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Advances in Brief |
Laboratory of Cellular and Molecular Biology [C. D. H., P. J. M.], Research Resources Branch [A. B. Z.], Gerontology Research Center, National Institute on Aging, Baltimore Maryland 21224; Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore, Maryland 21287 [P. J. M.]; Department of Pathology, The University of Michigan Medical School, Ann Arbor, Michigan 48109 [K. R. C., D. R. S.]
| ABSTRACT |
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| Introduction |
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Recent advances in the field of functional genomics have made it possible to study gene expression in EOC on a large scale. cDNA array technology has been used advantageously in the identification of numerous genes differentially expressed in EOC (20, 21, 22) . From these studies, many genes have emerged as promising biomarker candidates, including HE4, a secreted protease inhibitor. Using a specialized array, many angiogenesis genes were found differentially regulated in ovarian cancer (23) . In addition, we have used SAGE to identify genes differentially expressed in EOC (24) . Interestingly, several of the most up-regulated genes encode surface or secreted proteins, such as Kop, SLPI, claudin-3 and claudin-4, making these products attractive candidate biomarkers.
Although advancing our knowledge of genes expressed in EOC and generating a myriad of candidate biomarkers, functional genomics approaches have done little to improve our understanding of the molecular pathways involved in EOC. In addition, quantitative large-scale analysis of gene expression in primary tumors is technically challenging because of the requirement for relatively high amounts of intact RNA. In this report, we have chosen 13 highly relevant genes for quantitative analysis of expression in a panel of 39 microdissected ovarian cancers. Importantly, the genes under study were not chosen based on their importance in other cancer types but rather based on their relevance to EOC. We report the finding of many genes that are highly up-regulated in the vast majority of ovarian carcinomas. In addition, we show that the genes overexpressed in serous ovarian cancer are also overexpressed in other subtypes, making the genes studied here candidates as general EOC biomarkers. Finally, we find that many genes are up-regulated coordinately in ovarian cancer, which suggests the existence of a few dominant molecular pathways, whose abnormal regulation is responsible for the overexpression of many genes.
| Materials and Methods |
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The comparative CT method (PE Applied Biosystems) was used to determine relative quantitation of gene expression for each gene compared with the GAPDH control. First, the CT values from GAPDH reactions were averaged for each duplicate. Next, the relative difference between GAPDH and each duplicate was calculated (2 CT GAPDH - CT experimental). This value was then averaged for each duplicate set and divided by the value for HOSE, a short-term culture of ovarian surface epithelial cells, to determine the relative fold induction for each sample relative to these cells.
Sequencing of K-ras.
Mutations in the K-ras gene were identified by sequencing a 233-bp fragment encompassing codons 12, 13, and 61, which are frequently mutated in cancer. The fragment was obtained by PCR amplification of
5 ng of cDNA used for the real-time RT-PCR analyses. The PCR reactions were performed for all of the samples as follows: 35 cycles at 95°C for 30 s; 58°C for 1 min; and 70°C for 1 min, followed by a 5-min extension step at 72°C. The PCR amplification primers (forward, 5'-CCAGGTGCGGGAGAGAG-3'; reverse, 5'-CCCTCATTGCACTGTACTCC-3') were also used for sequencing the gel-purified fragments.
Multivariate Analyses.
Analyses were performed using S-PLUS 2000 for PC (Mathsoft 2000, Seattle, WA). We computed a matrix of Pearson product moment correlations to measure the strength of bivariate associations between pairs of genes. We used F-ratios to assess the likelihood that each bivariate correlation was different from zero. We considered F-ratios with P < 0.001 significantly different from zero because this probability level minimized the chance of declaring spurious correlations. We hypothesized that genes in the same pathway would correlate more highly among themselves than with other genes. If this were so, we further hypothesized that, if we found more than one cluster of associated genes, then this would imply the presence of multiple pathways with some genes in the same pathway and other genes in different pathways. Additionally, genes contributing to more than one cluster of associations might reflect connections between pathways.
We used maximum-likelihood factor analysis (27) with Promax rotation to examine the matrix of correlations for clusters of associated genes. This technique provides a goodness-of-fit test to determine the number of "factors" that are regarded as hypothetical constructs with which the measures (gene expression) are related (28) . Factor analysis is a technique that reduces the relationships among many measures to a smaller number of (hypothetical) constructs. These constructs are linear combinations of the measured variables, but are considered representations of underlying or common factors. The goodness-of-fit test expresses the extent to which the derived linear combinations reproduce the measured relationships. The appropriate number of factors are calculated when a smaller number of derived factors adequately reproduce a larger number of measured variables.
