We examined global gene expression patterns in primary ovarian cancers and malignant effusions and found differences that may be related to tumor progression. Our results are consistent with many reports that document the heterogeneity of gene expression patterns noted in ovarian cancer [14, 16–18, 20–22]. These data underscore the heterogeneity of this disease and the profound molecular differences within tumor sub-groups with comparable morphology.
Several clusters of variably expressed genes may have relevance to the biology of ovarian cancer. A large cluster of genes from chromosome 8q21-24 was more highly expressed among a subset of the cancers, suggesting an amplification of this region on chromosome 8. This was seen in both the primary and the effusions from the corresponding samples with these abnormalities. Transcripts over-expressed in this cluster include YWHAZ, that encodes the zeta isoform of 14-3-3 protein (tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein) family. 14-3-3 proteins are expressed in a number of cancers and are involved in the cell cycle and also in prolonging cell survival. TPD52 (hD52) that has been shown to be in the peak of the 8q21 amplicon in breast cancer cell lines was also over-expressed in a number of cancers in this cluster. A recent report suggests that TPD52 is a candidate target gene and putative oncogene at 8q21 . In addition, co-clustering of a number of genes in this region was also observed in the cluster resulting from the intrinsic genelist (Figure 5C, panel a).
Involvement of the MAP kinase pathway may be indicated in a large number of the cancers in our study based on the co-expression of the 3 sprouty transcripts (1, 2, and 4) (Figure 1C panel f). Expression of all three sprouty homologs has been observed before in mouse development , but not in human cancers. Human sprouty 2 has been shown to inhibit the mitogen-activated protein (MAP) kinase pathway , and sprouty proteins have been implicated in the negative regulation of the receptor tyrosine kinase-induced MAP kinase pathway. DUSP, another gene in our sprouty cluster, belongs to a family of 9 cytoplasmic and/or nuclear enzymes, that function by dephosphorylating threonine and tyrosine residues of p38, JNK and ERK [36, 37]. The transcriptional regulation of Ets transcription factors, including that of PEA3 (ETV4), on the other hand, involves signals initiated by growth factor signaling through tyrosine kinase receptors that may be mediated by MAPK . We have previously shown that PEA3 and DUSP member PAC-1 predict poor outcome in ovarian carcinoma, whereas expression of all three MAPK predicts improved survival [39–41]. The coordinated expression of 3 sprouty family members, DUSP6, and ETV4 and 5 in a subset of ovarian cancers therefore raises the possibility that the activity of a specific, MAPK-related signaling pathway may have a role in ovarian cancer.
We have previously shown that clinical and molecular markers that are of established prognostic role in primary ovarian cancer have little or no significance in effusions . Besides the obvious fact that cells at this site represent tumor progression, they also appear to be biologically different than tumor cells in both primary tumors and solid metastases. Using PAM to analyze the three different groups, primary tumors, and pleural and peritoneal effusions, we identified a subset of genes that is more highly expressed in the primary tumors, but fewer differences between pleural and peritoneal effusions. These genes are mainly characteristic of previously defined 'stromal' signature , but that are produced by both tumor and stromal cells including collagens, TIMP2, bFGF, vimentin and SPARC [28–30]. To study tumor progression we evaluated the expression levels in relation to clinical parameters using SAM, focusing on FIGO stage and grade. The most notable distinctions were based on grade rather than stage.
A large cluster of genes on chromosome segment 19q13.1 showed covarying expression among the cancers in this study, consistent with previous reports that the 19q13.1 region is amplified in some ovarian carcinomas [44, 45]. The AKT2 oncogene contained in this region of chromosome 19, has been shown to be associated with the progression of ovarian cancer [44, 45]. Interestingly, we found that some of the genes in the 'chromosome 19 cluster' including PDCD5 and PEN2, were more highly expressed in the Stage IV cancers than earlier-stage supporting the notion that amplification of the 19q13.1 region and concomitant elevated expression of these genes may play a role in the progression of the disease . Furthermore in a larger cohort of advanced ovarian carcinomas amplification of this region was found to be associated with poor survival (Wang et. al., manuscript to be submitted).
In summary, we have examined the relationship between primary tumors in ovarian cancer and their corresponding effusions. The most notable difference was observed in expression patterns between effusions and the primary tumors. There is significant molecular variation among the cancers. There are some hints of differences related to tumor grade and effusion versus primary tumor that will need further investigation to see whether these are significant. Finally, some consistent features of expression patterns in subsets of the cancers may suggest possible molecular alterations involved in the biology of the tumors.