Cancer Prevention Reversal of Hypermethylation and Reactivation of p16 INK4a, RARb, and MGMT Genes by Genistein and Other Isoflavones from Soy Ming Zhu Fang,1 Dapeng Chen,1 Yi Sun,1 Zhe Jin,1 Judith K. Christman,2 and Chung S. Yang1 Abstract Purpose: We have previously shown the reactivation of some methylation-silenced genes in cancer cells by ( )-epigallocatechin-3-gallate, the major polyphenol from green tea. To determine whether other polyphenolic compounds have similar activities, we studied the effects of soy isoflavones on DNA methylation. Experimental Design: Enzyme assay was used to determine the inhibitory effect of genistein on DNA methyltransferase activity in nuclear extracts and purified recombinant enzyme. Methylation-specific PCR and quantitative real-time PCR were employed to examine the DNA methylation and gene expression status of retinoic acid receptor h (RARb), p16INK4a , and O 6methylguanine methyltransferase (MGMT) in KYSE 510 esophageal squamous cell carcinoma cells treated with genistein alone or in combination with trichostatin, sulforaphane, or 2Vdeoxy-5-aza-cytidine (5-aza-dCyd). Results: Genistein (2-20 Amol/L) reversed DNA hypermethylation and reactivated RARb, p16INK4a , and MGMT in KYSE 510 cells. Genistein also inhibited cell growth at these concentrations. Reversal of DNA hypermethylation and reactivation of RARb by genistein were also observed in KYSE 150 cells and prostate cancer LNCaP and PC3 cells. Genistein (20-50 Amol/L) dose-dependently inhibited DNA methyltransferase activity, showing substrate- and methyl donor ^ dependent inhibition. Biochanin A and daidzein were less effective in inhibiting DNA methyltransferase activity, in reactivating RARb, and in inhibiting cancer cell growth. In combination with trichostatin, sulforaphane, or 5-aza-dCyd, genistein enhanced reactivation of these genes and inhibition of cell growth. Conclusions:These results indicate that genistein and related soy isoflavones reactivate methylation-silenced genes, partially through a direct inhibition of DNA methyltransferase, which may contribute to the chemopreventive activity of dietary isoflavones. Methylation of CpG islands in the promoter region is a key epigenetic mechanism for the silencing of many genes including tumor suppressor genes, as well as genes encoding hormone receptors, DNA repair enzymes, mediators of the apoptosis pathway, and detoxification enzymes (1, 2). Unlike many other genomic alterations that occur during carcinogenesis, DNA methylation is potentially reversible via the use of preventive or therapeutic agents (3, 4). 5-Aza-cytidine and 2Vdeoxy-5-aza-cytidine (5-aza-dCyd), nucleoside analogue inhibitors of DNA methytransferases, have been widely used in Authors’ Affiliations: 1Susan Lehman Cullman Laboratory for Cancer Research, Department of Chemical Biology, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey and 2Department of Biochemistry and Molecular Biology and UNMC Eppley Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska Received 2/24/05; revised 6/28/05; accepted 7/8/05. Grant support: NIH grants CA105331, CA88961, and CA65871 (C.S. Yang). 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. Requests for reprints: Chung S. Yang, Department of Chemical Biology, Ernest Mario School of Pharmacy, Rutgers University, 164 Frelinghuysen Road, Piscataway, NJ 08854-8020. Phone: 732-445-5360; Fax: 732-445-0687; E-mail: csyang@ rci.rutgers.edu. F 2005 American Association for Cancer Research. doi:10.1158/1078-0432.CCR-05-0406 www.aacrjournals.org attempts to reverse abnormal DNA hypermethylation in cancer cells and restore ‘‘silenced’’ gene expression. However, clinical utility of these nucleoside analogue DNA methyltransferase inhibitors has been somewhat limited by myelosuppression and other side effects (5). We have previously shown the reactivation of methylation-silenced retinoic acid receptor h (RARb), p16INK4a (p16), O 6-methylguanine methyltransferase (MGMT), and human mutL homologue 1 (hMLH1) genes by ( )-epigallocatechin-3-gallate (EGCG), the major polyphenol from green tea, and this activity has been attributed to the inhibition of DNA methyltransferase by EGCG (6). To determine whether other polyphenolic compounds have similar activities, we tested the ability of soy isoflavones to inhibit DNA methylation. Genistein (4V,5,7-trihydroxyisoflavone), the major isoflavone present in soy bean, has been shown to prevent carcinogenesis in animal models for tumor development at different organ sites (7). Many mechanisms have been proposed for this activity. Some are believed to be closely related to the estrogenic and antiestrogenic activities of genistein (7). Prepubertal exposure to soy or genistein reduced mammary carcinogenesis in rats treated with carcinogens, possibly by modulating the development of the mammary