Outcome-dependent global similarity analysis of imbalanced core signaling pathways in ischemic mouse hippocampus.

Analysis of the diverse interactions of multiple signaling pathways is an emerging challenge in the era of networking pharmacology. To reveal imbalanced signaling pathways and pharmacological mechanisms involved in ischemic process, we designed systemic experiments from top-down to bottom-up for investigating the variations of multiple pathways in mouse hippocampal cells. A total of 711 focal cerebral ischemia-reperfused animals (504 mice and 207 rats), induced by occlusion of the middle cerebral artery, were obtained to conduct 4 experiments. The mice were used to analyze the pharmacological effects of four single compounds, baicalin (BA), jasminoidin (JA), ursodeoxycholic acid (UA) and concha margaritifera (CM) and two combination therapies (BA+JA, and JA+UA). Moreover, the mouse models were also used for microarray and western blotting test. The rat models were used for infarction volume test, magnetic resonance imaging (MRI) test and neurological score analysis to validate the pharmacological effects in another species. The results of western blotting confirmed that the expression of the key proteins involved in the ischemiaactivated Wnt and nuclear factor κB (NF-κB) pathway was markedly altered. In addition, based on the screened gene expression profiles of ischemia hippocampus, a variety of altered genes contributed to the 9 stroke-related pathways based on literature review [Wnt, extracellular signal-regulated kinase (ERK), janus kinase (JAK), mitogen-activated protein kinase (MAPK), gonadotropin-releasing hormone (GnRH), calcium/calmodulin-dependent protein kinase (CaMK), vascular endothelial growth factor (VEGF), epidermal growth factor (EGF), and platelet-derived growth factor (PDGF)] in different groups. Thus, we believed that the 9 signaling pathways were significantly imbalanced in different groups. However, analysis of overlapping genes was insufficient to reveal the expression profiles of imbalanced pathways between or within various conditions treated with different compounds or compound mixtures. Therefore, global similarity index (GSI) is introduced to quantify the genotypic outcomes of gene expression profiles. Independent experiments in mice on the effects of infarction volume, neurologic deficit score and the results of MRI in rats showed that GSI was suitable for the spectral measurement of imbalance in those 9 biochemical pathways with a predictive accuracy of 81.0% as assessed by leave-one-out cross-validation.

Synergistic mechanism of gene expression and pathways between jasminoidin and ursodeoxycholic acid in treating focal cerebral ischemia-reperfusion injury.

AIM: Jasminoidin and ursodeoxycholic acid are 2 bioactive compounds extracted from Chinese medicine that have been proven to exert a synergistic effect as a combined administration for the treatment of stroke. The aim of this study was to reveal the pharmacogenomic mechanism of this synergistic effect of jasminoidin and ursodeoxycholic acid. METHODS: One hundred and fifteen mice with brain damage, induced by focal cerebral ischemia/reperfusion, were divided into 5 groups: jasminoidin-treated, ursodeoxycholic acid-treated, combination-treated, vehicle group, and sham-operated group. Comparative analysis of stroke-related gene expression profiles and Kyoto Encyclopedia of Genes and Genomes pathways among the 3 treatment groups were performed to reveal the mechanism of this synergistic effect. RESULTS: This study demonstrated that (1) treatment with jasminoidin alone caused similar changes in the pattern of gene expression as those treated with the combination; (2) jasminoidin treatment and the combination treatment had more overlapping changes in gene expression and activated pathways than the ursodeoxycholic acid treatment; (3) Hspa1a and Ppm1e were only up-regulated in the combination-treated group; (4) the nonoverlapping genes Fgf12, Rarα, Map3k4, paxillin (PXN) in the combination-treated group were markedly expressed, and P53 pathway was obviously activated in the combination-treated group. CONCLUSION: These findings may suggest that jasminoidin is the major component of the combination, and the combination plays an important role of the synergistic effect in up-regulating expression of gene Hspa1a, genes Fgf12, Rarα, Map3k4 and down-regulating gene PXN, as well as activating P53 pathway.

Comparison of the network structural characteristics of calcium signaling pathway in cerebral ischemia after intervention by different components of Chinese medicine.

OBJECTIVE: To explore the network control mechanism of the calcium signaling pathway in cerebral ischemic injury after intervention by the main components of Qingkailing (see text), i.e. Baicalin, Jasminoidin and their combination. METHODS: Thirty mice were randomly divided into 5 groups, a baicalin group, a Jasminoidin group, a baicalin plus Jasminoidin group, a nimodipine group, and a model group (n = 6). The global cerebral ischemia-reperfusion mouse model was established. The mice were administrated respectively by injection of baicalin, Jasminoidin, mixture of baicalin and Jasminoidin, and nimodipine into the caudal vein, with the model group given no any drug. Three hours after operation, the brain was removed and sectioned. After calculation of cerebral ischemic area by 2,3,5-triphenyltetrazolium staining, the percentage of infarct volume was calculated. The total RNA of the mouse brain tissue was extracted to obtain the whole genome expression profile, and the differentially expressed genes related to the calcium signaling pathway was analyzed with Bayesian network structures. RESULTS: Compared with the model group, the ischemic area was significantly reduced in the baicalin group, the Jasminoidin group, the Baicalin plus Jasminoidin group (all P < 0.05). The ischemic area in the baicalin plus Jasminoidin group was smaller than the other three groups (all P < 0.01). In the gene regulatory network structures of calcium signaling pathway, the average length and equitability were the highest in the baicalin plus Jasminoidin group, followed by the nimodipine group. CONCLUSION: Compared with a single component, combination of Baicalin and Jasminoidin can more obviously intervene in the overall expression of calcium signaling pathway, and the mechanism is related with the aggregation characteristic of the gene expression network.

Fusion of core pathways reveals a horizontal synergistic mechanism underlying combination therapy.

Combination therapies have recently been shown to be more effective than monotherapies that may provide synergistic effects in the treatment of stroke, but its selective mechanism still remains unclear. Based on the median-effect method, the combination therapy of jasminoidin and ursodeoxycholic acid had a synergic effect on reducing the infarct volume. The numbers of up- or down-regulated genes by at least 1.5-fold in the vehicle, jasminoidin, ursodeoxycholic acid, and the combination of jasminoidin and ursodeoxycholic acid treatment groups were 228, 95, 136, and 101, respectively. According to clustering and principal component analysis, the pattern of gene expression in the combination group was similar to that of jasminoidin group rather than ursodeoxycholic acid group. Based on these nine top sequences in the combination group excluding four overlapping pathways (MAPK-ERK, Kitlg, Icam1-Ap1, and prolactin), the jasminoidin group had four (PRLR-STAT1, AcvR2-AcvR1B, ACVR1/2A-SMAD1, GHR-NF-κB) contributing pathways, and the ursodeoxycholic acid group had one (IL-6) contributing pathway. Based on the multiple-pathway-dependent comparison analysis (MPDCA), it may lead to the conclusion that jasminoidin possibly contributes more important pharmacological effect in the combined treatment as jasminoidin regulated 80% of the pathways that the combination group mediated. The study reveals a horizontal synergistic effect by optimizing the fusion of more pathways from the compounds with more contribution to the combination therapy. Rather than selecting compounds only based on experience in the past, this study would give a new insight into the systematic strategies for designing synergistic combination therapies.