Temporal Regulation of Gene Expression Profiles in Rat Brains Following Ischemic Stroke

To improve understanding of the molecular mechanisms that underlie ischemic stroke, we analyzed early gene expression profiles in permanent middle cerebral artery occlusion (pMCAO) stroke model. Rats were allocated into 4 groups: control, 3h MCAO, 6h MCAO, and 12h MCAO. Cortical brain tissue was collected after stroke and subjected to microarray analysis. This information was then analyzed using a series of bioinformatic tools including Transcriptome Analysis Console (TAC), Genesis, Short time-series Expression Miner (STEM), and STRING. A number of differentially expressed genes were found to be either upregulated or downregulated in a temporal manner. At 3 hours post-stroke, 230 genes were upregulated and 21 downregulated, 635 were upregulated and 238 downregulated at 6 hours, 1033 were upregulated and 741 downregulated at 12 hours following MCAO. STEM analysis highlighted several distinct patterns of gene activity. Genes that were temporally upregulated were highly associated with inflammatory response and apoptosis, while genes that were temporally downregulated after stroke were strongly associated with cell membrane components and neurons. Genes that decreased at 3 hours and increased afterwards were also associated with inflammatory response. Genes that increased the 1st 6 hours and decreased slightly at 12 hours were associated with RNA binding with indication that a key regulator THOC1 may also be involved in apoptosis. Lastly genes that decreased at 6 hours but remained flat before and after were associated with hydroxy compound transport. The temporally upregulated genes separated into two distinct hubs: the 1st was mostly associated with cytokines and chemokines, and the 2nd was mostly made up of RGD, Rps, Eif, and ESNROG proteins which are mostly ribosomal or associated with translation. The main regulator in the 2nd hub Rsl1d1 is associated with apoptosis. The main regulators of inflammatory response appeared to be Il6, Il1b, and Ccl2. STRING analysis revealed no distinct pattern for the temporally downregulated genes. These results provide evidence that in addition to the neuronal death and inflammatory responses following stroke, regulation of translation may play an important role. Understanding the transcriptional mechanisms following ischemia may provide therapeutic targets for treating stroke