A crucial role for ATR in the regulation of deoxycytidine kinase activity

Biochemical Pharmacology 100 (2016) 40–50

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A crucial role for ATR in the regulation of deoxycytidine kinase activity Maxime Beyaerta , Eliza Starczewskaa , Eric Van Den Nestea,b , Françoise Bontempsa,* a b

de Duve Institute & Université catholique de Louvain, B-1200 Brussels, Belgium Department of Hematology, Cliniques universitaires Saint-Luc & Université catholique de Louvain, B-1200 Brussels, Belgium

A R T I C L E I N F O

A B S T R A C T

Article history: Received 25 August 2015 Accepted 20 November 2015 Available online 24 November 2015

Deoxycytidine kinase (dCK) (EC 2.7.1.74) is a key enzyme for salvage of deoxynucleosides and activation of numerous anticancer and antiviral nucleoside analogs. dCK activity is enhanced in response to several genotoxic treatments, which has been correlated with an increase of dCK phosphorylation at Ser-74. ATM was recently identified as the kinase responsible for Ser-74 phosphorylation and dCK activation after ionizing radiation (IR). Here, we investigated the role of ATM and the related kinase ATR in dCK activation induced by other types of DNA damage. Using ATM-deficient cells or the ATM inhibitor KU-60019, we found that ATM was not required for dCK activation caused by UV light, aphidicolin, cladribine, and unexpectedly also IR. On the other hand, the selective ATR inhibitor VE-821 significantly reduced upregulation of dCK activity induced by these genotoxic agents, though not IR, and also down-regulated basal dCK activity. A role for ATR in the control of dCK activity was confirmed by using ATR siRNA and ATR-Seckel cells. ATR was also found to directly phosphorylate dCK at Ser-74 in vitro. Further studies revealed that ATR, which is also activated in response to IR, although later than ATM, was responsible for IR-induced dCK activation in ATM-deficient cells or in the presence of KU-60019. Overall, our results demonstrate that ATR controls basal dCK activity and dCK activation in response to replication stress and indicate that ATR can activate dCK after IR if ATM is lacking or inhibited. ã 2015 Elsevier Inc. All rights reserved.

Chemical compounds studied in this article: Cladribine (PubChem CID: 20279) Aphidicolin (PubChem CID: 457964) KU-60019 (PubChem CID: 15953870) VE-821 (PubChem CID: 51000408) Keywords: Deoxycytidine kinase Ser-74 phosphorylation ATM ATR DNA damage Nucleoside analogs

1. Introduction Deoxycytidine kinase (dCK) catalyzes the phosphorylation of deoxycytidine, deoxyadenosine and deoxyguanosine into their monophosphate form. This reaction is the first and rate-limiting step of the deoxynucleoside salvage pathway that supplies cells with deoxyribonucleotides for DNA synthesis as an alternative to the de novo synthesis [1]. In addition to its natural substrates, dCK phosphorylates and activates a large number of nucleoside analogs used in the treatment of cancer and viral diseases [2,3], thereby playing an essential role in their therapeutic efficacy [4]. Given the important role of dCK in deoxynucleotide metabolism and in human chemotherapy, identification of the mechanisms that control its activity is of highest interest. We previously

Abbreviations: APC, aphidicolin; ATM, ataxia-telangiectasia mutated; ATR, ATM and Rad-3 related; CdA, cladribine; dCK, deoxycytidine kinase; DSB, double-strand break; IR, ionizing radiation; PP2A, protein phosphatase 2A; siRNA, small interfering RNA; ssDNA, single-stranded DNA. * Corresponding author at: de Duve Institute & Université catholique de Louvain, 75, Avenue Hippocrate, B1.75.08, B-1200 Brussels, Belgium. Fax: +32 2 764 7598. E-mail address: [email protected] (F. Bontemps). http://dx.doi.org/10.1016/j.bcp.2015.11.022 0006-2952/ ã 2015 Elsevier Inc. All rights reserved.

established that dCK is a phosphoprotein, containing at least four phosphorylation sites: Thr-3, Ser-11, Ser-15 and Ser-74, the latter being the major phosphorylated residue [5]. Site-directed mutagenesis demonstrated that Ser-74 phosphorylation increases basal dCK activity, whereas phosphorylation of the three other sites does not [5,6]. In addition, the use of a specific anti-phospho-Ser74 antibody showed that activation of dCK, which is observed in response to a series of genotoxic treatments, including ionizing radiation (IR), UV-C light, DNA synthesis inhibitors and chemotherapeutic nucleoside analogs [7–12], is correlated with an increase of the phosphorylation of dCK at Ser-74 [5,13]. Next step was to decipher the signaling pathway involved in the control of Ser-74 phosphorylation. The finding that dCK was activated by genotoxic stimuli suggested that a DNA damageactivated protein kinase could be involved in this process. In accordance with this hypothesis and the results from a global proteomic analysis [14], the ATM (ataxia-telangiectasia mutated) kinase, a master regulator of the DNA damage response, was identified as the protein kinase responsible for Ser-74 phosphorylation and dCK activation in response to IR [15,16]. Concerning dCK dephosphorylation, we recently showed that protein phosphatase 2A (PP2A) constitutively dephosphorylates Ser-74 and is therefore

