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Experimental Therapeutics, Molecular Targets, and Chemical Biology |
-H2AX as a Biomarker of DNA Damage1 Laboratory of Molecular Pharmacology and 2 Developmental Therapeutics Program, National Cancer Institute, Department of Health and Human Services, Bethesda, Maryland
Requests for reprints: Yves Pommier, National Cancer Institute, Department of Health and Human Services, NIH, 37 Convent Drive, 37-5068, Bethesda, MD 20892. Phone: 301-496-5944; Fax: 301-402-0752; E-mail: pommier{at}nih.gov.
| Abstract |
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/ß-mediated DNA cleavage in vitro and in cells. The phosphorylation of histone (
-H2AX) was tested to measure the extent of DNA damage. Kinetics of
-H2AX "foci" showed early activation with low µmol/L concentrations, thus presenting a useful early biomarker of DNA damage. The half-life of
-H2AX signal reversal after drug removal was consistent with reversal of DNA-protein cross-links. The persistence of the DNA-protein complexes induced by batracylin was markedly longer than by etoposide or camptothecin. The phosphorylated DNA damage–responsive kinase, ataxia telangiectasia mutated, was also found activated at sites of
-H2AX. The cell cycle checkpoint kinase, Chk2, was only weakly phosphorylated. Thus, batracylin is a dual Top1 and Top2 inhibitor and
-H2AX could be considered a biomarker in the ongoing clinical trials. [Cancer Res 2007;67(20):9971–9] | Introduction |
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Batracylin is undergoing evaluation as an anticancer agent at the NCI in patients. We therefore proposed to test the use of potential biomarkers of its DNA-directed actions. Members of the DNA damage response pathway are among the first responders to genomic alterations produced by topoisomerase-targeting agents. The ataxia telangiectasia mutated (ATM) kinase, a member of the PIKK family, is autophosphorylated on serine 1981 and acts on downstream substrates responsible for DNA repair, cell cycle arrest, and apoptosis. Histone H2AX phosphorylated on serine 139, termed
-H2AX, is one of the earliest markers of camptothecin-induced replication-associated DNA double-strand breaks (DSB; refs. 15, 16) and of etoposide (VP-16; ref. 17).
-H2AX is proposed to anchor broken chromosomes together and recruit DNA repair elements, including Mre11-Rad50-Nbs1 (18, 19). Another substrate of ATM is the cell cycle–associated kinase, Chk2 (2, 20). The Chk2 kinase undergoes a cascade of autophosphorylation, including on threonine 68, upon camptothecin-induced DNA damage (21).
In this report, we present results from our study on the topoisomerase-directed mechanism of actions of batracylin. We also present evidence for the use of phosphorylated histone
-H2AX as a biomarker of its DNA damage.
| Materials and Methods |
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was provided by Dr. John Nitiss (St. Jude Children's Research Hospital, Memphis, TN). Recombinant Top2ß was a kind gift from Dr. Neil Osheroff. T4 polynucleotide kinase, DNA polymerase I (Klenow fragment), deoxynucleotide triphosphates,
X174 DNA, agarose, and polyacrylamide/bis were purchased from Invitrogen or New England Biolabs. DNA Quick Spin columns were purchased from Roche Diagnostics. [
-32P]Deoxy-ATP and [
-32P]dGTP 5'-triphosphate were purchased from Perkin-Elmer Life and Analytical Science. Oligonucleotides were synthesized by MWG Biotech.
Cell Culture and Drug or Ionizing Radiation Treatment
Human colon carcinoma HT29, HCT116, and MCF-7 cells were obtained from the Developmental Therapeutics Program, NCI. HCT116-p53–deficient cells were obtained from Dr. Bert Vogelstein (Johns Hopkins University, Baltimore, MD). MCF-7/VP cells were maintained in 4 µmol/L VP-16 during culture. Cells were maintained in DMEM supplemented with 10% fetal bovine serum at 37°C before experimental use. Cells grown in T75 flasks were exposed to indicated doses of ionizing radiation from a 137Cs source in a Mark I irradiator (J.L. Shepherd and Associates).
Colony Formation Assay
Cell survival was determined using a colony formation assay after indicated treatments. HT-29 cells were trypsinized, counted, and plated (in triplicate, 50/500/5,000 cells) on six-well, 60-mm sterile polystyrene culture plates. The cells were maintained in 3 mL of culture medium and incubated unperturbed for 10 days. Before colony counting, culture medium was aspirated, and colonies were treated with 2 mL of fixation solution (50% methanol, 5% acetic acid) for 1 h. After removal of fixation solution, colonies were stained with 3 mL of Wright's Giemsa stain (Sigma Diagnostics) for 1 h. Colonies were counted manually.
