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Molecular Biology, Pathobiology, and Genetics |
1 Department of Molecular Oncology, John Wayne Cancer Institute at Saint John's Health Center; 2 The Angeles Clinic and Research Institute, Santa Monica, California; and 3 Department of Biomathematics, University of California at Los Angeles School of Medicine, Los Angeles, California
Requests for reprints: Dave S.B. Hoon, Department of Molecular Oncology, John Wayne Cancer Institute, 2200 Santa Monica Boulevard, Santa Monica, CA 90404. Phone: 310-449-5264; Fax: 310-449-5282; E-mail: hoon{at}jwci.org.
| Abstract |
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| Introduction |
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Investigators have shown the clinical utility of circulating tumor cells (CTC) in blood as surrogate markers for subclinical disease and prognostic factors of disease outcome and treatment response (710). CTC in blood are detected by quantitative real-time reverse transcription-PCR (RT-PCR) assay, which allows rapid and reproducible identification of a few tumor cells among millions of peripheral blood leukocytes (PBL; ref. 11). The presence of CTC in blood is associated with poorer disease outcome in melanoma patients (6, 12).
The epigenetic phenomenon of hypermethylation at promoter region CpG islands of tumor-related genes in various cancers has been implicated in cancer development and progression (1316). Hypermethylation of promoter region is a significant epigenetic mechanism that regulates gene transcription. Methylation-specific PCR (MSP) is a sensitive and specific assay for tumor-related DNA methylation in serum and/or plasma (17). A number of studies have evaluated the potential of circulating tumor-related methylated DNA in serum for the molecular diagnosis and prognosis of various types of cancer (5, 18, 19). However, the source of tumor-related cell-free DNA in serum is still unknown and it has been postulated to be from primary/metastatic tumors and/or CTC.
CTC and tumor-related methylated DNA in blood have been separately assessed for their clinical utility; however, no studies have looked into the relation between these two different types of molecular markers. Although the origin and mechanism of cell-free DNA in blood is still debated, death of CTC has been considered as one of the possible sources whereby DNA is released in blood (20, 21). If CTC are the source of cell-free DNA, their physiologic relation would justify coassessment of CTC and serum tumor-related methylated DNA as a potentially powerful composite molecular index of disease outcome in cancer patients.
Previous studies have suggested the benefit of biochemotherapy in advanced-stage melanoma (2228). Identifying surrogate markers of treatment response would be of tremendous clinical value to manage the patients receiving systemic therapy, such as biochemotherapy. Monitoring of surrogate molecular markers may be informative on whether to continue or alternate the treatment, and prediction of treatment efficacy can bring an improvement on the patients' quality of life. Because melanoma is a heterogeneous disease, multiple molecular marker assays may be more favorable compared with single-marker assays to detect tumor spreading in blood (4, 9, 19, 2931). Recently, we showed that sequential monitoring of CTC using a multimarker quantitative real-time RT-PCR assay could predict the treatment outcome in American Joint Committee on Cancer (AJCC) stage III melanoma patients receiving neoadjuvant biochemotherapy (6). We have also shown that serum tumor-related hypermethylated DNA at tumor-related gene promoter regions was frequently found in patients with metastatic tumors (31).
We hypothesized that CTC levels in blood may be correlated with tumor-related methylated DNA in serum and that the combination of these molecular variables may allow more accurate prognostic assessment in melanoma patients. In this study, we assessed a physiologic and prognostic correlation between CTC and tumor-related methylated DNA in the blood of 50 patients receiving biochemotherapy for AJCC stage IV melanoma.
| Materials and Methods |
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2b, interleukin 2, and tamoxifen, and clinical results of the trial were described as previously reported (22, 32). Fifty patients from this single-institute trial were retrospectively selected by the database coordinator based on availability of cryopreserved specimens, completion of the biochemotherapy treatment, and their clinical follow-up (38 males and 12 females; median age, 45 years; range, 18-70 years; Table 1
). Patients were categorized by their response to biochemotherapy (22): complete response (CR; n = 13), partial response (PR; n = 10), stable disease (SD; n = 3), and progressive disease (PD; n = 24; median follow-up time, 12.5 months; range, 1-79 months).
