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[Cancer Research 60, 1043-1048, February 15, 2000]
© 2000 American Association for Cancer Research


Molecular Biology and Genetics

Increasing Methylation of the CDKN2A Gene Is Associated with the Progression of Adult T-Cell Leukemia1

Kisato Nosaka, Michiyuki Maeda, Sadahiro Tamiya, Tatsunori Sakai, Hiroaki Mitsuya and Masao Matsuoka2,3

Department of Internal Medicine II, Kumamoto University School of Medicine, Kumamoto 860-8556 [K. N., S. T., T. S., H. M., M. Mat.], Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606-8507 [M. Mae.], Japan


    ABSTRACT
 Top
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 
In this study, we examined the methylation status of the CDKN2A gene in patients with different forms of adult T-cell leukemia (ATL) using Southern blot analysis, methylation-specific PCR (MSPCR), and nucleotide sequencing. We found that the CDKN2A gene was more frequently methylated in fresh tumor cells isolated from patients with acute ATL (47%) or lymphoma-type ATL (73%) than in those with less malignant chronic (17%) and smoldering (17%) ATL. In addition, deletions of the CDKN2A gene were found in 24% of acute ATL patients; thus, abnormalities of the CDKN2A gene totaled 71% in acute ATL patients. In contrast, no CDKN2A gene methylation was found in asymptomatic carriers or uninfected individuals. Methylation of the p15 gene was not found in any samples from 36 ATL patients. Direct sequencing of the CDKN2A gene after sodium bisulfite treatment of genomic DNA revealed that the methylation of CpG sites had occurred in 24 of 32 ATL cases (75%) including chronic and smoldering ATL, even when MSPCR and the Southern blot had failed to detect CDKN2A gene methylation. Among fresh ATL samples with methylation, methylation was detected in the promoter region and exon in 17 of 24 cases, and methylation in the exon without promoter region was detected in 7 of 24 cases. In one case, the pattern of methylation proved to be different between peripheral blood cells and lymph node cells, suggesting the presence of multiple subclones with regard to methylation patterns, despite the same HTLV-I integration site. Quantitative PCR showed a marked decrease in CDKN2A mRNA expression in the cells with a methylated CDKN2A gene, especially if the promoter region was methylated. These findings suggest that CpG methylation decreases CDKN2A expression and represents a critical factor in the disease progression of ATL.


    INTRODUCTION
 Top
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 
ATL4 is a highly aggressive neoplasm of helper T lymphocytes and is etiologically associated with HTLV-I (1, 2, 3, 4, 5, 6) . HTLV-I has a unique structure, named the pX region, between env and the 3' long terminal repeat. The pX region encodes at least three proteins, Tax, Rex, and p21. Among them, Tax protein is thought to play a central role in the leukemogenesis of ATL, because of its pleiotropic actions (7 , 8) . By binding to various cellular factors, such as nuclear factor-{kappa}B, serum response factor (SRF), and cyclic AMP-responsive element binding protein, Tax activates transcription of both viral and cellular genes; on the other hand, Tax can also trans-repress the transcription of certain genes, such as lck and DNA polymerase ß (9 , 10) . Moreover, Tax binds to I{kappa}B and p16, resulting in their functional suppression (11 , 12) . These multiple functions of Tax are believed to contribute to the immortalization of HTLV-I-infected cells, especially CD4-positive T lymphocytes. Indeed, the proliferation of HTLV-I-infected cells in vivo is generally clonal, as detected by analysis of integration sites, and persistent proliferation has been observed in HTLV-I carriers (13 , 14) . After initial infection with HTLV-I, a long-term latent period (~50 years in Japan) precedes the onset of ATL (15) . Such a long latent period suggests that multistep tumorigenesis is involved in the development of ATL. During the latent period, mutations are thought to accumulate in infected cells. Among subtypes of ATL, chronic and smoldering ATL are considered to be low-grade malignancies because of their insidious clinical courses, although they frequently progress to acute or lymphoma-type ATL after several years (16) . The presence of the HTLV-I provirus in ATL cells enables us to analyze each of these steps of leukemogenesis (carrier, smoldering, chronic, lymphoma-type, and acute ATL).

