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Regular Article |


§
From the Departments of Pathology,*
Biochemistry,
Community and Family
Medicine,
and
Medicine,§
Dartmouth Medical School, Hanover;
and The Norris Cotton Cancer Center, Dartmouth-Hitchcock Medical
Center, Lebanon, New Hampshire
| Abstract |
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| Introduction |
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Recently we described a common single nucleotide polymorphism (SNP) in the promoter of MMP-1, in which one allele is associated with enhanced transcription of this gene.8 The SNP is located at -1,607 bp and is represented by the presence or absence of a guanine (G) at this position. In the absence of the G, the sequence reads 5'-GAA-3', whereas the presence of an extra G gives the sequence 5'-GGAA-3', a consensus binding site for the ETS family of transcription factors. Indeed, MMP-1 genes with promoters carrying the 2G allele are transcribed at a significantly higher rate in both normal fibroblasts and in tumor cells than are MMP-1 genes with promoters carrying the 1G allele.8 The frequencies of the 1G and 2G alleles appear to be approximately equal in normal populations, whereas in a small sample of tumor cell lines tested, the frequency of the 2G allele was increased to 60%.8 In addition, there was a higher than expected proportion of apparent 2G homozygotes in these cell lines, suggesting that the 2G allele may be associated with aggressive and invasive cancers.8 This concept is supported by a significant association of the 2G allele with ovarian16 and endometrial cancer,17 and with increased expression of MMP-1 protein in these diseases.16,17 Although the findings in tumor cell lines may simply reflect a greater proportion of tumors derived from homozygous 2G hosts, it is also possible that these aggressive tumors result from the loss of the 1G allele in tumors from heterozygous hosts [loss of heterozygosity (LOH)].
LOH is a common event in many tumors and is often associated with advancing disease, presumably because of loss of tumor suppressor gene(s) at the deleted locus.18-26 LOH occurs at several chromosomal loci, including the MMP-1 locus at 11q22.23.27 We tested the hypothesis that if metastatic tumors were derived from cells that retained the 2G allele, they would have a selective invasive advantage and would, therefore, be overrepresented in heterozygous hosts compared to tumors that had retained the 1G allele. Accordingly, we genotyped normal and metastatic tumor tissues from patients with melanoma to determine the frequency of the 2G allele and the occurrence of LOH. To perform LOH studies with a relatively large number of patient samples, we developed a rapid method to screen samples for heterozygosity and precise quantitative techniques to objectively assess LOH.
| Materials and Methods |
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Samples were available from a total of 61 patients: frozen tumor and peripheral blood leukocytes from 12 patients; formalin-fixed, paraffin-embedded normal and tumor tissue from 44 patients; and both frozen and paraffin-embedded samples from five patients. The frozen tissues had been stored for up to 3 years at -70OC; the paraffin blocks had been stored for up to 7 years at room temperature.
In addition to these paired normal tissue and tumor samples, control germline DNA samples from known heterozygotes were run with each experiment to provide additional data for calculation of interassay variability.
DNA Isolation
Frozen Tumor Tissue and Peripheral Blood Leukocytes
Genomic DNA was isolated from frozen peripheral blood lymphocytes or from frozen single-cell tumor suspensions using Gentras Puregene (Minneapolis, MN) kit according to the manufacturers instructions. These tumor samples had been collected for the purpose of vaccine production and had been trimmed, originally, to be free of normal tissue; however, this was not confirmed at the time of this study.
Paraffin-Embedded Tissues
One 5-µm section and three adjacent 10-µm serial sections of formalin-fixed, paraffin-embedded tumor and normal tissue were mounted on glass slides. The 5-µm section was stained with hematoxylin and eosin. Under a dissecting microscope, normal and tumor tissue were identified by a pathologist on unstained sections by comparing these to the adjacent stained section, and were scraped separately with a sterile pin into a microfuge tube. The pathologist performing the dissections estimated that no more than 20% of the cells dissected from tumor were contaminating normal cells. Digestion buffer, consisting of 25 µl of 50 mmol/L Tris-HCl, pH 8.5, 2% Laureth-12, 400 µg/ml proteinase K, was added, and the samples were incubated overnight in a 55°C oven to minimize evaporation. An additional 25 µl of digestion buffer was added and the samples were incubated at 55°C for an additional 4 to 5 hours. The proteinase K was inactivated by heating to 95°C for 10 minutes. The samples were spun at 13,000 x g in a microcentrifuge for 2 minutes and the supernatant was used for polymerase chain reaction (PCR). DNA from some tumor samples could not be amplified using this lysis method, perhaps because of high melanin concentrations that may have interfered with the PCR reaction.28 Those samples were recut and DNA was isolated using the Puregene kit.