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CTC assay. Peripheral blood specimens were collected in sodium citratecontaining tubes and the first several milliliters were discarded to eliminate skin-plug contamination (29). Nucleated cell fractions were isolated from blood and cryopreserved in liquid nitrogen until thawed for the study as previously described (10). Briefly, the nucleated cells from blood were isolated using a gradient and Purescript RBC lysis solution (Gentra, Minneapolis, MN).
Tri-Reagent (Molecular Research Center, Cincinnati, OH) was used to isolate total cellular RNA from PBL (29). RNA was quantified and assessed for purity by UV spectrophotometry. Reverse transcription reactions were done using Moloney murine leukemia virus reverse transcriptase (Promega, Madison, WI) with oligo-dT primer (33).
The multimarker quantitative real-time RT-PCR assay was done to assess the presence of melanoma antigen recognized by T cells 1 (MART-1), ß1
4-N-acetylgalactosaminyltransferase (GalNAc-T), and melanoma antigen gene A3 family (MAGE-A3) mRNAs. The sensitivity and specificity of the quantitative real-time RT-PCR assay using three markers for detection of CTC have been validated and could be used as a surrogate of CTC in blood as previously described (6, 11). Multimarker quantitative real-time RT-PCR assay was done with the use of the ABI Prism 7900HT Sequence Detection System (Applied Biosystems, Foster City, CA). Primer and probe sequences were designed for quantitative real-time RT-PCR assay and sequences used have previously been reported (11). We transferred 4 µL of cDNA from 200 ng of total RNA to individual wells of a 384-well PCR plate, in which 0.5 µmol/L of each primer, 0.3 µmol/L probe, and 5 µL of iTaq custom supermix with ROX (Bio-Rad Laboratories, Hercules, CA) were added to a final volume of 10 µL. Samples were amplified with a precycling hold at 95°C for 10 minutes, followed by 40 cycles of denaturation at 95°C for 15 seconds, annealing/extension at 55°C for 1 minute for glyceraldehyde-3-phosphate dehydrogenase (GAPDH; at 59°C for MART-1, at 62°C for GalNAc-T, and at 58°C for MAGE-A3). The standard curve was generated with the threshold cycle (Ct) of seven serial dilutions of plasmid templates (106-100 copies). The Ct of each sample was interpolated from the standard curve and the number of mRNA copies was calculated. PCR efficiency, assessed from the slopes of standard curves, was between 90% and 100%. The correlation coefficients for all standard curves (Ct versus log copy number) in the study were
0.99.
Each quantitative real-time RT-PCR assay was done at least twice and included marker-positive and marker-negative controls and reagent controls (reagent alone without RNA or cDNA). GAPDH gene was used as a housekeeping gene. Any specimen with inadequate GAPDH mRNA copies (<10,000) was excluded from the study. No sample was excluded from the study. The mean mRNA copy number was used for analysis. All healthy normal donors' blood was processed and prepared as with the melanoma patients.
Serum methylated DNA assay. Ten milliliters of blood were collected in serum separator tubes (CORVAC, Sherwood-Davis & Geck, St. Louis, MO), centrifuged (3,000 rpm, 15 minutes), and passed through a 13-mm serum filter (Fisher Scientific, Pittsburgh, PA). Then serum was aliquoted and cryopreserved at 80°C until use. DNA was extracted from serum as previously described (31). The DNA quantification was assessed using the PicoGreen quantification assay (Molecular Probes, Eugene, OR; ref. 34). Only specimens with sufficient DNA (>1 µg) were further tested in the protocol. All patient specimens were used. All healthy normal donors' sera were processed and prepared in the same manner as the melanoma patients' sera. Controls were matched as closely as possible in gender and age range. The ratio of males and females was 67% and 33%, respectively, similar to the melanoma patients. The age range was 24 to 65 years, with a mean of 41 years.