The CDKN2A gene was isolated as a tumor suppressor gene that undergoes deletions and/or mutations in certain human tumors, including acute lymphoblastic leukemia, bladder cancer, and melanoma (17, 18, 19) . The p16 protein encoded by CDKN2A is an inhibitor of CDK4 and CDK6, competing with cyclin D to block CDK activity, resulting in G1 arrest (20) . Deletions or rearrangements of the CDKN2A gene have also been reported in ~20% of ATL cases, mostly acute or lymphoma-type ATL (21 , 22) . However, the loss of expression of the CDKN2A mRNA is seen in certain cancer cells without evidence of deletion or recombination, suggesting that epigenetic changes affect the expression of the CDKN2A gene (23) . Methylation of CpG sites in the promoter region of the CDKN2A gene was recently shown to be associated with its reduced expression, because demethylation by 5-aza-2'-deoxycytidine restored its expression (24) . These data suggest that epigenetic changes, such as methylation, may be involved in the inactivation of the CDKN2A gene.

In this study, we analyzed the methylation of CpG sites in the CDKN2A genes in ATL cells obtained from patients at various clinical stages and detected a high incidence of methylation in all stages of ATL. We also observed that the methylation of CpG sites in the CDKN2A gene increased as the disease progressed and caused the suppression of CDKN2A gene expression.


    MATERIALS AND METHODS
 Top
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 
ATL Patients.
PBMCs or lymph node cells were obtained from patients with various subtypes of ATL [smoldering (6 cases), chronic (16 cases), acute (38 cases), and lymphoma-type (8 cases)], three asymptomatic HTLV-I carriers, and three uninfected healthy individuals. Diagnosis was made based on the criteria proposed previously (25) , and monoclonal integrations of the HTLV-I provirus were confirmed by Southern blot analyses using a whole HTLV-I probe.

Cell Lines.
HTLV-I transformed cell lines and ATL-derived cell lines were used in this study (26 , 27) . ED, ATL-43T, SKT1B, ATL-55T, TL-Om1, and ATL-48T were cell lines derived from leukemic clones, as confirmed by Southern blot analysis with an HTLV-I probe or a T-cell receptor gene probe. MT-2, MT-4, ATL-2, ATL-14, ATL-16, ATL-17–2, ATL-18, ATL-22, ATL-35T, ATL-KI, ATL-40T, ATL-41T, and Sez627 were derived from nonleukemic clones. The human embryonic kidney cell line, 293, was studied as a control. To demethylate the CDKN2A gene, cell lines were grown in media supplemented with 10 µM 5-Aza-CdR (Sigma) for 3 days, and then RNAs were isolated using Trizol (Life Technologies, Inc., Paisley, United Kingdom). Reverse transcription-PCR using primers specific for the CDKN2A gene amplified transcripts of the CDKN2A gene.

Southern Blot Analysis.
Genomic DNA isolated from PBMCs or lymph node cells was first digested with a methylation-sensitive enzyme, SacII, then digested with EcoRI, and electrophoresed in a 1.0% agarose gel, transferred to nylon membrane, and subjected to hybridization with a probe corresponding to CDKN2A exon 1.

MSPCR.
MSPCR was performed as described previously by Herman et al. (28) . In brief, 2 µg of genomic DNA (10 µl) were denatured by the addition of an equal volume of 0.6 N NaOH for 10 min, and then 208 µl of 3.6 M sodium bisulfite and 12 µl of 10 mM hydroxyquinone were added. This mixture was incubated at 55°C for 16 h to convert cytosine to uracil. Treated genomic DNA was subsequently purified using the Wizard clean up system (Promega), precipitated with ethanol, and resuspended in 100 µl of distilled H2O. The genomic DNA obtained was used in MSPCR using primers as follows: CDKN2A M (methylated): sense primer 5'-TTATTAGAGGGTGGGGCGGATCGC-3', antisense primer 5'-CCACCTAAATCGACCTCCGACCG-3'; CDKN2A U (unmethylated): sense primer 5'- TTATTAGAGGGTGGGGTGGATTGT-3', antisense primer 5'-CCACCTAAATCAACCTCCAACCA-3'; p15 M (methylated): sense primer 5'-GCGTTCCTATTTTGCGGTT-3', antisense primer 5'-CGTACAATAACCGAACGACCGA-3'; and p15 U (unmethylated): sense primer 5'-TGTGATGTGTTTGTATTTTGTGGTT-3', antisense primer 5'-CCATACAATAACCAAACAACCAA-3'. The PCR mixture contained 1x buffer with 1.5 mM MgCl2, 0.2 µM of each primer, 0.1 mM deoxynucleotide triphosphates, 2 units of Taq DNA polymerase (Promega), and 100 ng of sodium bisulfite-treated genomic DNAs. Conditions of amplification were as follows: 95°C for 3 min and 35 cycles of 95°C for 30 s, 65°C for 30 s (60°C for CDKN2A U, p15 M, and p15 U primers), 72°C for 30 s, and finally 4 min at 72°C.

