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[Cancer Research 61, 2320-2327, March 1, 2001]
© 2001 American Association for Cancer Research


Tumor Biology

Elevation of Breast Carcinoma Nm23-H1 Metastasis Suppressor Gene Expression and Reduced Motility by DNA Methylation Inhibition

Melanie T. Hartsough1,,2, Susan E. Clare1,,3, Michael Mair, Abdel G. Elkahloun, Dennis Sgroi, C. Kent Osborne, Gary Clark and Patricia S. Steeg

Women’s Cancers Section, Laboratory of Pathology, Division of Clinical Sciences, National Cancer Institute, NIH, Bethesda, Maryland 20892 [M. T. H., S. E. C., M. M., P. S. S.]; Department of Molecular Pathology, Massachusetts General Hospital, Charlestown, Massachusetts 02129 [D. S.]; The Breast Center, Baylor College of Medicine, Houston, Texas 77030 [C. K. O., G. C.]; and Cancer Genetics Branch, National Human Genome Research Institute, Bethesda, Maryland 20892 [A. G. E.]


    ABSTRACT
 Top
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 
We hypothesize that elevation of Nm23-H1 expression in micrometastatic breast cancer cells may inhibit their metastatic colonization and further invasion, and induce differentiation, thus resulting in a clinical benefit. The current study investigated the possible contribution of DNA methylation to the regulation of Nm23-H1 expression, based on the observation that two CpG islands are present in its promoter. 5-Aza-2'-deoxycytidine (5-Aza-CdR), a DNA methylation inhibitor, increased the Nm23-H1 expression of 5 of 11 human breast carcinoma cell lines in vitro, including 3 of 3 metastatically competent lines. Increased Nm23-H1 expression was accompanied by a reduction in motility in vitro, with minimal effect on proliferation. Both increased Nm23-H1 expression and decreased motility were observed using low (75 nM) concentrations of 5-Aza-CdR. Array analysis of MDA-MB-231 breast carcinoma cells treated with 5-Aza-CdR confirmed the elevation of nm23-H1 mRNA, whereas relatively few other genes exhibited altered expression. Bisulfite sequencing of the two CpG islands in a panel of cell lines and in 20 infiltrating ductal carcinomas revealed that one island (-3090 bp to -3922 bp) exhibited infrequent differential methylation. The data indicate that DNA methylation inhibitors can directly or indirectly cause both elevation of Nm23-H1 expression and decreased function in one aspect of metastasis, motility.


    INTRODUCTION
 Top
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 
Metastasis suppressor genes are defined by their inhibition of tumor cell line metastatic capability in vivo on transfection, without the inhibition of primary tumor size. Several of these genes are thought to affect the non-angiogenesis-dependent colonization of tumor cells at the metastatic site and, therefore, constitute interesting translational targets (1 , 2) . The nm23 gene family, currently containing eight members, exhibits metastasis suppressor activity. Transfection of nm23 cDNAs into metastatically competent breast carcinoma (3, 4, 5) , melanoma (6, 7, 8, 9) , colon carcinoma (10) , and oral squamous cell carcinoma (11) cell lines resulted in 40–98% decreased metastatic potential in vivo. In the MDA-MB-435 breast carcinoma model system, overexpression of nm23-H1 resulted in a 50–90% inhibition of metastasis in vivo, reduced colonization in soft agar under both normal and transforming growth factor-ß stimulated conditions (3) , inhibition of motility to a variety of attractants (12, 13, 14) , and morphological and biosynthetic evidence of differentiation (15) .

Tumor cohort studies indicate that reduced Nm23 expression is associated with aggressive breast carcinomas, although it is not an independent prognostic factor. Reduced Nm23 expression has been correlated with poor patient survival, nodal metastases, or aggressive histopathological criteria in 18 of 24 recent breast cancer cohort studies (reviewed in 16 ). In the only large node-negative cohort study reported, low Nm23-H1 expression was a significant predictor of poor survival in univariate and multivariate analyses (17) , and comparison with other metastasis-associated proteins indicated that loss of Nm23-H1 is an early event (18) . In another cohort study, side-by-side analysis of allelic deletion at nm23-H1, Nm23-H1 expression and patient survival revealed that Nm23-H1 expression, but not allelic deletion, was a predictor of poor patient clinical course. Moreover, mutations in the nm23-H1 coding sequence were not observed (19) .

Because low nm23-H1 RNA and protein expression correlate with poor clinical course, we have focused on the regulation of nm23-H1 at the transcriptional level. One notable mechanism of transcription regulation that has been defined in cancer is aberrant methylation of genes. DNA methylation occurs at CpG dinucleotides on cytosine residues. Regions of a gene that contain a high frequency of CpG dinucleotides are defined as CpG islands. These islands are normally unmethylated except in particular instances such as X-chromosomal inactivation and genomic imprinting (20 , 21) . In the neoplastic process, hypermethylation of CpG islands within tumor and metastasis suppressor genes has been reported to silence a host of these genes by down-regulation of expression (reviewed in Refs. 22 , 23 ). DNA methylation inhibitors, such as 5-Aza-CdR4 , have been shown to demethylate these regions, thereby causing an increase in gene expression (22) .

