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Department of Pediatrics [R. S., P. A. M., R. G.], Department of Epidemiology and Biostatistics [J. Q.], Orthopaedic Surgery Service, affiliated with Weill Medical College of Cornell University [J. H. H.], Department of Pathology [A. H.], Memorial Sloan-Kettering Cancer Center, New York, New York 10021; The Cancer Institute of New Jersey, Robert Wood Johnson School of Medicine, New Brunswick, New Jersey 08903 [D. B., J. R. B.]; and Institute for Frontier Medical Sciences, Kyoto University, Kyoto, Japan [J. T.]
2 To whom requests for reprints should be addressed, at Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10021. Phone: (212) 639-8392; Fax: (212) 717-3792; E-mail: gorlickr{at}mskcc.org
| Abstract |
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| Introduction |
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The expression of TS, a major target of 5-fluorouracil and its correlation with response of colorectal cancer patients to this therapy, has been extensively studied. TS expression at both the mRNA and protein level can serve as prognostic indicators in that increased expression is associated with poor outcome (79). A close association of TS with E2F-1 expression has been shown in colorectal cancer patient samples (10). The E2F family of transcription factors is known to be involved in the transcriptional regulation of several DNA synthesis enzymes and common chemotherapeutic targets (11). E2F-1 is the transcription factor most closely associated with TS expression (10, 11), whereas E2F-4 has been shown to be a regulator of DHFR expression (12). HT-1080 (fibrosarcoma) cell lines transfected to overexpress E2F-1 had increased expression of TS and, to a lesser degree, DHFR at both the protein and the mRNA levels (11). Possible correlations between E2F family members and RFC have not been investigated previously in patient samples, but given the relationship between E2F family members and DHFR and TS, as well as the similar cell cycle-dependent levels and requirements for these proteins, it would not be unexpected for E2F to play a role in the transcriptional regulation of RFC. In fact, SP1 sites, the binding sites for the E2F transcription factors, have been shown to be present in the RFC promoter (13).
This study was performed to investigate the possible relationship, if any, between the mRNA expression of E2F-1 and E2F-4 transcription factors and RFC, DHFR, and TS mRNA expression levels in OS patient samples. Real-time quantitative fluorescent reverse transcription-PCR was used to measure the mRNA expression levels of DHFR, TS, RFC, E2F-1, and E2F-4 in the 112 OS patient samples.
| Materials and Methods |
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RNA and DNA Preparation.
Approximately 20 mg of fresh tumor tissue were frozen in Ultraspec Reagent (Biotecx, Houston, TX) and stored at -80°C. Total RNA was isolated using the Biotecx protocol with RNA resuspended in sterile, diethyl pyrocarbonate-treated water. To reduce the risk of genomic DNA contamination, mRNA was subsequently isolated from the total RNA suspension using a modified protocol from the Roche mRNA Isolation Kit (Indianapolis, IN). In short, a mixture of biotin-labeled oligo(dT) probe (30 pmol), hybridization buffer, and 300 µg of streptavidin magnetic particles was added to the total RNA suspension. After a 10-min 37°C incubation, the magnetic particles were separated using a magnet, and the supernatant was discarded. The remaining magnetic particles were washed twice (wash buffer), and the beads were resuspended in 20 µl of sterile, diethyl pyrocarbonate-treated water and incubated for 2 min at 70°C followed by magnetic separation. The supernatant (containing the mRNA) was immediately reverse transcribed using the Promega Reverse Transcription Kit (Madison, WI). After second strand synthesis, the cDNA was stored at -80°C.
Quantitative Real-Time PCR.
