Abstract 1620: Vulnerability to selective CTPS1 inhibition in cancers lacking CTPS2

Background De novo pyrimidine synthesis is a universal requirement for cancer cell proliferation; however, targeting this pathway results in toxicity to all dividing cells. The rate limiting conversion of UTP to CTP is catalysed by two isoforms with the same enzymatic activity (CTP synthase 1 and 2; CTPS1 & CTPS2). CTPS1 plays an essential role in lymphoid cell proliferation; differential targeting of CTPS1, sparing the paralog CTPS2, is a therapeutic strategy in lymphoid cancers that can potentially avoid toxicity. In epithelial tissues (and cancers derived from them), CTPS2 is also active and may compensate for CTPS1 inhibition. Somatic loss of CTPS2 would expose a synthetic lethal vulnerability to CTPS1 inhibition. A highly selective, orally available CTPS1 inhibitor has entered clinical development. Methods Pan-Cancer Analysis of Whole Genomes data were accessed via cBioPortal. Ovarian cancer tumour microarrays (n=117 tumours) were analysed by immunohistochemistry (IHC) using a monoclonal CTPS2 antibody. CTPS2 was disrupted in cancer cell lines by clustered regularly interspaced short palindromic repeats (CRISPR); protein loss was confirmed in clonal progeny by western blotting. STP-B is a potent and highly selective inhibitor of CTPS1 (PMID: 37008165); IC50 values for isogenic cell line pairs (n=5) and primary ovarian cancers (n=10) were assessed using CellTiter-Glo. Immunodeficient mice were transplanted subcutaneously with a CTPS2 positive or negative primary ovarian cancer (n=1 each) and treated with STP-B at 10-50 mg/kg/day or vehicle control (n=10 mice per arm). Results Hemi/homozygous loss of CTPS2 (chrX gene) was most prevalent in ovarian, lung, bladder and gastroesophageal cancer (17 to 19%). IHC analysis of tumour microarrays confirmed lack of CTPS2 protein in 24% of ovarian cancers, as well as in other cancer types at prevalences broadly commensurate with the genomic data. CRISPR-induced CTPS2 loss in cancer cell lines resulted in an 11-fold mean increase in sensitivity to CTPS1 inhibition by a highly selective small molecule (STP-B). CTPS2 null primary ovarian cancers showed uniformly greater sensitivity to STP-B in vitro and underwent tumour regression with STP-B treatment in vivo. CTPS2 loss was largely mutually exclusive with BRCA1/2 mutation in two independent ovarian cancer cohorts. Conclusions In vitro and in vivo studies demonstrate that loss of CTPS2 exposes a synthetic lethal vulnerability to selective CTPS1 inhibition. The prevalence of CTPS2 loss is >10% in a number of common cancer types. A highly selective oral CTPS1 inhibitor is currently in clinical development for the treatment of lymphoma (NCT05463263). Dose escalation in solid tumours commenced September 2024, and will be followed by a safety expansion cohort for patients with CTPS2 null ovarian cancer (NCT06297525). Citation Format: Philip A. Beer, John P. Thomson, Charlie Gourley, Alison Meynert, Andrew E. Parker, Brian Schwartz, Patricia Roxburgh. Vulnerability to selective CTPS1 inhibition in cancers lacking CTPS2 [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 1620.