At this point, 3116 probe sets indicated sellekchem genes that were differen tially expressed. Of these, 253 probe sets were upregulated, and 427 probe sets were down regulated in tumours with overexpressed KIT compared to those with low expression. Again, unsupervised hierarchi cal clustering showed that gene expression patterns of the individual tumour samples from these two groups clus tered together. No gene expression signature was found to be associated with tumour size, mitotic index, or risk category. Gene enrichment analyzes Differential expression was then analyzed on the level of GO categories and KEGG pathways. Functional features of the 311 and 680 genes that differentiated tumours according to KIT expression compared to those with high KIT expres sion.

Because previous studies indicated that KIT mutant and PDGFRA mutant GISTs may have features associated with activation of downstream Inhibitors,Modulators,Libraries pathways like ERK12, AKT, p7085S6K, STAT1STAT3, and PI3KmTOR, the lists of differentially expressed genes were compared with both lists of interacting partners of KIT and PDGFR, sum marized in Supplementary Table Inhibitors,Modulators,Libraries S5. According to our model of PDGFRA signalling path ways, the final data set contained 44 and 52 proteins inter acting with KIT and PDGFR, respectively, 13 of which were common for both pathways. Within the list of differentially expressed genes according to the mutation status only 3 genes corresponding to PDGFRA interactome were found. None of KIT genes encoding KIT signalling pathway pro teins was found within this list.

To further test other pathways described by Corless et al, we also analyzed genes from selected KEGG pathways involved Inhibitors,Modulators,Libraries in mitogenic signal transduction signalling. Inhibitors,Modulators,Libraries Those genes were compared with lists of differentially expressed genes Relative mRNA expression of accordingpanelsample mutation Relative mRNA expression of KIT and PDGFRA in GIST tumours according to sample mutation Inhibitors,Modulators,Libraries status. Black circles KIT mutations. gray circles PDGFRA mutations Interestingly, the expression of 7 genes annotated to syn aptic transmission, 15 genes annotated to blood vessel development, and 20 genes annotated to G protein sig nalling were at least 2 fold higher in tumours with low depending on KITPDGFRA mutation status. Apart from protein kinase C alpha, no other genes from such lists were found among the differentially expressed genes.

Among PKC isoforms selleck chemical Imatinib analyzed in this study by microar ray and quantitative RT PCR, expression of PKC alpha was significantly lower, while expression of PKC theta was significantly higher in tumours with KIT mutations compared to those with PDGFRA mutations and wild type tumours. Discussion GISTs express KIT, a 145 kD transmembrane glycoprotein that serves as the receptor for stem cell factor. KIT activates cellular signalling during embryogenesis and is critical for the development of germ cells, hemat opoietic progenitor cells, and mast cells.