The methodologies for the quantitative real-time PCR measurements have all been described previously. Standardization and validation of the assays have been described previously (10).4 Briefly, 5 µl of cDNA were added to 20 µl of Master Mix containing: 1x Taqman Buffer A (PE Biosystems, Foster City, CA); 3.5 mM MgCl2; 200 µM deoxynucleoside triphosphate; 0.025 units/µl Taq polymerase (AmpliTaq Gold; PE Biosystems); 900 nM each of forward primer and reverse primer; and 200 nM of probe. All probes were modified with a 6-carboxyfluorescein fluorophore at the 5' end and a 6-carboxytetramethylrhodamine quencher at the 3' end. All primers and probes (Table 1) were obtained from IDT (Coralville, IA) and validated for relative efficiency (14). All reactions were carried out using the Bio-Rad iCycler iQ (Bio-Rad, Hercules, CA) in 96-well plates. Cycling parameters were as follows: one 10-min hot start at 94°C; 45 cycles of 30-s denaturation at 94°C; 1 min of annealing at 55°C; 30-s extension at 72°C; and a final 5-min extension at 72°C. Each sample was run in triplicate for both the target gene and the housekeeping gene.
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CT. For each run, identical calculations were made for a known positive control reference cell line. The CCRF-CEM leukemia line was used for DHFR and RFC, HOS human OS line for TS and E2F-4, and SkBr3 breast cancer line for E2F-1. The
CT of the reference cell line was then subtracted from
CT yielding the 
CT, which was entered into the equation 2-
CT, accounting for the exponential amplification of PCR. The reference cell line for each gene was arbitrarily assigned an expression of one. The expression of the gene of interest therefore represents the fold-difference expression relative to the reference cell line.
Statistical Analysis.
The Spearman rank correlation coefficient (rs) was used to determine correlative values between genes and groups of genes (i.e., Huvos III versus Huvos IIIIV and primary versus metastatic) because the observed data are not normally distributed. Because some patients contributed multiple samples (biopsy, definitive and/or relapse/recurrent at primary site and/or metastatic site), we used the bootstrap method to take the dependent measurements within patients into account. We resampled patients 1000 times, then 1000 Spearman rank correlation coefficients were calculated.
| Results |
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The median levels of expression for TS, E2F-1, and E2F-4 in the total sample pool were 0.15, 0.52, and 1.45, respectively (Table 3, Fig. 1). When comparing median TS expression in the primary site samples versus the metastatic site samples, little difference was noted (0.02-fold). The good responders had a median TS expression 0.08 lower than the poor responders. E2F-1 and E2F-4 demonstrated similar expression levels in good and poor responders. In the primary versus metastatic site, E2F-1 median expression was essentially unchanged, whereas E2F-4 median expression was 0.21 higher in the metastatic site samples than in the primary site samples.
Spearman correlation values between E2F-1/E2F-4 and DHFR and RFC and TS are summarized in Table 4. With respect to the total sample pool, the tightest correlation appears to exist between E2F-1 and RFC (rs = 0.63, P < 0.001) and the weakest correlation between E2F-4 and TS (rs = 0.33, P < 0.001). Within the metastatic site sample pool, correlations for E2F-1:DHFR and E2F-4:TS were not significant with Ps > 0.150. The tight correlation that appears to exist between E2F-1 and RFC fluctuates slightly when the total sample pool is subdivided by either site of specimen or Huvos grade. No substantial fluctuations are noted in any of the Spearman correlation coefficients when the total sample population is divided into primary versus metastatic or Huvos I, II versus Huvos III, IV. DHFR and TS both appear to link more closely with E2F-1 than with E2F-4, whereas with RFC, the correlation values are comparable between E2F-1 and E2F-4.
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| Discussion |
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Briefly summarizing some of the information that is known about the E2F pathway, inactive E2F is complexed to the retinoblastoma gene product (pRB). Upon (hyper-) phosphorylation of pRB as part of the transition from the G1 to S phase of the cell cycle, the E2F protein is released from the E2F-pRB complex and along with its binding partners (DP protein family) becomes available to transcriptionally activate a plethora of target genes, including many genes involved in DNA synthesis and chemotherapy response (e.g., DHFR, TS, thymidine kinase, ribonucleotide reductase; Refs. 1517). E2F is known to be involved in the transcriptional regulation of DHFR and TS (15). Both E2F-1 and E2F-4 were investigated because prior studies have suggested E2F-1 is involved in TS regulation (10), whereas E2F-4 is involved in DHFR regulation (12). The RFC promoter is known to have many features in common with the DHFR promoter such as the presence of Sp1 sites, but its regulation has been less extensively characterized (13). The majority of OS samples have nonfunctional pRB usually through large gene deletions or rearrangements (1821). In SaOS-2, a human OS cell line known to have truncated and nonfunctional pRB, expression levels of DHFR and TS are 24-fold greater than the HT-1080 fibrosarcoma cell line with wild-type pRB, which would be expected secondary to increased levels of free E2F (22).
