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Objective To investigate the regulation of liver regeneration (LR) by changes in energy metabolites in the initiation phase during rat liver regeneration. Methods Rats were randomly divided into 3 groups with 5 rats in each group, including two partial hepatectomy (PH) groups and one normal control group. Selective reaction monitoring/multiple reaction monitoring (SRM/MRM) was employed in the targeted metabolomics identification of 29 energy metabolites. Ingenuity Pathway Analysis (IPA) was applied for integration analysis, including canonical pathway and molecular interaction network. Results The levels of 3-phospho-D-glycerate, AMP, cyclic AMP, D-fructose 1, 6-bisphosphate, dihydroxyacetome phosphate (DHAP), guanosine monophosphate (GMP), guanosine triphosphate (GTP), nicotinamide adenine dinucleotide (NAD) and nicotinamide adenine dinueleotide phosphate ( NADP ) significantly increased. The levels of alpha-ketoglutarate, beta-D-fructose 6-phosphate, cis-aconitate, D-glucose 6-phosphate, lactate, NADPH, oxaloacetate and pyruvate dramatically reduced. Through hierarchical clustering analysis of energy metabolisms, these energy metabolisms can be grouped into four clusters. IPA showed that the biomolecular changes in the priming phase of liver regeneration are mainly related to carbohydrate metabolism, cellular growth and proliferation, and organismal development. During the priming phase of liver regeneration, adenosine 5'-monphosphate-activated protein kinase (AMPK), hypoxia- inducible factor la (HIF-la), peroxisome proliferator-activated receptor (PPAR), protein kinase A (PKA) and phosphatidylinositol 3-kinase/protein kinase B (PI3K/Akt) signaling pathways are involved in energy metabolism, and glycolysis may be the main mode of energy supply. Conclusion The result suggests that the changes of energy matabolites during the initial stage of LR play a regulatory role in live regeneration.
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This present study aimed to explore the molecular mechanism of Erzhi Wan(a prescription of nourishing Yin and toni-fying liver and kidney) in treatment of aging by network pharmacology. The active constituents and target proteins of Erzhi Wan were searched from Traditional Chinese Medicine Systems Pharmacology Database(TCMSP) and PubChem databases respectively. Aging-related genes were searched from Gene and HAGR databases. Based on the Ingenuity Pathway Analysis(IPA), we analyzed the common molecular network, biological pathway and interaction sites between these two parts, and verified some of them by Western blot. Twelve active constituents of Erzhi Wan were screened by TCMSP databases, 69 protein targets were predicted through PubChem, and 148 aging-related genes were found in Gene and HAGR databases. IPA comparison showed that the molecular networks of these two were complex, with diversity of biological functions. The common pathways involved 292 pathways, mainly related to tumors. They acted on hypoxia inducible factor-1α gene(HIF1α), nuclear factor-E2 related factor(Nrf2/NFE2 L2), tumor necrosis factor(TNF) and other sites. Western blot results suggested that Erzhi Wan could down-regulate the expression of HIF1α, with statistical difference(P<0.05). It was concluded that, Erzhi Wan could intervene aging through improving pseudo-hypoxic microenvironment and inflammation. The molecular mechanism of Erzhi Wan in delaying aging was preliminarily revealed, which laid a foundation for further stu-dying the anti-aging mechanism of Erzhi Wan, and also provided a reference for the compatibility mechanism and extended application of Chinese medicine compounds.
