Loss of PPP2R2A Inhibits Homologous Recombination DNA Repair and Predicts Tumor Sensitivity to PARP Inhibition

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Loss of PPP2R2A Inhibits Homologous Recombination DNA Repair and Predicts Tumor Sensitivity to PARP Inhibition Published OnlineFirst October 18, 2012; DOI: 10.1158/0008-5472.CAN-12-1667 Cancer Molecular and Cellular Pathobiology Research Loss of PPP2R2A Inhibits Homologous Recombination DNA Repair and Predicts Tumor Sensitivity to PARP Inhibition Peter Kalev1, Michal Simicek1, Iria Vazquez1, Sebastian Munck1, Liping Chen2, Thomas Soin1, Natasha Danda1, Wen Chen2, and Anna Sablina1 Abstract Reversible phosphorylation plays a critical role in DNA repair. Here, we report the results of a loss-of-function screen that identifies the PP2A heterotrimeric serine/threonine phosphatases PPP2R2A, PPP2R2D, PPP2R5A, and PPP2R3C in double-strand break (DSB) repair. In particular, we found that PPP2R2A-containing complexes directly dephosphorylated ATM at S367, S1893, and S1981 to regulate its retention at DSB sites. Increased ATM phosphorylation triggered by PPP2R2A attenuation dramatically upregulated the activity of the downstream effector kinase CHK2, resulting in G1 to S-phase cell-cycle arrest and downregulation of BRCA1 and RAD51. In tumor cells, blocking PPP2R2A thereby impaired the high-fidelity homologous recombination repair pathway and sensitized cells to small-molecule inhibitors of PARP. We found that PPP2R2A was commonly downregulated in non–small cell lung carcinomas, suggesting that PPP2R2A status may serve as a marker to predict therapeutic efficacy to PARP inhibition. In summary, our results deepen understanding of the role of PP2A family phosphatases in DNA repair and suggest PPP2R2A as a marker for PARP inhibitor responses in clinic. Cancer Res; 72(24); 6414–24. Ó2012 AACR. Introduction during the DNA repair process (3, 4), suggesting that phos- Genome stability is essential for the prevention of undue phatases may serve not only as negative regulators but also as cellular death and cancer development. To maintain genome active modulators of DNA damage response. integrity, cells have evolved multiple DNA repair pathways (1). Protein phosphatase 2A (PP2A) refers to a large family of One of the most powerful activators of the DNA repair response heterotrimeric Ser/Thr phosphatases. The PP2A core enzyme is double-strand breaks (DSB). consists of a catalytic C subunit and a structural A subunit. In Initiation of DSB repair is controlled by the phosphoinosi- mammals, 2 distinct genes encode closely related versions of tide 3-kinase–like kinase (PIKK) family. A wave of phosphor- both the PP2A A (Aa/PPP2R1A and Ab/PPP2R1B) and C (Ca/ ylation events radiating from PIKKs is amplified to convey the PPP2CA and Cb/PPP2CB) subunits. The AC dimer recruits a signals to a large number of substrates. Although this cascade third regulatory B subunit, which is responsible for the sub- fi has been studied in a great detail, the biologic relevance of strate speci city and function of the PP2A heterotrimeric many of these phosphorylation events and the mechanisms complex. Four unrelated families of B subunits have been identified to date: B/B55/PPP2R2A, B0/B56/PR61/PPP2R5, that control their downregulation remain unknown (2). It is 00 conceivable that Ser/Thr protein phosphatases could be B /PR72/PPP2R3, and Striatin/STRN. Approximately 100 dis- responsible for keeping proteins involved in DNA repair tinct complexes can be formed through combinatorial asso- fi response in an inactive state under normal conditions or for ciation of these subunits, and it is believed that speci c PP2A inactivating the signaling once DNA has been repaired. How- complexes mediate particular physiologic functions (5, 6). ever, phosphorylation of a number of PIKKs, including ataxia PP2A has been directly implicated in the negative regulation telangiectasia mutated (ATM), ATR, and CHK2, oscillates of DSB DNA repair proteins, including g-H2AX, ATM, CHK1, and CHK2 (2). However, consistent with the idea that protein phosphatases are not just negative regulators of DNA repair Authors' Affiliations: 1VIB Center for the Biology of Disease; Center for signaling, selective inhibition of PP2A activity impairs DNA Human Genetics, KU Leuven, Leuven, Belgium; and 2Department of repair (7–9). PP2A function is also essential for activation of Toxicology, Faculty of Preventive Medicine, Guangdong Provincial Key Laboratory of Food, Nutrition and Health, School of Public Health, Sun Yat- cell-cycle checkpoints in response to irradiation (10, 11). One sen University, Guangzhou, China potential explanation for this apparent discrepancy is that Note: Supplementary data for this article are available at Cancer Research several distinct PP2A complexes may modulate different steps Online (http://cancerres.aacrjournals.org/). of the DNA repair process. fi Corresponding Author: Anna Sablina, CME Department, KU Leuven, O&N Here, we assessed the role of speci c PP2A complexes in I Herestraat 49, bus 602, Leuven, Belgium 3000. Phone: 32-163-30790; control of DSB repair and identify PPP2R2A as a critical Fax: 32-163-30145; E-mail: [email protected] effector of the homologous