Expression data from mouse ovarian surface epithelium cells at different stages of malignancy
ABSTRACT: Ovarian cancer is one of the most deadly cancers accounting for only 3% of diagnosed cancers, but is the fifth leading cause of cancer deaths among woman; however, the progression of ovarian cancer is poorly understood. To study and further understand the early events that lead to epithelial derived ovarian cancer, we previously developed a cell model of progressive ovarian cancer. Mouse ovarian surface epithelial (MOSE) cells have undergone spontaneous transformation in cell culture and represent pre-neoplastic, non-tumorigenic to an aggressive malignant phenotype. Microarray analysis was performed with RNA isolated from different stages of MOSE cells to examine changes in gene expression as MOSE cells transition from a pre-neoplastic to a malignant state. Overall design: RNA was isolated from MOSE early cell representing a pre-neoplastic, non-malignant stage, MOSE Intermediate cells representing a noeplastic, pre-invasive state, and MOSE Late cells representing a malignant, invasive stage. Three biological replicates were used to take into account variations within the heterogeneous cultures.
Project description:Ovarian cancer is one of the most deadly cancers accounting for only 3% of diagnosed cancers, but is the fifth leading cause of cancer deaths among woman; however, the progression of ovarian cancer is poorly understood. To study and further understand the early events that lead to epithelial derived ovarian cancer, we previously developed a cell model of progressive ovarian cancer. Mouse ovarian surface epithelial (MOSE) cells have undergone spontaneous transformation in cell culture and represent pre-neoplastic, non-tumorigenic to an aggressive malignant phenotype. Microarray analysis was performed with RNA isolated from different stages of MOSE cells to examine changes in gene expression as MOSE cells transition from a pre-neoplastic to a malignant state. RNA was isolated from MOSE early cell representing a pre-neoplastic, non-malignant stage, MOSE Intermediate cells representing a noeplastic, pre-invasive state, and MOSE Late cells representing a malignant, invasive stage. Three biological replicates were used to take into account variations within the heterogeneous cultures.
Project description:Background - The malignant potential of serous ovarian tumors, the most common ovarian tumor subtype, varies from benign to low malignant potential (LMP) tumors to frankly invasive cancers. Given the uncertainty about the relationship between these different forms, we compared their patterns of gene expression. Methods - Expression profiling was carried out on samples of 7 benign, 7 LMP and 28 invasive (moderate and poorly differentiated) serous tumors and surface epithelium of four normal whole ovaries using oligonucleotide microarrays representing over 21,000 genes. Results - We identified 311 transcripts that distinguished invasive from benign tumors, and 20 transcripts that were significantly differentially expressed between invasive and LMP tumors at p < 0.01 (with multiple testing correction). Five genes that were differentially expressed between invasive and either benign or normal tissues were validated by real time PCR in an independent panel of 46 serous tumors (4 benign, 7 LMP, 35 invasive). Overexpression of SLPI and WNT7A and down-regulation of C6orf31, PDGFRA and GLTSCR2 were measured in invasive and LMP compared with benign and normal tissues. Over-expression of WNT7A in an ovarian cancer cell line led to increased migration and invasive capacity. Conclusions - These results highlight several genes that may play an important role across the spectrum of serous ovarian tumorigenesis. Overall design: Common reference design.
Project description:To identify dysregulated miRNA(s) upon infection with H. pylori during different pre-malignant and malignant stages of gastric cancer in a mouse model miRNA expression in pre-neoplastic and neoplastic lesions in murine stomachs induced by H. pylori and N-methyl-N-nitrosourea (MNU) after 12 months was profiled by miRNA expression array.