end buds (8, 9). Various soy products containing genistein have been found to inhibit the growth of transplanted human prostate carcinoma, reduce the incidence of poorly differentiated 7033 Clin Cancer Res 2005;11(19) October 1, 2005 Cancer Prevention prostate adenocarcinoma in a transgenic mouse model, and inhibit 2-amino-1-methyl-6-phenylimidazo[4,5]pyridine induced rat prostate carcinogenesis (10 – 13). Carcinogenesis or metastasis in stomach, colon, bladder, and lung is also inhibited by genistein and related isoflavones (14 – 20). The effects of genistein on various cancer cell lines have been extensively studied. It has been reported that genistein can inhibit cancer cell growth (21 – 23), induce apoptotic cell death accompanied by cell cycle arrest at G2-M phase, and inhibit angiogenesis (17, 24 – 28). The precise molecular mechanisms responsible for these activities, however, are not clearly known. One potential mechanism that has recently received considerable attention is that genistein may be involved in regulation of gene activity by modulating epigenetic events such as DNA methylation and/or histone acetylation directly or through an estrogen receptor dependent process (29 – 31). This hypothesis is supported by a report indicating that dietary genistein causes epigenetic changes in mouse prostate (32). Genistein can also up-regulate mRNA expression of the BRCA1 gene during mammary tumorigenesis, which is frequently inactivated by epigenetic events in breast cancer (8). In this preclinical study, we examined the effect of genistein and its combination with other agents on the reactivation of methylation-silenced RARb, p16, and MGMT genes, as well as its effect on the activity of DNA methyltransferase and histone deacetylase (HDAC) in the esophageal squamous cell carcinoma cell line KYSE 510. These genes were selected for study because they have been shown to be progressively inactivated by DNA hypermethylation in human esophageal squamous carcinogenesis and to be reactivated in KYSE 510 cells by 5-azadCyd and EGCG (33 – 35). Our results show that genistein inhibits DNA methyltransferase and reverses the methylation status, with accompanying reexpression of RARb, p16, and MGMT genes. These activities may contribute to the chemopreventive activity of genistein. Materials and Methods Cell lines and cell culture The human esophageal squamous cell carcinoma cell lines KYSE 510 and KYSE 150 were a gift from Dr. Yutaka Shimada (Kyoto University, Kyoto, Japan). The cells were maintained in 5% CO2 atmosphere at 37jC in RPMI 1640/Ham’s F-12 mixed (1:1) medium containing 5% fetal bovine serum. To determine the dose-dependent changes, KYSE 510 cells were treated with 2, 5, 10, or 20 Amol/L of genistein (Sigma, St. Louis, MO) or 8.7 Amol/L of 5-aza-dCyd (Sigma) administered in fresh culture medium every other day, when the medium was changed, for 6 days. For the time-course study, cells were treated with 5 Amol/L of genistein in fresh culture medium on days 0, 2, 4, and 5. Prostate cancer cell lines LNCaP and PC3 were obtained from American Type Culture Collection (Manassas, VA) and were grown in RPMI 1640 containing 10% fetal bovine serum. KYSE 150, LNCaP, and PC3 cells were treated with 10 or 20 Amol/L of genistein for 6 days as described above. For the combination study, KYSE 510 cells were treated with either 5 Amol/L of genistein or 2 Amol/L 5-azadCyd for 5 days and then cultured for 1 additional day in fresh medium with 0.5 Amol/L trichostatin or 15 Amol/L sulforaphane; or treated with 5 Amol/L of genistein or 2 Amol/L 5-aza-dCyd alone or together for 5 days and 1 additional day in fresh medium. Bisulfite modification and methylation-specific PCR DNA was extracted from the cells using the DNeasy tissue kit (Qiagen, Valencia, CA) following the procedure of the manufacturer Clin Cancer Res 2005;11(19) October 1, 2005 and modified by a bisulfite reaction as described by Herman et al. (36). Primers specific for the methylated and unmethylated DNA were the same as we previously reported (6). To verify the specificity of the PCR, we used normal human placental DNA (Sigma) as a negative control and CpGenome universal methylated DNA (Chemicon, Temecula, CA) as a positive control for methylation-specific PCR. Methylation-specific PCR was carried out using a nested twostage PCR approach (37) with similar PCR conditions as previously described (6). In brief, stage I PCR was done on bisulfite-modified DNA to amplify the CpG-rich promoter regions of the p16, RARb, or MGMT gene with the primers that recognize the bisulfite-modified template, but do not discriminate between methylated and unmethylated alleles. DNA fragments from the first PCR were used for methylation-specific PCR with primers specific for methylated and unmethylated DNA. Amplification was carried out using a 