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Molecular Oncology, Markers, Clinical Correlates |
Departments of Surgery [H. W. C., A. C., W. I. W., A. P. W. Y.] and Clinical Oncology [D. L. W. K., J. S. T. S.], The University of Hong Kong, Hong Kong, Peoples Republic of China
| ABSTRACT |
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Experimental design: Methylation status of RIZ1 was evaluated by MSP on CNE-2 and M1 cell lines, 30 tumor biopsies, and their matched body fluid samples, including mouth and throat (M & T) rinsing fluid, NP swabs, plasma, and buffy coat. Normal controls included 8 normal NP biopsies and body fluid samples from 29 healthy volunteers. Sequencing was performed on MSP products from one NP tumor and one M & T rinsing fluid. Transcription of the RIZ1 gene before and after 5-aza-2'-deoxycytidine treatment was examined on CNE-2.
Results: The methylated RIZ1 gene was detected in both CNE-2 and M1, 18 (60%) NP tumors, but not in any of the normal controls. Of 30 matched body fluid samples, methylated RIZ1 DNA was found in 11 (37%) NP swabs, 9 (30%) M & T rinsing fluid, 7 (23%) plasma, and 3 (10%) buffy coat samples. Sequencing analysis confirmed all cytosines to uracils conversion, excluding cytosines in CpG dinucleotides in methylated PCR products. Promoter methylation correlated with loss of RIZ1 mRNA expression, and 5-aza-2'-deoxycytidine treatment restored its expression in CNE-2.
Conclusion: Our results suggest that promoter hypermethylation of the RIZ1 gene is commonly found in NPC. Its detection in body fluid samples of NPC patients but not in normal controls indicates that it is worth to further evaluate its clinical application in assisting screening of NPC and monitoring recurrence after treatment.
| INTRODUCTION |
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Applications of analysis of free DNA in circulation from tumor cells have been well documented (11 , 12) . These studies have shown that it is possible to identify tumor-specific alterations, such as loss of heterozygosity, microsatellite instability, and tumor-specific hypermethylation in the saliva, plasma, and serum DNA of patients with various cancers (13, 14, 15, 16) . We have also found hypermethylated DAP-K promoter DNA in peripheral blood plasma and buffy coat of NPC patients but not in normal controls (17) . Tumor-specific methylation of p16, MGMT, and DAP-K genes are also found in the saliva of head and neck cancer patients (16) . The high specificity of hypermethylation of many TSGs in cancer but not in normal tissue may be used as tumor marker in helping clinical screening of primary cancer of high-risk population and minimal residual cancer after treatment.
Cell cycle regulatory genes involved in growth control are often mutated or deleted in many human cancers but is rarely found in NPC (18 , 19) . Epigenetic inactivation of cell cycle genes is more commonly found in NPC, including p15, p16, RASSF1A, and DAP-kinase (18 , 20) . We have reported previously high frequency of DAP-kinase hypermethylation in NPC (17) . It would be of interest to know whether epigenetic change of the RIZ1 gene can be found in NPC, which might give additional growth advantage of tumor cells. In this study, we aim to: (a) evaluate the hypermethylation status of RIZ1 in NPC cell lines, NP tumors, and normal NP tissues; (b) test whether loss of its transcription is associated with promoter hypermethylation in the NPC cell line; and (c) evaluate the value of methylated RIZ1 DNA as tumor marker for screening NPC in body fluids, which include NP swab, M & T rinsing fluid, and peripheral blood of NPC patients.
| MATERIALS AND METHODS |
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DNA Extraction and Purification.
The blood and tissues were obtained with consent for research purposes. The NP biopsy tissues were immediately frozen in liquid nitrogen and subsequently stored in -80°C until use. The biopsies were treated with proteinase K (0.5 mg/ml) for 36 h at 50°C. High molecular weight genomic DNA was obtained by conventional phenol/chloroform and ethanol extraction (22)
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The peripheral venous blood of patients was collected by EDTA-containing tubes. The plasma was immediately separated from buffy coat fraction by centrifugation at 400 x g for 10 min, and the extracted plasma was transferred to a plain tube for further extraction by centrifugation at 1000 x g for 10 min. The M & T rinsing fluid and NP swabs of patients were collected by bottles containing saline and immediately separated by centrifugation at 400 x g for 10 min. After separation, the remaining cells of M & T rinsing fluid and NP swabs, plasma, and buffy coat fractions were transferred to eppendorf tubes and stored at -80°C until further processing. DNA isolation from M & T rinsing fluid and NP swabs was extracted by a Clontech Nucleospin Blood Mini Kit (Palo Alto, CA) using the protocol as recommended by the manufacturer.
