Abstract PR009: Cytidine diphosphate diacylglycerol synthase 2 is a synthetic lethal target in mesenchymal cancers

Abstract

Abstract Synthetic lethal interactions (SLIs) can provide a therapeutic index, as illustrated by PARP inhibition of BRCA-deficient cancers. This clinical success, and other examples, have spurred efforts to identify additional cancer-associated SLIs. Whereas additional SLIs based on genomic alterations in cancer have been identified, we set out to explore the SLI space as a function of differential RNA expression profiles in cancer and normal tissue, covering all ∼3.4e8 gene pairs. In our bioinformatic pipeline, synthetic lethality is scored by correlating DepMap dependency and expression data (n = 913 cancer cell lines), while cancer specificity is scored by comparing TCGA expression data for 9264 tumors and 741 healthy samples. Cancer specificity is confirmed by comparing also calibrated GTEx data for 17382 healthy tissue samples with calibrated DepMap expression data. With this pipeline we uncovered a frequent cancer-specific SLI between the paralogs cytidine diphosphate diacylglycerol synthase 1 (CDS1) and CDS2 (p<0.001 in all three analyses). Essentiality of CDS2 is observed in one third of cultured cancers (DepMap). Using CRISPR-Cas9 we confirm the CDS1-dependency for CDS2 essentiality in a panel of 12 cultured cancer cell lines, with lethality by CDS2 ablation reaching up to 98% in CDS1-negative cell lines. We also confirm the SLI using admixing experiments in tumor-bearing mice for two cell lines (6 mice per group, up to 95% synthetic lethality, p<0.001). The essentiality of CDS2 for cell survival is observed for mesenchymal-like cancers, which commonly express low levels of CDS1. To biochemically define the effects of CDS2 perturbation in CDS1-negative cancer cells, we performed multi-omic analyses in a panel of CDS1-negative cancer cell lines. The results show that mechanistically, the CDS1-2 SLI is accompanied by disruption of lipid homeostasis, including extensive accumulation of cholesterol esters and triglycerides. Additionally, quantitative western blotting for cleaved caspase-3 showed induction of apoptotic cell death (p<0.001 in 2 cell lines). To challenge the robustness of the SLI, we performed genome-wide CRISPR-Cas9 knockout screens in a panel of four CDS1-negative cancer cell lines. This failed to identify a common escape mechanism of death caused by CDS2 ablation. These findings suggest that no common escape to the combined loss of CDS1 and CDS2 is possible through loss-of-function. In conclusion, by computational, genetic, biochemical and functional analyses we demonstrate that CDS2 may serve as a target in mesenchymal cancers, meriting therapeutic exploration. Citation Format: Tim Arnoldus, Alex van Vliet, Adriaan F.H. de Groot, Niek Blomberg, Onno B. Bleijerveld, Susan E. van Hal-van Veen, Anita E. Grootemaat, Rolf Harkes, Nicole N. van der Wel, Maarten Altelaar, Martin Giera, Daniel S. Peeper. Cytidine diphosphate diacylglycerol synthase 2 is a synthetic lethal target in mesenchymal cancers [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Expanding and Translating Cancer Synthetic Vulnerabilities; 2024 Jun 10-13; Montreal, Quebec, Canada. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(6 Suppl):Abstract nr PR009.