9700 Perkin-Elmer thermal cycler (Applied Biosystems, Foster City, CA). Reverse transcription-PCR Total RNA was isolated from cells using Tri reagent (Sigma). Reverse transcription of RNA was done using the Advantage RT-for-PCR kit (Clontech, Palo Alto, CA). The primers and conditions used in the PCR for the genes analyzed were previously summarized (6). The PCR was carried out in an approximate linear range (for example, 25 to 28 cycles for p16, 30 to 35 cycles for RARb, and 30 to 35 cycles for MGMT). The PCR products were separated on 2% agarose gel containing ethidium bromide and then photographed. Negative controls for PCR were run under the same conditions without RNA or reverse transcriptase. Glyceraldehyde-3-phosphate dehydrogenase (G3PDH) mRNA was used as an endogenous control. Real-time PCR Total RNA was extracted using ABI Prism 6100 Nucleic Acid PrepStation. Analysis of relative gene expression for RARb, p16, and MGMT was done using real-time quantitative PCR and the comparative threshold cycle method (Ct). All reagents, kits, and instruments used in RNA extraction, reverse transcription, and realtime PCR were purchased from Applied Biosystems. In the reverse transcription step, 12.5 ng of RNA were reversely transcribed to cDNA using the High Capacity cDNA Archive Kit following the instruction manual. In the real-time PCR step, cDNA was amplified with Assayson-Demand Products containing two gene-specific primers for RARb, p16, and MGMT, respectively, and one TaqMan MGB probe (6-FAM dye – labeled) using the TaqMan Universal PCR Master Mix in ABI Prism 7000 Sequencing Detector. Thermal cycling conditions included 2 minutes at 50jC, 10 minutes at 95jC, 40 cycles of 95jC for 15 seconds, and 60jC for 1 minute according to the TaqMan Universal PCR Protocol. No-template control was included in each assay. b-Actin was used as an endogenous control and vehicle control was used as a calibrator. Each sample was run in triplicate. The comparative Ct method was used to calculate the relative changes in gene expression in the ABI Prism sequence detection system and Microsoft Excel as previously described by Livak and Schmittgen (38) and Ariani et al. (39). The relative changes of gene expression were calculated using the following formula: Fold change in gene expresDCt (untreated control)] sion, 2 – DDCt = 2 [DCt (genistein treated samples) , where DCt = Ct (detected gene) Ct (h-actin) and Ct represents threshold cycle number. DNA methyltransferase assays Assays with nuclear extracts as the source of DNA methyltransferase. Cultured KYSE 510 cells were harvested, and nuclear extracts were prepared with a nuclear extraction kit (Pierce, Rockford, IL). The DNA methyltransferase assay was modified in our lab according to the published methods (40, 41). In brief, the nuclear extracts (4.5 Ag of protein) were incubated for 1.5 hours at 37jC with 20 nmol/L (0.75 Ag) of poly(deoxyinosine-deoxycytosine) [poly(dI-dC)poly(dIdC)] and 10 Amol/L of S-adenosyl-L-[methyl-3H]methionine (2 ACi; 7034 www.aacrjournals.org Reactivation of p16 INK4a , RARb, and MGMT by Genistein and washed on glass fiber filters before analysis for 3H-methyl by liquid scintillation counting in aqueous fluor. To measure the effect of genistein on the rate of substrate methylation, sets of duplicate reactions were initiated by adding poly(dI-dC)poly(dI-dC) in the presence of increasing concentrations of EGCG or genistein dissolved in DMSO as described above. Cell growth inhibition and other studies KYSE 510 cells were treated with 1, 2, 5, 10, and 20 Amol/L genistein, biochenin A, or daidzein added in fresh culture medium every other day for 6 days or with 5 Amol/L genistein for 1, 2, 4, or 6 days. Living cells were counted after staining with 0.04% trypan blue. After treatment for 2 or 6 days, the cells were photographed under an inverted microscope for morphologic analysis. In other experiments, KYSE 510 cells were treated with 2, 5, 10, and 20 Amol/L genistein for 3 days; cell proliferation was determined with the BrdUrd ELISA method according to the instruction manual (Roche Diagnostics Co., Indianapolis, IN) and apoptosis was determined with fluorescence 4V,6-diamidino-2-phenylindole staining or caspase-3 immunocytochemistry staining. For colony formation efficiency assay, KYSE 510 cells were treated with 2, 5, 10, or 20 Amol/L genistein for 2 days and then cultured for 10 additional days in fresh medium, and then colony numbers were analyzed. Fig. 1. Alterations of methylation status and mRNA expression levels of RARb, p16, and MGMT genes after treatment of genistein. Methylation status and mRNA expression level were determined with methylation-specific PCR and RT-PCR, respectively. UMSB, unmethylation-specific band; MSB, methylation-specific band. A , dose- and time-dependent alterations of methylation status