6
[CANCER RESEARCH 47, 75-79, January 1, 1987] DNA Methylation Affecting the Transforming Activity of the Human Ha-ras Oncogene1 Maria Grazia Borrello, Marco A. Pierotti,2 Italia Bongarzone, Rosangela Donghi, Pierà Mondellini, and Giuseppe Della Porta Division of Experimental Oncology A, Istituto Nazionale Tumori, Via G. Venezian 1, 20133 Milan, Italy ABSTRACT A plasmid containing the transforming Ha-ros gene and designated pT24-C3 was methylated in vitro using the sequence-specific bacterial methyltransferases Hpa\l and Hha\. Aliquots of the plasmid were meth ylated by the single enzymes or by the two enzymes simultaneously (double methylation). The transforming activity of the treated plasmids was assayed in the standard transfection assay on NIH-3T3 cells. Double methylation reduced the transforming activity of pT24-C3 about 80%, whereas treatment with the single methylating enzymes did not signifi cantly affect the oncogene activity. Southern blot analysis of the trans formants obtained with the methylated or mock-methylated pT24-C3 plasmids indicated in all the examined DNAs the presence of human Ha- ras sequences with methylation degrees consistent with the treatment of the plasmids. The M, 21,000 oncogene protein p21 was also detected in several examined transformants. The DNA-demethylating agent 5-aza- cytidine restored the transforming activity of the double-methylated pT24-C3 upon 24 h incubation of transfected NIH-3T3 cells. Southern blot analysis showed integration of human I l:i-ra.v with a methylation profile intermediate between the double-methylated and mock-methyl ated plasmids. It is suggested that DNA methylation of specific ( G- containing target sites can affect the transforming activity of a human oncogene. INTRODUCTION Accumulated evidence has implicated DNA methylation of cytosine at critical CpG sites as a regulatory signal for the expression of some eukaryotic genes (1). Two basic observations led to the hypothesis that high levels of DNA methylation are associated with the absence of gene expression: (a) several experiments indicated that DNA methylation directly inhibits the expression of viral and eukaryotic genes (2-5); (b) 5-aza- Cyd,3 an analogue which causes DNA demethylation, was shown to switch on the expression of certain genes (6, 7). However, an univocal correlation was not detected for other genes, like the chicken vitellogenin gene and the homologous Xenopus genes (8, 9). Therefore, it appears that DNA methyl ation is only one of the multiple mechanisms which control the expression of eukaryotic genes. A link between DNA methyla tion and neoplasia was recently suggested in two reports which showed that ras and myc oncogenes are hypomethylated in tumors compared to the corresponding normal tissues (10, 11). An obvious, but still unproved, implication of these findings is that the reported oncogenes belong to the category of eukaryotic genes which are active only if undermethylated. In this study we have directly examined this possibility by methylating /// vitro the cloned human Ha-ras oncogene and by testing its transforming activity in the standard transfection assay on Received 4/1/86; revised 6/27/86, 9/17/86; accepted 9/19/86. 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. 1This work was supported by grants from the Italian National Research Council, Special Project "Oncology," Contract 84.00735.44, and the Associazione Italiana Ricerca Cancro. 2To whom requests for reprints should be addressed. 