Bisulfide Modification and MSP.
Methylation status of the samples was investigated by MSP as described by Du et al. (10)
. In brief, 1 µg of the genomic DNA was modified by sodium bisulfide using the CpGenome DNA Modification Kit (Intergen, Purchase, NY) using the protocol as recommended by the manufacturer. Modified DNA was amplified by two different primer pairs specific to the unmethylated (U) and methylated (M) RIZ1 sequences, respectively. For the methylated (M-) sequence, the forward and backward primers were 5'-GTGGTGGTTATTGGGCGACGGC-3' and 5'-GCTATTTCGCCGACCCCGACG-3', and those for the unmethylated (U-) sequences were forward 5'-TGGTGGTTATTGGGTGAT GGT-3' and backward 5'-ACTATTTCACCAACCCCAAGA-3'. The PCR amplification was performed for a total of 45 cycles with an annealing temperature of 68°C and 60°C for M-sequences and U-sequences, respectively. Universal methylated DNA was used as the positive control. The PCR products were then analyzed by a 3.5% agarose gel. The amplification by PCR would generate fragments of 177 and 175 bp using M- and U-primer pairs, respectively (10)
. To test the specificity of the U- and M-primer pairs on NP tissues, we applied the MSP on normal (unmethylated) controls and NPC cell lines.
Sequencing of RIZ1 MSP Products.
Both U and M products of the MSP from one NPC tumor biopsy and one M & T rinsing fluid sample were excised from the agarose gel and purified by Concert Matrix Gel Extraction System (Invitrogen, Carlsbad, CA). Subsequently, sequencing reactions were performed separately on the purified U and M products by the DNA sequencing kit (Perkin-Elmer Corp., Warrington, United Kingdom) and analyzed by 377 ABI prism automatic sequencer (Perkin-Elmer Corp., Foster City, CA).
Sensitivity and Specificity of RIZ1 MSP Analysis.
Sensitivity of RIZ1 MSP analysis was demonstrated by mixing different copies (10, 25, 50, 60, 70, 80, 90, 100, 250, 500, and 1000) of universal methylated human male genomic DNA (Intergen) with 1000 copies of unmethylated normal control DNA from one histologically normal NP tissue biopsy (adenoid 1080). A conversion factor of 6.6 pg of DNA/diploid cell was used for copy number calculation. Eight histologically normal NP biopsy tissues, body fluid samples of 20 M & T rinsing fluid and NP swabs, and 18 peripheral blood from 29 healthy subjects were included in this study as normal (negative) controls.
RT-PCR of RIZ1.
RNA isolation with TRIzol (Invitrogen) was performed according to the manufacturers instructions. The RNA was enriched for polyadenylated RNA molecules using the mRNA Capture Kit (Roche, Indianapolis, IN) according to the manufacturers instructions. In brief,
1 µg of total cellular RNA was transferred to a streptavidin-coated PCR tube to immobilize the mRNA, and reverse transcription was performed using Moloney murine leukemia virus reverse transcriptase (New England Biolabs) for 1 h at 37°C. Subsequently, PCR was performed with an initial hot start of 2 min at 94°C and followed by amplification of 15 s at 94°C, 15 s at 58°C, and 15 s at 72°C for a total of 40 cycles and a final extension of 10 min at 72°C using forward and backward primers RIZ1 5'-GAA CACTAC TGAGCCTGTGG-3' (sense) and RIZ2 5'-ACACCAATCCGGGTCTT GTC-3' (antisense). The primers for amplification of human glyceraldehyde-3-phosphate dehydrogenase were 5'-CGG AGT CAA CGG ATT TGG TCG TAT-3' (sense) and 5'-AGC CTT CTC CAT GGT GGT GAA GAC-3' (antisense).
