI-cmpd1, robustly induced RS biomarkers (e.g., pRPA) in ecDNA+ COLO320 tumor cells as compared to matched chromosomally-amplified (ecDNA-) COLO320 cells, consistent with the increased reliance on CHK1 to manage elevated RS in the ecDNA amplified setting. BBI-cmpd1 demonstrated potent anti-proliferative activity against a panel of ecDNA+ oncogene amplified tumor lines as compared to non-amplified lines demonstrating oncogene and indication agnostic efficacy in ecDNA-based tumors. Oral administration of BBI-cmpd1 resulted in on-target activity against CHK1 and anti-tumor activity in an ecDNA oncogene amplified tumor model in vivo. These findings support the clinical utility of potent, selective, and oral CHK1i to address the significant unmet need driven by ecDNA oncogene amplified cancers. Citation Format: Sudhir Chowdhry, Snezana Milutinovic, Edison Tse, Salvador Garcia, Dean Perusse, Melissa Ritland, Juyeon Ko, Deepti Wilkinson, Kristen Turner, Auzon Steffy, Joshua Plum, Ben Norman, AnnMarie Pferdekamper, Todd Meyer, Debbie Liao, Rachelle Elsdon, Joshua Lange, Anthony Pinkerton, Ryan Hansen, Christian Hassig, Shailaja Kasibhatla. Tumors driven by oncogene amplified extrachromosomal DNA (ecDNA) demonstrate enhanced sensitivity to cell cycle checkpoint kinase 1 (CHK1) inhibition [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1626.