The factors are interpreted by examining the weights from the linear combinations of measured variables. We interpret variables with large weights or "loadings" as sharing the same construct. Generally, the matrix of factor loadings is transformed to "simple structure," the goal of which is to produce large associations between each measure and one (and only one) factor. We performed Promax rotation, a transformational technique that allows correlated factors if, indeed. the data do not support orthogonal factors (29) . In the present analyses, correlated factors might arise when some genes are involved in more than one pathway. A loading factor of 0.4 is typically accepted to be significant.
| Results and Discussion |
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The genes analyzed generally exhibited various levels of up-regulation in the majority of the microdissected ovarian tumors studied (Fig. 1)
. Fold up-regulation compared with HOSE was highly variable. For example, ceruloplasmin was found at 10,000-fold above the levels in HOSE, whereas TIMP-2 was typically found elevated 2- to 3-fold. Interestingly, the induction levels as determined by RT-PCR were typically much higher than the figures obtained with SAGE. This may be attributable to two factors. First, the noncancerous components of the bulk tissue may have diluted the true fold induction. However, expression levels in RNA from microdissected specimens and SAGE tumors OVT6 and OVT8 were typically very similar (Fig. 1)
, which suggests that the dilution factor may not be a major contributor to the observed differences. Second, some of the genes that were found expressed at very low levels in normal tissues did not show a statistically significant number of tags in the SAGE analysis, which would bias the fold induction calculated using SAGE data. For example, the tag corresponding to ceruloplasmin was found 79 times in the tumors but was not found in any of the three normal samples (24)
. Although this led to a calculated 79-fold increase, it is clear that the real difference could be much higher. Indeed, using real-time RT-PCR, we found that ceruloplasmin was up-regulated an average of 10,000-fold in serous samples and even higher in clear cell specimens (60,000-fold; Fig. 1
). FR1 also exhibited up-regulation levels in the thousands of fold. In any event, real-time RT-PCR validated the use of bulk tissue as starting material for SAGE analysis. Importantly, the quantitative RT-PCR analysis allowed us to examine expression of genes identified by SAGE in various ovarian cancer subtypes in a highly quantitative manner. All of the genes overexpressed in serous ovarian cancers were also overexpressed at various levels in the other ovarian cancer subtypes. Intriguingly, GPX3 appeared to be overexpressed at even higher levels in clear cell ovarian carcinomas. Indeed, GPX3 was found at levels 30-fold higher on average in clear cell cancer compared with the other ovarian cancer subtypes (Fig. 1)
. The high level of expression of GPX3 in clear cell ovarian cancer is particularly obvious when values are plotted on a linear scale (Fig. 1)
. Ceruloplasmin was also found at very high levels in at least two clear cell ovarian cancers. It is intriguing that GPX3 and ceruloplasmin, two genes implicated in oxidative stress response, are highly overexpressed in clear cell carcinomas, an EOC subtype notorious for its aggressiveness and poor prognosis. High levels of antioxidants likely result from high amounts of reactive oxygen species, which have been implicated in mitogenic signaling (37)
and angiogenesis (38)
. In addition, high levels of antioxidant proteins may make cells more resistant to chemotherapy (39)
, which explains the poor response of clear cell ovarian cancer to treatment. These findings suggest that antioxidant inhibitors in combination with chemotherapy may improve response of clear cell ovarian cancers. In any event, GPX-3 may represent the first molecular marker that is highly specific for clear cell carcinomas.
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Association between the Expression of Various Genes.
We wondered whether overexpression of the 13 genes examined here were the result of the malfunction of numerous signaling pathways or a restricted number of pathways. It has been shown that expression of genes that are part of a common pathway tend to be coordinately regulated and that this behavior is apparent if a sufficient number of tumors are examined (40
, 41)
. On the other hand, an absence of coordinate regulation would result in random levels of overexpression for the different genes in a given tumor. On multivariate analysis of the 44 samples, we found that several gene expression patterns showed significant association (P < 0.001; Fig. 2A
). For example, whereas the expression patterns of clusterin/ApoJ and IGFBP-2 clearly did not exhibit any association (Fig. 2B)
, the expression patterns of STAT1 and Kop were very similar (Fig. 2C)
. Overall, we found 26 pairs of genes with a significant (P < 0.001) correlation coefficient. This result might be surprising considering that genes overexpressed in tumors are often assumed to be the result of the malfunction of a large number of pathways interacting in complex manners. However, it is important to remember that these genes were chosen because of high level of expression and consistency of up-regulation. Thus, there appears to be few pathways that meet these criteria, but these pathways may be highly relevant to ovarian oncogenesis.