Direct Sequencing after Sodium Bisulfite Treatment.
Sodium bisulfite-treated genomic DNAs (100 ng) were amplified with the CDKN2A gene-specific primers as follows (29) . Primers for amplification of the promoter region of the CDKN2A gene (from -378 to -89) were 5'-TTTTTAGAGGATTTGAGGGATAGG-3' (sense) and 5'- CTACCTAATTCCAATTCCCCTACA-3' (antisense). To obtain products for sequencing, a second round of PCR was performed with 20 pmol of nested primers: the sense primer, 5'-AGTATTAGGAGGAAGAAAGAGGAG-3', and the antisense primer 5'-TCCAATTCCCCTACAAACTTC-3'. Amplification was carried out for 35 cycles (30 s at 95°C, 1 min at 58°C, and 1 min at 72°C) and followed by a final 4-min extension at 72°C. Primers used for amplification of the promoter and exon 1 (from -115 to 119) were as follows: for the first PCR round, 5'-GAGGGGGTAGGGGATAT-3' (sense) and 5'-ACCAATCAACCRAAAACTCCATACTA-3' (antisense), and for the nested PCR, 5'-GTAGGTGGGGAGGAGTTTAGTT-3' (sense) and 5'-CCCACCCTATAATAACCAACCAA-3' (antisense). Conditions of amplification were as follows: 35 cycles (30 s at 95°C, 1 min at 52°C, and 1 min at 72°C) and then 4 min at 72°C. Sequencing was performed using Big Dye Terminator (Applied BioSystems) with an ABI 377 autosequencer. Six HTLV-I-transformed cell lines were analyzed [ED (CL-1), 43T (CL-2), SKT-1B (CL-3), ATL-55T (CL-5), and Tl-Om1 (CL-6) were derived from leukemic clones, whereas MT-2 (CL-4) was derived from nonleukemic cells].

cDNA Synthesis and Semiquantitative PCR.
Total RNA was prepared from cell lines or PBMCs from ATL patients using Trizol reagent (Life Technologies), and cDNAs were made from 5 µg of total RNAs using the Superscript Preamplification System (Life Technologies) according to the manufacturer’s protocol. Oligo dT primers were used to prime first-strand synthesis for all of the reactions. For PCR, 2 µl of the reverse transcriptase reaction mixture were diluted with 50 µl of PCR buffer containing 0.2 mM each of deoxynucleotide triphosphates, 1.5 mM MgCl2, 1.25 units of Taq DNA polymerase (Life Technologies), and 20 pmol of each primer. Primers specific for the CDKN2A gene were 5'-TTCGGCTGACTGGCTGGCCA-3' (sense, exon 1) and 5'-AGCTCCTCAGCCAGGTCCAC-3' (antisense, exon 2), and primers for the GAPDH gene used as a control were 5'-ATGGGGAAGGTGAAGGTCGGAGTC-3' (sense) and 5'-CCATGCCAGTGAGCTTCCCGTTC-3' (antisense). PCR was performed in a Robo Cycler (Stratagene, La Jolla, CA) for 30 cycles for the CDKN2A gene and 22 cycles for the GAPDH gene under the following conditions: 3 min at 94°C, 30 s at 94°C, 1 min at 60°C, 1 min at 72°C, and 4 min at 72°C. The PCR products were visualized by ethidium bromide staining in 2% agarose gels. The intensity of amplified bands was quantified by ATTO densitograph 4.0 (ATTO, Tokyo, Japan).