3 The abbreviations used are: 5-aza-Cyd, 5-azacytidine; SDS-PAGE, sodium dodecyl sulfate-polyacrylamide gel electrophoresis; p21, M, 21,000 protein. NIH-3T3 cell line. Our results show that the methylation of the human Ha-ras oncogene significantly affects its transform ing activity. Moreover, the methylation-induced inactivation of the oncogene was reversed by treating the transfected cells with 5-aza-Cyd. MATERIALS AND METHODS Cloned Human Ila-ras Genes. The plasmids containing the cloned Ha-ros gene were kindly provided by Dr. M. Barbacid (NCI-Frederick Cancer Research Facility, Frederick, MD). The plasmid designated pT24-C3 contains the transforming form of the human Ha-ros onco gene mutated by a G —» T transversion at the 12th codon (12). The plasmid pbc-Nl carries the Ha-ros normal alÃ-ele isolated from a library of human fetal liver DNA (12). Methylation Reaction. Bacterial DNA methyltransferases Hpa\\ and Hhal were purchased from Biolabs (Beverly, MA). Plasmid DNA was treated with a 10- to 20-fold excess of enzyme for 16 h in 50 mM Tris- HC1 (pH 7.5)-10 mM EDTA-80 MMS-adenosylmethionine-5 mM 0- mercaptoethanol. Mock-methylated p I 24 was similarly treated without the methyl donor 5-adenosylmethionine or without enzyme. Transfection. DNA transfection procedures were essentially as de scribed elsewhere (12). NIH-3T3 cells were used as recipients. In each transfection, 40 Mg of carrier DNA (high molecular weight mouse thymus DNA) were added to different doses of plasmid DNA (pT24- C3), precipitated with CaCl2 and phosphate buffer, and applied to each of at least three 100-mm plates containing 3-4 x IO5 NIH-3T3 cells. The appearance of foci was scored 15 days later and then followed for 2 weeks. 5-aza-Cyd Treatment. NIH-3T3 cell plates were treated for 24 h with 3 or 30 tiM 5-aza-Cyd 24 h after the addition of DNA and then washed with growth medium. Southern Blot Analysis. DNA was extracted and purified from un treated or transformed NIH-3T3 cells following the standard proce dures. Restriction enzymes were purchased from Biolabs, Boehringer (Mannheim, West Germany), and Amersham (Amersham, Bucking hamshire, England). DNA samples were digested using a 3-fold excess of BamHl or £coRIenzymes and a 6-fold excess of I/pall or Hhal and monitored for complete digestion by mixing an aliquot of the digest containing 1 tig of DNA with 0.6 ^g of an appropriate marker DNA for parallel digestion; a complete digestion pattern of the marker DNA was taken as evidence of complete digestion of the DNA sample. Digested DNA samples were fractionated in agarose gel, electropho- resed at 40 V for 16-20 h in horizontal 1.4-1.6% agarose gels, blotted to Gene Screen Plus sheets (New England Nuclear, Boston, MA) and hybridized for 16 h, as described by Southern (13), with 0.3-0.5 x 10* cpm of the nick-translated "P-labeled BamHl insert of the pbc-Nl plasmid (which represents the human Ha-ros gene). After being dried, filters were exposed at -70°C with Trimax 3M XR films with intensi fying screens for varying periods of time. p21 Immunoprecipitation and SDS-PAGE Analysis. The procedures were as previously described by Furth et al. (14) who kindly provided the anti-p21 monoclonal antibody Y13-259. As control, the rat mono clonal antibody 74/8' specific for the Ly-5 differentiation antigens (15) was used. RESULTS The plasmid pT24-C3 contains a BamHl 6.5-kilobase insert of the activated human Ha-ras oncogene which includes, up- 75 Research. on November 11, 2018. © 1987 American Association for Cancer cancerres.aacrjournals.org Downloaded from

