methylation of p16 cpg islands associated with malignant … · 90% of low-grade dys lesions do not...

Methylation of p16 CpG Islands Associated with MalignantTransformation of Gastric Dysplasia in aPopulation-Based Study

Yu Sun, Dajun Deng, Wei-Cheng You, Hua Bai,Lian Zhang, Jing Zhou, Lin Shen, Jun-Ling Ma,Yu-Quan Xie, and Ji-You LiPeking University School of Oncology and Beijing Institute forCancer Research, Beijing, People’s Republic of China

ABSTRACTPurpose: Inactivation of p16 by aberrant methylation of

CpG islands is a frequent event in carcinomas and precan-cerous lesions of various organs, including the stomach. Theaim of this study is to investigate the relationship betweenp16 methylation and malignant transformation of humangastric dysplasia (DYS) based on follow-up endoscopicscreening in a high-risk population.

Experimental Design: Genomic DNA samples were ex-tracted from paraffin blocks of gastric mucosal biopsies thatwere histopathologically diagnosed as low-grade DYS frompatients who developed gastric carcinomas [GCs (n � 21)]and those that did not do so (n � 21) during 5 years offollow-up. The methylation status of p16 CpG islands of eachsample was detected by methylation-specific PCR, dena-tured high-performance liquid chromatography, and se-quencing.

Results: Aberrant p16 methylation was observed in 5 of21 samples of DYS that progressed to GC but in 0 of 21samples that did not progress to GC (P � 0.048, two-sided).Sequencing results confirmed that all CpG sites were meth-ylated in the analyzed sequence from these five p16-methy-lated cases. Furthermore, p16 methylation was also observedin the five subsequent GCs. Unmethylated p16 CpG islandswere detected in all of the samples without p16 methylation.

Conclusions: Our findings suggest p16 methylation iscorrelated with the malignant transformation of gastric

DYS, and p16 methylation might be a useful biomarker forprediction of malignant potential of gastric DYS.

INTRODUCTIONGastric carcinoma (GC) is the second leading cancer death

in China and in the world. Gastric dysplasia (DYS) [noninvasiveneoplasia, the Padova International Classification] is a prema-lignant lesion of intestinal-type GC. It was reported that about90% of low-grade DYS lesions do not progress to malignancyduring long-term follow-up (1, 2).

Current diagnosis of DYS is based primarily on morpho-logical criteria (3). It is virtually impossible to identify themalignant potential of low-grade DYS lesions on histopatholog-ical grounds alone. Thus, predicting the malignant potential ofthis lesion is eagerly awaited.

P16INK4A (CDKN2/MTS1), an inhibitor of the cyclin D-dependent protein kinase 4/6, is a cell cycle regulator involvedin the inhibition of G1 phase progression (4). Loss of function ofp16 results in higher cyclin D-dependent protein kinase activityand thus leads to aberrant phosphorylation of retinoblastoma,which accelerates cell growth. Inactivation of p16 by homozy-gous deletion or point mutation is one of the most commonlyobserved aberrations in tumors, indicating that p16 is a tumorsuppressor gene (5). An alternative mechanism for inactivationof p16 is aberrant methylation of CpG island extending from thepromoter region to exon 1, which silences transcription of thisgene (6). Aberrant p16 methylation was reported to occur fre-quently in a variety of human cancers (6–8). In GC, the fre-quency of p16 inactivation by homozygous deletions rangedfrom 0% to 9%, the frequency of p16 inactivation by mutationranged from 0% to 2%, and the frequency of p16 inactivation bymethylation ranged from 32% to 42% (9–15), which suggeststhat methylation is a major mechanism for p16 inactivationin GC.

Aberrant p16 methylation was also observed frequently inpremalignant stages of GC (16). We previously reported apositive association between aberrant p16 methylation and theseverity of glandular stomach pathology of Wistar rats withcancer induced by chemical carcinogen (17). In the presentstudy, aberrant p16 methylation in relation to malignant pro-gression of DYS was investigated through a nested case-controlstudy in a population with a high risk of GC.