Project description:We have previously described differences in the expression profiles of tumors by comparing tumors of two known classes: low malignant potential versus highly malignant (invasive). This report presents an effort to discover unknown classes within a large heterogeneous set of ovarian tumors, using unsupervised learning approaches. We were able to define four classes in a set of 74 ovarian cancer tumors. Groups identified as A1 and A2 were closely related and correlated with the “invasive” pathology class while the group identified as B2 was correlated with low malignant potential tumors; group B1 consisted of a mixture of low potential and invasive samples. We selected characteristic candidate genes, which were validated by quantitative-PCR and by comparison to other published studies. Experiment Overall Design: We used unsupervised classification methods to identify unknown classes in a set of 74 cancer samples
Project description:Platinum-based compounds exert their anti-neoplastic effect through direct binding to DNA, which blocks fundamental cellular process ultimately resulting in apoptotic cell death. However, many ovarian cancers become refractory to treatment with platinum-based compounds. To improve the existing therapies for ovarian cancer, we sought to identify potent, nontoxic and specific drug candidates that have anti-neoplastic effects towards cisplatin-sensitive and cisplatin-resistant ovarian cancer cells. Using a cell-based screening assay, we evaluated 56 compounds-derived from the Chinese medicinal plant, Phytolaccae, and one phytoaccagenin compound (Hu-17) was selected on the basis of its ability to dramatically decrease the viability of cisplatin-resistant SK-OV-3 cells.Using high-throughtput microarray system, we identified GO terms and pathway signatures enriched in Hu-17 and/or cisplatin treated SK-OV-3 cells. Overall design: Ovarian cancer cells SK-OV-3 were cultured in McCoy's 5A medium supplemented with 10% fetal bovine serum, the cell were treated with Hu-17 and/or cisplatin for different time, and total RNA from SK-OV-3 cells was hybridized on Affymetrix U133 plus 2.0 genechip.
Project description:Epithelial ovarian cancer is morphologically and clinically heterogeneous. Transcriptional profiling has revealed molecular subtypes (referred to as “C-signatures”) that correlate to biological as well as clinical features. We aimed to determine gene expression differences between malignant, benign and borderline serous ovarian tumors, and to investigate similarities to the intrinsic molecular subtypes of breast cancer. Global gene expression profiling was performed using Illumina's HT12 Bead Arrays and applied to 59 fresh-frozen ovarian tumors. SAM analysis revealed enrichment of cell cycel processes among the malignant tumors, in line with malignant tumors being highly proliferative. The borderline tumors were split between the malignant and benign tumor clusters, indicating that borderline tumors have both malignant and benign features. Furthermore, nearest centroid classification was performed applying previously published gene profiles for the ovarian cancer C-signatures and the intrinsic breast cancer subtypes, respectively, and showed significant correlations between the malignant serous tumors and the highly aggressive C1, C2 and C4 ovarian cancer signatures, and the basal-like breast cancer subtype. The benign and borderline serous tumors together were significantly correlated to the normal-like breast cancer subtype and the ovarian cancer C3 signature. The borderline tumors, on the other hand, correlated significantly to the Luminal A breast cancer subtype. These findings remained when analyzed in a large, independent dataset. The data in this study link the transcriptional profiles of serous ovarian cancer to the intrinsic molecular subtypes of breast cancer, in line with the shared clinical and molecular features between high-grade serous ovarian cancer and basal-like breast cancer, including an aggressive phenotype, frequent TP53 mutations and a high degree of genomic instability, and suggest that biomarkers and targeted therapies may overlap between these subsets of ovarian and breast cancers. Finally, the link between benign and borderline ovarian cancer and luminal breast cancer may indicate endocrine responsiveness in a subset of ovarian cancers. Total RNA obtained from serous ovarian adenocarcinomas, adenomas and borderline tumors. Gene expression profiling using Illumina's HT12 v4 bead arrays. Application of ovarian cancer molecular subtypes and intrinsic breast cancer subtypes using nearest centroid classification. KRAS and BRAF mutation analyses in the malignant and borderline tumors.
Project description:The Homeobox (HOX) family of genes encodes transcription factors involved in basic developmental processes, most notably during embryogenesis. A possible HOX gene link between development and oncogenesis has recently been described. Dysregulation of HOX genes may be an early event in malignant transformation likely to induce antibody response and thus provide a potential marker for early diagnosis of cancer. Ovarian cancer is characterized by poor early detection and serves as an excellent model system to develop potential markers for early diagnosis. In this study we begin to characterize HOX gene expression in malignant tumors of the ovary and analyze the potential role of HOX genes as biomarkers for early detection of ovarian cancer. Microarray analysis of mRNA from human ovarian tissues was performed on 65 samples of normal, benign, borderline malignant and malignant ovarian tissue. These samples were analyzed using the Affymetrix Human Genome Focus GeneChip (HG-Focus) microarray to distinguish the differential pattern of mRNA expression between the four types of samples. Real-time reverse transcription PCR was utilized to confirm up-regulation of HOX genes as determined by microarray analysis. Our results demonstrate multiple HOX genes to be up-regulated in ovarian cancer. We have shown stepped increase in HOX expression comparing normal, benign neoplastic, and malignant human ovarian tissue samples. This suggests dysregulation of HOX genes may be an early event in malignant transformation and warrants additional studies to validate HOX gene products as potential markers for early detection of ovarian cancer. Experiment Overall Design: 67 samples were analyzed. 4 groupings based on pathology (normal, benign, borderline malignant, malignant). An average of normal samples was used as controls. Cell lines were used as ovarian cancer control samples.