and mRNA expression levels. Left, KYSE 510 cells were treated with 2, 5, 10, or 20 Amol/L of genistein or 8.7 Amol/L of 5-aza-dCyd (DAC) for 6 days. Right, the cells were treated for1, 2, 4, and 6 days with 5 Amol/L of genistein. B, alterations of methylation status and mRNA expression level of RARb gene in KYSE 150, LNCaP, and PC3 cells. Cells were treated with 10 or 20 Amol/L of genistein for 6 days. Amersham, Piscataway, NJ) in a total volume of 40 AL of reaction buffer (pH 7.4), containing 20 mmol/L Tris-HCl, 10% glycerol (v/v), 10 mmol/L EDTA, 0.2 mmol/L phenylmethylsulfonylfluoride, and 2 mmol/L 2-mercaptoethanol. Genistein was dissolved in DMSO, and all incubations were adjusted to contain an equivalent concentration of DMSO (10%), which had no significant effect on DNA methyltransferase activity. Reactions were initiated by the addition of nuclear extracts and stopped by mixing with 200 AL of a solution containing 1% SDS, 3% 4-aminosalicylate, 5% butanol, 2.0 mmol/L EDTA, 125 mmol/L NaCl, 0.25 mg/mL carrier salmon testes DNA (Life Technologies, Inc., Gaithersburg, MD), and 1 mg/mL protease K. DNA was extracted using the phenol/chloroform method, purified with ethanol precipitation, and then washed thrice with 70% ethanol. The radioactivity in the pellets was counted in a scintillation counter. Each assay was done in duplicate. Background levels were determined in incubations without the template poly(dI-dC)poly(dIdC). For kinetics, the results were analyzed using GraphPad Prism 4 (GraphPad Software, San Diego, CA). Assays with purified recombinant DNA methyltransferase 1. Recombinant murine DNA methyltransferase 1 (DNMT1) with an NH2terminal hexahistidine tag added for purification was expressed in Spodoptera frugiperda 9 cells and purified as previously described (42). Standard reaction mixtures (25 AL) contained 60 nmol/L recombinant DNMT1, 15 Amol/L S-adenosyl-L-[methyl-3H]methionine (specific activity, 275 GBq/mmol), and 10 ng poly(dI-dC)poly(dI-dC) (average chain length: 3,000) in M2 buffer [100 mmol/L Tris (pH 8), 10 mmol/L EDTA, 10 mmol/L DTT, 200 Ag/mL bovine serum albumin] and were incubated for 1 hour at 37jC. Reactions were terminated by the addition of NaOH to a final concentration of 0.3 mol/L. Salmon sperm DNA (100 Ag/mL) was added as a carrier, and the solution brought to 860 mmol/L with perchloric acid to precipitate DNA. Precipitated DNA was collected www.aacrjournals.org Fig. 2. Quantitative determination of mRNA expression levels of p16, RARb, or MGMT genes by real-time PCR. KYSE 510 cells were treated with 2, 5, 10, or 20 Amol/L of genistein (G) or 8.7 Amol/L of 5-aza-dCyd for 6 days and mRNA expression levels were determined using real-time PCR with TaqMan MGB system. The results were analyzed using a comparative Ct method. h-Actin was used as an endogenous control. Each sample was run in triplicate. A , amplification plots of RARb and b-actin are shown on right and left side, respectively. Y axis, DRn = Rn baseline (Rn, the normalized reporter). X axis, amplification cycle number. B, relative quantification for mRNA expression levels of p16, RARb, or MGMT. Columns, mean (n = 3); bars, SD. Genistein significantly induced reexpression of p16, RARb, and MGMT in a concentration-dependent pattern (r = 0.82-0.87, P < 0.0001). 7035 Clin Cancer Res 2005;11(19) October 1, 2005 Cancer Prevention Fig. 3. Induction of RARh mRNA expression by different isoflavonoids. KYSE 510 cells were treated with different concentrations of genistein, biochenin A, or daidzein for 6 days, and then the RARh mRNA levels were determined with RT-PCR. G3PDH was used as an internal control. Representative of three independent experiments. The band intensity was determined with densitometry; columns, mean (n = 3); bars, SD. Different letters indicate a significant difference (P <0.05) based on one-wayANOVA and Tukey’s honest significant difference test. The effect of genistein on HDAC activity was carried out according to the instruction manual of the HDAC Assay Kit (Fluorometric Detection, Upstate Biotechnology, Lake Placid, NY). In brief, the reaction mixture contained nuclear extract from KYSE 510 cells (4.0 Ag protein), substrate (CH3-CO-NH-CH2-(CH2)3-Lys-X2-, 48 Amol/L), and genistein (5, 10, 20, 50, or 100 Amol/L) in 40 AL total volume. Trichostatin (1 Amol/L) was used as a positive control. After incubation for 30 minutes at 25jC, activator solution was added to release a fluorophore from the deacetylated substrate. The product was determined by a fluorescence plate reader (excitation, 360 nm; emission, 465 nm). Each assay was done in triplicate. Statistical analyses Statistical significance between treatment and control groups was evaluated using the Student’s t test. One-way ANOVA and Tukey’s honest significant difference test were used for comparing the effects of