Variations in target gene expression and pathway profiles in the mouse hippocampus following treatment with different effective compounds for ischemia–reperfusion injury

Abstract

In order to elucidate the overlapping and diverse pharmacological protective mechanisms of different Chinese medicinal compounds, we investigated the alteration of gene expression and activation of signaling pathways in the mouse hippocampus after treatment of cerebral ischemia-reperfusion injury with various compounds. A microarray including 16,463 genes was used to identify differentially expressed genes among six treatment groups: baicalin (BA), jasminoidin (JA), cholic acid (CA), concha margaritiferausta (CM), sham, and vehicle. The US Food and Drug Administration (FDA) ArrayTrack system and Kyoto Encyclopedia of Genes and Genomes (KEGG) database were used to screen significantly altered genes and pathways (P < 0.05, fold change >1.5). Vehicle treatment alone resulted in alteration of 726 genes (283 upregulated, 443 downregulated) compared to the sham treatment group. BA, JA, and CA treatments, but not CM treatment, were effective in reducing infarct volume compared with vehicle treatment (P < 0.05). Compared with the CM group, a total of 167 (73 upregulated, 94 downregulated), 379 (211 upregulated, 168 downregulated), and 181 (76 upregulated, 105 downregulated) altered genes were found in the BA, JA, and CA groups, respectively. The numbers of overlapping genes between the BA and JA, BA and CA, and JA and CA groups were 28 (16 upregulated, 12 downregulated), 14 (4 upregulated, 10 downregulated), and 31 (8 upregulated, 23 downregulated), respectively. Three overlapping genes were identified among the BA, JA, and CA treatment groups: Il1rap, Gnb5, and Wdr38. Based on KEGG pathway analysis, two, seven, and four pathways were significantly activated in the BA, JA, and CA groups, respectively, when compared to the CM group. The ATP-binding cassette (ABC) transporters general pathway was activated by BA and JA treatment, and the mitogen-activated protein kinase (MAPK) signaling pathway was activated by JA and CA treatment. Alteration of IL-1 and Hspa1a expression was found by real time reverse transcription polymerase chain reaction, confirming the results of the microarray analysis. Our data demonstrated that polytypic profiles of 167-379 altered genes exist in the mouse hippocampus treated with different compounds known to be therapeutically effective in cerebral ischemia-reperfusion injury, and we were able to identify overlapping genes and pathways among these groups. Therefore, these different compounds may function through both overlapping and distinct pharmacological mechanisms to exert their therapeutic action.

Phenotype-dependent alteration of pathways and networks reveals a pure synergistic mechanism for compounds treating mouse cerebral ischemia

“…Images of these slices were captured by a digital camera (Color CCD camera TP-6001A, Topica Inc, Tokyo, Japan). The area of the infarction region was calculated using a Pathology Image Analysis System (Topica Inc), and the ratio of the infarction volume to the total slice volume was calculated as described in our previous study [21][22][23][24][25][26] .…”

“…The cDNA microarray, including 374 cDNA ischemia-related genes, was selected from the Science STKE database. The details of this process are described in our previous studies [21][22][23][24][25][26] .…”

“…The results were submitted to the Array Express database. All data were normalized by locally weighted scatter plot smoothing (Lowness) to reduce experimental variability [21][22][23][24][25][26] . One-way analysis of variance and significant analysis of micro-arrays were employed to compare the mean numbers of the altered genes between the vehicle and sham, CM and vehicle, UA and CM, JA and CM, and JU and CM groups.…”

“…The level of statistical significance was set at P<0.05. Finally, canonical pathways with a P value<0.05 and a >1.5-fold change were screened out and analyzed [21][22][23][24][25][26] .…”

“…Our previous studies have shown that ursodeoxycholic acid (UA) and jasminoidin (JA) can significantly reduce ischemic infarct volume [21][22][23][24][25] . In the current study, we further explored the pure synergistic mechanism of these drugs, excluding interference from any negative phenotype compounds.…”