Abstract 7126: Synergistic combinations and tissue type-specificity of compounds targeting components of the DNA damage response pathway in 2D culture and 3D spheroid cell viability assays
Authors: Melis Janneke J. , Kluitmans Daphne J. , Kooijman Jeffrey J. , Dylus Jelle , Wetemans Sabine , Geerdink-Datema Suzan , de Roos Jeroen A. , Grobben Yvonne , Zaman Guido J. 
Published: March 2024

Abstract
Poly (ADP-ribose) polymerase (PARP) inhibitors have changed the landscape of treatment for homologous recombination (HR)-deficient cancers. PARP inhibitors are synthetically lethal with deficiencies in genes involved in the HR pathway, such as BRCA2, but resistance against PARP inhibitors is a major problem in the clinic. The use of new synergistic drug combinations targeting different components of the DNA damage response (DDR) pathway may overcome PARP inhibitor resistance. Sixteen small molecule inhibitors acting on different targets in the DDR pathway (including PARP, Polθ and ATR) were profiled in 2D culture and 3D spheroid cell viability assays. Intracellular ATP content was used as an indirect readout of cell number. Compound synergies were determined by profiling combinations of compounds in a 6-by-6 matrix, and quantifying synergistic effects using the Excess over Bliss score [1]. A pair of isogenic BRCA2-deficient and -proficient DLD-1 colon adenocarcinoma cell lines was used as a model of BRCA2-deficient tumors. In 2D cell viability assays, PARP inhibitors and the Polθ inhibitor ART558 were more active in BRCA2-deficient compared to BRCA2-proficient DLD-1 cells, whereas an ATR inhibitor (ceralasertib) was equally potent in both cell lines. Combining olaparib with ART558 in 2D culture and 3D spheroid studies showed synergistic effects in BRCA2-deficient DLD-1 cells. Moreover, olaparib synergized with ceralasertib in both BRCA2-deficient and -proficient DLD-1 cells. Different DDR-targeting inhibitors were profiled in over a hundred cancer cell lines from diverse tumor tissue origin in 2D assays. This showed a relatively high potency for PARP inhibitors in ovarian cancer cell lines compared to cell lines derived from other tissue types, which is consistent with the clinical application of PARP inhibitors for treatment of ovarian cancers. For ATR inhibitors and ART558, kidney and myeloid cancer cell lines were found to be most sensitive, respectively, suggesting potential therapeutic utility of ATR and Polθ inhibitors for treatment of these cancer types. The genomic determinants of the different sensitivities were investigated by comparing compound potencies in the cell viability assays with the mutation status of more than 500 genes involved in cancer or the DDR pathway in the cell lines. Additionally, cancer cell line sensitivity was correlated with the expression levels of more than 19,000 genes in these cell lines to identify novel RNA signatures capable of predicting response to DDR-targeting inhibitors. This study uncovers new synergistic drug combinations that increase the efficiency of PARP inhibitors, and provides new insights into the determinants of cancer cell line sensitivity to compounds targeting different components of the DDR pathway. [1] Liu et al. Stat. Biopharm. Res. 10, 112-22; 2018
Citation Format: Janneke J. Melis, Daphne J. Kluitmans, Jeffrey J. Kooijman, Jelle Dylus, Sabine Wetemans, Suzan Geerdink-Datema, Jeroen A. de Roos, Yvonne Grobben, Guido J. Zaman. Synergistic combinations and tissue type-specificity of compounds targeting components of the DNA damage response pathway in 2D culture and 3D spheroid cell viability assays [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 7126.