Parallel gene expression monitoring using oligonucleotide probe arrays of multiple transcripts with an animal model of focal ischemia

High density oligonucleotide arrays offer tremendous potential to study gen e changes occurring in disease states. The authors described the first case of using a custom designed high density oligonucleotide probe array contai ning 750 genes to monitor the changes in mRNA transcript levels occurring a fter focal ischemia for a period of 3 hours. Permanent middle cerebral arte ry occlusion in the rat resulted in neuronal degeneration in the dorsolater al cortex and striatum over a time course of 24 hours. Comparing the change s in hybridization levels in the frontal and parietal cortices and the stri atum, between the ipsilateral and contralateral sides of the brain using th e probe arrays resulted in the up-regulation of 24 genes, which showed grea ter than a twofold change. Very few genes were found to be downregulated af ter the ischemic insult. Many of the immediate early genes (IEGs) such as c -Sas, NGFI-A, NGFI-C, and Krox-20 were found to be robustly upregulated in the three different regions studied. Other genes that were up-regulated in perifocal regions included Are, Inhibin beta-A, and the phosphatases MKP-1 and MKP-3. The hybridization signal intensity from the probe arrays enabled quantification of many genes relative to one another, and robust changes i n expression were obtained with very little interanimal variability. Furthe rmore, the authors were able to validate the increased expression of NGFI-C and Are using in situ hybridization. This represented the first example of using high density oligonucleotide probe arrays in studying the expression of many genes in parallel and in discrete brain regions after focal ischem ia.