different treatments. Pearson’s correlation coefficient (r) with P value was also determined to examine the association between concentration and efficacy. All statistical analyses were done using GraphPad Instat. genes began to appear after 2 days, whereas that from methylated p16 was only observed after 6 days (Fig. 1A). The mRNA expression of RARb, p16, and MGMT roughly correlated with the appearance of the unmethylated PCR products. Under these conditions, the loss of methylation was not apparent. Similar results were obtained in a repeated experiment. To determine whether the reactivation of methylationsilenced genes by genistein is a general phenomenon and occurs in other cell lines, we studied the effects of genistein treatment on the methylation status and mRNA levels of RARb in three other human cancer cell lines (Fig. 1B). The appearance of an unmethylation-specific band and mRNA band of RARb in KYSE 150 was observed after treating the cells with 10 or 20 Amol/L genistein for 6 days. In the LNCaP and PC3 cells, unmethylationspecific band and mRNA band of RARb only appeared after treating the cells with 20 Amol/L genistein for 6 days. Methylation-specific bands in all three cell lines were slightly decreased after treatment with 20 Amol/L of genistein. The results show that the reactivation of methylation-silenced genes by genistein does occur in different cell lines as a general phenomenon, although the effective concentrations are somewhat different in the different cell lines. To confirm the effect of genistein on the reactivation of these genes, real-time quantitative PCR with TaqMan MGB detector was employed to determine the mRNA expression levels of RARb, p16, and MGMT genes in the KYSE 510 cells after treatment with different concentrations of genistein. The results are summarized in Fig. 2. The results show that the relative amount of mRNA expression from these three genes was increased by treatment with 5 Amol/L of genistein and increased further with higher concentrations of genistein (10 or 20 Amol/L). However, genistein was not as effective as 5-aza-dCyd (8.7 Amol/L). This result was generally consistent with those from general reverse transcription-PCR (RT-PCR) shown in Fig. 1A. To compare the effects of different isoflavones from soy on the reactivation of RARb gene, KYSE 510 cells were treated with 5, 10, or 20 Amol/L of genistein, biochanin A, or daidzein for 6 days and mRNA levels of RARb were determined by RT-PCR (Fig. 3). All three compounds caused the reexpression of RARh mRNA, but biochanin A and daidzein were significantly less effective than genistein (P < 0.05). Results Inhibition of DNA methyltransferase and histone deacetylase activities Reversal of hypermethylation and reactivation of RARb, p16, and MGMT by genistein KYSE 510 cells, with hypermethylated RARb, p16, and MGMT genes, showed only the methylation-specific bands of these genes in methylation-specific PCR, with the loss of the respective mRNA expression, as we previously reported (6, 34). After treating the cells with 2, 5, 10, or 20 Amol/L genistein for 6 days, the unmethylation-specific bands of these three genes were detectable at 2 Amol/L, with higher intensity at 5 Amol/L and even higher intensity at 10 and 20 Amol/L (Fig. 1A). The expression of mRNA from all three genes increased approximately proportional to the appearance of unmethylated DNA, whereas PCR products from methylated DNA decreased as genistein concentration increased. The reversal of hypermethylation and reexpression of these three genes by genistein were similar to that produced by the classic DNA methyltransferase inhibitor 5-aza-dCyd. On treating the cells with 5 Amol/L genistein, PCR products from unmethylated RARb and MGMT Clin Cancer Res 2005;11(19) October 1, 2005 Genistein exhibited a dose-dependent inhibition of DNA methyltransferase activity with nuclear extracts from KYSE 510 cells as the enzyme source and poly(dI-dC)poly(dI-dC) as the substrate. The IC50 of genistein was f67 Amol/L. The structural analogues of genistein, biochanin A, and daidzein had weaker inhibitory activities than genistein (Fig. 4A). Genistein also showed a dose-dependent inhibitory effect on recombinant DNMT1 activity with an IC50 of 30 Amol/L (Fig. 4B). In kinetic studies with varying concentrations of poly(dI-dC)poly(dI-dC), genistein decreased V max and increased K m, showing a mixed inhibition with a K i c of 189.3 Amol/L for competitive and a K i n of 80.2 Amol/L for noncompetitive actions (Fig. 4C). With different concentrations of S-adenosyl-L-[methyl-3H]methionine, genistein decreased V max without a significant change of K m, suggesting a noncompetitive inhibition with a K i n of 140.5 Amol/L (Fig. 4D). The same conclusion was reached when this experiment was repeated thrice. 