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Leukemia cells rely on two nucleotide biosynthetic pathways, de novo and salvage, to produce dNTPs for DNA replication. Here, using metabolomic, proteomic, and phosphoproteomic approaches, we show that inhibition of the replication stress sensing kinase ataxia telangiectasia and Rad3-related protein (ATR) reduces the output of both de novo and salvage pathways by regulating the activity of their respective rate-limiting enzymes, ribonucleotide reductase (RNR) and deoxycytidine kinase (dCK), via distinct molecular mechanisms. Quantification of nucleotide biosynthesis in ATR-inhibited acute lymphoblastic leukemia (ALL) cells reveals substantial remaining de novo and salvage activities, and could not eliminate the disease in vivo. However, targeting these remaining activities with RNR and dCK inhibitors triggers lethal replication stress in vitro and long-term disease-free survival in mice with B-ALL, without detectable toxicity. Thus the functional interplay between alternative nucleotide biosynthetic routes and ATR provides therapeutic opportunities in leukemia and potentially other cancers., Leukemic cells depend on the nucleotide synthesis pathway to proliferate. Here the authors use metabolomics and proteomics to show that inhibition of ATR reduced the activity of these pathways thus providing a valuable therapeutic target in leukemia.

Pancreatic ductal adenocarcinoma (PDAC) is the third leading cause of cancer-related deaths in the United States, with an overall survival of less than one year. An improved knowledge of PDAC biology, to uncover vulnerabilities specific to cancer cells, is needed to develop more effective therapeutic options. We are investigating the intersection between three aspects of PDAC biology that can, ultimately, be developed for therapeutics: (i) cytokine signaling, with a particular focus on the metabolic effects of interferons (IFNs), which are present in the highly inflamed and dense PDAC stromal microenvironment; (ii) nucleotide metabolism, a network of tightly regulated biochemical pathways that produce deoxyribonucleotide triphosphates (dNTPs), which are required for DNA replication; and (iii) the replication stress response pathway, an intracellular signaling mechanism that is activated by perturbations in DNA replication, and has been recently shown to govern key aspects of nucleotide metabolism. We hypothesize that IFN signaling reduces the levels of already limited dNTP pools in PDAC cancer cells, which respond by initiating metabolic and signaling mechanisms that coordinately function to increase dNTP recycling and biosynthetic mechanisms while simultaneously reducing their consumption. Our results, which include integrated metabolic, transcriptomic, and proteomic analyses, indicate that IFN signaling in PDAC cells induces a switch in nucleotide metabolism from a biosynthetic to a predominantly dNTP catabolic phenotype. This switch appears to be mediated by dNTP phosphohydrolysis catalyzed by the Sterile Alpha Motif and Histidine/aspartic acid Domain-containing protein (SAMHD1). Furthermore, we have investigated the effects of IFN signaling on dNTP phosphohydrolysis to deoxyribonucleosides across a panel of PDAC cancer cells, resembling the spectrum of the human disease. We also examined the biochemical fates of the deoxyribonucleoside products of SAMHD1 using targeted LC-MS/MS metabolic tracing experiments. We have also demonstrated a role for the replication stress response kinase Ataxia Telangiectasia and Rad3-related protein (ATR) in regulating dNTP levels in PDAC cells exposed to IFN. Furthermore, we have demonstrated that ATR activity is an actionable co-dependency of IFN-exposed cells and that pharmacologic inhibition of ATR eradicates PDAC cells exposed to IFN. Collectively, these studies increase our understanding of the interplay between cell extrinsic (IFN signaling) and intrinsic (replication stress) signal transduction networks, and the regulation of nucleotide metabolism in PDAC, and uncovered critical vulnerabilities to be exploited by new therapeutic approaches against this extremely aggressive and difficult to treat malignancy. Citation Format: Evan R. Abt, Amanda Dann, Thuc M. Le, Joe R. Capri, Chloe M. Cheng, Juna Yi, Soumya Poddar, Woosuk Kim, Timothy R. Donahue, Caius G. Radu. Identification of new modulators of nucleotide metabolism and replication stress in PDAC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4971.