Screening of feature genes of the ovarian cancer epithelia with DNA microarray

Ovarian cancer is the fifth most common cause of cancer deaths among women and is the leading cause of death from gynecological neoplastic disease [1]. The average 5-year survival rate is approximately 40%; however, most ovarian cancers are diagnosed when the disease has progressed to the advanced stages III or IV. Patients with advanced disease (stages III and IV) have a significantly lower survival rate of only 10%–20% [2]. A high percentage of mortality results from low diagnosis rate. Survival rates can approach 90% when ovarian cancer is diagnosed at an early stage; however, early detection is challenging, because the relatively nonspecific symptoms of ovarian lesions may be overlooked until abdominal distension by ascites fluid or by large tumor masses becomes unmistakable. Even with extensive surgical debulking and aggressive chemotherapy, the prognosis for women with ovarian cancer currently is not hopeful.

The conventional view is that approximately 90% of ovarian cancers are derived from the single-cell layer of surface epithelium that surrounds the ovary [3]. As the ovarian epithelium transforms into a malignant phenotype, it differentiates into several subtypes that have been categorized into serous, mucinous, endometrioid and clear cell carcinoma, based on their morphology rather than their genotype [4]. Epithelial ovarian cancers show a high degree of genetic heterogeneity as a result of mutations, silencing, and deletions. Since changes in gene expression, either through mutation, epigenetic regulation, or differential splicing events, influence tumor development, progression, drug responsiveness and ultimately the survival of the patient, the identification of the tumor subtype and its genetic fingerprint is essential. Several studies have indicated that different histological subtypes of ovarian carcinoma are associated with different causes and underlying mechanisms, including gene amplification, genetic predisposition, and various carcinogens [5]. Nonetheless, the origin and causes of ovarian carcinoma remain to be elucidated.

The development of microarray technology has provided new insights into cancer diagnosis and treatment. Large-scale microarray studies in breast cancer have succeeded in clarifying 5 molecular subtypes based on gene expression profiles and in developing genomic biomarkers for predicting recurrence in early breast cancer [6]. Thus, breast cancer treatment strategies are being stratified according to molecular characteristics. In contrast, there are no gene expression signatures with high accuracy and reproducibility for clinical diagnosis and management in patients with ovarian cancer because there is a paucity of ovarian cancer samples available for microarray analysis compared with breast cancer. Although TP53 somatic mutation is present in almost all high-grade serous ovarian cancer and plays an important role in the pathogenesis [7, 8], high-grade serous ovarian cancer exhibits much biological and molecular heterogeneity that should be considered when developing a novel therapeutic strategy for ovarian cancer [8, 9]. A better understanding of the molecular mechanisms leading to ovarian cancer may provide new opportunities for the development of strategies for diagnosis and therapy.

In the present study, we compared the gene expression profile between ovarian surface epithelia (OSE) and laser capture microdissected serous ovarian cancer epithelia (CEPI) samples. Differentially expressed genes (DEGs) were analyzed using gene ontology (GO), molecular pathway, and gene set enrichment analysis algorithms methods. Here we highlight progressive changes that lead to a highly dysregulated cell cycle. These genes, their gene products and the associated signaling pathways may represent novel targets for intervention of ovarian cancer progression.

In the present study, we have identified genes and their functional categories that are altered in CEPI samples. The gene expression profiles displays statistically significant changes in cell cycle, signal pathway, metabolism and other functional categories that correspond well with many of the morphological changes and biological behaviors.

Dysregulation of the cell cycle is a hallmark of many cancers and control and timing of the cell cycle involves checkpoints and regulatory pathways that ensure the fidelity of DNA replication and chromosome segregation [19]. These processes involve a large collection of key molecules, which are excellent candidates for ovarian cancer susceptibility variants. These include the cyclins (CCNA1, CCNA2, CCNB1, CCNB2, CCND1, CCND2, CCND3, CCNE1, CCNE2, CCNG1, CCNG2), cyclin-dependent kinases (CDKS: CDK1, CDK2, CDK4, CDK6, CDK7, CDC2), CDK inhibitors (CDKN1A, CDKN1B, CDKN2A, CDKN2B, CDKN2C, CDKN2D) and CDC2 regulators (CDC25A, CDC25B, CDC25C) [19]. In the current study, CDK1, CDC6, CDC20, CDC25A, CDC25B, CDC25C, CDC45, Bub1, ORC6 were up-regulated. Studies have shown that up-regulation of CDC6, CDC 20, CDC25 family and Bub1 has relationship with human cancers.