Extracted DNA was subjected to sodium bisulfite modification (31). Briefly, DNA from 500 µL of serum was supplemented with 1 µg salmon sperm DNA (Sigma, St. Louis, MO) and denatured in 0.3 mol/L NaOH for 3 minutes at 95°C. Overall, 550 µL of a 2.5 mol/L sodium bisulfite/125 mmol/L hydroquinone solution were added. Samples were incubated under mineral oil in the dark for 3 hours at 60°C. Salts were removed using the Wizard DNA Clean-Up System (Promega) and samples were desulfonated in 0.3 mol/L NaOH at 37°C for 15 minutes. Modified DNA was precipitated with ethanol using Pellet Paint NF (Novagen, Madison, WI) as a carrier and then resuspended in molecular grade water.
We assessed the methylation status of Ras association domain family protein 1A (RASSF1A) and retinoic acid receptor-ß2 (RAR-ß2) as circulating DNA; RASSF1A and RAR-ß2 hypermethylation of the promoter region CpG islands was frequently detected in metastatic melanoma tumors (31). Each methylation status of the bisulfite-treated DNA was determined using two sets of fluorescently labeled primers designed to amplify methylated or unmethylated DNA sequences. The primer sets for MSP were as follows: RASSF1A, 5'-GTGTTAACGCGTTGCGTATC-3' (forward) and 5'-AACCCCGCGAACTAAAAACGA-3' (reverse); RAR-ß2, 5'-GAACGCGACCGATTCGAGT-3' (forward) and 5'-GACCAATCCAACCGAAACG-3' (reverse). The unmethylated-specific primer sets were as follows: RASSF1A, 5'-TTTGGTTGGAGTGTGTTAATG-3' (forward) and 5'-CAAACCCCACAAACTAAAAACAA-3' (reverse); RAR-ß2, 5'-GGATTGGGATGTTGAGAATGT-3' (forward) and 5'-CAACCAATCCAACCAAAACAA-3' (reverse). Forward methylated sequence-specific primers were labeled with D4pa dye and forward unmethylated sequence-specific primers were labeled with D2a dye. Optimized PCR assay condition and assessment of PCR product using capillary array electrophoresis (CAE, CEQ 8000XL, Beckman Coulter, Inc., Fullerton, CA) were previously described (31).
Lymphocyte DNA obtained from healthy donors underwent sodium bisulfite modification and a universal unmethylated control synthesized by
29 DNA polymerase from normal DNA served as positive unmethylated controls (35). Unmodified lymphocyte DNA was used as a negative control for methylated and unmethylated reactions. SssI methylasetreated (New England Biolabs, Beverly, MA) lymphocyte DNA was used as a positive methylated control. Blood processing, RNA and DNA extraction, PCR assay set-up, and post RT-PCR product analysis were carried out in separate designated rooms to prevent cross-contamination; RNA and DNA extraction and PCR studies were done by separate individuals.
Statistical analysis.
analysis was used to assess the correlation between any two markers. Cochran-Armitage trend test was used to examine the significance of association between marker detection and treatment response to biochemotherapy, and also between CTC and serum methylated DNA level.
2 test was used to assess the correlation between CTC/serum DNA methylation marker and prognostic factors [gender, age, Eastern Cooperative Oncology Group (ECOG) status, lactate dehydrogenase, number of metastatic sites, prior treatment, and biochemotherapy response]. Time to progression and overall survival from the start of biochemotherapy were used for outcome measurement. The correlation of marker detection with recurrence-free survival and overall survival was examined using the log-rank test. Kaplan-Meier survival curves were plotted. Two-sided P
0.05 was considered to be statistically significant.
| Results |
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Next, we assessed the correlation between CTC markers in blood and disease outcome. In patients with CR and PR (n = 23), individual CTC marker was detected in 3 (13%), 5 (22%), and 3 (13%) patients for MART-1, GalNAc-T, and MAGE-A3, respectively, and 9 (39%) patients had at least one CTC marker (Table 2A ). By contrast, in patients with PD (n = 24), individual markers were detected in 14 (58%), 6 (25%), and 5 (21%) patients, respectively, and 16 (67%) patients had at least one CTC marker. The number of CTC markers detected was significantly correlated with disease outcome (P = 0.03).
