Comparison of gene expression profiles between frozen original meningiomas and primary cultures of the meningiomas by GeneChip.

Objective: In vitro experiments are performed on a daily basis to study the molecular biology of tumors. For some benign tumors, however, established cell lines are not always available, or it may not be feasible to establish new ones. In such cases, primary cultures are used to perform in vitro experiments. Gene expression profiles in vitro differ from those in vivo, but information as to which genes have significantly altered levels is limited. In this study, gene expression profiles of meningiomas in primary cultures and frozen tumors were compared.

Methods: Affymetrix U95A chips were applied to three sets of meningiomas. For each tumor, the gene expression profiles in frozen specimens (Fr) and primary cultures from the same tumor at Pass 5 (P5) and Pass 10 (P10) were compared. A paired t test (P < 0.025) was applied between Fr and P5, and then between Fr and P10. Genes that demonstrated significantly different expression levels in both comparisons were then identified. The expression levels for a subset of these genes were confirmed by quantitative real-time reverse transcription-polymerase chain reaction.

Results: Among 12,000 genes examined, up-regulation of 51 genes by fivefold or more and down-regulation of 19 genes by twofold or more was found in primary cultures (P5 and P10) compared with the corresponding Fr. Up-regulation of genes encoding for extracellular matrix, cytoskeleton, and cell surface receptors was particularly notable.

Conclusion: Gene expression of tissue-cultured meningiomas and in situ meningiomas is significantly different for a large number of genes. Therefore, gene expression and therapeutic studies on cultured meningiomas need to be interpreted with caution.