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[CANCER RESEARCH 47, 75-79, January 1, 1987]

DNA Methylation Affecting the Transforming Activity of the Human Ha-rasOncogene1

Maria Grazia Borrello, Marco A. Pierotti,2 Italia Bongarzone, Rosangela Donghi, PieràMondellini, and

Giuseppe Della PortaDivision of Experimental Oncology A, Istituto Nazionale Tumori, Via G. Venezian 1, 20133 Milan, Italy

ABSTRACT

A plasmid containing the transforming Ha-ros gene and designatedpT24-C3 was methylated in vitro using the sequence-specific bacterialmethyltransferases Hpa\l and Hha\. Aliquots of the plasmid were methylated by the single enzymes or by the two enzymes simultaneously(double methylation). The transforming activity of the treated plasmidswas assayed in the standard transfection assay on NIH-3T3 cells. Doublemethylation reduced the transforming activity of pT24-C3 about 80%,whereas treatment with the single methylating enzymes did not significantly affect the oncogene activity. Southern blot analysis of the transformants obtained with the methylated or mock-methylated pT24-C3plasmids indicated in all the examined DNAs the presence of human Ha-ras sequences with methylation degrees consistent with the treatment ofthe plasmids. The M, 21,000 oncogene protein p21 was also detected inseveral examined transformants. The DNA-demethylating agent 5-aza-cytidine restored the transforming activity of the double-methylatedpT24-C3 upon 24 h incubation of transfected NIH-3T3 cells. Southernblot analysis showed integration of human I l:i-ra.v with a methylationprofile intermediate between the double-methylated and mock-methylated plasmids. It is suggested that DNA methylation of specific ( G-containing target sites can affect the transforming activity of a humanoncogene.

INTRODUCTION

Accumulated evidence has implicated DNA methylation ofcytosine at critical CpG sites as a regulatory signal for theexpression of some eukaryotic genes (1). Two basic observationsled to the hypothesis that high levels of DNA methylation areassociated with the absence of gene expression: (a) severalexperiments indicated that DNA methylation directly inhibitsthe expression of viral and eukaryotic genes (2-5); (b) 5-aza-Cyd,3 an analogue which causes DNA demethylation, was

shown to switch on the expression of certain genes (6, 7).However, an univocal correlation was not detected for othergenes, like the chicken vitellogenin gene and the homologousXenopus genes (8, 9). Therefore, it appears that DNA methylation is only one of the multiple mechanisms which control theexpression of eukaryotic genes. A link between DNA methylation and neoplasia was recently suggested in two reports whichshowed that ras and myc oncogenes are hypomethylated intumors compared to the corresponding normal tissues (10, 11).An obvious, but still unproved, implication of these findings isthat the reported oncogenes belong to the category of eukaryoticgenes which are active only if undermethylated. In this studywe have directly examined this possibility by methylating ///vitro the cloned human Ha-ras oncogene and by testing itstransforming activity in the standard transfection assay on

Received 4/1/86; revised 6/27/86, 9/17/86; accepted 9/19/86.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 inaccordance with 18 U.S.C. Section 1734 solely to indicate this fact.

1This work was supported by grants from the Italian National ResearchCouncil, Special Project "Oncology," Contract 84.00735.44, and the Associazione

Italiana Ricerca Cancro.2To whom requests for reprints should be addressed.3The abbreviations used are: 5-aza-Cyd, 5-azacytidine; SDS-PAGE, sodium

dodecyl sulfate-polyacrylamide gel electrophoresis; p21, M, 21,000 protein.

NIH-3T3 cell line. Our results show that the methylation ofthe human Ha-ras oncogene significantly affects its transforming activity. Moreover, the methylation-induced inactivation ofthe oncogene was reversed by treating the transfected cells with5-aza-Cyd.

MATERIALS AND METHODS

Cloned Human Ila-ras Genes. The plasmids containing the clonedHa-ros gene were kindly provided by Dr. M. Barbacid (NCI-Frederick

Cancer Research Facility, Frederick, MD). The plasmid designatedpT24-C3 contains the transforming form of the human Ha-ros oncogene mutated by a G —»T transversion at the 12th codon (12). Theplasmid pbc-Nl carries the Ha-ros normal alíeleisolated from a libraryof human fetal liver DNA (12).

Methylation Reaction. Bacterial DNA methyltransferases Hpa\\ andHhal were purchased from Biolabs (Beverly, MA). Plasmid DNA wastreated with a 10- to 20-fold excess of enzyme for 16 h in 50 mM Tris-HC1 (pH 7.5)-10 mM EDTA-80 MMS-adenosylmethionine-5 mM 0-mercaptoethanol. Mock-methylated p I 24 was similarly treated withoutthe methyl donor 5-adenosylmethionine or without enzyme.

Transfection. DNA transfection procedures were essentially as described elsewhere (12). NIH-3T3 cells were used as recipients. In eachtransfection, 40 Mg of carrier DNA (high molecular weight mousethymus DNA) were added to different doses of plasmid DNA (pT24-C3), precipitated with CaCl2 and phosphate buffer, and applied to eachof at least three 100-mm plates containing 3-4 x IO5 NIH-3T3 cells.

