Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of human ovarian cancer tumor samples to investigate heterogeneity

ABSTRACT: Women that underwent operation for what was expected to be epithelial ovarian cancer at Odense University Hospital, Denmark, from April 2004 to February 2005, were consecutively asked to participate in the study, and all gave written consent. In the operating theatre the tumors were removed as an entirety, and immediately transported to the pathology department without fixation. One senior pathologist was responsible for collection of samples. From each tumor three samples of about 200 300 mg each were taken with maximal mutual distance, taking into consideration that all samples should contain tumor tissue. This way of sampling was done without any kind of magnification and is mentioned as macro-dissection. The three samples were given the letters a, b and c. The three samples from each of the nine tumors are compared.

ORGANISM(S): Homo sapiens

SUBMITTER: qihua tan

PROVIDER: E-MEXP-935 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Gene expression in epithelial ovarian cancer: a study of intratumor heterogeneity.

Jochumsen K M KM Tan Q Q Hølund B B Kruse T A TA Mogensen O O

International journal of gynecological cancer : official journal of the International Gynecological Cancer Society 20070315 5

The aim of this study was to investigate the intratumor heterogeneity of gene expression profiles in epithelial ovarian cancer (EOC). This was done to evaluate whether sampling of a single macrodissected tissue sample from each EOC case would bias the data and result in, eg, prognostic studies based on gene expression microarray experiments. From nine EOCs removed at Odense University Hospital, Denmark, three tumor samples of 200-300 mg each were taken with greatest possible mutual distance. The ...[more]

PMID: 17367315

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Project description:Tumor specimens were collected from women with ovarian tumors at primary surgery in a study covering most of Denmark called the MALOVA-study (MALignant OVArian cancer study). This multidisciplinary study on ovarian cancer covers epidemiology (life style factors), biochemistry, and molecular biology with the purpose of identifying risk factors and prognostic factors for EOC. The study has been approved by the Scientific Ethic Committees in the study area (KF01-384/95). Sample collection went on from 1994 to 1999, and the study is described in details in other articles(20;21;24;30). Histopathological classification of the ovarian tumors was based on the typing criteria of the WHO. Pathology reports and tissue were collected from the participating hospitals. One pathologist specialized in ovarian tumors, reviewed the tissue specimens without knowledge of the primary diagnoses. Subsequently, the reviewed diagnosis was compared to the original diagnosis and agreement on invasiveness was present in 98 % of the cases. The histopathological type was refined in 14% of the cases. FIGO stages were obtained from clinical records and were reviewed by two gynecologists, both specialized in OC. Reviewed data were used for further analysis. Furthermore all other relevant hospital files were collected, and data concerning, debulking status, CA-125 level prior to operation, amount and type of chemotherapy and cause of death (if dead) were registered. Patients were scored as ÂradicalÂ (optimally debulked) if no macroscopic residual tumor nodules were left, and as Ânon-radicalÂ (sub-optimally debulked) if macroscopic nodules were left. All fresh tumor samples included in this study were intended to be snap frozen within 20 minutes after the tumor was removed, but exact transportation time is not known. All samples have been stored at -80ÂºC. We selected samples from the largest and most common histological subtype, the serous ovarian cancers, all stages. The tumor sample material consisted of 70 stage III/IV tumors and 19 stage I/II tumors. Further patient information can be obtained from the submitters on request.

Project description:The significant morphological differences observed during embryo development in angiosperms and gymnosperms are expected to be the result of a differential control of gene expression. We used a loblolly pine (Pinus taeda) cDNA microarray to analyze global transcriptional changes along zygotic embryogenesis in maritime pine (Pinus pinaster). A time-course analysis of the data obtained from the five embryo developmental groups used in this study led to the identification of 4,645 genes whose expression varied along P. pinaster embryogenesis. These transcripts were clustered into six distinct expression profiles. The grouping of these profiles in early, mid-embryogenesis and embryo maturation, according to the developmental period where most of the sequences were up-regulated, evidenced that characteristic transcriptional changes are associated to each developmental period. The application of a cut-off value of 1.95-fold change led to the identification of 1,838 differentially expressed transcripts that were categorized by biological process. Metabolism, interaction with the environment, oxidation-reduction and transport were some of the most represented categories. During early embryogenesis genes putatively involved in phytohormone-mediated signaling were identified, whereas in middle stages the overrepresented genes could be associated with cotyledon formation and induction of somatic embryogenesis. Genes associated with the synthesis of storage products were up-regulated in the latest stages of pine embryo development. It was also during this developmental period that the largest number of sequences putatively encoding transcription factors was identified. Pine immature zygotic embryos were pooled into five different developmental groups according to the collection date (Day0; Day5; Day11; Day15 and Day25). A common reference design was used. Total RNA was extracted from each sample. Three extractions were prepared per sample (biological replicates). A defined ammount from each RNA sample was pooled to use as reference. Messenger RNA was amplified for both test samples and reference. These were hybridized together in two separate experiments (technical replicates). In total, 30 slides were analyzed.

Dataset Information

Transcription profiling of human ovarian cancer tumor samples to investigate heterogeneity

Publications

Gene expression in epithelial ovarian cancer: a study of intratumor heterogeneity.

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