recombination (HR) repair through doi: 10.1158/0008-5472.CAN-12-1667 modulation of ATM phosphorylation. Critically, defects of HR Ó2012 American Association for Cancer Research. DNA repair in PPP2R2A-depleted cells dramatically increased 6414 Cancer Res; 72(24) December 15, 2012 Downloaded from cancerres.aacrjournals.org on September 23, 2021. © 2012 American Association for Cancer Research. Published OnlineFirst October 18, 2012; DOI: 10.1158/0008-5472.CAN-12-1667 The Role of PPP2R2A in DNA Repair their sensitivity to PARP enzyme inhibition. Finally, we show polyclonal anti-phospho-CHK1 (S296), rabbit polyclonal anti- that PPP2R2A is commonly downregulated in non–small cell phospho-CHK2 (T68), rabbit polyclonal anti-phospho BRCA1 lung carcinomas (NSCLC) and therefore propose PPP2R2A (S1524), rabbit polyclonal anti-CDC25A, rabbit polyclonal anti- status as a predictive marker for sensitivity to PARP inhibition. PPP2R2A, mouse monoclonal anti-phospho-ATM (S981; clone 10H11.E12), mouse monoclonal anti-CHK2 (clone 1C12), Materials and Methods mouse monoclonal anti-PP2A A (clone 4G7), rabbit polyclonal anti-phospho-CHK1 (S317), and rabbit monoclonal anti-phos- Plasmids and cell lines pho-CHK1 (S345; clone 133D3). Lentiviral pLA CMV N-Flag vector was used to generate Flag- tagged PPP2R2A. The pLKO.1-puro shGFP, pLKO.1-puro shLu- Neutral comet assay ciferase (shLuc), and pLKO.1-puro vectors containing short Microscope slides were precoated with a thin layer of normal hairpin RNA (shRNA) targeting specific PP2A subunits were melting point agarose. Cell suspensions were placed into a provided by the RNAi Consortium (12). The RNAi experiments tube containing low melting point agarose and transferred to a were carried out using ON-TARGETplus SMARTpools against glass microscope slide. Slides were placed in 2 mol/L NaCl, PPP2R2A and PPP2CA (Thermo Scientific). 30 mmol/L Na2EDTA, 10 mmol/L Tris-HCl, 1% Triton X-100, Cells were cultured in Dulbecco's Modified Eagle Medium and 10% dimethyl sulfoxide (DMSO), pH 8.0, for 1 hour at 4 C. or RPMI (GIBCO) supplemented with 10% FBS and penicillin/ After lysis, the slides were rinsed for 20 minutes in solution streptomycin. Lentiviral infections were carried out as 0.3 mol/L NaOH, 1 mmol/L EDTA and were subjected to described previously (12). To induce DSBs, cells were treated electrophoresis at 0.7 V/cm and 50 mA for 20 minutes. The with bleomycin (Sigma-Aldrich) or irradiated using the linear slides were then rinsed with 1 mol/L Tris-HCl, pH 7.5 and accelerator (6 MV photons, Varian Medical Systems). dried with prechilled absolute ethanol and stained with PI (2 mg/mL). Comet images were examined at Â200 magnifica- Cell-cycle analysis tion with Nikon ECLIPSE Ti microscope. The tail moment fi Cells were washed with PBS, xed with 70% ethanol, treated values were quantified by CometScore software v1.5. with 100 mg/mL RNase A, and stained with 50 mg/mL propi- 0 dium iodide (PI). 5-Bromo-2 -deoxyuridine (BrdUrd) incorpo- Immunofluorescent microscopy ration was analyzed using the In Situ Cell Proliferation Kit Cells were plated on cover slips or mClear-96 well plates FLUOS (Roche) according to the manufacturer's protocol. Cell- (Greiner Bio-One) and fixed with 4% paraformaldehyde for 10 cycle distribution and BrdUrd immunostaining were assessed minutes at room temperature and permeabilized with ice-cold by FACSCanto (Becton-Dickinson). methanol for 5 minutes at À20C. The cells were incubated in blocking buffer 3% bovine serum albumin (BSA) in PBS for 30 Immunoblotting and immunoprecipitation minutes at room temperature and then with primary anti- Cells were resuspended in 0.5% Triton X-100, 100 mmol/L bodies. After 3 washes with 0.3% BSA in PBS, the secondary NaCl, 3 mmol/L MgCl2, 300 mmol/L sucrose, 1 mmol/L EGTA, antibody was added. The following antibodies were used: 10 mmol/L PIPES, pH 6.8, containing protease inhibitor and mouse monoclonal anti-g-H2AX (S139; Millipore, clone phosphatase inhibitor cocktails (Roche). The cell lysates JBW301) and mouse monoclonal anti-RAD51 (Abcam, clone were incubated on ice for 10 minutes and then centrifuged at 14B4). 500 Â g for 5 minutes at 4C. The supernatant and pellet were Automated Image analysis was conducted using IN Cell designated as cytoplasmic and nuclear fractions, respectively. Analyzer 2000 (GE Healthcare; Supplementary Figs. S1 and S2). The nuclear fraction was resuspended in 10 mmol/L NaCl, 5 mmol/L MgCl2, 250 mmol/L sucrose, 1 mmol/L EGTA, Quantitative real-time reverse transcription PCR 10 mmol/L Tris-HCl, pH 7.6, containing protease and phos- Total RNA was isolated using RNeasy (Qiagen), and cDNA phatase inhibitor cocktails and treated with RNase-free DNase was synthesized using the Advantage RT-PCR Kit (Clontech). I (80 mg/mL; Roche) for 30 minutes at 37C. A list of primers used for real-time quantitative PCR is pre- Immunoprecipitations were conducted 24 hours after trans- sented in Supplementary Fig. S3A. Real-time PCRs were carried fection in lysis buffer containing 50 mmol/L Tris, pH 7.4, 1% out in a Roche LightCycler-480-96 (Roche), using SYBR Green NP-40, 250 mmol/L NaCl, and proteinase inhibitor cocktail PCR Master Mix (Roche).
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