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To explore the possibility of the existence of multiple pathways leading to the expression patterns observed, we conducted further statistical analyses. We hypothesized that genes in the same pathway would correlate more highly among themselves than with other genes. If this were so, we further hypothesized that if we found more than one cluster of associated genes, then this would imply the presence of multiple pathways with some genes in the same pathway and other genes in different pathways. Additionally, genes contributing to more than one cluster of associations might reflect connections between pathways. We used maximum-likelihood factor analysis to examine the matrix of correlations for clusters of associated genes. This technique provides a goodness-of-fit test to determine the number of factors (pathways) that are regarded as hypothetical constructs with which the measures (gene expression) are related. We found that the gene expression patterns could be explained by the existence of four independent pathways (Table 3)
. Pathway 1 was associated with high expression levels of EpCAM/GA733-2, Kop, TIMP3, FR1
SLPI, STAT1, and ApoE. Pathway 2 was associated with high expression of ApoJ/clusterin, EpCAM/GA733-2, Kop, TIMP3, FR1
SLPI, STAT1, ApoE, and ceruloplasmin. There is significant overlap between pathways 1 and 2. Additional experiments will be necessary to determine whether these hypothetical constructs represent two different molecular pathways with extensive cross-talk or two aspects of the same pathway. Pathway 3 was associated with expression of GPX3, ApoJ/clusterin, SLPI, and ceruloplasmin. Interestingly, pathway 4 appeared to be associated with high levels of expression of S100A2 only, which suggests a more restricted expression pattern corresponding to the activation of this pathway. SLPI expression was associated with three different pathways, which suggests that it may represent a useful marker for ovarian cancer. This is consistent with the data showing high levels and consistent overexpression of SLPI in all of the ovarian tumor subtypes (Fig. 1
; Table 2
). Overall, our data suggest that the activation of a restricted number of pathways may underlie much of the aberrant gene expression profiles in ovarian cancer.
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In this report, we have studied the expression of many genes up-regulated in EOC using real-time RT-PCR, a highly sensitive and reproducible technique. In addition, we have used microdissected specimens to maximize the proportion of tumor cells in the samples under study. The combination of real-time RT-PCR and microdissected specimens allowed a highly quantitative study of many genes in a relatively large number of ovarian tumors. We show that the genes that were suggested by SAGE to be relevant to EOC tumorigenesis are indeed highly elevated in the vast majority of ovarian carcinomas of various subtypes. Whereas most candidate biomarkers appear to be general markers of ovarian cancer, GPX3 appears to be specific for clear cell carcinoma. This represents the first systematic and highly quantitative study of gene expression in ovarian epithelial tumors of various subtypes. It is remarkable that several of the genes studied here are coordinately regulated in ovarian cancer. This finding suggests that a few pathways that are frequently activated in ovarian cancer are responsible for much of the aberrant gene expression observed consistently in EOC. Such an association is somewhat unexpected but suggests a certain amount of order in a disease that is known for its high level of heterogeneity. It will be interesting to identify the pathways up-regulated in ovarian cancer because they may provide new targets for effective therapeutic interventions.
| FOOTNOTES |
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1 To whom requests for reprints should be addressed, at Laboratory of Cellular and Molecular Biology, Gerontology Research Center, NIA, NIH, 5600 Nathan Shock Drive, Baltimore, MD 21224. E-mail: morinp{at}grc.nia.nih.gov Phone: (410) 558-8506; Fax: (410) 558-8386. ![]()
2 The abbreviations used are: EOC, epithelial ovarian cancer; SAGE, serial analysis of gene expression; HOSE, human ovarian surface epithelium; ApoJ, apolipoprotein J; GPX, glutathione peroxidase; SLPI, secretory leukocyte protease inhibitor; ApoE, apolipoprotein E; STAT, signal transducer and activator of transcription; GAPDH, glyceraldehyde-3 phosphate dehydrogenase; RT-PCR, reverse transcription PCR; TIMP, tissue inhibitor of metalloproteinase, IGFBP, insulin-like growth factor binding protein; FR, folate receptor; MGP, matrix gla protein. ![]()
Received 1/ 4/01. Accepted 3/26/01.
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