Assessment of Cell Survival
Cytotoxicity of batracylin was assessed by the sulforhodamine B (SRB; Sigma-Aldrich) assay as described previously (22). IC50 was calculated using the software Prism 4 (GraphPad Software, Inc.). Data were obtained from at least three independent experiments.
Alkaline Elution
DNA damage was detected using alkaline elution assays as described previously (22, 23). HT29 cells were prelabeled with [3H]thymidine (1 µCi/mL) for 72 h. Cells were chased overnight (16 h) with radioisotope-free medium before receiving drug treatments. The cells were harvested after specified incubations by scraping them into ice-cold HBSS.
Detection of DNA-protein cross-links and protein-associated strand breaks. DNA-protein cross-links (DPC) and protein-associated strand breaks were analyzed using DNA-denaturing (pH 12.1) alkaline elution carried out under nondeproteinizing conditions as described previously (24).
Detection of DNA single-strand breaks. DNA single-strand breaks (SSB) were analyzed using DNA-denaturing (pH 12.1) alkaline elution carried out under deproteinizing conditions as reported previously (24).
Detection of DSBs. DSBs were analyzed using non–DNA-denaturing (pH 9.6) elution carried out under deproteinizing conditions as described previously (23, 25).
Top1- and Top2-Induced DNA Cleavage Assays
Top-mediated reactions have been described previously (22). The 161-bp fragment from pBluescript SK(–) phagemid DNA (Stratagene) was 3'-end labeled with [
-32P]dGTP. For Top1 cleavage assays, labeled DNA (50 fmol/reaction) was incubated with 5 ng of recombinant Top1 with or without drug at 25°C in 10 µL reaction buffer [10 mmol/L Tris-Cl (pH 7.5), 50 mmol/L KCl, 5 mmol/L MgCl2, 0.1 mmol/L EDTA, and 15 µg/mL bovine serum albumin (BSA), final concentrations]. Maxam Gilbert loading buffer [3.3 volumes of 80% formamide, 10 mmol/L sodium hydroxide, 1 mmol/L sodium EDTA, 0.1% xylene cyanol, and 0.1% bromophenol blue (pH 8.0)] was added to the reaction mixtures. Aliquots were separated in 16% denaturing polyacrylamide gels (7 mol/L urea) in 1x Tris-borate EDTA (45 mmol/L Tris, 45 mmol/L boric acid, and 1 mmol/L EDTA) for 2 h at 40 V/cm at 50°C.
For Top2 assays, the same pSK fragment used for Top1 assays or single-stranded oligonucleotides were 5'-end–labeled with [32P]ATP and T4 polynucleotide kinase. Labeling mixtures were subsequently centrifuged through Mini Quick Spin DNA columns (for pSK fragment) or Oligo columns (for oligonucleotides; Roche Diagnostics) to remove the unincorporated label. Annealing to the complementary strand of the oligonucleotides was done by heating the reaction mixture to 95°C and overnight cooling to room temperature in 10 mmol/L Tris-HCl (pH 7.8), 100 mmol/L NaCl, and 1 mmol/L EDTA. DNA substrates (10 pmol/reaction) were incubated with 500 ng of Top2
or Top2ß (kind gift from Dr. Neil Osheroff) in the presence or absence of drugs for the indicated times at 25°C in 10 µL of reaction buffer [10 mmol/L Tris-HCl (pH 7.5), 50 mmol/L KCl, 5 mmol/L MgCl2, 1 mmol/L ATP, 0.2 mmol/L DTT, 0.1 mmol/L EDTA, and 15 µg/mL BSA]. Reactions were stopped by adding SDS (final concentration 0.5%). Samples were separated on 16% (for pSK DNA) or 20% (for the oligonucleotides) denaturing polyacrylamide gels (7 mol/L urea). Imaging and quantitation were done using a PhosphorImager (Molecular Dynamics).