7036 www.aacrjournals.org Reactivation of p16 INK4a , RARb, and MGMT by Genistein HDAC activity was assayed using an artificial fluorescence substrate, and the activity was completely inhibited by 1 Amol/L trichostatin. Significant inhibition was observed at 5 Amol/L genistein (13.2%), but the extent of inhibition was low even at 100 Amol/L genistein (33%; Fig. 5). Enhanced reactivation of RARb, p16, and MGMT and growth inhibition by combination of genistein with trichostatin, sulforaphane, or 2V-deoxy-5-azacytidine Treatment of KYSE 510 cells with trichostatin (0.5 Amol/L) alone for 1 day or with 5-aza-dCyd (2 Amol/L) alone for 5 days reactivated the RARb gene, but had little or no effect on p16 and MGMT (Fig. 6A). However, treatment of the cells with 5 Amol/L genistein for 5 days and then with 0.5 Amol/L trichostatin for 1 additional day significantly enhanced the reactivation of these three genes. In combination with 2 Amol/L 5-aza-dCyd, genistein also significantly enhanced the reexpression of RARb and p16, but not MGMT. The reactivation caused by the combination of genistein with trichostatin or 5-aza-dCyd was higher than the sum of the effect of individual agents, suggesting a synergistic action. The combination of 2 Amol/L 5-aza-dCyd and 0.5 Amol/L trichostatin seemed to produce an additive effect on RARb and a synergistic effect on p16 and MGMT. Under these experimental conditions, trichostatin (0.5 Amol/L) was more effective than genistein (5 Amol/L) in inhibiting cell growth, and the combination of these two agents caused a more pronounced inhibition (48%, P < 0.05). Similarly, 15 Amol/L sulforaphane alone can reactivate the RARb gene, but cannot induce reexpression of p16 and MGMT genes; however, treatment of the cells with 5 Amol/L genistein for 5 days and then with 15 Amol/L sulforaphane for 1 additional day significantly enhanced the reactivation of these three genes, especially p16 and MGMT, whereas the combination of genistein and sulforaphane significantly enhanced the inhibitory effect on cell growth (P < 0.05) compared with genistein or sulforaphane alone (Fig. 6B). Effects on inhibition of cell growth and other factors After treatment with genistein, biochanin A, or daidzein for 6 days, a dose-dependent inhibition of cell growth was observed (Fig. 7A). At concentrations as low as 2 Amol/L, Fig. 4. Inhibition of 5-cytosine DNA methyltransferase activity by genistein. A, dose-dependent inhibition of DNA methyltransferase activity of nuclear extracts from KYSE 510 cells by genistein, biochanin A, and daidzein. The reaction mixture contained nuclear extracts (4.5 Ag protein), poly(dI-dC)poly(dI-dC) (20 nmol/L), and S-adenosyl-L-[methyl-3H]methionine (10 Amol/L, 2.0 ACi) in 40 AL incubation mixture containing 10% glycerol and 2 mmol/L 2-mercaptoethanol. The incubation time was 1.5 hours. B, dose-dependent inhibition of recombinant DNMT1activity. Standard reaction mixtures (25 AL) contained 60 nmol/L recombinant DNMT1, 15 Amol/L S-adenosyl-L-[methyl-3H]methionine (specific activity, 275 GBq/mmol), and 10 ng poly(dI-dC)poly(dI-dC) (average chain length: 3,000) in M2 buffer [100 mmol/L Tris (pH 8), 10 mmol/L EDTA, 10 mmol/L DTT, 200 Ag/mL bovine serum albumin] and were incubated for 1hour at 37jC. C, kinetic study with varying concentrations of poly (dI-dC)poly(dI-dC). The reaction mixtures contained 20 Amol/L of S-adenosyl-L-[methyl-3H]methionine and different concentrations of poly(dI-dC)poly(dI-dC). Kin , noncompetitive inhibition constant; Kic , competitive inhibition constant. D, kinetic study with varying concentrations of S-adenosyl-L-[methyl-3H]methionine. The reaction mixtures contained 120 nmol/L poly(dI-dC)poly(dI-dC) and different concentrations of S-adenosyl-L-[methyl-3H]methionine. Points, mean of three sets of the same experiments; bars, SD. *, P < 0.05; **, P < 0.01, statistically significant difference from control according to Student’s t test. Genistein, biochanin A, and daidzein significantly inhibited DNA methyltransferase activity of nuclear extracts and recombinant DNA methyltransferase in a concentration-dependent pattern (r = 0.95 to 0.98, P < 0.0001). www.aacrjournals.org 7037 Clin Cancer Res 2005;11(19) October 1, 2005 Cancer Prevention Fig. 5. Inhibition of HDAC activity by genistein. The reaction mixture contained nuclear extract from KYSE 510 cells (4.0 Ag protein), substrate (48 Amol/L), and genistein (5,10, 20, 50, or100 Amol/L) in 40 AL total volume.Trichostatin (1 Amol/L) was used as a positive control. Incubation time is 30 minutes at 25jC. The product was determined by a fluorescence plate reader (excitation, 360 nm; emission, 465 nm). Columns, mean (n = 3); bars, SD. *, P < 0.05; **, P < 0.01, statistically significant difference from control according to Student’s t test. Genistein inhibited HDAC activity in a concentration-dependent pattern (r = 0.89, P < 