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a negative regulator of dCK activity [17]. Interestingly, we noted in this study that the PP2A inhibitor okadaic acid induced increase of Ser-74 phosphorylation and dCK activity in ATM-deficient cells, suggesting that another kinase than ATM was able to phosphorylate dCK at Ser-74 in basal conditions [17]. Whereas IR predominantly activates the kinase ATM, other genotoxic agents known to increase dCK activity, such as UV-C light and the DNA polymerase inhibitor aphidicolin, primarily activate ATR (ATM and Rad-3 related), another essential kinase involved in the DNA damage response. Both ATM and ATR promote cell cycle arrest and DNA repair or induce apoptosis if repair systems are overwhelmed [18], but they respond to distinct DNA lesions: ATM is activated in response to DNA double-strand breaks (DSBs), such as induced by IR, while ATR is activated by single-stranded DNA (ssDNA) [19]. This ssDNA structure is generated during processing of DSB or arises when DNA replication forks stall, which can occur during normal replication (for instance at fragile sites) or in response to DNA synthesis inhibitors, chemotherapeutic drugs or UV irradiation [20,21]. Like ATM, ATR phosphorylates its targets on Ser or Thr residues that are followed by Gln (SQ/TQ motifs) [14], as is Ser-74 of dCK, suggesting that ATR could phosphorylate Ser74 and activate dCK in response to certain genotoxic stimuli. In the present study, we aimed to compare and investigate the roles of both ATM and ATR in Ser-74 phosphorylation and dCK activation in response to various DNA-damaging agents, and particularly to UV light and genotoxic drugs that cause replication stress. Our results show that ATR, besides ATM, plays an important role in the regulation of dCK activity, not only after DNA damage, but also in unperturbed cells.

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conditions, except that FCS was used at a concentration of 10%. MCF-7 and PANC-1 cells were cultured in DMEM medium supplemented with 10% FCS, 2 mM ultraglutamine and penicillin-streptomycin (100 U/ml). When used, inhibitors were added 1 h before genotoxic treatment. Hydrophobic compounds were dissolved in DMSO and equal amounts of DMSO were added in untreated and treated cells. The final DMSO concentration was 0.2%. In some experiments, cells were UV-C-irradiated as described in [7] or submitted to IR using a 137Cs source at a dose rate of 2.43 Gy/min at room temperature. 2.3. dCK assay in cell lysates GM0536, GM1526, GM18367A, EHEB, HL-60, MCF-7 and PANC-1 cell extracts were prepared as previously reported [5,12]. dCK activity was measured by a radiochemical assay as described in [5], using 30–100 mg of cellular protein or 0.25 mg of recombinant dCK, with 10 mM [5-3H]-deoxycytidine (1000 cpm/pmol) and 5 mM Mg-ATP as substrates. The protein content of samples was determined by the method of Bradford, using BSA as a standard [22]. To facilitate the comparison between the different experimental conditions and cell lines, dCK activities were expressed as fold change. Basal dCK activities in wild-type (GM0536) and ATM/ (GM1526) cells were 13.5  1.0 (n = 18) and 11.1 1.6 (n = 9) pmol/min/mg protein, respectively. For other cell lines, dCK activities are given in the legend of the figures. 2.4. Immunoblot analysis

2. Materials and methods 2.1. Reagents RPMI-1640 and all cell culture reagents were from Gibco/ Invitrogen (Carlsbad, CA, USA). Fetal calf serum (FCS) and ultraglutamine were purchased from Lonza (Basel, Switzerland). Cladribine (2-chloro-20 -deoxyadenosine, CdA) was synthesized and supplied by Prof J. Marchand (Laboratory of Organic Chemistry, Université catholique de Louvain, Louvain-la-Neuve, Belgium). [5-3H]-deoxycytidine (18 Ci/mmol) was from Moravek Biochemicals (Brea, CA, USA). KU-60019 and VE-821 were purchased from Bio-Connect (Huissen, The Netherlands). The protein A/G PLUSagarose beads were from Santa Cruz Biotechnology (Santa Cruz, CA, USA). Other chemicals, materials and reagents were from Sigma, Calbiochem or Bio-Rad Laboratories. 2.2. Cell culture and treatments The EBV-immortalized lymphoblastoid cell lines GM0536 (ATM+/+), referred here as wild-type cells, and GM1526 (ATM/  ), which were derived from a healthy control or an ataxia telangiectasia patient, respectively, were obtained from the NIGMS Human Mutant Cell Repository (Camden, NJ, USA). The Seckel lymphoblastoid cell line GM18367A was kindly provided by Dr. X. Liu (Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA). The human leukemia cell lines EHEB (chronic B-cell leukemia) and HL60 (acute myeloid leukemia) were purchased from DSMZ-German Collection of Microorganisms and Cell Culture (Braunschweig, Germany). MCF-7 (breast) and PANC-1 (pancreatic) cancer cell lines were kind gifts from Dr. A. Decottignies and Dr. G. Bommer (de Duve Institute), respectively. GM0536, GM1526 and GM18367A cells were cultured in RPMI-1640 medium with Glutamax supplemented with 15% FCS at 37  C in humidified air containing 5% CO2. EHEB and HL-60 cells were cultured in the same