Immunocomplex of Top1-DNA Detection Assay
Top1-DNA adducts were detected as described previously (16, 26). Briefly, 106 treated or untreated cells were pelleted and immediately lysed in 1% sarkosyl. Following homogenization with a Dounce homogenizer and pestle B, cell lysates were gently layered on cesium chloride step gradients and centrifuged at 165,000 x g for 20 h at 20°C. Half-milliliter fractions were collected and the fractions 6 to 10 were pooled together. The pooled fractions were then diluted with 25 mmol/L sodium phosphate buffer (pH 6.5) to make a 1x, 2x, 4x, or 8x scaled dilution for better resolution of differences and applied to Immobilon-P membranes (Millipore) in a slot-blot vacuum manifold. Top1-DNA complexes were detected using the C21 Top1 monoclonal antibody (gift from Yung-Chi Cheng, Yale University, New Haven, CT) using standard Western blotting procedures. Top2
and top2ß antibodies were obtained from Abcam.
Confocal Microscopy of Nuclear Protein Localization, Antibodies Used
Cells grown in Nunc chamber slides (Nalgene) using 0.5 mL of tissue culture medium were fixed and permeabilized as described previously using 4% paraformaldehyde and ice-cold 70% ethanol (16). Nonspecific binding was blocked using 8% bovine serum albumin in PBS. Fixed cells were stained overnight with primary antibodies (in 1% BSA at 4°C) and tagged with fluorescent secondary antibodies (Molecular Probes) for 2 h at room temperature. Slides were mounted using Vectashield mounting liquid (Vector Labs) and sealed. Immunofluorescence microscopy was done in a Nikon Eclipse TE-300 confocal laser scanning microscope system. The mouse anti–
-H2AX antibody was purchased from Upstate USA, Inc., and the rabbit anti–
-H2AX antibody was obtained from Dr. William Bonner (NCI). The phosphorylated S1981-ATM and phosphorylated T68-Chk2 antibodies were purchased from Cell Signaling Technologies. Images were collected as tif files and processed with Adobe Photoshop (Adobe Systems, Inc.). Images were converted to black and white and ellipses were drawn over the nuclear boundaries for clarity.
| Results |
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Topoisomerase-directed actions of batracylin. The favored production of SSBs over DSBs by batracylin led us to hypothesize that batracylin could be targeting Top1. Induction of DNA cleavage in the presence of Top1 was tested using recombinant Top1 on a purified DNA fragment (Fig. 3A
; ref. 22). The cleavage sites observed with camptothecin are indicated by arrows for comparison. Batracylin showed a DNA cleavage pattern distinct from the known Top1-targeting drugs, camptothecin, and the indenoisoquinoline, MJ-III-65 (NSC 706744) (2). We also tested the actions of batracylin on Top2
and Top2ß. VP-16 (100 µmol/L) was used as a positive control in these experiments. Shown in Fig. 3B, batracylin exhibits extremely low Top2
inhibition compared with VP-16. We found mainly Top2ß-mediated DNA cleavage in the presence of increasing concentrations of batracylin (Fig. 3C). Thus, batracylin is a dual inhibitor of both Top1 and Top2ß enzymes.
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, and Top2ß after batracylin treatment at 3 h in HT-29 cells. Camptothecin (1 µmol/L) or VP-16 (100 µmol/L) were used as positive controls. The pooled fractions were diluted as described in Materials and Methods and probed for Top 1, Top2
, or Top2ß. Batracylin at 100 and 300 µmol/L showed increased enzyme complexes at 3 h (Fig. 3D). The complex formation was most apparent for Top1. Thus, batracylin exhibits in vivo trapping of both Top1 and Top2 enzymes.
Batracylin cell killing in cells deficient for p53 and Top1, or resistant to VP-16. Loss in cellular viability by batracylin was assayed using a SRB dye–based test (22). A dose-dependent reduction in cell survival at 72 h was observed in HCT116 colon carcinoma cells deficient or proficient for p53 (Fig. 4A
), suggesting a p53-independent mode of cell killing. MCF-7 breast cancer cells stably transfected with Top1 siRNA (27) were partially resistant to batracylin (
2.9-fold reduction in IC50 value). MCF-7 cells that are resistant to VP-16 (MCF-7/VP; ref. 28) were 5.4-fold resistant to batracylin compared with their sensitive parental cells. Thus, batracylin displays a p53-independent but partially Top1- and Top2-mediated cell killing.
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-H2AX, as a biomarker of batracylin-induced DNA damage. We tested the phosphorylation of a variant of histone H2A, termed
-H2AX, as a viable biomarker for the early detection of DNA damage by batracylin. We analyzed whether we would be able to detect nuclear aggregates ("foci") of
-H2AX before the earliest detection of DNA breaks that would be indicative of DNA damage. In Fig. 5A
, we used confocal microscopy to detect the formation of
-H2AX foci with increasing concentrations of batracylin for 3 h. Doses as low as 1 µmol/L were able to increase the number of cells that were positive for
-H2AX. VP-16 was included as a positive control and the time course of
-H2AX formation in response to batracylin was determined. Figure 5B shows distinct foci formation after 1 h of treatment. The signal for
-H2AX seemed to increase with time up to 15 h.