Bub1 encodes a kinase involved in spindle checkpoint function. Several studies have found high Bub1 levels in subsets of breast and gastric cancers, and lymphomas. Furthermore, independent studies of diverse tumor types have identified Bub1 as a gene whose up-regulation correlates with poor clinical prognosis [20].

It is reported that Cdc20 functions as an oncoprotein to promote the development and progression of human cancers [21]. Microarray studies have recently reported overexpression of CDC20 in various tumors, such as tumors of the oral cavity [22], stomach [23], brain (glioblastoma) [24], urinary bladder [25], uterine cervix [26], and ovary [27]. Meta-analysis of cancer microarray data also identifies CDC20 as one of the highly expressed genes in various human cancer tissues [28]. Furthermore, expressions of specific genes including CDC20 consistently correlate with total functional aneuploidy and are predictive of poor prognosis in several cancer types using a computational method [29]. Particularly in serous epithelial ovarian cancer, overexpression of CDC20 is a prognostic factor associated with clinical stage of disease, irrespective of tumor grade [27].

The cell division cycle 25 (CDC25) families of proteins is a group of highly conserved dual-specificity phosphatases. There are three isoforms: CDC25A, CDC25B and CDC25C. They are key regulators of normal cell division and the cell response to DNA damage, and play a fundamental role in transitions between cell cycle phases during normal cell division, via the activation of CdK/cyclin complexes. Their abnormal expression, detected in a number of tumors, often correlated with a poor clinical prognosis, implies that their dysregulation is involved in malignant transformation [30]. In the context of the progression of cell division, the A and B isoforms of CDC25 have been reported as potential oncogenes, being overexpressed in more than ten types of human cancer, including prostate and breast cancers, as well as vulvar squamous cell carcinomas. In contrast, CDC25C is expressed at a far lower level in a limited number of tumors [30].

Module analysis showed that the modules containing the down-regulated DEGs were related with lipid metabolic process and cytoskeletal structure. The modules containing up-regulated DEGs were related with signal transduction. In the last decade, the altered lipid metabolism has increasingly been recognized as another common property of malignant cells [31, 32]. Like glucose metabolism, lipid metabolism in cancer cells is also regulated by the common oncogenic signaling pathways, and is believed to be important for the initiation and progression of tumors [32]. Some newly generated lipids molecules, such as phosphatidic acid (PA), diacylglycerol (DAG), and lysophosphatidic acid (LPA), also mediate signal transduction in cancer cells [32]. These lipids regulate a variety of cellular functions including cell proliferation, survival and migration by either activating other signaling proteins inside the cells, or binding to a series of G protein-coupled receptors (GPCRs) on the cell surfaces. It has been reported that inhibitors of lipid metabolic pathways, particularly drugs targeting the mevalonate pathway, have been suggested to be valuable in enhancing the effectiveness of epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKIs) [33]. On the other hand, oncogenic signaling pathways can regulate lipid metabolism at multiple steps, including transcriptional, translational and post-translational levels.

The cytoskeleton plays an important role in tumor cell progression and events such as migration and invasion, allowing the cells to adapt and survive in different microenvironments; compounds that regulate cytoskeleton organization have been used as cancer therapeutics [34]. On the other hand, the organization of the cytoskeleton affects cellular organization, adhesion complexes and polarity, and vesicular transports. Creekmore et al. demonstrate that cytoskeleton disorganization can have profound effects on the subcellular localization of important signaling intermediates, which ultimately may lead to modulated signaling pathways contributing to ovarian cancer development [4].

The complex molecular processes underlying the onset and development of epithelial ovarian cancer is only beginning to be unraveled. Our results indicate that cell cycles, lipid metabolic pathways, cytoskeleton changes and some signal transduction pathways are involved in the establishment and development of ovarian cancer. While many of these pathways have previously been either directly or indirectly implicated in ovarian cancer, detailed network analyses of our gene expression data led to the identification of linkages between these pathways attributable to the altered expression of key regulatory genes.