Aliquots of cell lysates containing 30–150 mg of protein or 0.25 mg of recombinant dCK were subjected to SDS-PAGE in 12% (w/v) polyacrylamide gels and transferred to Immobilon-P Transfer membranes (PVDF) (Millipore, Billerica, USA). After transfer, the membranes were blocked at room temperature for 1 h in Odyssey blocking buffer, or in PBS or TBS containing 5% (w/v) fat-free milk powder or BSA, and then probed overnight at 4  C with primary antibodies. After extensive washing in either PBS-T or TBS-T, the membranes were incubated with the secondary antibody at room temperature for 1 h. After washing, the membranes were scanned with the Odyssey Infrared Imaging System from LI-COR Biosciences (Nebraska, NE, USA) and fluorescence intensities were used to quantify dCK expression or phosphorylation [6]. Other proteins analyzed in this work were visualized using the ClarityTM Western ECL Substrate from Bio-Rad (Hercules, CA, USA) and band intensities were calculated using the image J software. Phosphorylations of dCK, Chk1 and Chk2 were normalized to dCK, Chk1 and Chk2 protein levels, respectively. Mean values obtained from three independent experiments are given under a representative Western blot image, the values found in untreated cells being set at 1 for comparison. Primary antibodies used in this study were: anti-ATR (sc-1887) and anti-p53 (sc-126) from Santa Cruz Biotechnology, anti-p53pS15 (9284L), anti-ATM (2873S), anti-ATM-pS1981 (5883S), antiChk1 (2360S), anti-Chk1-pS317 (2344S), anti-Chk2 (2662S), antiChk2-pT68 (2197S) from Cell Signaling Technologies (Beverly, MA, USA) and anti-b-actin (A5441) from Sigma–Aldrich (St. Louis, MO, USA). Anti-phospho-Ser-74 and anti-dCK antibodies were generated as previously described [5]. Anti-poly(His) antibody used to detect recombinant dCK was from GE Healtcare (Machelen, Belgium). Secondary antibodies were from Sigma–Aldrich (antirabbit and anti-mouse IG conjugated to horseradish peroxidase) or from Westburg (Leusden, The Netherlands) (IRDye1 800CW donkey anti-goat, IRDye1 800CW goat anti-rabbit and IRDye1 680 goat anti-mouse).

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2.5. ATR immunoprecipitation and kinase assay ATR was immunoprecipitated from ATM-deficient cells to avoid potential interference of ATM in the ATR kinase assay or from ATRSeckel cells characterized by impaired ATR expression. For each assay, 500 mg of precleared protein extract were incubated overnight at 4  C with 40 ml of protein A/G PLUS-Agarose beads and 2.4 mg of ATR antibody. The beads were then washed twice with 1 ml of ice-cold protein extraction buffer [5] and twice with 1 ml of the kinase assay buffer containing 10 mM HEPES (pH 7.5), 50 mM NaCl, 10 mM MgCl2, 10 mM MnCl2, 10 mM ATP, 10 mM NaF, 50 mM b-glycerophosphate, 1 mM dithiothreitol and freshly added protease or phosphatase inhibitors (5 mM benzamidine, 1 mM p-toluenesulfonyl fluoride, 5 mg/ml leupeptin/antipain and 1 mM orthovanadate). Immunoprecipitates were then mixed with 40 ml of the kinase buffer containing 1 mg of human recombinant dCK expressed in Escherichia coli as previously reported [23]. After 30 min at 30  C, aliquots (10 ml) were withdrawn for immediate measurement of dCK activity, as described above, or stopped in Laemmli SDS-PAGE buffer for analysis of Ser-74 phosphorylation by immunoblotting. When the ATR inhibitor was used, it was added to immunoprecipitated ATR, on ice, for 30 min before kinase assay. 2.6. RNA interference GM0536 cells were transfected using AmaxaTM nucleofector and nucleofection Kit V (Amaxa, Cologne, Germany) according to the Amaxa guidelines. Briefly, 2  106 cells were resuspended in 100 ml of the Nucleofector solution V. Targeting or not-targeting small interfering RNAs (siRNAs) were added at a concentration of 600 nM to the cell suspensions and the mixtures were transferred to the Amaxa certified cuvettes. Nucleofection was performed using M-013 program. After 24 h, cells were re-transfected with siRNA at the same concentration and incubated for additional 48 h before utilization in subsequent experiments. siRNA duplexes were from Dharmacon (Lafayette, CO, USA): ATM siRNA (SMARTpool: ON-TARGETplus ATM siRNA), ATR siRNA (SMARTpool: ON-TARGETplus ATR siRNA), and the non-targeting control (ON-TARGETplus Non-targeting Pool). 2.7. Statistical analysis Results are expressed as the means  SEM of at least three independent experiments. Statistical analysis was performed with the GraphPad Prism 6.0 software using the one- or two-way ANOVA, as indicated, followed by the Turkey’s post hoc test. Changes were considered significantly different at P values <0.05. Statistical significance for quantified Western blot data is indicated in the figure legends. 3. Results 3.1. ATM is dispensable for dCK activation following DNA damage To investigate whether ATM was required for dCK activation induced by chemotherapeutic nucleoside analogs, DNA synthesis inhibitors or UV-C light, we analyzed dCK activation in response to these genotoxic agents in ATM-deficient lymphoblastoid cells (ATM/) as compared to wild-type cells. Treatment of cells with IR, which was previously shown to increase dCK activity in an ATM-dependent manner [15,16], was used as a positive control. We found that activation of dCK by the nucleoside analog cladribine (2-chloro-20 -deoxyadenosine, CdA), aphidicolin, UV light, and unexpectedly IR, could be induced whether ATM was present or not in cells (Fig. 1A). Moreover, the extent of dCK activation