In this report, we examined the contribution of DNA methylation to the regulation of Nm23-H1 expression, based on the finding that the nm23-H1 promoter contains two CpG islands. We present evidence herein that the DNA methylation inhibitor 5-Aza-CdR increases the Nm23-H1 expression of 5 of 11 human breast carcinoma cell lines, including 3 of 3 with metastatic competence in vivo. Increased Nm23-H1 expression was accompanied by minimal growth inhibition, but significantly lower motility in vitro.


    MATERIALS AND METHODS
 Top
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 
Cell Lines, Tissue Specimens, and Reagents.
RPMI 1640 supplemented with 10% FCS and glutamine (RPMI complete medium) and DMEM supplemented with 10 mM HEPES, 100 units/ml penicillin G sodium, 100 units/ml streptomycin sulfate, and 0.25 µg/ml amphotericin B (DMEM serum-free medium) was purchased from Life Technologies. Oligonucleotides were synthesized by Lofstrand Labs and Life Technologies. TSA and 5-Aza-CdR were obtained from Sigma. MDA-MB-231, MDA-MB-435, ZR-75–1, MCF7, HBL-100, MDA-MB-157, BT-474, MDA-MB-468, SK-BR-3 and MDA-MB-157 cell lines were obtained from American Type Culture Collection. MDA-MB-231 and MDA-MB-435 cells were also a generous gift of Dr. Janet Price (M. D. Anderson, Houston, TX), and equivalent results were obtained. The LCC15-MB cell line was a generous gift from Dr. Robert Clarke (Georgetown University, Washington D.C.). All of the cells were grown in RPMI complete medium at 5% CO2.

Twenty unlinked and unlinkable human infiltrating ductal breast carcinomas were obtained from the Baylor University SPORE National Breast Cancer Tissue Resource. These tumors were designated exempt from further review by the NIH Office of Human Subjects Research. For the 20-tumor cohort, mean estrogen receptor expression was 109 fmol/mg protein (range, 0–763), progesterone receptor expression was 215 fmol/mg protein (range, 0–1270), and S phase was 7.7% (range, 0.9–21.9%). A direct correlation of estrogen receptor and progesterone receptor expression was observed in the cohort (Spearman correlation coefficient, 0.465; P = 0.039) as was an indirect correlation of progesterone receptor expression and S phase (Spearman correlation coefficient, 0.490; P = 0.028).

5-Aza-CdR Treatment.
MDA-MB-231, MDA-MB-435, ZR-75–1, MCF7, HBL-100, MDA-MB-157, BT-474, MDA-MB-468, LCC15-MB, SK-BR-3, and MDA-MB-157 cells were plated at densities of 4.0 x 103, 3.25 x 104, 4.0 x 104, 7 x 104, 1.0 x 104, 4.0 x 103, 3.2 x 104, 1.0 x 105, 2 x 104, 1 x 104, 3 x 104, and 4 x 104 cells/100 mm dish, respectively (three plates per cell line), in RPMI complete media. The medium was changed to fresh RPMI complete media on day 3. On day 4, one plate of each cell line was treated with RPMI complete media containing 0, 0.075, or 0.75 µM 5-Aza-CdR. The medium was changed on day 6, maintaining 5-Aza-CdR treatment. On day 7, the cells were harvested and counted via hemacytometer. The cells were then centrifuged at 1500 rpm, 4°C for 1 min, washed with cold 1x PBS, recentrifuged and resuspended in cold lysis buffer [50 mM Tris-HCl (pH 7.6), 5 mM EDTA, 150 mM NaCl, 1% NP40, 10 µg/ml Aprotinin, 10 µg/ml Leupeptin, 1 mM PMSF, 10 mM NaF, 0.1 mM NaVO4, and 10 µg/ml Pepstatin A]. The cells were incubated on ice for 10 min and then frozen at -80°C until needed.

For reversal experiments, MDA-MB-231 cells were plated at densities of 2 x 105, 1 x 105, 5 x 104, 2.5 x 104, and 2 x 104 cells/100-mm plate and incubated with 0.75 µM 5-Aza-CdR for 3 days (treatment started on day 2). On day 5, the media was changed to fresh RPMI complete media without 5-Aza-CdR. Cells were harvested on days 5, 7, 9, 11, and 13, respectively, resulting in the withdrawal of 5-Aza-CdR for 0, 2, 4, 6, and 8 days. Harvested cells were counted and lysed, as described previously, and frozen at -80°C until needed.

For immunoblotting, lysates were thawed and centrifuged at 13,000 rpm, 4°C, for 15 min to remove particulate matter. One x 105 cells/sample were separated on 15% SDS/PAGE gels, transferred to PVDF, and immunoblotted with anti-Nm23-H1 (Ab11; Ref. 24 ) or anti-E-cadherin (H-108; Santa-Cruz) for 1 h at room temperature or 4°C, overnight, respectively, followed by a second incubation with IgG-horseradish peroxidase conjugate for 1 h at room temperature. Nm23-H1 and E-cadherin proteins were visualized by ECL (Amersham). Protein densities of Nm23-H1 were determined by densitometry (AlphaEase 5.1; Alpha Innotech Corp).

TSA Treatment.
MDA-MB-231 and MCF7 cells were plated, as described above, except that the cells were either untreated or treated with TSA (0.3 µM) or 5-Aza-CdR (0.75 µM), alone or in combination. 5-Aza-CdR was added to the cells on day 4, and TSA was added on day 6. On day 7, the cells were harvested and counted. Nm23-H1 protein expression was then determined as described for 5-Aza-CdR treatment.

