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| Status |
Public on Dec 19, 2007 |
| Title |
Gene expression profiling in glioblastoma and immunohistochemical evaluation of IGFBP-2 and CDC20 |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
The different clinical behavior of low and high grade gliomas and the chance to develop novel selective agents that specifically target tumor-associated proteins in gliomas stimulate the research of molecules playing a role in glioma progression.
Gene expression profiling using microarrays allows the study at the same time of the expression patterns of thousands of genes in tumor cells.
In the present study microarrays with about 20,000 genes have been employed to discover the gene expression profile in 39 glial neoplasias (28 glioblastomas (GBM) and 11 low grade gliomas, namely 4 oligodendrogliomas, 5 pilocytic astrocytomas (PA), 2 fibrillary astrocytomas (FA)).
Unsupervised classification through hierarchical cluster analysis identified 2 groups of tumours: one group mainly composed of low grade malignant tumours (10 low grade gliomas and 3 GBM), the other one constituted by GBM, with the exception of one low grade case.
The nearest shrunken centroid classification method was used to identify genes useful to classify and best characterize high and low grade gliomas. [Tibshirani et al. 2002]
This procedure selected 9 genes as most informative for the classification task:
Among them 7 genes were overexpressed in low grade gliomas, but underexpressed in GBM; on the contrary 2 genes were overexpressed in GBM, but underexpressed in low grade tumours
Forty five tumors were immunostained for IGFBP-2 . 81,5% GBM resulted immunopositive. On the contrary only one low grade glioma was positive.
Gene expression profiling and immunohistochemistry suggest that IGFBP-2 may play a role in glioma progression. IGFBP-2 appears to be a novel immunohistochemical marker of malignancy in glial tumours and probably is the basis for targeted chemotherapy.
Keywords: glioblastoma, gene expression analysis, IGFBP-2, Hiearchical clustering
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| Overall design |
We retrieved for this study 185 randomly selected cases of gliomas. All the cases had been received unfixed. A sample of neoplastic tissue had been flash frozen over liquid nitrogen and stored at -80°C into the frozen tissue bank of the Section of Pathology of Bellaria Hospital between 1990 and 2002. The remaining (specular) tissues were formalin fixed and paraffin embedded for routine histologic diagnosis.
In the present investigation, only samples with rRNA 28S/18S ratio > 1.0 measured by Bioanalyzer 2100 (Agilent)and no evidence of ribosomal degradation were included. Some cases were excluded as the tissue samples were composed only by necrosis; other cases did not show neoplastic proliferation. Therefore only 39 glial neoplasias were suitable for the study: i.e. 28 GBMs and 11 low grade CNS tumors, namely 4 oligodendrogliomas (OL), 5 pilocytic astrocytomas (PA), 2 fibrillary astrocytoma (FA) showed a good quality of RNA.
All the tumors were re-staged and graded according to 2000 WHO criteria at time of gene expression analysis by two pathologists (GM and VE).
39 glial neoplasias were labeled by Cy5. Common reference pool consisted of a mixture of total RNA from the low grade CNS tumor group (4 OL, 5 PA, 2 FA) labeled by Cy3. A series of the most informative genes were confirmed by RT-qPCR.
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| Contributor(s) |
Marucci G, Morandi L, Magrini E, Franceschi E, Miglio R, Calo' D, Pession A, Foschini M, Eusebi V, Farnedi A |
| Citation(s) |
18953566 |
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| Submission date |
Dec 14, 2007 |
| Last update date |
Dec 06, 2012 |
| Contact name |
Luca Morandi |
| E-mail(s) |
[email protected]
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| Organization name |
University of Bologna
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| Department |
Oncology Dept
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| Lab |
Anatomia Patologica Bellaria Hospital
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| Street address |
Via Altura 3
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| City |
Bologna |
| ZIP/Postal code |
40139 |
| Country |
Italy |
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| Platforms (2) |
| GPL885 |
Agilent-011521 Human 1A Microarray G4110A (Feature Number version) |
| GPL887 |
Agilent-012097 Human 1A Microarray (V2) G4110B (Feature Number version) |
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| Samples (39)
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| Relations |
| BioProject |
PRJNA103879 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE9885_RAW.tar |
219.1 Mb |
(http)(custom) |
TAR (of TXT) |
| Processed data included within Sample table |
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