SNP Determination by Restriction Fragment Length Polymorphism (RFLP) Analysis
An RFLP method to distinguish the SNP was developed to screen
samples rapidly and to identify heterozygotes for LOH studies.
Restriction enzyme sites were introduced into the PCR amplicon at the
SNP locus by making a single base change in the downstream primer, such
that the 1G allele digested with BglII and the 2G allele
digested with Alw I (Figure 1A)
. Purified DNA (100 ng) or lysate (5
µl) from the paraffin-embedded samples was amplified using 50 pmol of
each primer (RFLP forward: GTC TTC CCA TTC TTC TTA CC; RFLP reverse:
ATT GAT TTG AGA TAA GTC AGA TC) in 1x Qiagen (Valencia, CA) PCR buffer
(Tris-Cl, pH 8.7, at 20°C, KCl,
(NH4)2SO4,
1.5 mmol/L MgCl2), 200 µmol/L each dNTP, 1.5
mmol/L additional MgCl2, for a total of 3 mmol/L
MgCl2, 2.5 U HotStarTaq (Qiagen) in a 100 µl
reaction. Cycling conditions were 95°C for 15 minutes followed by 35
cycles of 95°C for 30 seconds, 50°C for 30 seconds, and 72°C for
30 seconds with a final 72°C extension for 2 minutes. Samples (20
µl) were digested using 10 U of Alw I or BglII
(New England Biolabs, Beverly, MA) at 37°C for 2 to 3 hours. The
digests were electrophoresed on 3% SFR Agarose (Amresco, Solon, OH)
and visualized with ethidium bromide.
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Tumor and normal tissue samples from heterozygotes were analyzed
by two quantitative PCR assays, using sets of nonoverlapping primer
pairs, that generated either a 72-bp amplicon or an 82-bp amplicon.
This dual amplification with no overlap between the primer sets
controlled for the possibility that a point mutation was present under
either of the primer binding sites in the tumor DNA (that might alter
the relative amplification of the 1G and 2G alleles), thereby giving a
false indication of LOH. The primers for the 72-bp product were:
forward: GTT ATG CCA CTT AGA TGA GG, end-labeled with
-32P ATP (3,000 Ci/mmol); reverse: CTT GGA TTG
ATT TGA GAT AAG (Figure 1B)
. The primers for the 82-bp product were:
forward: GAA ATT GTA GTT AAA TAA TTA G, end-labeled with
-32P ATP; reverse: GCT TAC TCA TAA ACA ATA CTT
CAG (Figure 1B)
. The reverse primer of the 82-bp set was modified by
the addition of a 5' terminal G that, along with the cycling
conditions, helped drive the PCR reaction to allele + A.29
This modification eliminated shadow bands seen in previous studies
using a different primer set.8,30
For both PCR reactions 100 ng of purified DNA or 5 µl lysate from the paraffin-embedded samples was amplified using 50 pmol of each primer in 1x Qiagen PCR buffer (Tris-Cl, pH 8.7, at 20°C, KCl, (NH4)2SO4, 1.5 mmol/L MgCl2), 200 µmol/L each dNTP, 1.5 mmol/L additional MgCl2, for a total of 3 mmol/L MgCl2, 2.5 U HotStarTaq (Qiagen) in a 100 µl reaction. Samples containing known ratios of 1G and 2G DNA were prepared for a standard curve (see Results) using purified peripheral blood DNA from 1G and 2G homozygotes. For the 72-bp product, cycling conditions were 95°C for 15 minutes, followed by 30 cycles of 95°C for 30 seconds, 50°C for 30 seconds, and 72°C for 30 seconds with a final 72°C extension for 2 minutes. For the 82-bp product, cycling conditions were 94°C for 15 minutes, followed by 10 cycles of 94°C for 15 seconds, 50°C for 30 seconds, and 72°C for 60 seconds, then 20 cycles of 89°C for 15 seconds, 50°C for 30 seconds, and 72°C for 60 seconds with a final 72°C extension for 30 minutes.