The appearance of foci was scored 15 days later and then followed for2 weeks.

5-aza-Cyd Treatment. NIH-3T3 cell plates were treated for 24 h with3 or 30 tiM 5-aza-Cyd 24 h after the addition of DNA and then washedwith growth medium.

Southern Blot Analysis. DNA was extracted and purified from untreated or transformed NIH-3T3 cells following the standard procedures. Restriction enzymes were purchased from Biolabs, Boehringer(Mannheim, West Germany), and Amersham (Amersham, Buckinghamshire, England). DNA samples were digested using a 3-fold excessof BamHl or £coRIenzymes and a 6-fold excess of I/pall or Hhal andmonitored for complete digestion by mixing an aliquot of the digestcontaining 1 tig of DNA with 0.6 ^g of an appropriate marker DNAfor parallel digestion; a complete digestion pattern of the marker DNAwas taken as evidence of complete digestion of the DNA sample.Digested DNA samples were fractionated in agarose gel, electropho-resed at 40 V for 16-20 h in horizontal 1.4-1.6% agarose gels, blottedto Gene Screen Plus sheets (New England Nuclear, Boston, MA) andhybridized for 16 h, as described by Southern (13), with 0.3-0.5 x 10*cpm of the nick-translated "P-labeled BamHl insert of the pbc-Nlplasmid (which represents the human Ha-ros gene). After being dried,filters were exposed at -70°Cwith Trimax 3M XR films with intensi

fying screens for varying periods of time.p21 Immunoprecipitation and SDS-PAGE Analysis. The procedures

were as previously described by Furth et al. (14) who kindly providedthe anti-p21 monoclonal antibody Y13-259. As control, the rat monoclonal antibody 74/8' specific for the Ly-5 differentiation antigens (15)

was used.

RESULTS

The plasmid pT24-C3 contains a BamHl 6.5-kilobase insertof the activated human Ha-ras oncogene which includes, up-

75

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DNA METHYLATION AND ONCOGENE TRANSFORMING ACTIVITY

stream of the first coding exon, a 1.6-kilobase noncoding regionwith a potential TATA box at position 1334, preceded by a CG-rich region (16, 17). We have numbered a total of 372 CpGdinucleotides in the cloned Ha-ras sequence, about 50% ofwhich are clustered in the first 1330 base pairs. Moreover, asshown in Fig. 1, about 50 and 70% of the total Hpall (CCGG)and H hai (GCGC) restriction sites, respectively, are representedin the 5 ' end region. This portion of the gene has been shown

to be essential for its transforming activity (18). For this reason,we used the prokaryotic methyltransferases specific for Hpalland Hhal target sites.

In Vitro Methylation of pT24-C3. The in vitro methylationof pT24-C3 plasmid was performed in two experiments withconsistent results. In both cases equal aliquots of plasmid weremethylated at Hpall, at Hhal, and at both the restriction sites(hereafter double-methylated) or were mock-methylated. Fig. 2shows the results of Southern blot analysis of the plasmidsobtained in one of the two methylation experiments. Afterlinearization by EcoRl digestion (Fig. 2/1), the methylated ormock-methylated plasmids were found apparently intact and inalmost the same amount. As shown in Fig. 2Ä,when the sameplasmids were treated by BamHl followed by Hpall digestion,the mock-methylated (Lane 1) or the //Aal-methylated (Lane3) plasmids were fully susceptible to Hpall digestion, and thedouble-methylated or //pall-methylated plasmids were foundto be completely protected from Hpall digestion (Lanes 2 and4). Analogous results were obtained when the methyl-sensitive

restriction enzyme Hhal was used after BamHl digestion (Fig.2C). Only a partial digestion of part of the double-methylatedplasmid was detected following Hhal treatment (Lane 2).