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-H2AX has been associated with the kinase activity of ATM, a large protein mutated in the disorder ataxia telangiectasia (20, 29). ATM itself is autophosphorylated at S1981 (pS1981-ATM) and is emerging as yet another responsive element to DNA damage (20, 29). We tested the formation of pS1981-ATM along with
-H2AX and found an equivalent increase in nuclear foci for pS1981-ATM with 3-h treatment of batracylin in HT29 cells (Fig. 5C). The signal for
-H2AX seemed to colocalize with that of pS1981-ATM. Additionally, we tested the phosphorylation of the cell cycle checkpoint kinase, Chk2 (pT68-Chk2), a substrate of ATM and other phosphatidylinositol 3-kinases (30, 31). In Fig. 5D, we observe weak induction of pT68-Chk2 compared with
-H2AX. The pT68-Chk2 signal was also colocalized with
-H2AX.
Thus,
-H2AX could serve as a biomarker for early detection of DNA damage by batracylin.
Slow reversibility of the DPCs and
-H2AX foci induced by batracylin. To ascertain the reversibility of DNA damage induced by batracylin, we measured the reversal of
-H2AX after a 3-h exposure to 10 µmol/L of drug. In Fig. 6A
, we show persistence of
-H2AX foci after 3-h incubation in drug-free medium. By 15 h, most cells had returned to their untreated state for
-H2AX signal. We then measured the stability of Top1- and Top2-DNA cleavage complexes by alkaline elution. The reversal of DPC after batracylin removal was found to be in agreement with
-H2AX disappearance (Fig. 6B). The DPC reversal was compared with that of VP-16 and observed to be significantly slower. The half-life of VP-16–induced DPCs was within minutes (<30 min), whereas that of batracylin was between 1 and 2 h. Thus, the reversibility of DNA damage by batracylin was slower than for VP-16.
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| Discussion |
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The topoisomerase-directed actions of batracylin. We confirmed the toxicity of batracylin in colon carcinoma cell line HT29 by colony formation assay and provided evidence for a dose-dependent cell killing (Fig. 1). The COMPARE algorithm was used to analyze sensitivity patterns in the NCI-60 human tumor cell line panel, and activity of batracylin was most comparable with the Top2 class of drugs. The Top2 inhibitory actions of batracylin were hypothesized to reveal predominantly DSB in cells. However, when alkaline elutions were done to measure DSB and SSB, we observed almost none at 3 h under conditions where SSB were clearly detected. Only a few DSB were detectable at longer times (6 h; Fig. 2D). This led us to hypothesize that batracylin might be targeting Top1 in addition to Top2. In the present study, we show batracylin activity on both Top1- and Top2-mediated DNA cleavage (Fig. 3A–C). Batracylin exhibited a unique cleavage pattern when compared with VP-16 or camptothecin or VP-16, suggesting that it might also target distinct genomic sites. These DNA breaks observed were protein associated because no significant breaks could be measured in the presence of proteinase K (Fig. 2A). Also, we present evidence for increasing DPCs after batracylin exposure with time and increasing concentration (Fig. 2B). Thus, batracylin seems to possess the properties of a dual topoisomerase inhibitor. We confirmed the cellular activity of batracylin on Top1 and Top2 using the immunocomplex of enzyme assay (ref. 26; Fig. 3D). The activity of batracylin was only partially diminished in Top1-deficient or VP-16–resistant cells, confirming the redundancy of the topoisomerase targeting (Fig. 4). The varying expression level of Top1 and Top2 in cancer cells treated with a selective inhibitor can potentially be overcome by use of a dual inhibitor such as batracylin. Thus, batracylin seems to be a nonclassic topoisomerase inhibitor. It belongs to the group of dual topoisomerase inhibitors. A limited number of dual topoisomerase inhibitors have been identified and some are being developed as anticancer agents. These include the anthracycline-like anthraquinone saintopin, indenoquinolones (TAS-103), quaternary alkaloids (fagaronine), the indolocarbazole NB-506, GA3P polysaccharide, the acridine DACA and pyrazoloacridine, the pyridoindole intoplicin, XR5944, and the homocamptothecin derivative BN-80297 (32–40). The DPCs produced by batracylin had a significantly longer half-life than those induced by VP-16 (Fig. 6) and camptothecin (data not shown; ref. 41). Hence, similar to the bisindenoisoquinolines (22), batracylin has an advantage of producing cleavage complexes with slower reversibility than conventional topoisomerase-targeting drugs that require longer treatment schedules. Only a few dual topoisomerase inhibitors have been identified and are being developed as anticancer agents (42, 43). Further preclinical studies on batracylin are therefore warranted to evaluate its clinical potential.