MATERIALS AND METHODSSpecimens. In 1989, 1994, and 1999, the Beijing Insti-

tute for Cancer Research conducted three surveys of precancer-ous gastric lesions in Linqu County, a rural area in whichresidents had a high risk of GC, in Shandong Province, China (1,18–20). The Institutional Review Boards of the Beijing Institutefor Cancer Research approved these surveys, and all participants

Received 11/21/03; revised 3/5/04; accepted 3/8/04.Grant support: Key Technologies Research & Development Program2002BA711A06 and National Basic Research Priorities Program 973Project 1998051203 from the Ministry of Science and Technology ofChina, a grant from Peking University School of Oncology and BeijingInstitute for Cancer Research, Grant 3171045 from the National NaturalScience Foundation of China, and Grant H020920030130 from theBeijing Science and Technology Commission.The costs of publication of this article were defrayed in part by thepayment of page charges. This article must therefore be hereby markedadvertisement in accordance with 18 U.S.C. Section 1734 solely toindicate this fact.Requests for reprints: Ji-You Li or Dajun Deng, Peking UniversitySchool of Oncology, Hai-Dian District, Beijing, 100036, China. Phone:8610-88122450; Fax: 8610-88122437; E-mail: [email protected] [email protected].

5087Vol. 10, 5087–5093, August 1, 2004 Clinical Cancer Research

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gave written informed consent. Briefly, an endoscopic screeningprogram for GC was launched among 3399 residents aged35–64 years in 1989, and a repeat endoscopic screening wasoffered to 83% of eligible follow-up members in 1994 and 94%of eligible follow-up members in 1999 to determine the pro-gression of precancerous gastric lesions at baseline. The endo-scopic biopsy specimens were taken from seven standard sites inthe stomach (four from the antrum, one from the angulus, andtwo from the body of the stomach). The biopsies were fixedimmediately in buffered formalin and then embedded, sec-tioned, and stained with H&E. The microscopic slides werestudied by a panel of three senior pathologists at the Departmentof Pathology, Beijing Institute for Cancer Research. The pres-ence or absence of DYS, carcinoma, and other pathologicalchanges was recorded for each biopsy, and a global diagnosis ofeach case represented the most advanced lesion. The threesurveys used the same endoscopic and histopathological proce-dures, and histopathological diagnoses were made by the samepathologists blinded to the previous evaluations.

Biopsies with low-grade DYS (the global diagnosis) in1989 and 1994 at baseline that either progressed to GC orpersisted in DYS at the corresponding sites during the follow-up(in 1994 and 1999, respectively) were selected for detection ofp16 promoter methylation. All biopsy samples (n � 21) of DYSthat progressed to GC were used if sections were available fromthe paraffin block. An equal number of DYS samples (n � 21)that persisted in DYS were selected from the tissue blockarchive, according to pathological grade, sampling site, age, andsex.

Genomic DNA Extraction and Bisulfite Treatment.All sections from the margin of the gastric tissue biopsiesembedded in paraffin that were not eligible for preparation ofdiagnosis slides were collected into 1.5-ml microcentrifugetubes. After the collected sections were dewaxed by xylene andrehydrated with graded ethanol, they were mixed with lysisbuffer containing proteinase K and digested at 37°C overnight.Genomic DNA (about 10 ng) was extracted with a genomicDNA purification kit (Promega, Madison, WI) and modifiedwith sodium bisulfite to convert the unmethylated cytosines touridines (17, 21).

Amplification of the Methylated p16 CpG Island. Themethylation status of the bisulfite-modified p16 CpG island(GenBank accession No. GI 16944057, antisense strand) wasanalyzed with methylation-specific PCR (MSP) as describedpreviously (22). The primers for the methylated p16 CpG islandwere 5�-TTATTAGAGGGTGGGGCGGATCGC-3� (sense)and 5�-GACCCCGAACCGCGACCGTAA-3� (antisense). Hot-start MSP was used for amplification of the methylated p16CpG islands. Thermal cycles were as follows: denaturation at97°C for 5 min, followed by addition of DNA polymerase;amplification for 35 cycles (95°C for 45 s, 64°C for 45 s, and72°C for 45 s); and extension at 72°C for 10 min. The reactionmixture (20 �l) contained about 10 ng of templates, 10 pmol ofeach primer, 40 nmol of deoxynucleotide triphosphate, 1 unit ofTaq DNA polymerase (Takara, Kyoto, Japan), and 10 �l of 2�GC buffer I (Takara). Distilled water and genomic DNA ofhuman GC (p16 unmethylated by sequencing) or lymphocyteswere used as template for negative control. Genomic DNA ofp16-methylated human GC (p16 methylated by sequencing) or

colon cancer cell line RKO (23) was used as positive control.The control MSP products were run on the gel first. When nofalse positive or false negative methylated p16 MSP productswere observed, the sample MSP products were analyzed fur-ther by denaturing high-performance liquid chromatography(DHPLC). In the pilot study, positive detection of p16 methyl-ation by the above-mentioned MSP protocol correlated nega-tively with P16 expression in surgically obtained GCs by im-munohistochemistry. Methylated p16 was detectable in 80% ofP16-negative tissues and 32% of P16-positive samples (P �0.003). Therefore, this protocol was used in the present nestedcase-control study.