Transforming Activity of Methylated pT24-C3 Plasmids. Weperformed four separate transfection experiments in which the

I II II I lili III II Mlfri"|É|VÌ

1I..:.::; v '"..Mia «WO

Fig. 1. Restriction map of the Hpall (above) and Hhal (below) sites in a 6.5-kilobase BamHl fragment of the human Ha-ras oncogene cloned in pBR322(pT24-C3). •.exons; E3,variable tandem repetition region ( VTR). The fragmentsgenerated by Sad treatment are also indicated.

A

234

B234

C

234kb

-10.8-6.4

-1.8

s• — -0.6

«B -0.4• •-0.35

Fig. 2. Blot hybridization analysis of pT24-C3 plasmid, mock-methylated(Lane I), methylated at both Hpall and Hhal sites (Lane 2), at Hhal sites (Lane3), and at Hpall restriction sites (Lane 4). The plasmids (0.5 ng) were digestedwith £coRI(A) or with BamHl followed by Hpall (B) or Hhal (C) restrictionenzymes. All hybridizations were with the nick-translated BamHl fragment ofthe pbc-Nl plasmid containing a normal alíeleof the human Ha-ras gene. Sizemarkers were a mixture of XHindlll and pBR322 Taal fragments, kb, kilobases.

transforming efficiency of the oncogene methylated at bothHpall and Hhal sites was compared with that of the mock-methylated gene. We used different plasmid DNA doses, ranging from 1 to 100 ng, and scored the resulting foci of transformation 15 days after addition of DNA to cultures.

The results reported in Table 1, Experiment A and those ofthe other unreported experiments indicated that the simultaneous methylation at both Hpall and Hhal sites reduced thedose-dependent transforming activity of pT24-C3 about 80%.The methylation at each single restriction site did not significantly modify the transforming efficiency of the oncogene (Table 1, Experiment B).

Moreover, we observed that, besides a significant lower number of foci that persisted until week 4, the double-methylatedoncogene yielded foci with a delay of about 2-3 days comparedwith that of foci obtained with the control oncogene.

Several foci obtained in transfection experiments were analyzed in Southern blot to certify the presence of human Ha-rassequences. In all the foci investigated, i.e.. 6 foci obtained withmock-methylated plasmids and 20 foci derived by the double-methylated plasmid, integrated human Ha-ras sequences weredetected. Fig. 3 reports a Southern blot analysis of high molecular weight DNA prepared from representative NIH-3T3 transformants obtained with differently treated pT24-C3 plasmids.As shown in Fig. 3A we did not detect any signal with themouse DNA prepared from untreated NIH-3T3 cells (LaneNIH) whereas in the transformants the human gene was foundto be integrated in various numbers of copies (see Lanes 3 and6). In the recombination processes accompanying the integration events, some plasmids lost at least one of the originalBamHl sites (see Lanes 2, 4, and 6).

Several of the NIH-3T3 transformants showing the presenceof integrated human Ha-ras sequences were analyzed by SDS-PAGE after immunoprecipitation of their 35S-metabolically

labeled and solubili/ed proteins, for the expression of humanHa-ras p21 molecules. Fig. 4 shows that a molecule of a sizecompatible with the p21 was specifically immunoprecipitatedby the anti-p21 rat monoclonal antibody Y13-259 (Fig. 4, Laneb). The specificity of the reaction was certified by the lack ofreactivity of Y13-259 for untreated NIH-3T3 cells (Fig. 4, Lanea) and of the unrelated rat monoclonal 74/8' for the transform-

ant (Fig. 4, Lane c).

Table 1 Effect of methylation on the transforming activity of the human Ha-rasoncogene (pT24-C3) on mouse NIH-3T3 cells

Mouse NIH-3T3 cells were transfected with in vitro methylated pT24-C3 atHpall, Hhal or at both restriction sites or mock-methylated pT24-C3 and foci oftransformed cells were scored after 15 days. Some foci from the different experimental groups were shown to form tumors in nude mice and were analyzed bySouthern blot for the presence of human Ha-ros-related sequences (see the text).Mock-methylated plasmid DNAs were prepared by the usual in vitro methylationprocedure in the absence of methyltransferase (Experiment A) or of S-adenosyl-methionine, the methyl donor in the reaction (Experiment B).