0.0001). genistein inhibited cell growth by f30%, and at 20 Amol/L, by more than 90%. The inhibitory effects of biochanin A and daidzein were weaker, with biochanin A the weakest. In a timedependent study with 5 Amol/L genistein, slight growth inhibition was seen after 4 days and significant inhibition was observed after 6 days (Fig. 7A). Signs of toxicity and growth inhibition were observed in cells treated for 2 or 6 days with 10 or 20 Amol/L genistein; the greatest effect was observed in cells treated with 20 Amol/L genistein for 6 days (Fig. 7B). In cells treated with different concentrations of genistein for 3 days, cell proliferation was significantly inhibited after treatment with 10 or 20 Amol/L genistein (Fig. 7C), but induction of apoptosis was not observed even after treatment with 20 Amol/L genistein (data not shown). In colony formation assays of KYSE 510 cells, treatment with genistein, especially at 10 or 20 Amol/L, for 2 days, significantly decreased the number of colonies formed (Fig. 7D). RT-PCR results with total RNA of KYSE 510 cells treated with 1, 2, 5, 10, and 20 Amol/L genistein for 6 days indicated that genistein treatment did not affect the mRNA expression levels of DNMT1, DNMT3a, DNMT3b, and methyl-CpG binding domain 2. The protein level of 5-methylcytosine DNA glycosylase, an enzyme that may be involved in the removal of methylated DNA (43), also did not change after treatment with 10 or 20 Amol/L of genistein for 24 hours (data not shown). Discussion The present study clearly shows that genistein reverses DNA hypermethylation and reactivates the methylation-silenced genes RARb, p16, and MGMT. This activity is similar to our previous observations with EGCG. Genistein is also an inhibitor of DNA methyltransferase activity in nuclear extracts from KYSE 510 cells, with 14% inhibition at 20 Amol/L (IC50, f67 Amol/L), and this activity is weaker than that of EGCG Fig. 6. Effects of combination of genistein and trichostatin, sulforaphane, or 5-aza-dCyd on the reactivation of p16, RARb, and MGMT genes and cell growth. A, KYSE 510 cells were treated with or without either 5 Amol/L genistein or 2 Amol/L 5-aza-dCyd alone or together for 5 days and cultured for 1additional day in fresh medium with or without 0.5 Amol/L trichostatin (TSA). B, KYSE 510 cells were treated with or without 5 Amol/L genistein for 5 days and cultured for 1additional day in fresh medium with or without 15 Amol/L sulforaphane (SFN). The mRNA expression levels of p16, RARb, and MGMT genes were determined by RT-PCR and the band intensity was quantified using densitometry and normalized to each control (mean F SD, n = 2). Representative of two independent experiments. Cell growth was analyzed using trypan blue exclusion assay. Different letters indicate a significant difference (P < 0.05) based on one-wayANOVA and Tukey’s honest significant difference test (mean F SD, n = 3). Clin Cancer Res 2005;11(19) October 1, 2005 7038 www.aacrjournals.org Reactivation of p16 INK4a , RARb, and MGMT by Genistein Fig. 7. Effects of genistein on cell growth, morphologic change, cell proliferation, and colony formation efficiency assay. A , KYSE 510 cells were treated with different concentrations of genistein, biochenin A, or daidzein for 6 days, or with 5 Amol/L genistein for different time periods, and then their effects on cell growth were determined by trypan blue exclusion assay. Genistein, biochanin A, and daidzein significantly inhibited cell growth with regard to concentration (r = 0.94 to 0.99, P < 0.0001) and time (r = 0.65, P = 0.0017). B, after treatment for 2 days (a-c) or 6 days (d-f), the morphology of the cells treated with 0 Amol/L (a and d), 10 Amol/L (b and e), or 20 Amol/L (c and f) genistein was photographed. Magnification, 100. C, KYSE 510 cells were treated with different concentrations of genistein for 3 days, and then cell proliferation was determined with the BrdUrd ELISA method. Genistein significantly inhibited cell proliferation in a concentration-dependent pattern (r = 0.85, P < 0.0001). D, KYSE 510 cells were treated with different concentrations of genistein for 2 days and cultured for 10 additional days in fresh medium, and then colony numbers were analyzed. Genistein significantly inhibited colony formation efficiency in a concentration-dependent pattern (r = 0.96, P < 0.0001). *, P < 0.05; **, P < 0.01, statistically significant difference from control according to Student’s t test. (IC50, f20 Amol/L). Kinetic studies indicate that genistein inhibits DNA methyltransferase activity in a substrate- and methyl donor – dependent manner, which differs from our previous results with EGCG as a competitive inhibitor of DNA methyltransferase. The inhibition activity of genistein was also observed using recombinant DNMT1 as the enzyme source, showing an IC50 of 30 Amol/L. In