Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of human neuroblastoma tissue samples

ABSTRACT: The prognosis of the patients with neuroblastoma largely depends on the biological characteristics. Neuroblastoma tissues obtained before any treatments were analyzed for gene expression using Affymetrix array. We used microarrays to detail the global programme of gene expression distinguishing tumor biology of neuroblastoma tissues from the prognosis of the patients. Experiment Overall Design: 51 neuroblastoma samples were selected those resected from the patients who died of tumor progression and those whose tumor regressed or matured spontaneously. Total RNA was extracted from these tissues samples and hybridized on Affymetrix microarrays. We sought to obtain genes to distinguish unfavorable tumors from favorable tumors.

ORGANISM(S): Homo sapiens

SUBMITTER: Eiso Hiyama

PROVIDER: E-GEOD-16237 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

A robust method for estimating gene expression states using Affymetrix microarray probe level data.

Ohtaki Megu M Otani Keiko K Hiyama Keiko K Kamei Naomi N Satoh Kenichi K Hiyama Eiso E

BMC bioinformatics 20100412

<h4>Background</h4>Microarray technology is a high-throughput method for measuring the expression levels of thousand of genes simultaneously. The observed intensities combine a non-specific binding, which is a major disadvantage with microarray data. The Affymetrix GeneChip assigned a mismatch (MM) probe with the intention of measuring non-specific binding, but various opinions exist regarding usefulness of MM measures. It should be noted that not all observed intensities are associated with exp ...[more]

PMID: 20380745

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Project description:Purpose: In this study, we try to investigate the possible signaling pathways involved in the tumorigenesis of fibroblastic and anaplastic meningiomas. We also attempt to investigate EGFL6 gene expression in brain arachnoidal tissues and various tumors and to measure EGFL6 levels in serum samples from healthy people and patients with various tumors by using ELISA. Experimental Design: Differential gene expression profiles between meningiomas and brain arachnoidal tissues were established by using Affymetrix GeneChip Human U133 Plus 2.0 Array. KEGG pathway analysis was performed to identify potential gene pathways that may be involved in the pathogenesis of meningiomas. Quantitative real-time PCR (qRT-PCR) was performed to validate the differentially expressed genes in the KEGG pathways. EGFL6 mRNA levels were also determined in brain arachnoidal tissues, meningiomas, and other tumors by qRT-PCR. EGFL6 levels were measured in serum samples from healthy people and patients with various tumors by using ELISA. Results: Fibroblastic meningioma exhibited upregulated PI3K/Akt and TGFÎ² signaling pathways, and accelerated G1/S progression cell cycle. KEGG analysis also demonstrated that focal adhesion and ECM-receptor interaction pathways were activated in anaplastic meningioma. Benign meningiomas had significantly higher levels of EGFL6 mRNA than brain arachnoidal tissues and atypical and anaplastic meningiomas (P<0.001). EGFL6 gene was also highly expressed in ovarian cancer, but expressed lowly in all other investigated tumors. EGFL6 was hardly detectable in serum samples of healthy people. The mean serum EGFL6 concentration was 675, 118, and 126 pg/ml in patients with benign, atypical, and anaplastic meningiomas respectively. Patients with ovarian cancers also had high serum EGFL6 levels (mean concentration: 617 pg/ml). Patients with all other investigated tumors, however, had low levels of serum EGFL6 with mean concentration less than 240 pg/ml. Conclusion: We proposed that deregulation of cell cycle and PI3K/Akt pathways might play important roles in the tumorigenesis of fibroblastic meningioma. It was also suggested that the activated integrin-mediated signaling pathways were involved in the pathogenesis of anaplastic meningioma. We presented evidence that EGFL6 might serve as a novel serum biomarker for benign meningioma and ovarian cancer. It was also suggested that EGFL6 could help discriminate benignancy or malignancy of meningiomas before surgery or at early time points. Differential gene expression profiles between meningiomas and brain arachnoidal tissues were established by using Affymetrix GeneChip Human U133 Plus 2.0 Array. KEGG pathway analysis was performed to identify potential gene pathways that may be involved in the pathogenesis of meningiomas. Quantitative real-time PCR (qRT-PCR) was performed to validate the differentially expressed genes in the KEGG pathways. EGFL6 mRNA levels were also determined in brain arachnoidal tissues, meningiomas, and other tumors by qRT-PCR. EGFL6 levels were measured in serum samples from healthy people and patients with various tumors by using ELISA.

Dataset Information

Transcription profiling of human neuroblastoma tissue samples

Publications

A robust method for estimating gene expression states using Affymetrix microarray probe level data.

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