Five µl of PCR product from each reaction was then mixed with 5 µl
of formamide loading buffer and denatured at 95°C for 5 minutes. Five
µl aliquots of the sample mixtures were loaded on an 8% denaturing
acrylamide gel and run at 55 W constant power until the xylene cyanol
was
6 cm from the bottom of the gel. Under these conditions there
was excellent resolution of the 1G and 2G alleles for both the 72/73-bp
and 82/83-bp products (see Results). Gels were exposed to a
phosphorimager screen (Molecular Dynamics, Sunnyvale, CA) for 15 to 60
minutes and to film for 30 minutes to several hours.
For quantitative analysis of allele intensity, the phosphorimager screens were scanned and the band intensities quantified using ImageQuant v. 1.2 (Molecular Dynamics) by drawing a 2 by 1 matrix around each lane, placing the 2G allele in the upper box and the 1G allele in the lower box. The percent 2G was calculated by dividing the signal in the upper box by the total signal in both boxes and multiplying by 100. The signals were not corrected for background.
Statistical Testing Methods
Under the null hypothesis, assuming that allele retention is a random event, we would expect the 1G or 2G allele to be retained in an equal number of tumors (ie, a genotype ratio of 1:1). We calculated an exact P value using a binomial distribution31 for the likelihood that the observed genotype ratio in the 12 tumors with LOH was a chance finding.
| Results |
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Normal DNA from 61 patients was genotyped using the RFLP method,
yielding 102- or 103bp products. There were 31 1G/2G heterozygotes, 16
1G/1G homozygotes, and 14 2G/2G homozygotes (allele frequencies:
1G = 0.52, 2G = 0.48). Figure 2
demonstrates the RFLP pattern after digestion with BglII
(the 102-bp 1G allele is cleaved) and after digestion with
Alw I (the 103-bp 2G allele is cleaved). This method is
rapid and does not require radioactivity, and the use of separate
restriction enzymes to recognize each of the two alleles serves as an
internal control.
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Of the 31 heterozygous patients identified by RFLP analysis, one patient had three metastases available for study, one patient had two metastases available for study (both of which were refractory to DNA amplification), and 29 had one metastasis available for study (one of which was refractory to amplification). The three samples refractory to DNA amplification were from paraffin blocks. In summary, 31 tumors and normal tissue from 29 patients were tested successfully for LOH at the SNP locus with the quantitative 72-bp and 82-bp amplicon assays.
The most sensitive means of detecting LOH was by visual inspection of
exposed film, the unaided eye readily seeing small deviations from the
pattern of equal allele intensity seen with normal DNA from
heterozygotes. However, at the outset of the study it was decided that
an objective, quantitative method of assessing allelic imbalance was
preferable to visual inspection to eliminate any possibility of
observer bias. Accordingly, each experiment included seven standards,
composed of various proportions of DNA from 1G and 2G homozygotes
(0/100, 25/75, 40/60, 50/50, 60/40, 75/25, 100/0) expressed as
"percent 2G" (Figure 3)
. A standard
curve (x axis = actual percent 2G, y
axis = observed percent 2G) was plotted and analyzed by linear
regression, and the regression equation was used to calculate the
actual percent 2G in the unknown samples. Because the
phosphorimager data used to determine observed percent 2G were not
corrected for background (see Materials and Methods), the regression
line has a positive intercept on the y axis. The standard
curves from successive experiments with each primer pair were
remarkably reproducible and linear (Figure 4)
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Twelve of the 31 tumors (39%) showed marked or consistent deviation
from the 1G/2G ratio characteristic of normal heterozygous tissue and
were classified as having undergone LOH. Each of these tumors was from
a different patient. Ten (83%) of the tumors underwent LOH with
retention of the 2G allele, and two (17%) tumors underwent LOH with
retention of the 1G allele (Figure 5)
. This departure from the expected
1:1 ratio was statistically significant (P =
0.04).