Analysis by DHPLC. DHPLC is used frequently to sizedouble-stranded DNA fragments and detect point mutation andCpG methylation (22, 24–26). In the present study, the MSPproducts (150 bp) of p16 CpG island were detected by DHPLCat 48°C, the nondenaturing temperature suitable for sizing of theamplicons of bisulfite-modified DNA samples (22). In brief,DHPLC was performed with the WAVE DNA Fragment Anal-ysis System (Transgenomic, Inc.). MSP products were intro-duced into the mobile phase at an injection volume of 5 �l bythe autosampler. A DNASep analytical column was used as thesolid phase. The products were eluted from the column with abinary gradient of 0.1 M triethylammonium acetate and 0.1 M

triethylammonium acetate in 25% acetonitrile during mobilephase at a flow rate of 0.9 ml/min at 48°C. Elution gradientswere predicted automatically by WAVEMaker 4.0 software(Transgenomic, Inc) according to the target size (150 bp). Theeluted products were detected by UV analysis at 260 nm.

Confirmation of the Existence of the Modified Tem-plates in MSP. If the methylated p16 CpG island was notobserved by DHPLC, the unmethylated p16 CpG islands werefurther amplified by MSP to exclude the possibility of a falsenegative result of unsuccessful DNA preparation and bisulfitemodification, which would result in the negative detection ofmethylated products by DHPLC. Because of the difficulty inobtaining additional sections from the invaluable biopsy paraf-fin archives, the above p16 methylation-negative MSPs weredirectly used in the confirmation assay.

The primers for unmethylated p16 CpG island and 1 unit offresh DNA polymerase were added to each of the above MSPs,including negative control. The primers for the unmethylatedisland were 5�-TTATTAGAGGGTGGGGTGGATTGT-3�(sense) and 5�-CAACCCCAAACCACAACCATAA-3� [anti-sense (21)]. Touchdown MSP was used. Thermal cycles were asfollows: denaturation at 95°C for 5 min; followed by 30 cyclesof amplification (95°C for 30 s362°C (�0.3°C/cycle) for 30s372°C for 30 s); 10 additional cycles of annealing at 53°C;and a final extension at 72°C for 10 min. The reamplified MSPswere analyzed again by DHPLC as described above.

Sequencing of the MSP Products of Methylated p16CpG Islands. To further confirm the specificity of MSP andthe reliability of DHPLC analysis, the MSPs in which themethylated p16 fragments were observed by DHPLC analysiswere subsequently purified and sequenced as described previ-ously (25).

Statistical Analysis. Comparisons were made with the�2 test, t test, and Fisher’s exact test.

5088 Methylation of p16 and Gastric Dysplasia Progression



RESULTSA total of 42 patients (21 cases progressed to GC, and 21

cases remained with DYS on follow-up) were studied. Informa-tion on the sex, age, lesion site, and DYS grade of each of thecases enrolled in the present study is presented in Table 1 andFig. 1. The period ratio, sex ratio (1989–1994/1994–1999),average age, and lesion site were similar in both groups [P �0.750, 0.214, 0.903, and 1.00, respectively].

A chromatographic peak corresponding to the 150-bp MSPproduct of the methylated p16 CpG island was observed unam-biguously at a retention time of 5.6 min. The p16 methylationpeak was detectable in dysplastic biopsy samples of 5 of 21progressive DYS cases (23.8%; Fig. 2A), whereas none wasfound in any biopsy samples of 21 DYS cases without progres-sion (Fig. 2B; two-sided Fisher’s exact test, P � 0.048). Fur-thermore, the methylated p16 MSP products were observed inall five GCs that originated from the p16-methylated DYSlesions on PAGE gel (Fig. 3) and DHPLC chromatograms (datanot shown).

The MSP products of all five p16-methylated DYS sampleswere further analyzed by sequencing. Sequence information wasobtained from four of five processed p16-methylated samples,Dys3245, Dys3504, Dys0335, and Dys3002 (Fig. 4). Resultsshowed that all cytosines in the CpG sites in the testing se-quence persisted as cytosines and that cytosines not in the CpGsites were converted to thymidines, indicating that all CpG sitesanalyzed were methylated.