Project description:The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in breast tissues from women with and without breast cancer. Breast tissue samples were drawn from 114 breast cancers and 23 non-neoplastic breast tissues. The breast cancer tissue samples were from women (mean age 59.4) who were diagnosed with breast cancer. Among the cancers, 33 were at stage 1 and 81 at stage 2/3/4; 34, 59, and 19 were grade 1, 2, and 3 respectively;and 91 were invasive ductal carcinoma breast cancers. The 23 non-neoplastic samples are from healthy woman (mean age 47.6). Bisulphite converted DNA from the 137 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2
Project description:Purpose: The aim of this study is to identify known and novel small RNAs (Piwi-interacting RNAs and microRNAs) in normal ovary and epithelial ovarian malignancies by adopting high-throughput RNA sequencing (RNA-Seq) and unveil their possible functions in neoplastic pathways of the two most frequently observed and highly lethal subtypes of epithelial ovarian cancers, endometrioid ovarian cancer (ENOCa) and serous ovarian cancer (SOCa). The study has been performed in normal ovarian tissues as well as malignant tissues of these cancer subtypes. Methods: 1 µg of total RNA was used as the starting material for library preparation as prescribed by Illumina Truseq small RNA library protocol. Small RNA sequencing was carried out by Genotypic Technology, Bangalore, India on Illumina Next-Seq 500 platform. Library preparation was done by performing 3' and 5' adapter ligation followed by reverse transcription of cDNA and amplification of the library. The construct of the library was fractionated to select 16-40 nucleotide insert of small RNAs using PAGE. The quality check of the library was done in Agilent Technologies 2100 Bioanalyzer using a DNA-specific chip, such as High Sensitivity DNA. The sequence reads that passed through Quality Check by FastQC and aligned to the human genome (hg19) were further analysed using in-house pipelines and set of known and novel piRNAs and miRNAs were identified. The sets of known piRNAs and miRNAs identified were assessed for their involvement in neoplastic processes of ovarian cancer subtypes by performing target analysis and GO enrichment studies. Results: Using an in-house prediction pipeline, we mapped about 10-15 million sequence reads per sample to the human genome (hg19) and detected 256, 234 and 219 annotated piRNAs in ENOCa, SOCa, and normal ovary respectively; whereas the average number of known miRNAs present in each sample was estimated to be 480. The annotated piRNAs obtained from each sample exhibited varied length distribution between 26-32 nts. Conclusions: For the first time, our study reported the presence of piRNAs in ENOCa, SOCa and normal ovarian tissue from the next-gen sequencing of small RNAs of 16-40 nts length. The extensive catalogue of human EOCa small RNAs (both piRNAs and miRNAs) detected in this study provides a useful resource to dissect complex neoplastic events that are possibly mediated by these ncRNAs, especially by piRNAs. Moreover, these piRNAs could be used as probable small RNA biomarkers for the EOCa. Overall design: Small RNA profile of human epithelial ovarian cancer and normal epithelial ovarian tissue was generated by deep sequencing using Illumina Next-Seq 500
Project description:Gene expression profiles of malignant carcinomas surgically removed from ovarian cancer patients pre-treated with chemotherapy (neo-adjuvant) prior to surgery group into two distinct clusters. One group clusters with carcinomas from patients not pre-treated with chemotherapy prior to surgery (C-L) while the other clusters with non-malignant adenomas (A-L). Although the C-L cluster is preferentially associated with p53 loss-of-function (LOF) mutations, the C-L cluster cancer patients display a more favorable clinical response to chemotherapy as evidenced by enhanced long-term survivorships. Keywords: Patient Tumor Samples Overall design: A set of 43 ovarian tumors was obtained from the Ovarian Cancer Institute (Atlanta). Tissue was collected at the time of surgery and preserved in RNAlater (Ambion, Austin, TX) within one minute of collection. Labeled probe was hybridized to the Affymetrix HG-U95Av2 arrays.