ExperimentABTreatment ofpT24-C3Mock-methylated

controlMethylated

(Hpall +Hhal)Mock-methylated

controlMethylated(Hpall)Methylated(lilialiMethylated

(Hpall + Hhal)Amount

(ng)151015105555No.of foci/

plate6,7,8°9,

11,1335,36,380,

1,11,2,36,

8, 1110.5

±2.94*8.4

±4.629.8±5.551.6±l.5c

" Number of foci in each of three different plates.* Mean ±SD of different plates (from 6 to 11 plates).' Significantly different (P < 0.01) from the other treatments (Waller-Duncan

test).

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DNA METHYLATION AND ONCOGENE TRANSFORMING ACTIVITY

NIH 1 23 45612345

ababab ab ab

23.7-9.5-6.7-

2.3-2.0-

kb-8.4_6.4-4.8-3.6

-2.3

Fig. 3. Detection of human Ha-raj sequences in transformants obtained byDNA-tnediated gene transfer of pT24-C3 plasmids differently treated in vitro inNIH-3T3 cells. In A, high molecular weight DNA from NIH-3T3 normal cellline (Lane NIH), four NIH-3T3 tumor cell lines obtained by double-methylatedpT24-C3 (Lanes I, 2, 3, and 4), or two lines induced by mock-methylated pT24-C3 (Lanes 5 and 6) was digested by BamH\ and analyzed by Southern blothybridization with the Ha-ros probe described in the legend of Fig. 2. In B, highmolecular weight DNA from the NIH-3T3 tumor cell lines described in A wasrestricted with Bamttl followed by //pall (Lanes a) or Hhal (Lanes b) digestionand analyzed as described in A. \ Hindl\\ and X BslEll fragments were used assize markers. Kb, kilobases.

b ckd

-69-46

-30

— - -18

Fig. 4. SDS-PAGE analysis of "S-metabolically labeled NIH-3T3 untreated(Lane a) or transformed by mock-methylated Ha-rai oncogene (pT24-C3) andimmunoprecipitated with an anti-p21 (Y13-259) (Lane b) or anti-Ly-5 (74/8')

rat monoclonal antibody (Lane c). Kd, molecular weight in thousands.

Next, we examined the methylation status of the transform-ants at both Hpall and Hhal CG target sites, to verify whetherthe transforming activity of pT24-C3 was correlated with aparticular methylation degree of the oncogene. Southern blotanalysis of the same DNAs shown in Fig. 3/4 (except transformant 6), which after BamHl were digested with Hpall (Lanesa) or Hhal (Lanes b), is reported in Fig. 3A. The transformantsobtained with the double-methylated oncogene were susceptible, to a different degree, to the digestion with Hpall and Hhalrestriction enzymes. In some cases, the two protected sitesappeared equally susceptible (Lanes 3 and •/):in other instances,one of the two Hpall or Hhal sites resulted less methylated(Lanes I and 2; compare a versus b). The lowest methylationdegree detectable in the transformants was seen in the DNAfrom an NIH tumor cell line induced by the mock-methylatedoncogene (Lane 5).

In a different experiment, the same transformants were analyzed using as a probe the 0.8-kilobase SacI fragment, comprising the promoter region, or the 2.9-kilobase SacI fragment,representative of Ha-ros coding sequences (see Fig. 1). In allthe transformants the promoter region was fully demethylatedwhereas the coding region was methylated at varying degree

depending also from the pT24-C3 (methylated or wild-type)used for the induction of the particular transformant (data notshown).