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50) was significantly correlated with detection of CTC markers (P = 0.04).
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Patients with at least one methylated DNA marker had significantly lower time to progression (P = 0.004) and overall survival (P = 0.008) than patients without methylated DNA markers (Fig. 2 ). For patients without methylated DNA markers, the estimated overall survival was 76% (95% CI, 66-83%) at 12 months and 57% (95% CI, 44-69%) at 24 months. For patients with at least one methylated marker, the estimated overall survival was 43% (95% CI, 26-62%) at 12 months and 19% (95% CI, 7-40%) at 24 months.
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Next, we evaluated the correlation of these variables with survival. We divided the patients into three groups: patients without CTC and serum methylated DNA, those with either type of molecular marker, and those with both type of molecular markers. Patients with both blood molecular markers had significantly lower time to progression (P = 0.009) and overall survival (P = 0.02) among these three groups (Fig. 3 ). For patients without CTC and serum methylated DNA, the estimated overall survival was 81% (95% CI, 69-88%) at 12 months, 65% (95% CI, 49-78%) at 24 months, 52% (95% CI, 34-70%) at 36 months, and 42% (95% CI, 24-62%) at 48 months. For patients with either marker, the estimated overall survival was 63% (95% CI, 46-77%) at 12 months, 40% (95% CI, 22-60%) at 24 months, 25% (95% CI, 11-48%) at 36 months, and 16% (95% CI, 5-38%) at 48 months. For patients with both blood molecular markers, the estimated overall survival was 50% (95% CI, 27-65%) at 12 months, 21% (95% CI, 8-45%) at 24 months, 9% (95% CI, 2-31%) at 36 months, and 4% (95% CI, 7-22%) at 48 months. These analyses showed that the combination of both blood molecular markers improves the assessment of prognosis in stage IV melanoma patients treated with biochemotherapy.
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| Discussion |
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We selected three CTC markers and two serum methylated DNA markers for this study based on our previous findings (11, 31). All the markers were frequently found in blood from metastatic melanoma patients but not in blood from healthy donors. As expected, detection rates of multimarker assay were higher than any individual marker assay and these findings were consistent with previous studies (29, 36, 37). Detection rate of individual CTC marker was higher in patients with serum methylated DNA marker and the number of CTC markers significantly increased in patients with serum methylated DNA. These findings strongly suggest that CTC is a potential source of circulating methylated DNA.
To our knowledge, this is the first report that shows the correlation between two different molecular marker types in cancer patients' blood. Recently, DNA methylation status of tumor-related gene promoter region has turned out to be one of the most common tumor-related molecular alterations in various cancers, and many studies have shown tumor-related methylated DNA recovered from plasma or serum of cancer patients. Several sources of the cell-free DNA are suggested (i.e., lysis of CTC or micrometastases in organs, DNA leakage from cell as the result of tumor necrosis or apoptosis, or spontaneous release of DNA into circulation from primary and metastatic tumors; refs. 20, 38). However, to date, there is no agreement on the origin and mechanism that produces cell-free DNA in blood. This issue is important and still remains enigmatic. Although it is difficult in human patients to directly elucidate the origin of cell-free DNA in circulation, the significant correlation between CTC and serum methylated DNA implicates CTC as a possible candidate of serum methylated DNA. DNA degradation occurs in normal and tumor cells by apoptosis, producing small fragmented DNA, which is rapidly cleared out (20, 39). However, other mechanisms of tumor cell destruction may involve nonapoptotic process, and it has been suggested that circulating DNA may be produced by cells undergoing nonapoptotic death in blood, resulting in larger fragments of DNA in serum. Lysis of CTC due to physiologic forces or nonapoptotic factors in the blood circulation may contribute to an increase in circulating methylated DNA. This would yield more circulating DNA if more CTC were in circulation. Our findings indicated that the number of CTC markers correlated with detection of serum tumor-related methylated DNA; thus, greater number of CTC in blood is likely to release larger amount of DNA. The issues about spontaneous release of DNA from CTC in blood and half-life of circulating cell-free tumor-related DNA have been poorly understood. The destruction of CTC in blood and the immediate release of DNA may account for greater frequency of cell-free DNA in advanced-stage melanoma patients.