Re-expression of RIZ1 by 5-Aza-dC Treatment.
The NPC cell line, CNE-2, was grown for 4 days in the presence of various concentrations of 5-Aza-dC (1, 5, and 10 µM). RNA and DNA were separately isolated. MSP and RT-PCR were performed afterward as described above.
| RESULTS |
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All normal controls from eight histologically normal NP tissue biopsies and body fluid samples of 20 M & T rinsing fluid and NP swabs and 18 peripheral blood from 29 healthy subjects showed only unmethylated sequence amplified (Fig. 2)
. The results suggested that RIZ1 gene promoter was unmethylated in all normal control tissue specimens, including NP tumors biopsies, M & T rinsing fluid, NP swabs, and peripheral blood.
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RIZ1 promoter was found to be methylated in 18 of 30 (60%) primary tumors, including 33% (1 of 3) stage I, 64% (7 of 11) stage II, 40% (2 of 5) stage III, and 73% (8 of 11) stage IV tumors (Spearman correlation, P = 0.651). Methylation was unaffected by sex (Fishers test, P = 1.00) and age (t test, P = 0.967). Representative MSP results of primary tumor, M & T rinsing fluid, NP swabs, buffy coat, and plasma are shown in Fig. 3
and summarized in Table 1
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Hypermethylated RIZ1 gene was found in 4 patients in their M & T rinsing fluid but not in the NP swabs, 6 patients in the NP swabs but not in the M & T rinsing fluid, and 5 patients in both M & T rinsing fluid and NP swabs. Methylation of the RIZ1 gene was detectable in 15 (50%) samples from either or both M & T rinsing fluid and NP swabs. Although aberrant methylation was detected in primary tumors, 3 patients had no detectable hypermethylated RIZ1 gene in both M & T rinsing fluid and NP swabs. Methylated RIZ1 gene promoter DNA had lower detectable rate in plasma 7 (23%) and buffy coat 3 (10%) specimens. All plasma and buffy coat samples with methylated RIZ1 gene detected showed promoter hypermethylation in their corresponding primary tumors. Hypermethylated RIZ1 promoter was found in 5 patients in the plasma but not in the buffy coat, 1 patient in the buffy coat but not in the plasma, and 2 patients in both buffy coat and plasma samples. All together, methylation of the RIZ1 gene was detected in 8 (27%) samples from either or both buffy coat and plasma.
Expression of RIZ1 mRNA in NPC Cell Lines Before and After Demethylation Agent 5-Aza-dC Treatment.
The expression of RIZ1 was examined on CNE-2 cell line by RT-PCR. No detectable RIZ1 mRNA was detected (Fig. 4A)
, although mRNA extracted from normal NP frozen tissue biopsies (adenoid 1080), which had no promoter hypermethylation, showed RIZ1 expression. In this experiment, the expression of glyceraldehyde-3-phosphate dehydrogenase was served as an internal index gene to ensure the integrity of mRNA.
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| DISCUSSION |
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Epigenetic silencing of RIZ1 by methylation was found in 11 of 25 (44%) breast cancer specimens and 20 of 32 (62%) liver cancer (10) . In this study, we have demonstrated the high frequency of RIZ1 promoter methylation in 60% NPC tumors. There was no correlation of clinical stage, sex, and age with RIZ1 methylation. Methylation of RIZ1 was detected in both early and late stage of tumors, indicating that the inactivation of the RIZ1 gene might be essential in the early development of NPC and persist throughout the course of this development. Because all 30 NPC patients in this study were followed up to 1 year, we couldnt evaluate the prognostic value of RIZ1 methylation.