Effect of 5-Aza-Cyd Treatment of Transfected NIH-3T3 Cells.To verify whether the abrogation of the transforming activitycould be reversed, cells were incubated in two repeated experiments for 24 h with 0, 3, and 30 pM 5-aza-Cyd, 24 h aftertransfection with double-methylated or mock-methylated pT24-

C3. The results are reported in Fig. 5. The control plates, i.e.,not treated with 5-aza-Cyd, yielded an average of 1.5 and 10.5foci after transfection with methylated and mock-methylatedplasmids, respectively. The lower dose of 5-aza-Cyd did notaffect the final number of foci (2 versus 8). It produced however,early focal morphological alterations. Some of the 5-aza-Cyd-induced foci, that morphologically were readily distinguishablefrom genuine Ha-ras-induced foci, grew in nude mice, but didnot contain human Ha-ras sequences (data not shown). The 30ßMdose resulted in a significant cytotoxicity for both trans-fected and control cultures. However, after the reconstitutionof the cellular monolayer, no significant morphological perturbations were observed and a similar average number of focideveloped in cultures treated with mock-methylated (4.5 foci)and methylated (5 foci) oncogene. The 30 ^M 5-aza-Cyd-in-duced cytotoxicity (about 50%), estimated by counting thenumber of viable cells in plates treated or not treated with thecompound, was in good agreement with the number of fociobtained with the mock-methylated oncogene in plates with orwithout the addition of 30 /¿M5-aza-Cyd (on average 4.5 versus10.5 foci).

Six of the foci obtained from 5-aza-Cyd-treated culturespreviously transfected with the double-methylated oncogenewere analyzed by Southern blot and all showed the presence ofintegrated human Ha-ras sequences (data not shown). Fig. 6shows a comparative analysis of the restriction patterns of DNAfrom transformants each representative of the groups obtainedwith mock-methylated or methylated pT24-C3 plasmid, followed or not by 5-aza-Cyd treatment. The methylation degreeof Ha-ras sequences integrated in the foci obtained by trans-fecting the cultures with the double-methylated plasmid followed by the demethylating analogue (Fig. 6, Lanes 2) fit inbetween those displayed by the oncogene sequences derivedfrom transformants induced by double-methylated (Lanes 1) ormock-methylated (Lanes 3) pT24-C3. The peculiar restrictionpatterns of the six foci rescued by 5-aza-Cyd treatment can betaken as a molecular proof of the action of the compound andlead us to conclude that the methylation-induced silencing ofthe human Ha-rai oncogene can be abrogated by a demethylating treatment.

u, 15

* 10(JOLL.

fe 5

0 3 30pH 5'-AZACYTlDINE

Fig. 5. Effect of 5'-aza-Cyd treatment on the transforming activity of thehuman Ha-roj oncogene in mouse NIH-3T3 cells. 5-Azacytidine (3 or 30 JIM)was added to the cultures transfected 24 h before with 5 ng of double-methylated(•)or mock-methylated (D) pT24-C3. After 24 h, the compound was removed bywashing the cultures with the standard transfection medium. Foci of transformedcells were detected and scored after IS days. Data represent the mean number offoci scored in six plates from two different experiments. Bars, SD.

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DNA METHYLATION AND ONCOGENE TRANSFORMING ACTIVITY

kb8.5-

5.7-

3.7-

2.3-1.9-

1.4-1.3-

0.7-

1 2 3

B1 2 3

Fig. 6. Blot hybridization analysis of the restriction pattern for the methyla-tion-sensitive restriction enzymes Hpall (A) and Hhal (B) of the human Ha-rasBamHl fragments sequences integrated in the DNA of NIH-3T3 tumor cell linesobtained by transfection with double-methylated (Lane I), double-methylatedand 5-aza-Cyd-treated (Lane 2), and mock-methylated (Lane 3) pT24-C3. Allhybridizations were with the nick-translated probe described in Fig. 2. Sizemarkers were ABstEH and pBR322 Taq\ fragments, kb, kilobases.

DISCUSSION

Methylation of cytosine at critical CG sites provides one ofthe regulatory mechanisms for the expression of eukaryoticgenes, and some reports have indicated, without direct proof,that DNA methylation could be associated with the activity ofsome human oncogenes (10, 11). We explored this possibilitydirectly by using a biologically active human Ha-ras oncogene(pT24-C3) that was originally derived from a human bladdercarcinoma cell line (12).