    RESULTS
 Top
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 
Methylation of the CDKN2A Gene Detected by Southern Blot and MSPCR.
We analyzed the methylation of the CDKN2A gene of HTLV-I-transformed cell lines and fresh ATL cells using Southern blot analysis and MSPCR. Digestion of the CDKN2A gene with a methylation-sensitive restriction enzyme, SacII, produced a 3.3-kb band when detected with the exon 1 probe; however, when methylation occurred in the SacII site (within exon 1) of the CDKN2A gene, a 4.3-kb band was detected (data not shown). In addition to methylation, Southern blot analysis also revealed deletions of the CDKN2A gene. MSPCR was performed after sodium bisulfite treatment of the genomic DNA (Fig. 1)Citation . MSPCR relies on the fact that methylated cytosines are resistant to sodium bisulfite treatment, and thus primers can be made to distinguish between unmethylated and methylated templates. In samples with highly methylated CpG sites, only the methylated band was detected (Fig. 1Citation , no. 3). When the CDKN2A gene was methylated partially, both methylated and unmethylated bands were found (Fig. 1Citation , no. 6). A total of 71 samples of primary cells (38 cases with acute ATL, 8 cases with lymphoma-type ATL, 16 cases with chronic ATL, 6 cases with smoldering ATL, and 3 asymptomatic carriers) and 19 HTLV-I-associated cell lines were analyzed with Southern blot and MSPCR. This experiment detected a high incidence of methylation in both cell lines and fresh samples, and methylation was more prevalent in the more malignant forms of ATL, although MSPCR can detect methylation of CpG sites only in the exon. In contrast, no methylation was detected in asymptomatic HTLV-I carriers and uninfected healthy individuals. In acute ATL, methylation and deletion of CDKN2A was found in 47 and 24% of cases, respectively, resulting in either genetic or epigenetic changes of CDKN2A in 71% of acute ATL patients. In lymphoma-type ATL, methylation of the CDKN2A gene was found in 73% of cases without deletion. Methylation was less frequent in chronic (17%) and smoldering ATL (17%), as assessed by MSPCR and Southern blot analysis. Moreover, MSPCR with primers specific to the p15 gene failed to detect the methylation in 36 ATL samples (20 cases with acute ATL, 11 cases with chronic ATL, 3 cases with lymphoma-type ATL, and 2 cases with smoldering ATL). Because the CDKN2A gene is adjacent to the p15 gene, these data support the idea that the CDKN2A gene is preferentially methylated in lymphoid cells in contrast to the p15 gene.



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Fig. 1. Methylation-specific PCR detects methylation of the CDKN2A gene. Sodium bisulfite-treated DNA was amplified with each primer pair designed to detect the methylated or unmethylated CDKN2A gene. Lane M, methylated DNA; Lane U, unmethylated DNA. Lane 1, U937 (positive control); Lane 2, uninfected control; Lanes 3 and 4, acute ATL; Lane 5, lymphoma-type ATL; Lane 6, chronic ATL.

 
Nineteen cell lines transformed with HTLV-I were analyzed in this study. There were two types of HTLV-I-transformed cell lines: those derived from leukemic clones (identified by comparison of leukemic cells and cell lines with the Southern blot method using the HTLV-I provirus or T-cell receptor gene as a probe), and those derived from nonleukemic clones. All six cell lines derived from leukemic clones had methylation of the CDKN2A gene; however, there were 3 methylation-negative cell lines of 13 cell lines derived from nonleukemic clones, suggesting that methylation of the CDKN2A gene is more common in leukemic cells.

Direct Sequencing of Sodium Bisulfite-modified Genomic DNA.
A major limitation of Southern blot analysis and MSPCR is that these methods detect methylation in only a few CpG sites in the CDKN2A gene. In contrast, direct sequencing after treatment with sodium bisulfite enables us to identify the methylation state of all of the CpG sites in the amplified sequences. Therefore, we amplified and sequenced the promoter region and exon 1 of the CDKN2A gene using sodium bisulfite-treated genomic DNAs obtained from PBMCs of patients at various clinical stages (13 cases with acute ATL, 4 cases with lymphoma-type ATL, 11 cases with chronic ATL, and 4 cases with smoldering ATL) and three carriers. The level of methylation of the CpG sites (42 sites) was judged from the pattern of the electropherogram. When >20% methylation of a CpG site was seen, that site was determined to be a methylated one. Representative data from this analysis are shown in Fig. 2Citation . Most of the CpG sites were heavily methylated in a case of acute ATL, as shown in Fig. 2ACitation . Only partial methylation was observed in a case of chronic ATL and another case with lymphoma type ATL (Fig. 2, B and C)Citation . A summary of this analysis is shown in Fig. 3Citation , in which each column represents one CpG site of the CDKN2A gene and the extent of its methylation. We frequently observed complete methylation in HTLV-I-transformed cell lines, although the extent of methylation differed among cell lines. Cell lines derived from leukemic clones, like ATL-43T (CL-2), had heavily methylated CpG sites; however, MT-2 cells (CL-4), which were derived from a nonleukemic cell (30) , had partially methylated CpG sites (Fig. 3)Citation . The 5' region of the promoter was particularly less methylated.