To verify the existence of amplifiable templates in MSPsthat did not exhibit methylated p16 products by DHPLC, the

unmethylated p16 CpG islands in the same reaction were am-plified with primer specific for nonmethylation and analyzedagain by DHPLC. The unmethylated p16 products were ob-served in all of the samples examined (Fig. 2, C and D).

DISCUSSIONAberrant methylation of the p16 promoter CpG islands is

the major cause of inactivation of this tumor suppressor gene inGC (13–15) and various other human cancers (6–8). In thepresent study, we observed for the first time that aberrantmethylation of p16 CpG island was correlated with malignanttransformation of DYS. The methylated p16 CpG island wasalso present in all the GCs that progressed from the p16-methylated DYS lesions. Recent dynamic studies on a rat modelfor gastric carcinogenesis and on precursor lesions of human GCsuggested that p16 methylation might be an early event in thedevelopment of GC (16, 17). Taken together, these resultsindicate that inactivation of p16 might play an important role inearly-stage gastric carcinogenesis and thus may provide a spe-cific biomarker for prediction of the malignant potential ofDYS.

Aberrant p16 methylation has also been observed fre-quently in DYS of the cervix, esophagus, lung, and oral mucosa(27–31). It has been reported that aberrant p16 methylationcould not predict the evolution of precancerous bronchial le-sions within a 2-year follow-up (32). The follow-up time mightbe too short to display the effect of aberrant p16 methylation oncarcinogenesis. More studies are needed to evaluate whether

Table 1 Clinicopathological information on two groups of subjects with low-grade gastric dysplasia

Progressive dysplasiaa Persistent dysplasiab

Case no. Periodc Sex Age (yrs)d Site Case no. Period Sex Age (yrs) Site

Dys8201 94–99 M 34 Ae Dys2176 89–94 M 32 BDys2054 94–99 M 44 B Dys2112 89–94 M 38 BDys2184 94–99 M 44 B Dys4232 89–94 M 41 ADys1582 89–94 M 48 B Dys3170 94–99 M 42 ADys0185 94–99 M 50 A Dys5043 94–99 M 44 ADys0124 94–99 M 51 A Dys2542 94–99 M 49 BDys3554 94–99 M 52 B Dys3103 89–94 M 50 ADys0335f 89–94 M 52 B Dys4711 89–94 M 51 ADys2952 89–94 M 54 A Dys3426 89–94 M 51 ADys4415 89–94 M 54 B Dys2695 89–94 M 55 ADys5626 89–94 M 57 A Dys3909 89–94 M 55 ADys3002 94–99 M 57 B Dys4635 89–94 M 59 ADys5411 89–94 M 60 A Dys3585 89–94 M 59 ADys4531 89–94 M 60 A Dys0222 89–94 M 59 BDys2521 89–94 M 61 A Dys4665 89–94 M 60 ADys3504 89–94 M 61 B Dys1011 89–94 M 61 BDys4034 89–94 M 61 B Dys3456 89–94 F 43 ADys2104 89–94 M 63 A Dys3460 94–99 F 51 BDys2003 94–99 M 64 A Dys2120 94–99 F 54 BDys3245 89–94 F 59 A Dys5552 94–99 F 60 BDys2703 89–94 F 59 A Dys5022 94–99 F 61 B

a Twenty-one cases; period ratio (1989–1994/1994–1999), 8:13; sex ratio (M:F), 9:1; average age, 54.5 years; site ratio (body:antrum), 4:6.b Twenty-one cases; period ratio (1989–1994/1994–1999), 7:14; sex ratio (M:F), 8:2; average age, 51.2 years; site ratio (body:antrum), 4:6.c Period: 94–99, 1994–1999; 89–94, 1989–1994.d Age when endoscopic biopsy was taken.e Lesion sites: A, antrum; B, body.f Bold indicates samples with aberrant p16 methylation that progressed to gastric carcinoma.

5089Clinical Cancer Research



Fig. 1 Photo of gastric dysplasia (DYS) lesions and carcinomas, stained with H&E. A�E (Dys4635, Dys4711, Dys1011, Dys2120, and Dys0222),gastric DYS lesions without progression (�200); F�J (Dys3504, Dys3245, Dys2003, Dys2184, and Dys0335), gastric DYS lesions that progressedto gastric carcinoma (�200); K�O, gastric carcinomas that originated from DYS lesions F�J (�100).




p16 methylation could predict malignant transformation of DYSand other precancerous lesions of these organs.