Tumor Protein Analysis.
Tumor tissue (50–100 mg) was lysed in 1% SDS, vortexed vigorously, boiled for 3 min, revortexed, and spun at room temperature for 10 min at 14,000 x g. Protein concentration of the supernatant was determined by the BCA method (Pierce). Fifty µg of protein were loaded on a 15% SDS-PAGE gel and transferred to PVDF. Nm23 (Ab11) protein expression was determined by ECL. Data were analyzed by densitometry of the Nm23-H1 band (AlphaEase 5.1).

Cell Motility Assay.
Cell motility was determined using 48-well Boyden chemotaxis chambers (Neuro Probe; Ref. 13 ). The chemoattractant, FCS (Clonetics), was diluted in DMEM serum-free media containing 0.1% BSA. Serial dilutions of FCS were placed in the lower wells of the chamber at 0.01%, 0.5%, and 0.1%. A 8 µm pore size polycarbonate PVP-free filter (Poretics Corp.), precoated in 0.1 M acetic acid containing 40 µg/ml type IV collagen (Collaborative Biomedical Research), was sandwiched between the upper and lower wells of the chamber. MDA-MB-231 and MDA-MB-435 cells were plated and treated with 5-Aza-CdR, as described above. After a 3-day incubation, cells were trypsinized, rinsed once in PBS, and resuspended in DMEM serum-free media at a density of 2.0 x 106 cells/ml. Fifty-six µl of cells were added to the upper wells of the chamber, and the chambers were incubated for 3 h at 37°C in a humidified 5% CO2 incubator. The filters were then stained with Diff Quick (Baxter Healthcare Corp.), and the migrating cells counted by light microscopy in 6–9 fields at x20. Data for a particular concentration represents the mean of three replicate wells.

Proliferation Assay.
Cell viability was determined by using the CellTiter 96 Non-Radioactive Cell Proliferation Assay (Promega), as per manufacturer’s instructions. Briefly, cells were plated in a 96-well plate at 5000 cells/well in 75 µl and were incubated overnight at 37°C, 5% CO2. The next day, the cells were treated, in triplicate, with 0, 0.075, or 0.75 µM, 5-Aza-CdR (final volume of 100 µl) and incubated for 3 days at 37°C, 5% CO2. On the 3rd day, 15 µl of dye solution were added to each well, and the cells were incubated at 37°C, 5% CO2 for 3 h. Solublization/stop solution (100 µl) was then added to each well, and the plates were incubated overnight at room temperature for complete color development. Cell viability was then determined by spectrophotometry (A562 nm)(Vmax kinetic microplate reader; Molecular Devices). Cell proliferation was calculated as mean percentage of control (no 5-Aza-CdR); data represent the mean of three replicate wells.

Sodium Bisulfite Treatment of DNA.
Genomic DNA was extracted from one 150-mm plate of cells treated with or without 0.75 µM 5-Aza-CdR (as described above) using the Nucleon 8Acc-2 Kit (Pharmacia) and from 25 mg of tumor tissue using the Dneasy Tissue Kit (Qiagen), as per instructions. One µg of DNA was then subjected to sodium bisulfite modification using the CpGenome DNA modification kit (Intergen), as per manufacturer’s instructions. Universal methylated DNA was used as the positive control (Intergen). Treated DNAs were stored at -20°C until needed.

Sodium Bisulfite DNA Sequencing.
Bisulfite converted DNA (~50 ng) was amplified with 5' primer: tattttgggcgatttggtaaggttt (-3658 bp to -3634 bp) and 3' primer: ccaaaacactccaacctaaat (-3337 bp to -3358 bp). These primers encompass a region within the most 5' CpG island (-3634 bp to -3337 bp) of the promoter, generating a 321-bp PCR product. Conditions for the PCR were 1 cycle at 94°C for 10 min; 25 cycles at 94°C for 30 s, at 60°C for 1 min, and at 72°C for 2 min, and 1 cycle at 72°C for 7 min. The PCR product was cloned into the TA vector pCR2.1 (Invitrogen). Ten subclones were confirmed by restriction analysis and sequenced using the M13 reverse primer (Invitrogen) with a Prism 377 DNA Sequencer (Perkin-Elmer Applied Biosystems).

Microarray Analysis of MDA-MB-231 Cells.
Poly(A) RNA was extracted from two 150-mm plates of MDA-MB-231 cells (treated or untreated with 5-Aza-CdR for 3 days) using the FastTrac2.0 mRNA isolation kit (Invitrogen). Microarray hybridization was then performed with 1 µg of DNase-treated poly(A) RNA, as described previously (25) . Briefly, the RNA was reverse-transcribed in the presence of 50 µCi of [33P]dCTP or 50 µCi [33P]dATP, 500 ng of oligo-dT, and 200 units of Superscript II RT (Life Technologies, Inc). The second strand was synthesized in the presence of 50 µCi [33P]dCTP or 50 µCi [33P]dATP, 500 ng of random hexamers, and 2500 units of large DNA polymerase I (Life Technologies, Inc). The labeled DNA was denatured and hybridized to the GF211 GeneFilter as described previously (25) . The filters were then exposed on a Packard screen and scanned at 50-µm resolution in a phosphoimager instrument (Cyclone instrument; Packard Inc). The tiff images resulting from the phosphoimager were directly imported into the image analysis software Pathways and analyzed (Research Genetics, Inc).

Statistical Analysis.
Student’s t test was used for the analysis of motility data.