triggered by these different treatments did no significantly differ between wild-type and ATM/ cells (P = 0.76). In accordance with previous results obtained in leukemic cells [5,13], we detected an increase in Ser-74 phosphorylation in response to all the genotoxic agents investigated, including IR, in both cell lines (Fig. 1A). Our observation that dCK activity and Ser-74 phosphorylation increased in response to IR in ATM-deficient cells was in contradiction with results previously obtained in the same cell line after the same incubation time [15]. Western blot analysis confirmed that ATM was deficient in our ATM/ cell line (Fig. 1A). Moreover, a dose-response analysis (Fig. 1B) showed that increase of dCK activity and Ser-74 phosphorylation could be observed in ATM/ cells at all the doses investigated, including the dose (6 Gy) used in the aforementioned study [15]. Altogether, these results suggested that another kinase than ATM could phosphorylate Ser-74 and activate dCK in response to DNA damage, even following IR. To corroborate this hypothesis, we tested the effect of KU-60019, a specific ATM inhibitor [24], on the activation of dCK in wild-type cells. Results showed that KU-60019, used at a concentration of 10 mM, did not prevent dCK activation induced by CdA, aphidicolin, UV light or IR, but rather tended to enhance dCK activity (Fig. 1C, left panel). Also, the ATM inhibitor did not prevent the increase of Ser-74 phosphorylation induced by these various DNA-damaging agents, but, as observed for dCK activity, tended to increase it (Fig. 1C, left panel). We verified that ATM was actually inhibited in the presence of 10 mM KU-60019 by analyzing IRinduced autophosphorylation of ATM at Ser-1981 and phosphorylation of key ATM targets, namely Chk2 at Thr-68 and p53 at Ser-15 [14,25], which were found to be completely abrogated by the inhibitor (Fig. 1C, right panel). Finally, to further emphasize that ATM is not essential for dCK activation in response to genotoxic stress, wild-type cells were transiently transfected with scrambled or ATM siRNA for 72 h and then treated with CdA or IR. Although ATM was no longer detectable after transfection with ATM siRNA (Fig. 1D, right panel), neither dCK activation (Fig. 1D, left panel), nor Ser-74 phosphorylation (Fig. 1D, right panel) was modified in response to CdA or IR. 3.2. ATR is involved in the control of dCK activity As several lines of evidence suggested that dCK could be activated by a kinase distinct from ATM, we focused on ATR, which is activated in response to a broad spectrum of genotoxic stimuli including UV light and DNA replication inhibitors [26], but also IR as a result of DSB resection [27]. To explore the role of ATR in the control of dCK activity, we used VE-821, a potent ATR inhibitor with high selectivity for ATR versus ATM [28]. Significant reduction of dCK activity was observed in wild-type cells upon addition of 10 mM VE-821, in control conditions as well as after treatment with CdA, aphidicolin and UV (Fig. 2A, left panel). Decrease in Ser74 phosphorylation was also detected (Fig. 2A, left panel) in parallel with decrease in dCK activity. In contrast, the ATR inhibitor did not significantly modify IR-induced dCK activation or Ser74 phosphorylation. Inhibition of ATR by 10 mM VE-821 was confirmed by the lack of phosphorylation of two of its specific targets after UV irradiation: Chk1 at Ser-317 and p53 at Ser-15 [14,29] (Fig. 2A, right panel). Overall, these results strongly suggested that ATR is involved in the control of dCK activity not only in response to certain genotoxic agents, but also in control conditions. To assess more directly the role of ATR in the control of dCK activity, wild-type cells were transiently transfected with scrambled siRNA or ATR siRNA before induction of DNA damage by CdA or UV light. ATR siRNA markedly decreased ATR protein level as well as the phosphorylation of its target Chk1 in response to CdA or UV light (Fig. 2B, lower panel). Silencing of ATR also resulted in