TS protein or mRNA levels have been shown to be a major determinant of response to 5-fluorouracil chemotherapy in colorectal adenocarcinoma (2326). 5-Fluorouracil is not used in the treatment of OS. TS was primarily included in this study to allow comparability with prior studies. Consistent with prior observations in other tumor systems, E2F-1 correlated most strongly with TS expression. E2F-4 also correlated significantly with TS expression.
In contrast to what is observed in colorectal adenocarcinoma, levels of E2F and TS expression are not markedly higher in the pulmonary metastases as compared with the primary tumor in OS (10). This may reflect differences between the two tumor types. OS metastasizes to the lungs much earlier in its clinical course and has much more frequent alterations in the pRB pathway both of which may account for the difference. The relationships between E2F-1:DHFR and E2F-4:TS in metastatic site samples were statistically insignificant (P = 0.337 and P = 0.202). Data from the total sample population suggests that E2F-1 transcription factor could be an important regulator of DHFR expression, but whether this relationship is maintained through metastasis cannot be determined. DHFR amplification in metastatic samples has not been demonstrated in prior studies, but those studies have relied on Southern blots that are relatively insensitive. Studying metastatic OS samples for low-level DHFR amplification with PCR or dot blots should be considered in subsequent studies.
Also in contrast to prior studies, decreased RFC mRNA expression did not correlate with an inferior histological response to induction. The basis for the conflicting results is unknown, but prior studies have used relatively small numbers of OS samples. Additional prospective studies will need to be performed to determine the potential prognostic value of RFC expression in OS. When comparing the poor responders (Huvos grade I and II) to good responders (Huvos grade III and IV), there is a decreased median expression of all genes assessed in this study. It may be postulated that increased DHFR expression in the OS samples results in MTX resistance and therefore inferior response, but this explanation could not be used for the RFC because, historically, decreased expression has been associated with MTX resistance. If decreased RFC expression is indeed an indicator of inferior histological response, the uniformly higher RFC mRNA expression of the poor responders in our study may be secondary to the tumors cell cycle or proliferative state, which is being reflected in the expression of these S-phase genes. Additional studies will be necessary to determine which factors are primary determinants of histological response in OS and which are downstream events.
The association between E2F-1/E2F-4 and RFC should be regarded as preliminary yet informative. Identifying one of the transcriptional factors regulating RFC expression is important, but it is likely to be only one of many factors that contribute to the regulation of this protein involved in MTX transport and resistance. For example, RFC promoter methylation has been shown to be associated with decreased RFC expression in some cell lines (27).
To understand these findings and their correlation with histological response to induction chemotherapy in OS, additional studies of the genes upstream of the E2F transcription factors should be performed. These studies should focus on pRB as well as other regulators of the pathway, including the cyclins, cyclin-dependent kinases, and cyclin-dependent kinase inhibitors. A simultaneous study of the various components of the pRB pathway along with the downstream target genes in OS tumor samples may allow the identification of which factors are independent determinants of chemotherapy response and subsequently patient outcome.
| Footnotes |
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3 The abbreviations used are: MTX, methotrexate; RFC, reduced folate carrier; DHFR, dihydrofolate reductase; OS, osteosarcoma; TS, thymidylate synthase. ![]()
4 A. S. Levy, H. Sather, P. Steinherz, R. Sowers, M. La, J. Moscow, P. S. Gaynon, F. Uckun, J. R. Bertino, and R. Gorlick. Reduced folate carrier and dihydrofolate reductase expression correlate with outcome in acute lymphocytic leukemia: a childrens cancer group study, submitted for publication. ![]()
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.
Received 11/11/02; revised 3/ 7/03; accepted 3/26/03.
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