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Fig. 2. Electropherogram of direct sequencing of CDKN2A gene amplified with sodium bisulfite-treated genomic DNAs. In a patient with acute ATL, most CpG sites were resistant to sodium bisulfite treatment because of heavy methylation (A). In a patient with lymphoma-type ATL (B) and another patient with chronic ATL (C), partial methylation (a mixture of converted T and unconverted C) was observed. Arrows, methylated CpG sites. D, a distinct methylation pattern was found in the same patient in lymph node cells and PBMCs.

 


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Fig. 3. Summary of methylation of CpG sites in the CDKN2A gene. A total of 42 CpG sites in the CDKN2A gene were analyzed by direct sequencing after amplification of sodium bisulfite-treated genomic DNA. CpG sites are numbered from the ATG site. Each column represents the extent of methylation of a CpG site measured from electropherogram data. CL, cell lines; A, acute ATL; L, lymphoma-type ATL; C, chronic ATL; S, smoldering ATL.

 
Direct sequencing after treatment with sodium bisulfite detected the methylation of the CDKN2A gene, even in cases (five cases: A-8, L-3, C-7, C-8, and C-9) in which methylation of the CDKN2A gene could not be found by Southern blot or MSPCR. Because the single methylation of a single site is unlikely to suppress transcription, only cases with more than two methylated CpG sites were judged as methylation positive. Methylation of the CDKN2A gene was detected in 24 of 32 ATL cases (75%), including chronic and smoldering ATL, and on the other hand, no methylation was detected in asymptomatic carriers (data not shown). CpG sites in exon 1 tend to be methylated in all cases. Methylation of the CDKN2A gene was observed in the exon region without upstream methylation in 7 of 32 cases. In 17 of 32 fresh ATL cases and all cell lines, methylation was also detected in the promoter region in addition to exon. In the promoter region, the -17 CpG site was preferentially methylated among fresh ATL samples (10 cases of 32; 31%).

Although none of methylation-negative cases (C-10, C-11, S-3, and S-4) among chronic and smoldering type ATL showed progression to acute ATL, the clinical progression was frequently observed in methylation-positive ATL cases (8 of 11 cases), which showed that methylation-negative ATL cases had more indolent clinical courses than methylation-positive cases. Two different subgroups among patients with chronic ATL have been reported; patients in one group progress to acute crisis within a few years, and patients in the other group have indolent clinical courses (31) . Chronic ATL patients with risk factors identified previously (high WBC counts and high lactate dehydrogenase) had more methylation of the CDKN2A gene (C-1–6) when compared with those without risk factors (C-7–11).

In one case, partial methylation (~50%) of the CDKN2A gene was found in PBMCs, whereas no methylation was identified in lymph node cells (Fig. 2D)Citation . It was confirmed that both ATL cell samples had the same HTLV-I provirus integration site, showing that multiple subclones with different methylation patterns were present in the patient.

Semiquantitative Reverse Transcription-PCR of the CDKN2A Gene.
Methylation of the CDKN2A gene may result in the suppression of its transcription, leading to decreased expression. Therefore, we analyzed the expression of the CDKN2A gene using semiquantitative PCR (30 cycles) using primers specific for the CDKN2A gene. As shown in Fig. 4ACitation ,293 cells (Lane 1) and normal T lymphocytes stimulated in the presence of interleukin 2 (Lane 6) contain CDKN2A gene transcripts (330 bp) and were used as positive controls. The relative levels of expression of the CDKN2A gene were shown by the histogram after normalization with the GAPDH transcript. Transcripts of the CDKN2A gene could not be detected in any cell line, such as ED (Lane 3) or ATL 43T (Lane 4), which had a heavily methylated CDKN2A gene (Fig. 3)Citation , and the MT-2 cell line, which contains a partially methylated gene, showed a markedly suppressed expression of the CDKN2A gene (Lane 5). Thus, expression of CDKN2A gene was inversely correlated with its methylation. For example, ATL cells with extensive methylation, which ranged to the promoter region, were found to express low levels of CDKN2A gene transcripts (Lanes 7; A-5 in Fig. 3Citation and Lane 8; C-1 in Fig. 3Citation ) when compared with controls. On the other hand, ATL cells with no methylation had equivalent amounts of CDKN2A gene transcripts (Lane 9, A-13; Lane 12, C-4). These results suggest that the decreased expression of the CDKN2A gene is caused by the methylation of the gene. To confirm this possibility, we tested whether a demethylating agent, 5-Aza-CdR, reversed the suppressive effects of methylation. As shown in Fig. 4BCitation , an exposure of ATL cell lines (ED, ATL-43T, and MT-2) to 5-Aza-CdR for 3 days reactivated or potentiated the expression of CDKN2A mRNA, corroborating our observation that the methylation of the CDKN2A gene was associated with CDKN2A gene silencing in ATL cells.