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Fig. 1. ATM is not required for dCK activation in response to DNA damage. (A) Comparison of dCK activation and Ser-74 phosphorylation in wild-type and ATM/ cells in response to various genotoxic agents. dCK activity (n = 3–7) and Ser-74 phosphorylation (n = 3) were analyzed in cells incubated for 4 h with 10 mM CdA, for 1 h after UV-C irradiation (18 J/m2), for 2 h with 10 mM aphidicolin (APC) or for 2 h after IR (10 Gy). dCK activities are expressed as means  SEM. pS74-dCK was normalized to dCK protein level (pS74/dCK) in three independent experiments and the mean values are given under a representative Western blot image, the value found in untreated cells being set at 1 for comparison. Significance relative to untreated cells was analyzed by twoway ANOVA: *P < 0.05; **P < 0.01; ***P < 0.001; ****P < 0.0001 for dCK activity, and P < 0.05 for pS74-dCK. (B) IR dose-effect on dCK activity and Ser-74 phosphorylation in ATM/ cells. Cells were exposed to IR at the indicated doses and incubated for 2 h before analysis of dCK activity (n = 3) and Ser-74 phosphorylation (n = 3). Significance relative to untreated cells was analyzed by one-way ANOVA: *P < 0.05 for dCK activity and P < 0.01 for pS74dCK. (C) Left panel: effect of 10 mM KU-60019 on dCK activation and Ser-74 phosphorylation induced by various genotoxic treatments. dCK activity (n = 5) and Ser-74 phosphorylation (n = 3) were analyzed in cells incubated as described in (A). Significance relative to the absence of KU-60019 was analyzed by two-way ANOVA: *P < 0.05 for dCK activity in the CdA condition, not significant in the other conditions and for pS74-dCK. Right panel: effect of 10 mM KU-60019 on ATM, Chk2 and p53 phosphorylation in cells incubated for 2 h after exposure, or not, to IR (10 Gy). (D) Left panel: effect of ATM silencing on dCK activation by CdA or IR. Wild-type cells were transfected with scrambled (siCTL) or ATM siRNA (siATM) for 72 h and then incubated for 4 h with or without 10 mM CdA or for 2 h after IR (10 Gy) before measurement of dCK activity (n = 3). Right panel: effect of ATM silencing on ATM protein level and Ser-74 phosphorylation (n = 3). No significant difference was found between siCTL- and siATM-treated cells for dCK activity or pS74-dCK using two-way ANOVA.

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M. Beyaert et al. / Biochemical Pharmacology 100 (2016) 40–50

Fig. 2. ATR is involved in the regulation of dCK activity. (A) Left panel: effect of 10 mM VE-821 on dCK activation and Ser-74 phosphorylation induced by various genotoxic agents. dCK activity (n = 5) and Ser-74 phosphorylation (n = 3) were analyzed in wild-type cells incubated as described in Fig. 1A. Significance relative to the absence of VE-821 was analyzed by two-way ANOVA: *P < 0.05; ***P < 0.001 for dCK activity, and P < 0.001 for pS74-dCK. No significant changes were found in the IR condition. Right panel: effect of 10 mM VE-821 on Chk1 and p53 phosphorylation in cells incubated for 1 h after exposure, or not, to UV irradiation (18 J/m2). (B) Upper panel: effect of ATR silencing on basal dCK activity (n = 6) or dCK activation by CdA (n = 3) or UV (n = 3). Wild-type cells were transfected with scrambled (siCTL) or ATR siRNA (siATR). After 72 h, cells were incubated for 2 h without or with 10 mM CdA, or for 30 min after UV irradiation (18 J/m2). Effect of ATR siRNA was investigated in the presence or absence of 10 mM VE-821. Significance relative to siCTL-treated cells was analyzed by two-way ANOVA: *P < 0.05; **P < 0.01; ***P < 0.001; ****P < 0.0001. Lower panel: effect of ATR silencing on ATR protein level and Chk1 or dCK phosphorylation. Phosphorylation of dCK at Ser-74 was analyzed in three independent experiments. Significance relative to siCTL-treated cells was analyzed by two-way ANOVA: P < 0.01. (C) Upper panel: Effect of various genotoxic treatments on dCK activity in ATR-Seckel cells. Cells were treated as described in Fig. 1A before analysis of dCK activity (n = 3). dCK activity in the absence of treatment was 3.3  0.6 pmol/min/mg protein. Significance relative to untreated cells was analyzed by one-way ANOVA: **P < 0.01. Lower panel: ATR protein level (n = 3) in WT and ATR-Seckel cells.

significant decrease of dCK activity (Fig. 2B, upper panel), both in control conditions and after genotoxic treatment, in parallel with a decrease of Ser-74 phosphorylation (Fig. 2B, lower panel). If 10 mM VE-821 was added to ATR-silenced cells, the phosphorylation of Chk1 in response to CdA or UV was completely abolished, indicating a more complete inhibition of ATR, and dCK activity and Ser-74 phosphorylation were further decreased. In these conditions, activation of dCK by CdA or UV was virtually suppressed, corroborating the major role of ATR in this process.

Next, we examined the activation of dCK in a B-lymphoblastoid Seckel cell line (GM18367A), characterized by impaired expression of ATR, due to a splicing mutation in the ATR gene, and severe defects in the ATR signaling pathway [30,31]. In contrast with the results obtained in wild-type cells (as illustrated in Fig. 1A), no significant changes in dCK activity were observed in ATR-Seckel cells after treatment with CdA, UV, or aphidicolin (Fig. 2C, upper panel). However, ATR defect did not prevent IR-induced dCK activation. Phosphorylation of dCK could not be analyzed in this