    RESULTS
 Top
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 
The DNA Methylation Inhibitor 5-Aza-CdR Elevates the Nm23-H1 Expression of Human Breast Carcinoma Cell Lines in Vitro.
A schematic of the nm23-H1 promoter is shown in Fig. 1Citation . The initiating ATG is located in exon 2, preceded by a large intron. A small exon 1 contains the transcriptional initiation site. The frequency of CpG dinucleotides through the nm23-H1 promoter is shown in Fig. 1Citation . Two areas of high CpG dinucleotide frequency occur: (a) bases, -1672 to -2343 (island B), which includes the translation initiation site; and (b) additional 5' between bases, -3090 and -3922 (island A). CpG islands were not present in the Nm23-H1 coding sequence (data not shown). The presence of these CpG islands suggested the hypothesis that DNA methylation may contribute to the regulation of Nm23-H1 expression levels.



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Fig. 1. CpG Islands of nm23-H1 gene. Schematic of the 5'-most region of the nm23-H1 (NME1) gene from -6 bp to -4922 bp; the translation start site is position 1. There are two CpG rich islands -3922 bp to -3090 bp (A) and -2343 bp to -1672 bp (B) within this region of the gene. CpG island A contains untranscribed DNA, whereas CpG island B includes the entire exon 1 and a portion of intron 1. CpG densities were calculated using MacVector software (Oxford Molecular Group), and CpG islands were delimited based on the definition reported in Gardiner-Garden and Fromer (70) .

 
To determine whether alterations in DNA methylation could influence Nm23-H1 expression, cells from the human breast carcinoma cell line MDA-MB-231 were incubated for 3 days in 5-Aza-CdR, and a Western blot was processed for Nm23 proteins. Low nanomolar (<=7.5 nM) concentrations of 5-Aza-CdR elevated Nm23-H1 expression ~4-fold by densitometry; elevated Nm23-H1 expression was maintained at higher 5-Aza-CdR concentrations. Nm23-H2 expression was coordinately induced (see Fig. 2Citation ). To determine the generality of this finding, cultures from 11 human breast carcinoma cell lines were incubated with or without 5-Aza-CdR for 3 days, and the Nm23 expression levels were determined (Fig. 3)Citation . A dose-dependent increase in Nm23-H1 and -H2 expression was observed in 5 of 11 cell lines, including all 3 of the in vivo metastatically competent cell lines (26 , 27) . The data are grouped by the extent of change in Nm23-H1 expression in response to 5-Aza-CdR. In Fig. 3ACitation , two low-Nm23-H1-expressing, in vivo metastatically competent cell lines, MDA-MB-231 and LCC15-MB, exhibited a 4- to 5- and 6- to 9-fold increase in Nm23-H1 in response to 75 nM and 0.75 µM 5-Aza-CdR, respectively. The remaining low-Nm23-H1-expressing, in vivo metastatically competent cell line, MDA-MB-435 (26) , was present in the moderately increased expression group (Fig. 3B)Citation . Nm23-H1 overexpression in this group ranged from 1.5- to 2.5-fold and 2- to 3-fold for 75 nM and 0.75 µM 5-Aza-CdR, respectively. The cell lines shown in Fig. 3CCitation showed no repeatable elevation of Nm23 proteins in response to 5-Aza-CdR. Among these cell lines are two high-Nm23-expressing, low-to-nonmetastatic lines (MCF7 and ZR-75–1; Ref. 28 ), as well as lines thought to be more aggressive because of specific molecular alterations (Her-2 and EGFR amplification in SKBR3 and MDA-MB-468, respectively).



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Fig. 2. Dose response of 5-Aza-CdR on Nm23-H1 and -H2 protein expression in the MDA-MB-231 human breast carcinoma cell line in vitro. MDA-MB-231 cells were treated for 3 days with 0 (Lane 1), 0.001 (Lane 2), 0.005 (Lane 3), 0.0075 (Lane 4), 0.01 (Lane 5), 0.05 (Lane 6), 0.075 (Lane 7), 0.1 (Lane 8), 0.5 (Lane 9), 0.75 (Lane 10), and 1.0 (Lane 11) µM 5-Aza-CdR. The cells were then harvested and counted. Lysates from 1 x 105 cells were separated on a SDS-PAGE and transferred to PVDF. The membrane was then immunoblotted with Nm23 (AB11) antibody, and Nm23-H1 protein was visualized by ECL.

 


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Fig. 3. Effect of 5-Aza-CdR on the Nm23-H1 and -H2 protein expression of 11 human breast carcinoma cell lines in vitro. Each cell line was cultured in the absence (Lane 1) or presence of 0.075 (Lane 2) or 0.75 (Lane 3) µM 5-Aza-CdR for 3 days. Lysates from equivalent numbers of cells were processed as a Western blot and Nm23-H1 and Nm23-H2 proteins were detected as for Fig. 2Citation . The cell lines are grouped based on their response to 5-Aza-CdR, with high levels of Nm23-H1 induction (A), moderate levels (B), and no reproducible increase (C). Each cell line shown represents a separate experiment, and Nm23 levels between cell lines cannot, therefore, be compared.

