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Transcription profiling of human ependymoma tumors with known clinical outcomes

ABSTRACT: Ependymoma, the 3rd most common brain tumor in children, recurs in approximately 50% of patients. There is currently no robust marker that predicts for recurrence, which is a significant clinical problem; We used global gene expression profiling of 19 patient surgical samples obtained at initial diagnosis and with known clinical outcomes to discover novel prognostic markers. Experiment Overall Design: Gene expression profiles were generated from surgical tumor samples using Affymetrix HG-U133plus2 chips. Profiles were divided into recurrent and non-recurrent groups in order to identify differentially expressed genes that were associated with risk of recurrence. In addition, time to progression was correlated with gene expression as a continuous variable in the recurrent group.

ORGANISM(S): Homo sapiens

SUBMITTER: Donson Andrew

PROVIDER: S-ECPF-GEOD-16155 | biostudies-other |

REPOSITORIES: biostudies-other

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Transcription profiling of human ependymoma tumors with known clinical outcomes

Project description:Ependymoma, the 3rd most common brain tumor in children, recurs in approximately 50% of patients. There is currently no robust marker that predicts for recurrence, which is a significant clinical problem; We used global gene expression profiling of 19 patient surgical samples obtained at initial diagnosis and with known clinical outcomes to discover novel prognostic markers. Experiment Overall Design: Gene expression profiles were generated from surgical tumor samples using Affymetrix HG-U133plus2 chips. Profiles were divided into recurrent and non-recurrent groups in order to identify differentially expressed genes that were associated with risk of recurrence. In addition, time to progression was correlated with gene expression as a continuous variable in the recurrent group.

2009-10-10 | E-GEOD-16155 | biostudies-arrayexpress

Transcription profiling of primary human breast tumors showing poor clinical prognosis

Project description:Using microarray analysis, we identified a unique ras superfamily gene, termed RERG (ras-related and estrogen-regulated growth inhibitor), whose expression was decreased or lost in a significant percentage of primary human breast tumors that show a poor clinical prognosis. Importantly, high RERG expression correlated with expression of a set of genes that define a breast tumor subtype that is estrogen receptor-positive and associated with a slow rate of tumor cell proliferation and a favorable prognosis for these cancer patients. RERG mRNA expression was induced rapidly in MCF-7 cells stimulated by beta-estradiol and repressed by tamoxifen treatment. Like Ras, RERG protein exhibited intrinsic GDP/GTP binding and GTP hydrolysis activity. Unlike Ras proteins, RERG lacks a known recognition signal for COOH-terminal prenylation and was localized primarily in the cytoplasm. Expression of RERG protein in MCF-7 breast carcinoma cells resulted in a significant inhibition of both anchorage-dependent and anchorage-independent growth in vitro and inhibited tumor formation in nude mice. These features of RERG are strikingly different from most Ras superfamily GTP-binding pro-teins and suggest that the loss of RERG expression may contribute to breast tumorigenesis.

| S-ECPF-SMDB-1443 | biostudies-other

Transcription profiling of human glial brain tumors

Project description:Gene expression profiling in 50 glial brain tumors and 4 normal brains using 42,000-feature cDNA microarrays (from total RNA). Tumors: 50 fresh-frozen glioma specimens subjected to standard WHO classification. Specimens included astrocytic [2 juvenile pilocytic astrocytomas, 1 low-grade astrocytic glioma, 1 anaplastic astrocytomas, 31 glioblastomas (of these 2 secondary glioblastomas and 2 gliosarcomas)], oligodendroglial [5 oligodendrogliomas, 3 anaplastic oligodendrogliomas], and 6 anaplastic oligoastrocytomas tumors. One tumor had been classified as glioneuronal neoplasm. Normal brain was purchased from Stratagene. Stratagene Universal Common Reference was used as reference RNA. The results provide insights into molecular mechanisms and pathways associated with gliomagenesis.

| S-ECPF-SMDB-3152 | biostudies-other

Transcription profiling by array of human pancreatic tumors

Project description:We used microarrays to identify the expression differences of FKBP5 gene between the pancreatic tumor and normal samples. On average normal samples had more FKBP5 expression compared to tumor samples .Experiment Overall Design: This experiment consists of 36 tumor samples and 16 normal samples; a total of 52 samples. 16 samples consist of both tumor and normal expression data, whereas 20 samples consist of only tumor data.