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cell line due to very low dCK protein level. Analysis of ATR protein expression by Western blot (Fig. 2C, lower panel) confirmed that ATR level was strongly reduced in ATR-Seckel compared to wildtype cells. Finally, we investigated whether ATR was also involved in the regulation of dCK activity in cancer cells. As illustrated in Fig. 3, the ATR inhibitor VE-821 was found to decrease dCK activity and dCK Ser-74 phosphorylation in all the cancer cell line investigated, namely the leukemic cell lines EHEB and HL-60 and the tumor cell lines MCF-7 and PANC-1, both in control conditions and after DNA damage induced by either CdA, UV or aphidicolin, indicating that the regulation of dCK activity by ATR may be generalizable to various types of cells. 3.3. ATM and ATR can both play a role in dCK activation after IR As illustrated in Figs. 1 B and 2 A, IR-induced dCK activation in wild-type cells was prevented neither by the ATM inhibitor, nor by the ATR inhibitor. On the other hand, IR could induce dCK activation in ATM-deficient cells as well as in ATR-Seckel cells (Figs. 1 A and 2 C), suggesting that neither ATM, nor ATR was essential for dCK activation induced by IR. Therefore, we wondered whether ATM and ATR could both phosphorylate and activate dCK and compensate for each other under this genotoxic condition. In

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line with this hypothesis, we observed that the increase of dCK activity and Ser-74 phosphorylation induced by IR in wild-type cells could be abrogated if KU-60019 and VE-821 were combined (Fig. 4A). We also found that the ATR inhibitor VE-821 almost completely prevented dCK activation and Ser-74 phosphorylation induced by IR in ATM/ cells (Fig. 4B), showing that IR-induced dCK activation is achieved by ATR when ATM is deficient. In order to better define the respective roles of ATM and ATR in dCK activation after IR, we performed a time-course analysis of the phosphorylation of their respective targets, Chk2 and Chk1, which is commonly used as readout of their activation [32]. Within 5–10 min after IR, Chk2 was already highly and maximally phosphorylated, while Chk1 phosphorylation was ongoing (Fig. 5A and B, upper left panel). Thereafter, Chk2 phosphorylation markedly declined, whereas that of Chk1 further increased. These data show that ATM is much more rapidly and potently activated than ATR after IR, as previously reported [33]. In contrast, treatment of cells with CdA, UV or aphidicolin predominantly induced Chk1 phosphorylation while Chk2 phosphorylation was delayed and markedly lower, in accordance with a key role of ATR in the cellular response to these agents (Fig. 5A and B, upper right and lower panels). Since ATM was found to be maximally activated within short time after IR while ATR activity started just to increase, we sought

Fig. 3. Effect of ATR inhibition on dCK activity in cancer cells. The effect of 10 mM VE-821 on dCK activity (n = 3) and Ser-74 phosphorylation (n = 3) was analyzed in EHEB, HL-60, MCF-7 and PANC-1 cells incubated for 2 h with 10 mM CdA or 10 mM aphidicolin (APC) or for 1 h after UV-C irradiation (18 J/m2), as indicated. dCK activities in untreated EHEB, HL-60, MCF-7 and PANC-1 cells were 32.1  0.9, 95.0  3.9, 18.9  4.7, and 51.3  6.2 pmol/min/mg protein, respectively. Significance relative to the absence of VE-821 was analyzed by two-way ANOVA: *P < 0.05; **P < 0.01; ***P < 0.001; ****P < 0.0001 for dCK activity, and at least P < 0.05 for pS74-dCK.

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However, at longer time, dCK activation could be carried out by ATR. In accordance with a delayed activation of ATR compared to ATM, we found that activation of dCK by IR in ATM/ cells started later than in wild-type cells, being undetectable until at least 10 min (Fig. 6B). 3.4. ATR directly phosphorylates dCK at Ser-74 in vitro Experiments reported above strongly indicated that ATR, in addition to ATM, is involved in the control of dCK activity. To determine whether ATR could directly phosphorylate dCK at Ser74, ATR was immunoprecipitated from ATM/ cells and incubated with purified human recombinant dCK in the presence of ATP. After 30 min of incubation with immunoprecipitated ATR, initial dCK activity was increased by more than three-fold in parallel with phosphorylation at Ser-74 (Fig. 7). To validate the role of ATR in these dCK changes, we performed the same assay in the presence of the ATR inhibitor VE-821 or with ATR immunoprecipitated from ATR-Seckel cells. In both cases, dCK activation and phosphorylation were strongly reduced. Taken together, these data indicate that ATR, like ATM [15], can directly phosphorylate dCK at Ser-74 in vitro and thereby increase its activity. 4. Discussion

Fig. 4. Analysis of the roles of ATM and ATR in dCK activation following IR. (A) Effect of the ATM and ATR inhibitors, alone or combined, on dCK activation and Ser-74 phosphorylation induced by IR. dCK activity (n = 3) and Ser-74 phosphorylation (n = 3) were analyzed in wild-type cells incubated for 2 h after exposure, or not, to IR (10 Gy), in the absence or presence of 10 mM KU-60019, 10 mM VE-821, or both (KU + VE). Significance relative to the absence of inhibitors was analyzed by twoway ANOVA: *P < 0.05; ****P < 0.0001 for dCK activity, and P < 0.001 for pS74-dCK in the IR condition in the presence of KU + VE. (B) Effect of the ATR inhibitor on dCK activation and Ser-74 phosphorylation induced by IR in ATM/ cells. dCK activity (n = 5) and Ser-74 phosphorylation (n = 3) were analyzed in cells incubated for 2 h after exposure, or not, to IR (10 Gy), in the presence or absence of 10 mM VE-821. Significance relative to the absence of VE-821 was analyzed by two-way ANOVA: *P < 0.05; ***P < 0.001 for dCK activity, and P < 0.001 for pS74-dCK.