 
Several additional aspects of 5-Aza-CdR elevation of Nm23-H1 expression were investigated. In the experiment shown in Fig. 4Citation , MDA-MB-231 cells were incubated with 0.75 µM 5-Aza-CdR for 3 days; the culture medium was then removed and replaced with medium lacking 5-Aza-CdR (shown as day 0). Elevated Nm23-H1 and -H2 levels were observable after 2 and 4 days of culture without drug, respectively. The potential interaction between 5-Aza-CdR and TSA, a histone deactylase inhibitor, was determined (Fig. 5)Citation . A representative cell line from the high-, moderate-, and no-induction groups from Fig. 2Citation was incubated with 5-Aza-CdR, TSA, or combinations thereof, and Nm23 expression was determined on Western blots. In contrast to other reported genes, the combination of 5-Aza-CdR and TSA was not synergistic in inducing Nm23 expression.



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Fig. 4. Elevated Nm23-H1 and -H2 expression is maintained after removal of 5-Aza-CdR in vitro. MDA-MB-231 cells were cultured in the absence or presence of 0.75 µM 5-Aza-CdR for 3 days. The medium was then changed to fresh RPMI complete medium containing no 5-Aza-CdR, and the cultures were maintained in the absence of drug for an additional 0, 2, or 4 days. The cells were then harvested and the lysates analyzed for Nm23-H1 and -H2 expression, as described in Fig. 2Citation .

 


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Fig. 5. Lack of synergy between 5-Aza-CdR and TSA in the induction of Nm23-H1 and -H2 in vitro. Cell lines representing high- (MDA-MB-231, A), medium- (MDA-MB-435, B), and nonresponders (MCF7, C) to 5-Aza-CdR, as listed in Fig. 3Citation , were incubated in the absence or presence of 0.75 µM 5-Aza-CdR or 0.3 µM TSA, alone or in combination. Lysates from equivalent numbers of cells were processed as a Western blot for Nm23-H1 and -H2 expression as described in Fig. 2Citation .

 
It has been estimated that the genome contains thousands of CpG islands that could participate in gene regulation through altered DNA methylation. Thus, any potential phenotypic effect caused by elevation of Nm23 expression in response to DNA methylation inhibitors could be offset by numerous other changes. To ascertain the degree to which other gene expression changes occurred in response to DNA methylation inhibition, MDA-MB-231 cells were treated with or without 0.75 µM 5-Aza-CdR for 3 days; mRNA was then extracted and hybridized to a Genefilter array. Of the 4000 genes that were quantitated, the expression of 22 (0.6%) changed. All showed a modest (2- to 3-fold) increase in the 5-Aza-CdR-treated cells (Table 1)Citation . One of the genes identified was Nm23-H1 (NDPKA), confirming our protein observations at the mRNA level. The listed genes have been reported to have a wide variety of functions in vitro and in vivo, including three involved in general transcription and translation, two with glutathione S-transferase activity, and two that suppress the transformed phenotype in vitro. PECAM-1 and glutathione S-transferase have been previously reported to be regulated by DNA methylation. Surprisingly, no increase in E-cadherin expression was observed in the 5-Aza-CdR-treated MDA-MB-231 cells. This protein has been reported to be regulated by DNA methylation in some, but not all, breast cancer studies (29) . To confirm the mRNA data, we performed a Western blot analysis of E-cadherin expression at multiple days of culture (Fig. 6)Citation . Induction of E-cadherin expression was not observed on day 3 of culture, confirming our array data; 8-fold induction of E-cadherin expression was observed on day 5 of culture but remained 6-fold less than that of the MCF7 cell line.


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Table 1 Array analysis of gene expression changes in 5-Aza-CdR-treated MDA-MB-231 human breast carcinoma cells

 


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Fig. 6. Effect of 5-Aza-CdR on E-cadherin protein expression in high responder MDA-MB-231 cells. MDA-MB-231 cells were incubated in the absence or presence of 0.75 µM 5-Aza-CdR for 1, 3, 5, and 7 days. The cells were harvested, and lysates from an equal number of cells were separated on a SDS-PAGE, transferred to PVDF, and immunoblotted with E-cadherin antibody. The E-cadherin protein was visualized by ECL. Lysate from untreated MCF7 cells is included as a positive control.

 
Treatment of Human Breast Carcinoma Cells with 5-Aza-CdR Suppresses Cellular Motility in Vitro.
Transfection of nm23-H1 into breast carcinoma cell lines has been associated with reduced colonization and motility, and increased differentiation in vitro (3 , 12, 13, 14, 15) , as well as with reduced tumor metastatic potential in vivo (3, 4, 5, 6, 7, 8, 9, 10, 11) . Of the transfection experiments, none have reported either a reduction in proliferation in vitro or of primary tumor size in vivo (3 , 6 , 7 , 30) . Thus, if the elevation of Nm23-H1 expression by 5-Aza-CdR was to have a relevant phenotypic effect, we hypothesized that metastasis-associated functions such as motility would be most affected. The effect of 5-Aza-CdR on anchorage-dependent proliferation in vitro is shown in Fig. 7Citation . Cells from the eleven breast carcinoma lines were incubated with 75 nM or 0.75 µM 5-Aza-CdR for 3 days, and their proliferation was measured. Data are shown as the percentage of control, untreated cultures. In general, 5-Aza-CdR exerted only minor antiproliferative effects on day 3 of culture, and its effects did not correlate with elevation of Nm23 expression. For 10 of 11 cell lines, little effect was observed on proliferation at 75 nM 5-Aza-CdR, and the log higher dose resulted in less than a 25% decrease in cell growth. The exception to this trend was the MDA-MB-468 cell line, which was inhibited by 5-Aza-CdR in a dose-dependent manner.