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Fig. 4. Expression of CDKN2A mRNA. A, semiquantitative PCR (30 cycles) specific for the CDKN2A gene was performed using cDNAs from various cell lines and ATL samples. PCR products of the CDKN2A gene (330 bp) were detected, and the GAPDH gene was used as an internal control (694 bp). Expression of the CDKN2A gene and GAPDH gene transcripts were measured with a densitometer. The histogram shows the relative levels of expression after normalization with the GAPDH transcript. Lane 1, 293 cells (positive control); Lane 2, Jurkat cells (negative control); Lane 3, ED; Lane 4, ATL-43T; Lane 5, MT-2; Lane 6, IL-2 stimulated T lymphocytes; Lane 7, acute ATL (A-5); Lane 8, chronic ATL (C-1); Lane 9, acute ATL without methylation (A-13); Lane 10, acute ATL (A-4); Lane 11, acute ATL (A-6); Lane 12, chronic ATL (C-4); Lane 13, chronic ATL (C-11). B, influence of 5-Aza-CdR on CDKN2A gene expression in HTLV-I-transformed cell lines. HTLV-I-transformed cell lines (ED, MT-2, and ATL-43T) were cultured in media supplemented with 10 mM 5-Aza-CdR for 3 days. Expression of the CDKN2A gene was examined by semiquantitative PCR. Lane 1, ED untreated; Lane 2, ED cultured with 5-Aza-CdR; Lane 3, MT-2 untreated; Lane 4, MT-2 cultured with 5-Aza-CdR; Lane 5, ATL-43T, untreated; Lane 6, ATL-43T cultured with 5-Aza-CdR.

 

    DISCUSSION
 Top
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 
Inactivation of the CDKN2A gene by deletions has been reported in cancer cells of various types, indicating that CDKN2A is a tumor suppressor gene (17, 18, 19) . The methylation of CpG sites in the CDKN2A gene has been recognized as another mechanism of suppressing its transcription in lymphoma, myeloma, melanoma, and bladder cancer (23 , 24 , 32) . The INK4 family includes the p15, p18, and p19 genes in addition to the CDKN2A gene, and the methylation of p15 was also reported in gliomas and leukemia cells (33) . In contrast to the methylation of the p15 gene observed predominantly in myeloid cells, the CDKN2A gene has been reported to be preferentially methylated in lymphoid malignant cells (34) , which is consistent with our findings in this study. Such preferential silencing specific for cell lineages suggests that each gene in the INK4 family is functionally predominant in a lymphoid lineage.

Deletion of the CDKN2A gene was reported in 27% (21) and 11.4% (22) of ATL cases, whereas this study revealed that methylation of this gene was a more common phenomenon in ATL, suggesting that methylation is the predominant mechanism of suppressing the expression of the CDKN2A gene in ATL cells. In this work, we reported an increasing methylation as the disease progressed. Increasing methylation is also associated with progressive suppression of CDKN2A expression, as shown by analysis of CDKN2A transcripts. Examination of ATL cells at each clinical stage showed that methylation first occurs in the exon region and progresses to the promoter region with clinical progression of ATL. It has been reported that methylation in the exon region does not have any effect on the expression of the CDKN2A gene (29 , 35) . This study supports that finding because the ED and ATL-43T cell lines, which had completely methylated CDKN2A genes, did not express CDKN2A gene transcripts, whereas the MT-2 cell line with a less methylated promoter region expressed low levels of CDKN2A gene transcripts. Methylation of the promoter region is thought to be related to the silencing of CDKN2A gene transcription because 5-Aza-CdR could restore the transcription of the CDKN2A gene.

