I. A. Elliott1, J. L. Williams2, R. Ghukasyan1, C. C. Matsumura1, N. Wu1, L. Li1, W. Kim3, S. Poddar3, E. R. Abt3, A. M. Dann1, H. DeRubertis1, D. Braas4, T. M. Le3, C. G. Radu3, T. R. Donahue1,3 1University Of California – Los Angeles,Department Of Surgery,Los Angeles, CA, USA 2Harbor-UCLA Medical Center,Department of Surgery,Torrance, CA, USA 3University Of California – Los Angeles,Department Of Molecular And Medical Pharmacology,Los Angeles, CA, USA 4University Of California – Los Angeles,Metabolomics Center,Los Angeles, CA, USA
Introduction:
Autophagy is a critical source of nucleotides, which are rate-limiting for Ras-driven cancer cell proliferation. Genetically disabling autophagy impairs energy and redox homeostasis by depletion of nucleotide pools, and sensitizes cancer cells to radiation. We hypothesized that the autophagy inhibitor chloroquine (CQ) would deplete deoxyribonucleotide triphosphate (dNTP) availability for incorporation into DNA, thus sensitizing cancer cells to replication stress and revealing a targetable liability in Ras-driven pancreatic ductal adenocarcinoma.
Methods:
Human (MiaPaCa-2) and murine (KPC) PDAC cells were treated with CQ +/- the replication stress response (RSR) inhibitor VE822. S-phase cells were labeled by pulsing with 5’-ethynyl-2’-deoxyuridine (EdU) and cell cycle progression measured by flow cytometry. Newly synthesized dNTP incorporation into DNA was measured via [13C6]glucose labeling and our novel liquid chromatography mass spectrometry (LC-MS) platform. Global metabolomics analyses were performed by detection of relative amounts of metabolites using LC-MS. Western blots (WB) were done on cell lysates. Cell viability was measured by Cell-Titer-Glo assay. MiaPaCa-2 or KPC cells were injected s.q. in the flanks of NSG or C57BL/6 mice. Mice were treated 5x/week with CQ+/-VE822 (60mg/kg p.o.). Immunohistochemistry (IHC) was performed on explanted KPC tumors after 3 days of CQ+VE822.
Results:
We found that CQ caused S-phase arrest in MiaPaCa-2, and impaired incorporation of newly synthesized dNTPs into replicating DNA(Fig.1a), indicating nucleotide pool insufficiency. Global metabolomic profiling of MiaPaCa-2 revealed that this was due to depletion of purine and pyrimidine substrates for dN synthesis under CQ, and this was exacerbated by addition of the RSR inhibitor VE822(Fig.1b). We then tested the impact of this nucleotide depletion on cell fate; CQ+VE822 treatment led to synergistic induction of DNA damage (reflected by pH2A.X WB), and decreased viability of MiaPaCa-2 and KPC in vitro (Fig.1c). We also observed increased IHC staining for pH2A.X in KPC tumors and impaired growth of MiaPaCa-2 tumors after CQ+VE822 treatment in vivo. Finally, we confirmed the ability of CQ to induce oxidative stress as indicated by HO-1 levels on WB. Management of redox balance and DNA damage are critical to recovery from radiation; accordingly, we found that CQ+VE822 profoundly impaired survival after radiation of MiaPaCa-2 and KPC cells.
Conclusion:
Pharmacologic inhibition of autophagy by CQ impairs incorporation of dNTPs into DNA by depleting substrates for nucleotide biosynthesis. When combined with an RSR inhibitor, this leads to induction of DNA damage and synthetic lethality in PDAC cells in vitro and in vivo.
