V. M. Kavsan

Comparison of microarray and SAGE techniques in gene expression analysis of human glioblastoma

To enhance glioblastoma (GB) marker discovery, we compared gene expression in GB with human normal brain (NB) by accessing the SAGE Genie web site and compared the results with published data. Nine GB and five NB SAGE libraries were analyzed using the Digital Gene Expression Displayer (DGED); the results of DGED were tested by Northern blot analysis and RT-PCR of arbitrarily selected genes. Review of available data from the articles on gene expression profiling by microarray-based hybridization showed as few as 35 overlapped genes with increased expression in GB. Some of them were identified in four articles, but most genes were identified in three or even in two investigations. Some differences were also found between SAGE results of GB analysis. The Digital Gene Expression Displayer approach revealed 676 genes differentially expressed in GB vs. NB with cutoff ratio: twofold change and P ≤ 05. Differential expression of selected genes obtained by DGED was confirmed by Northern analysis and RT-PCR. Altogether, only 105 of 955 genes presented in published investigations were among the genes obtained by DGED. Comparison of the results obtained by microarrays and SAGE is very complicated because the authors present only the most prominent differentially expressed genes. However, even available data give quite poor overlapping of genes revealed by microarrays. Some differences between results obtained by SAGE in different investigations can be explained by high dependence on the statistical methods used. As for now, the best solution to search for molecular tumor markers is to compare all available results and to select only those genes where significant expression in tumors combined with very low expression in normal tissues was reproduced in several articles. One hundred five differentially expressed genes, common to both methods, can be included in the list of candidates for the molecular typing of GBs. Some genes, encoded cell surface or extracellular proteins may be useful for targeting gliomas with antibody-based therapy.

Expression of genes belonging to the IGF-system in glial tumors

Increased expression of the insulin-like growth factor (IGF) family members, IGF1, IGF2, their receptors and binding proteins, or combinations thereof has been documented in various malignancies including gliomas. The results of multiple investigations suggest that the IGFs can play a paracrine and/or autocrine role in promoting tumor growth in situ during tumor progression but that these roles may vary depending on the tissue of origin. Enhanced IGF1 expression was not found in glioblastomas and it was supposed that IGF1 participation in the development of glial tumors may be substituted by protein products of highly expressed other genes, also participating in PI3K and MAPK pathways. Increased expression of IGF-binding protein genes in brain tumors makes the picture even more complicated. As other binding proteins, IGFBPs regulate the activity of their ligands by prolonging their half-life. The discrepancies arising from conflicting evidence on the results obtained by different laboratories in human gliomas are discussed. Our data highlight the importance of viewing the IGF-related proteins as a complex multifactorial system and show that changes in the expression levels of any one component of the system, in a given malignancy, should be interpreted with caution. As IGF targeting for anticancer therapy is rapidly becoming clinical reality, an understanding of this complexity is very timely.