to re-investigate the effect of ATM and ATR inhibitors during this early time period. We found that dCK was already maximally activated 5 min after IR and that this activation as well as the increase in Ser-74 phosphorylation could be prevented by the ATM inhibitor, but not the ATR inhibitor (Fig. 6A). Similar results were recorded 10 min after IR, but no effect of the ATM or ATR inhibitor could be evidenced at 120 min, as previously noted in Figs. 1 B and 2 A. These results showed that ATM is the kinase that triggers the activation of dCK after IR in wild-type cells, as previously stated [15,16], and the only kinase involved in this activation at early time.

Most dCK activators share the feature of inducing DNA damage followed by DNA damage response, a complex signaling network aimed to preserve genome integrity. At the core of the DNA damage signaling are the related protein kinases ATM and ATR, which, once activated, initiate a phosphorylation cascade leading to cell cycle arrest, DNA repair or apoptosis [18]. ATM, which is primarily activated in response to DSBs, has recently been identified as the kinase responsible for dCK activation after IR through Ser74 phosphorylation [15,16]. The results presented here show that ATM is not an absolute requirement for dCK activation in response to DNA damage. Indeed, we observed that dCK activity can be increased by various genotoxic agents, including IR, in ATM-deficient cells and that chemical inhibition of ATM or ATM silencing by siRNA does not impair the activation of dCK in response to these agents in wildtype cells. That ATM was not essential for dCK activation in response to IR was in apparent contradiction with previous studies [15,16]. Still, we observed that complete inhibition of IR-induced dCK activation could be achieved by the ATM inhibitor KU-60019 at early time points, indicating that ATM is the kinase that triggers dCK activation after IR in normal cells. Since activation of dCK by IR was not prevented by KU-60019 at longer times, but could be suppressed if the ATR inhibitor was combined with the ATM inhibitor, we propose that dCK is activated by ATR when ATM is inhibited. Consistent with this hypothesis, the ATR inhibitor VE-821 was able to prevent IR-induced dCK activation in ATM-deficient cells. In contrast, the same inhibitor had no effect on IR-induced dCK activation in normal cells, confirming the major role of ATM in this process. This might be explained by the fact that dCK is already fully phosphorylated and activated by ATM at the time of ATR activation. In short, IR-induced dCK activation appears to be mediated by ATM in normal cells and by ATR in cells devoid of ATM activity. The reasons why dCK activation by IR was not previously detected in ATM-deficient cells [15] or could be prevented by the ATM inhibitor KU-55933 in a murine leukemia cell line [16] are not clear. Indeed, neither the time of analysis, nor the irradiation dose can be invoked. The most logical explanation might be that ATR, for yet unidentified reasons, was not activated after IR in the experimental conditions used in these studies, so that ATR could not substitute ATM to activate dCK. Activation of ATR in response to

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Fig. 5. Time-course analysis of Chk2 and Chk1 phosphorylation after various genotoxic treatments. Wild-type cells were analyzed at the indicated times for Chk2 and Chk1 phosphorylation after exposure to IR (10 Gy), 10 mM CdA, UV light (18 J/m2) or 10 mM aphidicolin (APC). (A) Representative Western blots. (B) Quantitative analysis of Western blot data (n = 3). pChk2 () and pChk1 (&) were normalized to Chk2 or Chk1 protein level and mean values  SEM are shown, the values found in untreated cells being set at 1 for comparison.

IR is well documented in wild-type [27,33–36] as in ATM-deficient cells [35,37,38]. The mechanisms that underlie this activation are not yet fully elucidated, but it becomes now accepted that activation of ATR by IR results from the resection of DSBs into ssDNA during the repair process, which causes an ATM-to-ATR switch [33]. Resection could be initiated either ATM-dependently by the MRN (Mre11-Rad50-Nbs1) complex [27,39–42] or ATMindependently by the nuclease Exo1 [35,38]. Whereas ATM, in accordance with previous results [15,16], appears to play the major role in dCK activation induced by IR in

normal cells, ATR has emerged from this study as the kinase responsible for dCK activation in response to treatment with CdA, aphidicolin and UV light, which all induce replication stress in proliferating cells. This statement is supported by the following observations: (i) the specific ATR inhibitor VE-821 has the capacity to reduce dCK activation and Ser-74 phosphorylation induced by these agents, (ii) the effect of VE-821 is closely mimicked by ATR siRNA and finally (iii) CdA, UV and aphidicolin do not induce significant activation of dCK in ATR-Seckel cells, characterized by severe ATR defect. While it was well established that UV light and

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Fig. 6. ATM triggers dCK activation following IR in wild-type cells. (A) Effect of 10 mM KU-60019 or 10 mM VE-821 on dCK activation (n = 3) and Ser-74 phosphorylation (n = 3) at different times after IR (10 Gy). Significance relative to the absence of inhibitors was analyzed by two-way ANOVA: *P < 0.05; ***P < 0.01 for dCK activity, and P < 0.05 for pS74-dCK in the three conditions where there was a significant change in dCK activity. (B) Time-course activation and phosphorylation of dCK after IR in wild-type compared to ATM/ cells. dCK activity (n = 3) and Ser-74 phosphorylation (n = 3) were measured at the indicated times after exposure of cells to IR (10 Gy). Significance relative to time zero was analyzed by two-way ANOVA: **P < 0.01; ***P < 0.001 for dCK activity, and P < 0.01 for pS74-dCK in the conditions where there was a significant change in dCK activity.

