A cell-based screen identifies ATR inhibitors with synthetic lethal properties for cancer-associated mutations

Abstract

Oncogene activation has been shown to generate replication-born DNA damage, also known as replicative stress. The primary responder to replicative stress is not Ataxia-Telangiectasia Mutated (ATM) but rather the kinase ATM and Rad3-related (ATR). One limitation for the study of ATR is the lack of potent inhibitors. We here describe a cell-based screening strategy that has allowed us to identify compounds with ATR inhibitory activity in the nanomolar range. Pharmacological inhibition of ATR generates replicative stress, leading to chromosomal breakage in the presence of conditions that stall replication forks. Moreover, ATR inhibition is particularly toxic for p53-deficient cells, this toxicity being exacerbated by replicative stress-generating conditions such as the overexpression of cyclin E. Notably, one of the compounds we identified is NVP-BEZ235, a dual phosphatidylinositol-3-OH kinase (PI3K) and mTOR inhibitor that is being tested for cancer chemotherapy but that we now show is also very potent against ATM, ATR and the catalytic subunit of DNA-dependent protein kinase (DNA-PKcs).

Figure 1

Screening strategy for the identification of ATR inhibitors. (a) Schematic representation of the pipeline followed for the identification of ATR inhibitors (see Methods for a full description). Data were represented in a color-coded table of a 96 well plate, in which potential ATR inhibitors could be identified as black wells that had lost the 4-OHT-induced γH2AX signal. (b) Effect of increasing doses of caffeine on the nuclear γH2AX signal induced by 4-OHT. Error bars indicate s.d. AU: Arbitrary Units.(c) Results of the screening performed at 10 μM for the 623 compounds tested (average of 3 different experiments performed in duplicate). Highlighted in red are compounds that presented more than 70% inhibition and that were taken for further analysis. (d) Image illustrating the relative activity of 8 of the compounds from the secondary screen at decreasing concentrations, 2 of which show almost full activity at 100 nM (asterisks).(e) H2AX and Chk1 phosphorylation in TopBP1-ER cells exposed to 4-OHT, in the presence of absence of the compounds identified in (b). Caffeine (5mM) was used as a positive control of ATR inhibition.

Figure 2

Effect of the compounds in the G2/M checkpoint. (a) Cell cycle distribution of U2OS cells 4 hr after a treatment with 10 Gy of IR, in the presence of the indicated chemicals (UCN-01: 0.3 μM; compounds: 1 μM). H3 Ser10 phosphorylation (y axis) is used to distinguish mitotic cells from G2 cells. Cells were kept on taxol for the 4 hr period to capture all cells undergoing mitosis during that time. The percentage of mitotic cells is indicated in red. (b) Examples of the typical aberrations observed in IR-treated cells in the presence of the drugs. In this case, no taxol was added to prevent the influence of the drug in mitotic abnormalities. (c) Structures and formal names of the 2 compounds that are analyzed in the rest of the manuscript.

Figure 3

ATM-, ATR- and DNA-PKcs-dependent phosphorylations in vivo. Levels of ATM, Chk2 and Chk1 (a); DNA-PKcs (b) and H2AX (c) phosphorylation analysed in U2OS cells upon exposure to 10 Gy at increasing concentrations of the inhibitors. Note that ATR levels are not affected by the use of these compounds.

Figure 4

The identified compounds prevent the breakage of stalled replication forks. (a) The capability to restart DNA synthesis from stalled replication forks was quantified by a pulse of EdU (1 hr), performed at different times after the release from a 3hr exposure to HU. Note that whereas replication can readily restart in control U2OS cells, the presence of either inhibitor stops fork progression. (b) Cells taken from (a) were stained for 53BP1 to visualize the presence of DNA breaks 16 hr after the release from HU. The presence of the ATR inhibitors together with HU leads to a very high accumulation of DNA breaks (HTM quantification of these data is available in Supplementary Fig. 2).(c) Western blot analysis of HU treated U2OS cells (3hrs) in the presence of the inhibitors. (d) Cell cycle profiles of HU treated U2OS cells (1mM, 3hrs) 16 hrs after being released in fresh media free of HU and inhibitors. A dramatic G2 arrest is observed in the inhibitor treated cells.

Figure 5

Inhibition of ATR generates RS. (a) Illustration of the type of pan-nuclear γH2AX staining that is observed upon exposure of U2OS cells to ATR inhibitors (5 μM) or UCN-01 (0.3 μM) for 8 hrs. (b) Representation of the levels of pan-nuclear γH2AX signal obtained in (a) as automatically identified through HTM. (c,d) Representation of the levels of pan-nuclear γH2AX observed when combining lower doses of the ATR inhibitors (1 μM) with low doses of UCN-01 (c), or HU (d). (e) Illustration of the type of pan-nuclear γH2AX staining that is observed upon exposure of wt and p53^-/- MEF to UCN-01 (0.3 μM). (f) Pan-nuclear γH2AX in wt and p53 deficient MEF treated with ATR inhibitors (5 μM) or UCN-01 (0.3 μM), as represented in (a). AU: Arbitrary Units.

Figure 6

Synthetic lethality of ATR inhibition with cyclin E overexpression and/or p53 loss. (a) Example of the type of pan-nuclear γH2AX staining that is observed upon overexpression of cyclin E in wt primary MEF. (b) Quantification of the type of staining shown in (a) through HTM, in wt and p53^-/- MEF in the presence or absence of the ATR inhibitors (5 μM) for 8 hrs. AU: Arbitrary Units. (c) Cell cycle profiles of cyclin E overexpressing wt and p53^-/- MEF in the presence or absence of the DDRi (5μM) and/or UCN-01 (0.3 μM) for 48 hrs.