Histone
-H2AX as a biomarker of the DNA damage by batracylin. We have previously presented
-H2AX as an experimental biomarker of replication-mediated DNA damage by anticancer agents (16, 22). Phosphorylation of histone H2AX occurs rapidly after replication stress and can be readily detected by microscopic analysis of the nuclear foci that appears after fluorescent antibody staining (44). The phosphorylation of H2AX is mediated, among other kinases, by the ATM kinase. We show clear increase in
-H2AX foci formation along with an increased colocalized signal for phosphorylated ATM and Chk2 (Fig. 5). The
-H2AX signals are within similar dose range as the antiproliferative activity of batracylin, as indicated in Fig. 4. Lower doses of batracylin used for these microscopic analyses of
-H2AX are indicative of the high sensitivity of this assay (15, 45, 46). Pilot studies, including those from our group, with surgical tissue specimens and cell lines have shown that the
-H2AX foci are present at higher levels in cancerous samples when compared with normal tissue of the same origin (15, 44, 47). These foci are suggested to be indicative of aggressive replication stress–mediated genomic instability in these cells. The early detection of such foci is an early hallmark of DNA damage caused by batracylin and similar to other replication stress models likely signals for the concentration of DNA repair factors at the lesion sites (45, 48). Efforts are under way to characterize the low basal level of
-H2AX foci in various cancer models (44). An increase in
-H2AX foci signal is being tested in the clinic as a biomarker of increased DNA damage by ionizing radiation (49) and computed tomography examination (50). The slower rate of reversal of DPCs by batracylin was in agreement with the rate of reversal of
-H2AX foci after drug removal (Fig. 6). Consequently, batracylin caused DNA damage after topoisomerase inhibition that was measured by alkaline elution as well as
-H2AX foci formation. We have also previously presented evidence for the use of
-H2AX in the measurement of DNA damage by camptothecin, 4-nitroquinoline 1-oxide, and aminoflavone in cancer cell lines (14, 24, 25). Thus,
-H2AX presents a sensitive biomarker of therapeutic efficacy of anticancer drugs that could be readily measured in tissue biopsies or blood cells. It would be most beneficial to use it in combination with other biomarkers of disease progression during the upcoming clinical trials of batracylin.
| Acknowledgments |
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The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked advertisement in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.
We thank Dr. Jerry Collins for encouraging this work; Drs. Kurt Kohn, Bill Bonner, Andy Jobson, and Melanie Simpson for helpful discussions; and Dr. Neil Osheroff and Jo Ann Byl (Department of Biochemistry, Vanderbilt University, TN) for generously providingTop2
and Top2ß enzymes.
| Footnotes |
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3 http://dtp.nci.nih.gov/docs/compare/compare.html ![]()
Received 2/27/07. Revised 7/ 9/07. Accepted 8/ 8/07.
| References |
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H2AX in Cancer Cells: A Potential Biomarker for Cancer Diagnostics, Prediction and Recurrence. Cell Cycle 2006;5:2909–13.[Medline]
, and colocalization with
-H2AX after topoisomerase I-induced replication damage. Mol Cell Biol 2005;25:8925–37.
-H2AX detection. Methods Enzymol 2006;409:236–50.[Medline]
-H2AX foci at DNA double-strand breaks sites. Biochem Cell Biol 2003;81:123–9.[CrossRef][Medline]
-H2AX antibody. Radiat Res 2002;158:486–92.[CrossRef][Medline]
-H2AX as a therapeutic target for improving the efficacy of radiation therapy. Curr Cancer Drug Targets 2006;6:197–205.[CrossRef][Medline]This article has been cited by other articles:
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J. Kitagaki, K. K. Agama, Y. Pommier, Y. Yang, and A. M. Weissman Targeting tumor cells expressing p53 with a water-soluble inhibitor of Hdm2 Mol. Cancer Ther., August 1, 2008; 7(8): 2445 - 2454. [Abstract] [Full Text] [PDF] |
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