aphidicolin induce ATR activation [20,21], the DNA damage signaling pathway specifically triggered by the nucleoside analog CdA had not yet been investigated. Our analysis of Chk1 phosphorylation, used as readout of ATR activation, clearly indicates that CdA mainly activates ATR, most probably by inducing stalled replication forks as reported for other nucleoside analogs [43]. It is noteworthy that regulation of dCK activity by ATR is expected to take place not only in healthy, but also in cancer cells since the ATR inhibitor VE-821 significantly decreased dCK activity in leukemic and tumor cell lines in addition to lymphoblastoid cells. The biological relevance of dCK phosphorylation at Ser-74 in response to DNA damage is a fundamental question that has already been explored after IR. First, ATM-mediated Ser-74 phosphorylation has been shown to play a role in the activation of the G2/M checkpoint, which has been explained by the interaction of Ser-74-phosphorylated dCK with cyclin-dependent kinase (CDK1), a major regulator of the G2/M transition [15]. In addition to this function, which appears to be independent on the enzymatic activity of dCK, IR-induced dCK activation has been found to increase intracellular dCTP pool and enhance the rate of DNA repair [16]. As these two important roles are both mediated via Ser74 phosphorylation, we can expect similar effects if Ser-74 is

Fig. 7. ATR phosphorylates dCK at Ser-74 in vitro. The in vitro kinase assay was performed using human recombinant dCK (rec dCK) and ATR immunoprecipitated from ATM/ cells (ATR) or from ATR-Seckel cells (ATR-Seckel), as described in the Methods. When used, VE-821 was present at 10 mM. dCK activity (n = 3) and Ser-74 phosphorylation (n = 3) were analyzed after a 30 min-incubation at 30  C. Recombinant dCK had a basal activity of 3868  288 pmol/min/mg protein. Significance was analyzed by one-way ANOVA: ****P < 0.0001 for changes in dCK activity, and P < 0.05 for changes in pS74-dCK.

phosphorylated by ATR instead of ATM. Therefore, by phosphorylating Ser-74 and activating dCK, ATR, like ATM, could endorse DNA repair in response to DNA damage, including those induced by chemo- or radiotherapy, thereby limiting their efficacy. This supports the emerging concept of utilizing ATR inhibitors to enhance efficacy of cancer therapeutics [44]. Previous studies of our group have shown that dCK is already phosphorylated at some level under basal conditions [5,13], leading to the assumption that the protein kinase responsible for basal Ser-74 phosphorylation should be constitutively active. The data reported in this manuscript strongly suggest that this constitutively active kinase is ATR. If we consider the decrease in dCK activity induced by the combination of VE-821 and ATR siRNA in untreated cells (Fig. 2B), we can postulate that ATR accounts for almost 50% of dCK activity in basal conditions. This confirms that ATR possess intrinsic activity in the absence of exogenous stress [45]. The presence of an active ATR in unperturbed cells is also corroborated by results of our in vitro kinase assay, in which ATR immunoprecipitated from untreated cells was found to be able to phosphorylate Ser-74 of dCK. Unlike ATM, ATR is essential for the survival of replicating cells even in the absence of exogenous DNA damage [36], most probably because the ATR/Chk1 pathway is required during unperturbed S phase to ensure normal replication fork progression and stabilize the genome during DNA replication [45–47]. Additional functions of ATR, like an adequate control of dNTP pools, might be also considered. It has indeed been reported that the essential function of Mec1/ATR in Saccharomyces cerevisiae can be rescued in unperturbed cells by introducing mutations in ribonucleotide reductase that lead to an increase in dNTP pools [48]. By increasing basal dCK activity level, ATR could help to maintain adequate concentration of dNTPs for DNA repair in response to endogenous DNA damage or for DNA replication in

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rapidly dividing cells. In link with this, ATR regulation of dCK could also be important for T and B lymphocyte development, which has been shown to be particularly sensitive to dCK deletion [49], but also to reduction of its activity due to S74A mutation [16]. In summary, we have identified dCK as a novel ATR substrate and demonstrated that ATR, besides ATM, plays an important role in the regulation of dCK activity in response to DNA damage. We propose that ATR could activate dCK in response to all the situations that generate ssDNA, including stalled replication forks and DSBs resection, whereas ATM mediates dCK activation in response to DSBs. Therefore, activation of dCK by DNA damage will be mediated by ATR or ATM, depending on their relative activation state in response to a particular genotoxic stress. In addition, our data reveal that regulation of dCK activity by ATR takes place not only in DNA-damaged cells, but also in unperturbed cells, and in normal as in cancer cells from hematopoietic or epithelial sources. Overall, this study provides new insights on the regulation of dCK activity, which can shed light on the control of deoxynucleotide synthesis and DNA repair, and hence on the biological function of dCK.

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