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Fig. 7. 5-Aza-CdR exerts minimal effects on human breast carcinoma cell line proliferation in vitro. Each cell line was cultured in 75 nM (black bars) or 0.75 µM (white bars) 5-Aza-CdR for 3 days. Cell viability was estimated using the Non-Radioactive Cell Proliferation Assay kit (Promega). Data are shown as the mean ± SE percentage of control (unstimulated) cell number.

 
The effect of 5-Aza-CdR on cell motility in Boyden chamber assays to the combination of attractants present in FCS is shown in Fig. 8Citation . Cell lines from the high and moderately increased expression groups delimited in Fig. 3Citation were incubated for 3 days with 0, 75 nM, or 0.75 µM 5-Aza-CdR and were harvested and assayed for motility to three different concentrations of FCS. MCF7 cells from the no-induction group in Fig. 3Citation were virtually nonmotile (data not shown) and excluded from further analysis. Untreated MDA-MB-231 breast carcinoma cells exhibited a dose-dependent increase in directed motility toward FCS. Preincubation with 75 nM 5-Aza-CdR resulted in a 3-fold decrease in motility, which was further reduced by 0.75 µM preincubation. MDA-MB-435 breast carcinoma cells exhibited a similar trend, albeit at lower overall levels of motility. Thus, in an in vitro assay representative of one aspect of the tumor metastatic process, induction of Nm23 protein expression by 5-Aza-CdR correlated with reduced biological function.



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Fig. 8. 5-Aza-CdR pretreatment of human breast carcinoma cells inhibits stimulated motility in vitro. Cells from the high-responder line MDA-MB-231 (A) and medium-responder line MDA-MB-435 (B), as listed in Fig. 3Citation , were incubated in 0, 0.075, or 0.75 µM 5-Aza-CdR for 3 days. Cells were then harvested and used in Boyden chamber motility assays, with 0.01, 0.05, and 0.1% of FCS as a chemoattractant. The mean ± SE cells migrating to the FCS in triplicate chambers was counted under x20 magnification.

 
DNA Sequencing of CpG Islands in the nm23-H1 Promoter.
The two CpG islands in the nm23-H1 promoter were examined in human breast carcinoma cell lines for DNA methylation patterns by bisulfite sequencing. Briefly, DNA extracted from each cell line was bisulfite treated, amplified by PCR, and cloned; 10 clones per line were sequenced. The percentage of clones exhibiting methylation at CpGs in the island, as evidenced by lack of conversion of a cytosine to uracil, was determined. For CpG island B (-1672 bp to -2343 bp), no CpG methylation was apparent at 53 CpGs in the MDA-MB-231, MDA-MB-435, or MCF7 breast carcinoma cell lines, nor in two infiltrating ductal carcinomas (data not shown). For CpG island A (-3090 bp to -3922 bp), 19 CpGs were analyzed by bisulfite sequencing (Table 2)Citation . The low-Nm23-H1-expressing MDA-MB-231 cell line was highly methylated (all CpGs, 80–100% methylated) throughout this island. Treatment of MDA-MB-231 cells with 0.75 µM 5-Aza-CdR uniformly reduced methylation levels to 40–50% coincident with re-expression of Nm23-H1. Thus, 5-Aza-CdR elevation of Nm23-H1 expression in MDA-MB-231 cells is associated with demethylation of a specific CpG island.


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Table 2 DNA methylation status of 19 CpG dinucleotides (-3364 to -3634) in the nm23-H1 promoter

 
We asked whether relative Nm23-H1 expression levels among several breast carcinoma cell lines were correlated with specific changes in the DNA methylation status of CpG island A (-3090 bp to -3922 bp). The low-Nm23-H1-expressing MDA-MB-435 cell line was highly methylated (80–100% methylation of all CpGs) throughout the island in a manner similar to that in MDA-MB-231 cells. High-Nm23-H1-expressing MCF7 and ZR-75–1 breast carcinoma cells exhibited only minor and focal reductions in DNA methylation. The same question was asked of 20 infiltrating ductal breast carcinomas. The Nm23-H1 content of the tumors was determined on Western blots normalized by total protein loaded, and divided into high-, medium-, and low-expression groups. CpG island A was highly methylated in all of the tumors examined except in one medium-Nm23-expressing tumor (T-15). Tumor 15 exhibited low but positive estrogen receptor expression (8 fmol/mg protein) and was progesterone receptor negative, aneuploid (DNA index 2.08), and high in S-phase (11.5%). Minor and focal differential methylation was occasionally observed at other sites.


    DISCUSSION
 Top
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 
The use of DNA methylation inhibitors to increase gene expression is an attractive model system for the study of several cancer-related genes. In breast cancer cell lines or tumor specimens, altered expression of a host of genes has been associated with aberrant DNA methylation, including BRCA1 (31 , 32) , RAR-ß (33) , 14-3-3 (34) , Wilms’ tumor 1 (35) , p16 (36 , 37) , uPA (38) , estrogen receptor (39) , E-cadherin (40) , maspin (41) , and others. Whereas the potential re-expression of genes thought to be inhibitory to tumorigenesis and metastasis is of interest, the clinical utility of DNA methylation inhibitors will require that these genes actually alter cellular phenotypes, such as growth, metastasis, apoptosis, and so forth. We report herein that nanomolar concentrations of 5-Aza-CdR elevated expression of the Nm23-H1 metastasis suppressor gene in vitro in 5 of 11 human breast carcinoma cell lines tested, including the 3 in vivo metastatically competent breast carcinoma cell lines available. When the growth phenotype was investigated, minimal inhibition of anchorage-dependent proliferation was observed in response to 5-Aza-CdR. In contrast, 5-Aza-CdR treatment of breast cells significantly reduced their in vitro motility in Boyden chamber assays, an in vitro assay for one part of the tumor metastatic process. These data suggest that DNA methylation inhibitors may impact the breast cancer metastatic process in vivo, for which experiments are under way in animal models in our laboratory.

