Robustness of gene expression profiling in glioma specimen samplings and derived cell lines
Author(s): Mehrian SR, Reichardt Juergen KV, Ya-Hsuan H, Kremen Thomas J, Liau Linda M, Cloughesy Timothy F, Mischel Paul S, Nelson Stanley F
Publication: Brain Res Mol Brain Res, 2005, Vol. 136, Page 99
PubMed ID: 15893592 PubMed Review Paper? No
Purpose of Paper
Conclusion of Paper
Studies
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Study Purpose
The purpose of this study was to determine levels of intra- and inter-tumoral variability in gene expression via microarray analysis and real-time quantitative RT-PCR (qRT-PCR) in glioblastoma and oligodendroglioma tissue samples. Tumor specimens from 6 patients were analyzed, with 2-4 biopsy samples that were at least 3 cm apart were collected from each tumor.
Summary of Findings:
Of the 7129 cDNAs examined via microarray, 931 (or 13%) were differentially expressed. When analyzed by hierarchical clustering, gene expression profiles of samples collected from a single tumor were highly similar, with the exception of a single sample that clustered with two different tumor classes. Histological examination of adjacent regions confirmed that the sample likely contained a mix of cells from the two different tumor classes. The authors conclude that gene expression variance introduced by tumor heterogeneity is small in comparision to that observed between different tumor grades and classes, and between individuals. Results of real-time quantitative RT-PCR (although not shown) confirmed microarray data, as TAF15 expression was reduced in samples from the oligodendroglioma tumor class.
Biospecimens
Preservative Types
- Frozen
Diagnoses:
- Neoplastic - Other
Platform:
Analyte Technology Platform RNA DNA microarray RNA Real-time qRT-PCR Morphology H-and-E microscopy Pre-analytical Factors:
Classification Pre-analytical Factor Value(s) Real-time qRT-PCR Specific Targeted nucleic acid TAF15
Biospecimen Aliquots and Components Biospecimen heterogeneity Intratumoral sampling (exact positions not specified)
Preaquisition Diagnosis/ patient condition Glioblastoma brain tumor
Oligodendroglioma brain tumor
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Study Purpose
The purpose of this study was to determine whether primary human brain tumor culture (after 10 passages) retained parental gene expression profiles using microarray and real-time qRT-PCR (for angiotensinogen and fibronectin 1) analyses.
Summary of Findings:
Microarray analysis of primary cell cultures resulted in differential gene expression compared to parental samples, and similar gene expression profiles when compared to one another. Although data was not shown, the authors report angiotensinogen and fibronectin 1 expression were reduced and elevated in primary cell cultures compared to parental samples, respectively, when assessed by real-time qRT-PCR.
Biospecimens
Preservative Types
- None (Fresh)
Diagnoses:
- Neoplastic - Other
Platform:
Analyte Technology Platform RNA Real-time qRT-PCR RNA DNA microarray Pre-analytical Factors:
Classification Pre-analytical Factor Value(s) Biospecimen Aliquots and Components Number of cell passages 1 passage
10 passages
Real-time qRT-PCR Specific Targeted nucleic acid Angiotensinogen
Fibronectin 1