comparison with genistein, biochanin A and daidzein are weaker inhibitors of DNA methyltransferase, and they are also less effective in the reactivation of RARb gene, suggesting a correlation between the inhibition of DNA methyltransferase activity and reactivation of methylation-silenced genes by these dietary isoflavonoids. However, the fact that the effective concentrations of genistein in the inhibition of DNA methyltransferase are higher www.aacrjournals.org than those for the reactivation of methylation-silenced genes suggests that other factors are involved in the action of genistein. Our results, however, suggest genistein did not exert its effect by modulating the expression levels of DNMT1, 3a, and 3b, methyl-CpG binding domain 2, and 5-methylcytosine DNA glycosylase. For the DNA hypermethylation-related silencing of RARb, p16, and MGMT genes, histone deacetylation is also known to be involved (44, 45). In addition to inhibition of DNA methyltransferase, the presently observed weak inhibitory effect of genistein on HDAC activity (13-17% inhibition at 5-20 Amol/L) may also contribute to the reactivation of these genes. The weak inhibitory effects of genistein on DNA methyltransferase and HDAC may have an intrinsic synergistic 7039 Clin Cancer Res 2005;11(19) October 1, 2005 Cancer Prevention effect on the reactivation of methylation-silenced genes. Genistein may also be expected to have a synergistic or an additive effect with other HDAC or DNA methyltransferase inhibitors. Indeed, our results (Fig. 6) indicate that genistein, at 5 Amol/L, enhanced the activity of lower concentrations of 5-aza-dCyd (2 Amol/L) or trichostatin (0.5 Amol/L) in the reactivation of RARb, p16, and MGMT genes. In addition, combination of genistein and sulforaphane, a HDAC inhibitor found in broccoli (46), also enhanced the reactivation of these genes, especially p16 and MGMT genes. The possible synergistic actions in the combination of these agents warrant detailed investigation. In theory, the demethylation and reactivation of p16 and RARb by genistein should result in cell growth inhibition. Genistein (5-20 Amol/L) significantly inhibited cell proliferation without induction of apoptosis and also affected long-term cell survival after only 2 days of treatment, and this could be related to the reexpression of p16. More studies, however, are needed to determine the relationship between the reactivation of these genes and the growth inhibition by genistein. Oral administration of soy products containing genistein and other isoflavones has been shown to inhibit tumorigenesis in different organs, and different mechanisms have been proposed (7). In our present study, the effective concentration of genistein for DNA demethylation, transcriptional reactivation of these three genes, and cell growth inhibition was 2 to 10 Amol/L. These concentrations are lower than those used in many other studies (26, 47, 48). A concentration of 10 Amol/L is higher than the plasma level of genistein in women consuming soy products (0.74-6.0 Amol/L; http:// www.aminoup.co.jp; refs. 49, 50), but lower micromolar concentrations of genistein are still achievable. Because genistein is a weak inhibitor of DNA methyltransferase, genomic global hypomethylation is not expected to occur due to dietary intake of soy isoflavones. Even if hypomethylation occurred, it would not be to the extent as to induce genomic instability as has been reported with some DNA methyltransferase inhibitors (51, 52). In this study, we showed that genistein and related soy isoflavones can inhibit DNA methyltransferase activity, reverse DNA hypermethylation, and reactivate methylationsilenced genes. Genistein in combination with other DNA methyltransferase or HDAC inhibitors can enhance the reactivation of methylation-silenced genes. It remains to be determined whether dietary administration of genistein or soy products could cause the reactivation of methylationsilenced genes in vivo. An attractive approach that needs to be explored in vivo is the combination of genistein with sulforaphane, and low concentrations of these two dietary factors may produce a synergistic effect in the prevention of hypermethylation-induced inactivation of tumor suppressor genes. The combination of genistein with low doses of trichostatin or 5-aza-dCyd for the prevention or reversal of hypermethylation also warrants further investigations in vitro and in vivo. Acknowledgments We thank Drs. Jungil Hong, Shengmin Sang, and Charles desBordes for helpful discussions. References 1. Herman JG, Baylin SB. Gene silencing in cancer in association with promoter hypermethylation. N Engl J Med 2003;349:2042 ^ 54. 2. Egger G, Liang G, Aparicio A, Jones PA. Epigenetics in human disease and prospects for epigenetic therapy. 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