The numbers of CTC markers and serum methylated DNA markers detected were significantly correlated with treatment response. Combination assessment clearly showed that status of CTC and serum methylated DNA could predict tumor progression and survival. These findings suggested the high risk and aggressiveness of tumors in patients with large amounts of CTC and tumor-related DNA in bloodstream, resulting in systemic tumor spreading and failure of the treatment. Assessment of CTC and/or circulating tumor-related DNA can provide useful information on ongoing tumor spreading and treatment response in advanced-staged patients receiving adjuvant therapy, as well as early detection of tumor metastasis.
Although CTC and/or serum tumor-related methylated DNA predicts the disease outcome, the particular role of resistance to drugs might be considered because investigators have reported that resistance to cisplatin and tamoxifen, both of which were components of this biochemotherapy regimen, has been associated with RASSF1A hypermethylation in other malignancies (16, 40). The association between RASSF1A serum hypermethylation and poor clinical response to biochemotherapy may in part be mediated by melanoma resistance to the tamoxifen and cisplatin components of the regimen. These findings suggested that appropriate selection of specific markers based on functional role of the genes was important to assess the response to adjuvant therapy and to predict disease outcome.
Molecular detection of real-time tumor spreading is highly important for predicting the treatment efficacy and the management of melanoma patients. Patients with CTC or tumor-related methylated DNA showed poorer disease outcome compared with the patients without blood markers, and patients with both markers showed worst disease outcome. Thus, the composite assay system based on assessment of two different variables, CTC and serum tumor-related methylated DNA, enabled a more informative assessment as "lethal molecular biomarkers" and has greater advantage for predicting the outcome. Although we simultaneously assessed the blood specimens obtained before biochemotherapy treatment and showed the significance of blood molecular markers as a prognostic marker, serial monitoring of surrogate markers will provide more useful information for deciding on therapeutic strategy. As treatment regimens become multimodal and multiphasic, there will be an urgent need for clinically relevant surrogate markers that can be used to determine treatment response. To verify the clinical utility of CTC and serum methylated DNA, we are currently investigating the association between these two molecular markers and their significance as a potential prognostic factor using sequential blood specimens in a multicenter trial.
| Acknowledgments |
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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.
| Footnotes |
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Received 11/23/05. Revised 1/18/06. Accepted 3/13/06.
| References |
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for the treatment of metastatic melanoma. J Clin Oncol 1999;17:6517.
2B in patients with metastatic melanoma. Clin Cancer Res 2002;8:307581.This article has been cited by other articles:
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M. Widschwendter and U. Menon Circulating Methylated DNA: A New Generation of Tumor Markers Clin. Cancer Res., December 15, 2006; 12(24): 7205 - 7208. [Full Text] [PDF] |
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V. Muthusamy, S. Duraisamy, C. M. Bradbury, C. Hobbs, D. P. Curley, B. Nelson, and M. Bosenberg Epigenetic Silencing of Novel Tumor Suppressors in Malignant Melanoma Cancer Res., December 1, 2006; 66(23): 11187 - 11193. [Abstract] [Full Text] [PDF] |
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