Metastastic tumor cells may also enter the circulation and can be detected in the buffy coat layer of peripheral blood. NPC cells may detach from the primary tumor and can be collected by NP swabs or M & T rinsing fluid. Tumor DNA may be released after cell death into the nasopharynx or absorbed into the systemic circulation. We have found previously the presence of NP carcinoma cells in cytological swabs of the nasopharynx that can be used as diagnostic adjunct (21) . Cytological evaluation is labor intensive, requiring a high degree of experience to accurately identify morphologically suspicious cells. Studies have shown promising applied molecular approach to detect cancer-specific alterations like epigenetic change by hypermethylation, loss of heterozygosity, the presence of Epstein-Barr virus latent membrane protein, and so forth in cancer cells from mouth washes and NP swabs (16 , 24 , 25) . The collection of NP swabs, M & T rinsing fluid, and blood can be easily performed as a screening procedure by family physician or paramedics without the necessity of the more complicated, invasive endoscopic biopsy by a trained otorhinolaryngologists. MSP is a powerful technique in the identification of small quantity of cancer cells or cancer DNA. The PCR amplification has advantages of sensitive and accurate detection of small quantity of cancer cells or cancer DNA within the background of normal cells or normal DNA in tumors or body fluids (26) . This is particularly important if methylated DNA is to be used as tumor marker in screening primary NPC of high-risk asymptomatic population or patients with early symptoms suspected of having NPC or in the early detection of minimal residual tumor or asymtomatic stage of recurrence after treatment. From the sensitivity test, the MSP was able to detect a minimum of 70 methylated RIZ1 gene copies. With this sensitivity, methylated RIZ1 DNA was detectable in 50% of the samples from either or both M & T rinsing fluid and NP swabs and in 27% peripheral blood samples. Specificity of RIZ1 analysis was demonstrated in this study in which all normal controls, including 8 histologically normal NP tissue biopsies and body fluid samples from 29 healthy subjects and the 12 matched body fluid samples with methylated RIZ1 gene undetectable in primary tumors, showed methylation free.
Because RIZ1 methylation is not histological specific for NPC and can be found in other cancers or premalignant conditions other than NPC in the body, the source of methylated DNA in body fluid is therefore not specific for NPC. The NP swab contains DNA from nasal and NP tissues; M & T rinsing fluid DNA comes from whole upper aerodigestive tract, and peripheral blood plasma and buffy coat can come from any organs of the whole body. Methylation marker is a screening tool to assist clinical management and not by itself sufficient for definitive diagnosis. Histopathological examination of biopsy tissue should still be the gold standard for cancer diagnosis that cannot be replaced with molecular tumor marker. The present problem is the difficulty of screening or early detection of primary and minimal residual/recurrent NPC in their asymptomatic stage based on clinical examination. Molecular tools like methylation of the RIZ1 gene are developed to help in screening of cancer and early detection of residual or recurrent tumor after treatment. In case a positive molecular finding is found, it can help the clinician to further investigate and confirm with histopathological examination. A second cancer other than NPC should also be considered in the differential diagnosis. Treatment of primary and recurrent tumors in their early stage will significantly improve the outcome. With the relatively high sensitivity and specificity of MSP, screening with methylated promoter DNA as tumor marker is still potentially valuable to assist clinical management.
The present study shows the possibility of PCR-based MSP method to detect small quantity of cellular or cell-free DNA in body fluid, including NP swab, M & T rinsing fluid, and circulating blood of NPC patients. Additional large scale prospective studies are worthwhile to fully elucidate its sensitivity and specificity of screening high-risk population and early detection of residual or recurrent NPC after treatment.
| FOOTNOTES |
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1 Supported by Betty and Kadoorie Cancer Research Fund, Ho Hung Chiu Cancer Research Fund, and a research grant of the University of Hong Kong. ![]()
2 To whom requests for reprints should be addressed, at Department of Surgery, Queen Mary Hospital, 102 Pokfulam Road, Hong Kong, China. Fax: (852) 2855 3464; E-mail: pwyuen{at}hkucc.hku.hk ![]()
3 The abbreviations used are: TSG, tumor suppressor gene; NPC, nasopharyngeal carcinoma; M & T, mouth and throat; RT-PCR, reverse transcription-PCR; MSP, methylation-specific PCR; 5-Aza-dC, 5-aza-2'-deoxycytidine; NP, nasopharyngeal. ![]()
Received 7/ 1/02; revised 10/28/02; accepted 10/28/02.
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