Table 1
lists some of the clinical
characteristics of the patients whose tumors had undergone LOH, the
tissue source of the metastatic tumors that were analyzed, and the
likely mode of spread (lymphatic or hematogenous) of each of the
metastases.
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| Discussion |
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The varying degrees of LOH observed in our study most likely reflect either the presence of contaminating stromal cells and/or tumor heterogeneity, with only a portion of the sampled tumor having undergone allelic loss. An alternative explanation is that there was amplification of one MMP-1 allele, not allelic loss. Indeed, there are examples of amplification at 11q13 associated with aggressive breast carcinoma32 and rare examples of MLL amplification at 11q23 associated with acute myelogenous leukemia.33 Although we did not investigate this possibility, it seems to be an unlikely explanation for our findings, because a large body of literature has documented frequent LOH at this locus, not gene amplification, in many tumors including melanoma. Furthermore, we have preliminary data from analysis of satellite markers flanking the MMP-1 locus that large regions of LOH occurred in five metastatic melanomas that were tested, in some cases extending at least over the region 11q21-q24 (data not shown). Finally, a recent report describes allelic loss at 11q23 in regional lymph node metastases in melanoma, providing further support for our findings.34
Loss of regions of chromosomes 1, 3, 6, 7, 8, 9, 10, and 18 has been documented in many tumors,18-26 suggesting that genes in several chromosomal locations may be involved in tumor formation and/or progression. LOH is often thought to indicate the loss of one copy of a tumor suppressor gene at that locus, the other copy previously having undergone loss or inactivation by another mechanism, such as point mutation. LOH at 11q22-q23 has been described in numerous cancers, including melanoma, breast, ovarian, lung, and oral squamous cell carcinomas.18-26 The region involved includes a known tumor suppressor gene, ATM,19 as well as several candidate tumor suppressor genes, eg, IGSF4,35 VACM-1,36 and PPP2R1B.20
It is likely that deletion of one or more of these or other genes at this locus is a major determinant of aggressive behavior and metastasis in melanoma, independent of the patients MMP-1 genotype. Because deletions at this locus may be large, it is also likely that the deleted region will often include the MMP-1 gene. Furthermore, because it is reasonable to assume that LOH is a random event, there is an equal probability of retaining either of the two MMP-1 alleles. Consequently, if a patient is a 1G/2G MMP-1 heterozygote, and deletion occurs on the chromosome that carries the 1G allele, leaving behind an active 2G allele, that tumor cell may have an additional growth advantage over a cell that undergoes a similar deletion of 11q on the chromosome carrying the 2G allele.
A model of how a tumor suppressor gene and MMP-1 may cooperate to enhance tumor growth and invasion is suggested by a recent study of PPP2R1B, a candidate tumor suppressor gene located in an interval that flanks the MMP-1 locus.20 PPP2R1B encodes an isoform of the A subunit of the serine/threonine protein phosphatase 2A. Deletion/mutation of this gene generates a truncated protein that is unable to bind to the catalytic subunit of the PP2A holoenzyme, suggesting that the PP2R1B gene product may suppress tumor development through its role in cell cycle regulation and control of cell growth. If loss of this tumor suppressor gene coincides with LOH at the MMP-1 locus, tumor growth may be enhanced through de-regulation of cell growth, and the invasive potential of the tumor is maximized if the 2G allele is retained.
Increasing evidence suggests that elevated MMP-1 expression is associated with tumor invasiveness and with a poor prognosis in a variety of cancers, including colorectal, esophageal, breast, ovarian and endometrial carcinomas, and melanoma.12-17 Genotyping for the MMP-1 SNP, and rapid quantitative analysis of LOH in tumors may, therefore, serve as an additional prognostic indicator.
| Acknowledgements |
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| Footnotes |
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Supported by National Institute of Health grants CA-77267 (to C. E. B.), ST32-CA09658 (to J. L. R.), CA-23108 to the Norris Cotton Cancer Center from the National Cancer Institute, and a grant from the Ronya and Gregory Kozmetsky Foundation (to C. E. B.).
Present address of Joni L. Rutter, Ph.D.: National Cancer Institute, NIH, DCEG, Lab of Population Genetics, 41 Library Dr./Bldg. 41/Room D701, Bethesda, MD 20892 MSC 5060.
Accepted for publication October 4, 2000.
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