| S-ECPF-GEOD-16515 | biostudies-other

Transcription profiling of human age-dichotomized ER+ breast tumors

Project description:To investigate the biological basis between aging and sporadic breast cancer incidence and prognosis, RNA samples from matched ER+ invasive breast cancers diagnosed in either young (≤45) or old (≥70) women were analyzed by expression microarrays Experiment Overall Design: ER+ breast cancers collected from either young or old women, well matched for other clinical parameters were analyzed using expression microarrays. Age associated tumor subtypes and enrichment of pre-defined gene signatures were identified. Age associated differential expression and an age signature (gene-based classifier) was assessed

| S-ECPF-GEOD-8193 | biostudies-other

Optimized ChIP-seq method facilitates transcription factor profiling in human tumors.

Project description:Chromatin immunoprecipitation (ChIP)-seq analyses of transcription factors in clinical specimens are challenging due to the technical limitations and low quantities of starting material, often resulting in low enrichments and poor signal-to-noise ratio. Here, we present an optimized protocol for transcription factor ChIP-seq analyses in human tissue, yielding an ?100% success rate for all transcription factors analyzed. As proof of concept and to illustrate general applicability of the approach, human tissue from the breast, prostate, and endometrial cancers were analyzed. In addition to standard formaldehyde fixation, disuccinimidyl glutarate was included in the procedure, greatly increasing data quality. To illustrate the sensitivity of the optimized protocol, we provide high-quality ChIP-seq data for three independent factors (AR, FOXA1, and H3K27ac) from a single core needle prostate cancer biopsy specimen. In summary, double-cross-linking strongly improved transcription factor ChIP-seq quality on human tumor samples, further facilitating and enhancing translational research on limited amounts of tissue.

| S-EPMC6311467 | biostudies-literature

Transcription profiling of human breast tissue tumors vs. normal tissue

Project description:bulk breast tumor RNA from patient; Abstract: Sporadic basal-like cancers (BLC) are a distinct class of human breast cancers that are phenotypically similar to BRCA1-associated cancers. Like BRCA1-deficient tumors, most BLC lack markers of a normal inactive X chromosome (Xi). Duplication of the active X chromosome and loss of Xi characterized almost half of BLC cases tested. Others contained biparental but nonheterochromatinized X chromosomes or gains of X chromosomal DNA. These abnormalities did not lead to a global increase in X chromosome transcription but were associated with overexpression of a small subset of X chromosomal genes. Other, equally aneuploid, but non-BLC rarely displayed these X chromosome abnormalities. These results suggest that X chromosome abnormalities contribute to the pathogenesis of BLC, both inherited and sporadic. total 62 sample incudes 43 tumor, 7 normal breast and 12 normal organelle Experiment Overall Design: compare expression of tumor to normal breast tissue

| S-ECPF-GEOD-7904 | biostudies-other

Transcription profiling of 67 human lung tumors representing 56 patients

Project description:The global gene expression profiles for 67 human lung tumors representing 56 patients were examined by using 24,000-element cDNA microarrays. Subdivision of the tumors based on gene expression patterns faithfully recapitulated morphological classification of the tumors into squamous, large cell, small cell, and adenocarcinoma. The gene expression patterns made possible the subclassification of adenocarcinoma into subgroups that correlated with the degree of tumor differentiation as well as patient survival. Gene expression analysis thus promises to extend and refine standard pathologic analysis.

| S-ECPF-SMDB-810 | biostudies-other

microRNA profiling and clinical outcomes in human osteosarcoma (biopsies)

Project description:Osteosarcoma is a malignancy with variable outcomes that are not tightly aligned with chemotherapy response. Previous work has suggested a possible role for microRNAs (miRNAs) in determining the susceptibility of osteosarcomas to treatment but formal miRNA-based outcome models have not been reported. Formalin-fixed, paraffin-embedded (FFPE) specimens may be a unique approach for such studies in a rare malignancy. We used supervised principal components analysis and logistic regression to study survival and chemoresponse endpoints, and miRNA activity and gene set analysis algorithms to study miRNA regulatory networks using mRNA data. Our study also creates a paradigm for FFPE-based miRNA clinical biomarker research in rare tumors.

2013-01-22 | GSE39040 | GEO

mRNA profiling and clinical outcomes in human osteosarcoma (biopsies)

2013-01-22 | GSE39055 | GEO

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