Several aspects of the in vitro data are noteworthy. Among the five responding breast carcinoma cell lines, a 1.5- to 5-fold increase in Nm23-H1 was observed on incubation with 75 nM 5-Aza-CdR, (and 2- to 9-fold increased Nm23-H1 at 0.75 µM 5-Aza-CdR). For the MDA-MB-231 cell line, induction of Nm23-H1 expression was observed at >=1 nM 5-Aza-CdR. Thus, the elevation of Nm23-H1 appears sensitive to low concentrations of 5-Aza-CdR in vitro. Other breast-related genes have been tested only at higher concentrations of DNA methylation inhibitors, 0.5–0.75 µM for 14-3-3, Wilms’ tumor 1, and estrogen receptor (34 , 35 , 39) , and >1 µM for maspin and RAR-ß (33 , 41) . Elevation of Nm23-H2 expression at comparable levels was also observed. We have not yet examined the nm23-H2 promoter for CpG islands. The high level of Nm23-H1 expression in MDA-MB-231 cells induced by 5-Aza-CdR was maintained for 2 days of culture without agent, and was still 2.5-fold induced over controls at 4 days without agent.

Estimates of the abundance of CpG islands within the human genome vary from ~60% of all genes (42) to 45,000 (43) . In a study of 1,184 unselected CpG islands in 98 tumors of various origins, an average of 600 CpG islands (range, 0–4,500) were estimated to be aberrantly methylated. Both heterogeneous and tissue-specific patterns of methylation were found (43) . These data prompt the question of the relative specificity of DNA methylation inhibitors. To test this question, we performed DNA array analysis of MDA-MB-231 breast carcinoma cells that were treated with and without 5-Aza-CdR. Surprisingly, only a handful of the 4,000 genes analyzed were elevated in expression, including nm23-H1 and two other genes previously reported to be methylation sensitive. All were induced 2- to 3-fold at the mRNA level, the limit of sensitivity for this assay. Further validation of these results are required. It remains likely that other genes are induced by 5-Aza-CdR in this cell line, for instance, E-cadherin over a longer time course. These data, as well as ongoing proteomics evaluations,5 suggest that only a limited number of alterations in gene expression accompany 5-Aza-CdR treatment of a breast cell line in vitro, which indicates that specificity in phenotypic alterations may be observed.

In general, limited data concerning the phenotypic consequences of DNA methylation inhibition is available in the literature. The most compelling experiments are in vivo; these include the inhibition of intestinal neoplasia in the Apcmin mouse by 5-Aza-CdR (44) , the inhibition of tumorigenicity of a adrenocortical tumor in LAF1 mice by antisense to DNA methyltransferase (45) , and the reduction of T24 tumor size in response to 5-Aza-CdR (46) . Our examination of the biological phenotypes induced by 5-Aza-CdR included anchorage-dependent proliferation and motility in vitro. Minimal (<25%) inhibition of proliferation was observed in 10 of 11 breast carcinoma cell lines. None of the 10 lines exhibited a >10% inhibition of proliferation at the lower 75-nM dose. Inhibition of proliferation by 5-Aza-CdR, to the extent that it occurred, was not correlated with the induction of Nm23-H1 expression. These data stand in general agreement with Bovenzi et al., who found that 1–1000 ng/ml (~4 nM–4 µM) 5-Aza-CdR inhibited the growth of MDA-MB-231 cells by <20–69% on day 3 of culture (47) . Other reports have used nonbreast cell lines: a 1.5- to 2-fold extension of bladder and colon carcinoma and melanoma cell line doubling times was reported after 9 days of treatment with 0.5 µM 5-Aza-CdR (46) . An antisense oligonucleotide to DNA methyltransferase (48) also inhibited the growth of T24 cells. The relationship of DNA methylation to proliferation is complex in fields other than cancer, because embryonic stem cells from DNA methyltransferase knockout mice proliferated normally (49) , but the knockout mice exhibited histological evidence of reduced proliferation (50) .

In contrast to the proliferation data, both high-responder MDA-MB-231 and moderate-responder MDA-MB-435 cells exhibited reduced motility in vitro to multiple doses of attractant after preincubation with 5-Aza-CdR. Motility was suppressed several-fold by 75 nM 5-Aza-CdR, confirming the sensitivity observed at the Nm23-H1 protein expression level. Nonresponder MCF7 breast carcinoma cells were nonmotile and remained nonmotile after 5-Aza-CdR treatment (data not shown). Although the Western blot and array data suggest that increased Nm23-H1 expression is participatory in this phenotype, other molecular events may also contribute. Although limited by the number of breast carcinoma cell lines that exhibit motile behavior in vitro, the data to date suggest a degree of uniformity in the phenotypic consequences of DNA methylation inhibition, and that the metastatic process may be a sensitive target.