The 5' end of the gene comprises a CG-rich region (17) which

has been found to be essential for its transforming activity (18)and that accounts for about 50 and 70% of the total Hpall andHhal sites, respectively. Therefore, the cloned human Ha-ras

gene is an attractive model to assay directly the effect of DNAmethylation on the expression of an oncogene by using, asmethylating agent, prokaryotic methyltransferases specific forthe Hpall and Hhal restriction sites. In our study we assayedthe oncogene expression at the level of the induced phenotypeby scoring the number of transformation foci obtained in astandard transfection assay.

The specificity of our results was certified by Southern blotanalysis which showed the presence of integrated human Ha-ras sequences, with particular and specific methylation patterns,in all the foci we have collected and analyzed in the differenttransfection experiments. Moreover, the SDS-PAGE analysisof immunoprecipitates from transformants with integrated Haras gene showed that p21 was appropriately expressed.

Our results showed that methylation at both Hpall and Hhalsites affects the transforming efficiency of the human oncogeneHa-ros. A simultaneous double methylation of the gene resultedin the abrogation of about 80% of its transforming potential.No significant effect was observed when the methyltransferaseswere used individually. Therefore, it is possible that the criticalCG sites for the oncogene expression are contained at bothHpall and Hhal restriction sites mapping, most likely, at the5' end of the gene. The degree of methylation-induced inhibi

tion of the oncogene transforming activity did not reach the

level of magnitude registered in other experimental systems,especially when cloned viral genes and eukaryotic-derived methyltransferases were used (2). It was, however, comparable withthe degree of inhibition observed in eukaryotic systems whichmade use of prokaryotic methylating enzymes (4). The lowefficiency can be attributed to the specificity of the methylationtargets that include only the CG dinucleotides of the sequencesCCGG and GCGC. Moreover, because methylation-sensitiverestriction enzymes do not cut hemimethylated sites, we cannotexclude the occurrence of hemimethylated DNA strands. Alternatively, the methylation pattern fixed on the cloned gene bythe prokaryotic enzymes could be copied with a low fidelity inmouse cells, eventually resulting in an activating demethylation(19, 20). In agreement with these possibilities, we observed adelay in the appearance of foci in the cultures transfected withthe double-methylated oncogene. A delay of growth is compatible with requirement of a certain number of cell divisions inorder to obtain an appropriately demethylated and thus activeoncogene. However, we never found a transformed cell line thegenome of which contained integrated human Ha-ras oncogenedisplaying a methylated 5' promoter region.

The effect of DNA methylation on the oncogene transforming activity was confirmed by the experiments which used 5-aza-Cyd to reactivate the gene. The consistency of the resultsobtained in the transfection experiments received a molecularsupport by the Southern blot analysis of the rescued foci, whichindicated a specific methylation pattern of the oncogene derivedfrom cultures transfected with the double-methylated Ha-rasand then treated with the demethylating agent. We are currentlypreparing, by cotransfection with a selectable marker, NIH-3T3 cell lines containing a fully methylated oncogene to explorethis phenomenon further.

All together, our results indicate that the transforming activity of the human Ha-ras oncogene can be abrogated by DNAmethylation. The fact that an epigenetic and reversible mechanism, like DNA methylation, can silence a genetically activatedhuman oncogene could lead to a modified transfection approachfor revealing activated oncogenes in human tumor DNA.

ACKNOWLEDGMENTS

We thank Dr. Catia Traversari for the p21 analysis, Maria TeresaRadice and Mario Azzini for excellent technical assistance, and Giovanna Raineri for typing the manuscript.

REFERENCES

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DNA METHYLATION AND ONCOGENE TRANSFORMING ACTIVITY

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1987;47:75-79. Cancer Res   Maria Grazia Borrello, Marco A. Pierotti, Italia Bongarzone, et al.  

OncogenerasHuman Ha-DNA Methylation Affecting the Transforming Activity of the

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