Epigenetic alterations, in addition to multiple genetic ab-normalities, are involved in the development of carcinoma (33).Hypermethylation or imprinting of several genes was used topredict susceptibility to human cancer development. For exam-ple, malignant progression of myelodysplastic syndromes was

associated with methylation of p15INK4B (34, 35). The majorityof microsatellite-unstable sporadic colon cancers were corre-lated with transcription silence of hMLH1 by CpG methylation(36). Disorders of imprinting of H19, SNRPN, Igf2, Igf2r, andothers are involved in syndromes that are frequently accompa-nied by predisposition to childhood tumors (37).

Aberrant p16 methylation silences transcription of this

Fig. 3 Detection of p16 methylation in gastric carcinomas by methylation-specific PCR. Distilled water and genomic DNA of human lymphocytes(unmethylated p16) were used as negative controls. Genomic DNA of human colon cancer cell line RKO (methylated p16) was used as positivecontrol. Gastric carcinomas GC2003, GC3245, GC3504, GC0335, and GC3002 originated from the p16-methylated low-grade dysplasia lesionsDys2003, Dys3245, Dys3504, Dys0335, and Dys3002, respectively. Methylation-specific PCR products were run on a 12% PAGE gel.

Fig. 2 Denaturing high-performance liquid chromatography chromatograms of methylation-specific PCR (MSP) products of p16 promoter CpGislands in gastric dysplasia (DYS) lesions. MSP products were sized directly at 48°C. The peaks corresponding to the 150-bp methylated and 151-bpunmethylated MSP fragments of p16 CpG islands were clearly observed at a retention time of 5.6 min. A and B, p16 MSP products obtained by themethylated p16-specific primers; C and D, MSP products obtained by the unmethylated p16-specific primers; A and C, MSP products fromrepresentative DYS samples that progressed to gastric carcinoma; B and D, MSP products from representative DYS samples that did not progress togastric carcinoma.




tumor suppressor gene and consequently promotes cell prolif-eration through the cyclin D-dependent protein kinase 4-retino-blastoma 1-transcription factor pathway (4, 6). In present study,we observed that aberrant p16 methylation correlated positivelywith the malignant transformation of DYS. However, suchepigenetic alteration of p16 was detectable only in 5 of 21progressive DYS cases. This indicates that aberrant p16 meth-ylation may be one of the molecular pathways of gastric carci-nogenesis. Thus, it is reasonable that aberrant p16 methylationmay account for malignant transformation of a proportion ofDYS cases (24% in present study). Other genetic and epigeneticabnormalities that occur in gastric DYS are currently underinvestigation.

The advantages of using DHPLC (as compared with aga-rose gel and PAGE) to size DNA fragments include its highsensitivity, high efficiency, and high reproducibility. It is easy toclarify chromatogram data by using the typical criteria of 3 �peak signal versus baseline noise (3S/N) as the minimum de-tection limit. Therefore, if possible, it might be better to useDHPLC to size the MSP products. Results obtained by DHPLCanalysis were confirmed by sequencing.

MSP is a very sensitive assay for detection of CpG meth-ylation (21). Methylation of CpG islands in a few cells willresult in positive detection. MSP is useful in precancerouslesions such as DYS, in which genes might be inactivated onlyin a very limited number of cells. This is different from othergene expression assays, such as protein immunostaining andmRNA reverse transcription-PCR, which present the gene ex-

pression status in the majority of cells. The combination of MSPand DHPLC analyses demonstrates clear advantages for clinicalapplications.

In conclusion, methylation of p16 CpG island was posi-tively correlated with progression of gastric DYS to GC in thishigh-risk population. Aberrant methylation of p16 promoterCpG islands therefore might be useful to predict the malignantpotential of DYS identified specifically in gastric biopsies.

ACKNOWLEDGMENTSWe sincerely thank Dr. Steven M. Powell (Department of Gastro-

enterology and Hepatology, University of Virginia Health Science Cen-ter) for critical reading of the manuscript.

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Fig. 4 Sequence chromatograms of the methylation-specific PCR products of p16 promoter CpG islands in gastric dysplasia lesions usingmethylation-specific primers. The methylation-specific PCR products exhibiting methylation were sequenced by the p16 methylation-specific forwardprimer. The predicted sequence of the bisulfite-modified p16 CpG island was also included in the top part. Arrows point to the methylated CpG sites.The red Ts in the predicted sequence were converted from Cs residing outside of CpG sites by bisulfite.




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2004;10:5087-5093. Clin Cancer Res Yu Sun, Dajun Deng, Wei-Cheng You, et al. StudyTransformation of Gastric Dysplasia in a Population-Based

CpG Islands Associated with Malignantp16Methylation of

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