Our data showed that 5-Aza-CdR inhibited the methylation of one of the two CpG islands in the MDA-MB-231 nm23-H1 promoter coincident with increased protein expression. No synergy with TSA was observed in cell lines, which suggests that the global remodeling of the nm23-H1 promoter associated with histone organization is not operative. However, it is apparent that aberrant methylation of this CpG island is not a mechanism used frequently to maintain high Nm23-H1 expression, in either cell lines or tumors. Only 1 of 12 moderate-to-high-expression tumors exhibited uniform low methylation within this CpG island. Several possible explanations may underlie these data: (a) high Nm23-H1 expression may occur independently of DNA methylation through regulation by transcription factors that act independently of CpG island methylation; (b) elevation of Nm23-H1 may occur in a DNA-methylation-sensitive manner in nature, but indirectly. A fascinating possibility was recently suggested by the report that in hepatocellular carcinoma cells, retinoic acid (ATRA) induced Nm23-H1 expression and reduced motility in vitro (51) , similar to the effects noted herein. ATRA functions through binding to a RAR, which is known to be induced by DNA methylation in breast cancer (33) . Further investigation of the RAR response elements of the nm23-H1 promoter is warranted to determine whether they contribute to the 5-Aza-CdR effect; (c) aberrant DNA methylation may be masked by the use of whole, ground tumors. Because these tumor samples also include normal epithelial cells, stroma components and fat cells, microdissection of the relevant high- and low-Nm23-expressing epithelial cells may be further foretelling; and (d) DNA methylation of other specific transcription factor binding sites, and not entire CpG islands, may be contributory. CpGs 2, 9, 11, 14, and 18–19 were partially methylated in high-Nm23-H1-expressing cell lines, and computer analysis predicts many potential transcription factor binding sites. Moreover, aberrant focal methylation has been reported to occur outside of a CpG island (23) . Given the elevation of Nm23-H1 expression and suppression of the motility phenotype by 5-Aza-CdR, the lack of differential methylation in moderate-to-high Nm23-H1 expressing human cell lines and tumors does not overrule this strategy as a promising therapeutic treatment. Further investigation of the molecular mechanism of the phenotypic effects of 5-Aza-CdR, as well as in vivo studies are under way.


    FOOTNOTES
 
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.

1 M. T. H. and S. E. C. contributed equally to this work. Back

2 To whom requests for reprints should be addressed, at National Cancer Institute, NIH, Building 10, Room 2A33, Bethesda, MD 20892. Fax: (301) 402-8910; E-mail: hartso{at}box-h.nih.gov Back

3 Present address: Department of Surgery, Northwestern University School of Medicine, 300 East Superior Street, Chicago, IL 60611-3095. Back

4 The abbreviations used are: 5-Aza-CdR, 5-aza-2'-deoxycytidine; ATRA, all-trans-retinoic acid; RAR, retinoic acid receptor; TSA, trichostatin A; PVDF, polyvinylidene difluoride; ECL, enhanced chemiluminescence. Back

5 J. D. Wulfkuhle and P. S. Steeg, unpublished data. Back

Received 12/ 1/00. Accepted 1/17/01.


    REFERENCES
 Top
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 

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D. Palmieri, D. O. Halverson, T. Ouatas, C. E. Horak, M. Salerno, J. Johnson, W. D. Figg, M. Hollingshead, S. Hursting, D. Berrigan, et al.
Medroxyprogesterone Acetate Elevation of Nm23-H1 Metastasis Suppressor Expression in Hormone Receptor-Negative Breast Cancer
J Natl Cancer Inst, May 4, 2005; 97(9): 632 - 642.
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Clin. Cancer Res.Home page
A. Irie, A. Yamauchi, K. Kontani, M. Kihara, D. Liu, Y. Shirato, M. Seki, N. Nishi, T. Nakamura, H. Yokomise, et al.
Galectin-9 as a Prognostic Factor with Antimetastatic Potential in Breast Cancer
Clin. Cancer Res., April 15, 2005; 11(8): 2962 - 2968.
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Clin. Cancer Res.Home page
M. Zollo, A. Andre, A. Cossu, M. C. Sini, A. D'Angelo, N. Marino, M. Budroni, F. Tanda, G. Arrigoni, and G. Palmieri
Overexpression of h-prune in Breast Cancer is Correlated with Advanced Disease Status
Clin. Cancer Res., January 1, 2005; 11(1): 199 - 205.
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Endocr Relat CancerHome page
M Lacroix, R-A Toillon, and G Leclercq
Stable 'portrait' of breast tumors during progression: data from biology, pathology and genetics
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W. J. Meehan, R. S. Samant, J. E. Hopper, M. J. Carrozza, L. A. Shevde, J. L. Workman, K. A. Eckert, M. F. Verderame, and D. R. Welch
Breast Cancer Metastasis Suppressor 1 (BRMS1) Forms Complexes with Retinoblastoma-binding Protein 1 (RBP1) and the mSin3 Histone Deacetylase Complex and Represses Transcription
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Clin. Cancer Res.Home page
T. Ouatas, D. Halverson, and P. S. Steeg
Dexamethasone and Medroxyprogesterone Acetate Elevate Nm23-H1 Metastasis Suppressor Gene Expression in Metastatic Human Breast Carcinoma Cells: New Uses for Old Compounds
Clin. Cancer Res., September 1, 2003; 9(10): 3763 - 3772.
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