Analysis of bladder cancer cell lines with reactivated CDKN2A gene expression after 5-Aza-CdR treatment revealed that a small number of CpG sites can significantly down-regulate CDKN2A promoter activity (29) . In this study, methylation of a specific CpG site (-17) was observed frequently in ATL samples; this site may influence the expression of the CDKN2A gene. Transcriptional repression by DNA methylation has also been reported for other tumor suppressor genes such as E-cadherin (36) and the VHL tumor suppressor gene (37) . These reports suggest that methylation is a common mechanism of inhibiting tumor suppressor genes.

Among chronic ATL cases, there are variations in clinical course; some patients progress to acute or lymphoma-type ATL shortly, and other patients show no progression for a long time. Thus, the identification of the subgroup of chronic ATL cases who will progress to acute crisis is clinically important. Chronic ATL cases without CDKN2A gene methylation had more indolent clinical courses than those with methylation. Thus, analysis of the methylation status of the CDKN2A gene may be useful in predicting when the patients will progress to acute ATL.

In this study, we found different methylation patterns of the CDKN2A gene within a single patient, demonstrating the presence of subclones within leukemic cells carrying a single integration site of HTLV-I provirus. Cells with different methylation pattern of the CDKN2A gene in the same patient may have different tissue affinities, perhaps reflecting different patterns of expression of adhesion molecules.

Of various proteins associated with Tax, p16 has been shown to be functionally inactivated, resulting in cell cycle perturbation (12) . However, at the late stage of leukemogenesis, such as acute or lymphoma-type ATL, the expression of tax is significantly lower than in asymptomatic carriers (38) . Fresh leukemic cells in some acute ATL patients do not produce Tax in vitro because of deletion of the long terminal repeat and other mechanisms (39 , 40) . Thus, whether Tax expression is required in ATL cells remains unclear. On the other hand, such deletions in the HTLV-I provirus are rare in low-grade malignant ATL cases (smoldering or chronic ATL), suggesting that Tax may play an important role at such stages but may not be essential for late stages of leukemia. The increasing methylation of the CDKN2A gene shown in this study suggests that at an early stage of leukemogenesis, Tax is responsible for inactivating the p16 protein, whereas at a late stage, methylation or even deletion of the CDKN2A gene abolishes the expression of p16. Methylation might be a way to transform HTLV-I infected T cells in the absence of Tax expression. ATL cells express activation antigens like CD25 and secrete various cytokines; their phenotype resembles that of cells expressing Tax in vitro. Modification of methylation in ATL cells might fix a phenotype initially induced by Tax and replace the functions of Tax.

The progressive methylation of the CDKN2A gene in ATL cells observed in this study suggests that methylation suppresses the expression of the CDKN2A gene, which initially is functionally inactivated by Tax. Therefore, cells with methylated CDKN2A gene may not depend on the expression of viral proteins for their growth and thus may escape host immune surveillance.


    ACKNOWLEDGMENTS
 
We are grateful to Dr. Mitsuaki Yoshida for helpful discussion and Dr. Linda Kingsbury for critical reading of the manuscript.


    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 Supported by a grant-in-aid for Scientific Research from the Ministry of Education, Science, Sports and Culture of Japan. Back

2 To whom requests for reprints should be addressed, at Department of Internal Medicine II, Kumamoto University School of Medicine, 1-1-1 Honjo, Kumamoto 860-8556 Japan. Phone: 81-96-373-5156; Fax: 81-96-363-5265; E-mail: matsuoka{at}kaiju.medic.kumamoto-u.ac.jp Back

3 Present address: Laboratory of Virus Immunology, Research Center for AIDS, Institute for Virus Research, Kyoto University, 53 Shogoin Kawaramachi, Sakyo-ku, Kyoto 606-8507, Japan. Phone: 81-75-751-4048; Fax: 81-75-751-4049; E-mail: mmatsuok{at}virus1.virus.kyoto-u.ac.jp Back

4 The abbreviations used are: ATL, adult T-cell leukemia; HTLV-I, human T-cell leukemia virus type I; CDK, cyclin-dependent kinase; PBMC, peripheral blood mononuclear cell; 5-Aza-CdR, 5-aza-2'-deoxycytidine; MSPCR, methylation-specific PCR; GAPDH, glyceraldehyde-3-phosphate dehydrogenase. Back

Received 5/ 3/99. Accepted 12/15/99.


    REFERENCES
 Top
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 

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