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Humans , Aging , Drugs, Chinese Herbal , Medicine, Chinese Traditional , Neoplasms , Proteins , Tumor MicroenvironmentABSTRACT
Objective: To study the potential mechanisms of Yiwei Decoction on intervening gastric precancerous lesions by using metabolomics technology combined with ingenuity pathway analysis (IPA). Methods: Gastric precancerous lesion rat model induced by N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) was established and ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF/MS) was utilized to detect and characterize rat serum metabolites. Metabolites with significant changes in model group and Yiwei Decoction group were screened out; The IPA software was used to analyze the potential targets and mechanisms. Results: Yiwei Decoction effectively interfered with the progress of gastric precancerous lesions. A total of 23 metabolites in the serum of gastric precancerous lesion rat model were significantly changed (P < 0.05), 13 metabolites were significantly regulated to normal level in Yiwei Decoction group (P < 0.05), the metabolic pathways mainly involved in the biosynthesis of unsaturated fatty acids, biosynthesis of valine, leucine and isoleucine, sphingolipid metabolism, arachidonic acid metabolism and steroid hormone synthesis, etc. The effect of Yiwei Decoction on intervening with the progression of gastric precancerous lesions was related to the inhibition of ET-1 and IL-8 signaling pathway. Conclusion: Yiwei Decoction can inhibit the progress of gastric precancerous lesions and improve the inflammatory environment by regulating arachidonic acid metabolism and inhibiting ET-1 and IL-8 signaling pathways.
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Objective: To investigate the changes of expressions of the related genes in the triple-negative breast cancer (TNBC) MDA-MB-231 cells after knockout of Rab7a gene, and to elucidate the roles of Rab7a-related genes in TNBC. Methods: The breast cancer ZR-75-30, MCF-7, T-47D, MDA-MB-231 and HCC-1937 cells in the logarithmic phase were selected. The expression levels of Rab7a protein in the breast cancer ZR-75-30, MCF-7, T-47D, MDA-MB-231, and HCC-1937 cells were detected by Western blotting method. The Rab7a gene in the MDA-MB-231 cells was knockout with lentivirus and the cells were divided into negative control group and Rab7a knockout group. According to the four different knockout Rab7a sequences, the Rab7a knockout group was divided into KD1 group, KD2 group, KD3 group and KD4 group. The knockout efficiencies of Rab7a gene in the MDA-MB-231 cells in various groups were detected by qPCR method, the differential genes in the highest knockout efficiency group (KD2 group) and negative control group were detected by full gene expression microarray, and the interaction between Rab7a gene and other genes was analyzed by integrated pathway analysis (IPA) software. Results: The Rab7a protein was expressed in the TNBC MDA-MB-231 cells. Compared with negative control group, the knockout efficiency of Rab7a gene in the MDA-MB-231 cells in KD2 group was the highest (P
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Objective • To explore the differences in morphology, molecular characteristics and biological functions of different types of mouse fetal liver stromal cells. Methods • E13.5 mouse fetal liver stromal cells were obtained by adherent culture, and different cell types were distinguished by morphology and expression of surface markers, such as CD44, CD29, CD106, CD45 and Sca-1. Then microarray assay was conducted by Mouse Genome 430 2.0 Array and analyzed at P3 or <-2 to identify differential expression genes. Canonical pathway and biological function analyses were performed by using ingenuity pathway analysis (IPA software). Results • Spindle-like (CD45+CD106-CD29+CD44+Sca-1-) and fibroblast-like (CD45-CD106+CD29+CD44+Sca-1-) fetal liver stromal cells were isolated in this study according to the cell morphology. The 1 485 highly-expressed genes in spindle-like cells mainly involved in immune and inflammation-related signaling pathways; while the 3 374 highly-expressed genes in fibroblast-like cells mainly involved in extracellular matrix formation and cellular adhesion. Conclusion • Mouse fetal liver stromal cells have strong heterogeneity in biological characteristics and functions, especially in hematopoietic promoting capability.
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OBJECTIVE@#To decipher the possible mechanisms of Sinomenium Acutum (SA) in treating diseases by a bioinformatics method.@*METHODS@#SA ingredients were searched according to Chinese Pharmacopoeia, Chinese Medicine Dictionary and Traditional Chinese Medicines Database (TCMD). Active compounds and target proteins of SA were acquired through the Pubchem platform. Pathway, network and function analyses of SA were performed with ingenuity pathway analysis (IPA), a bioinformatics analysis platform. Disease, biofunction-target networks were established with Cytoscape.@*RESULTS@#Eighteen ingredients from SA were obtained. Seven active ingredients with 31 active target proteins were acquired according to PubChem Bioassay test. By IPA analysis, 277 canonical pathways belonging to 17 function categories were collected, 23 kinds of diseases, 21 categories bio-functions were obtained. Based on P value, calculated by IPA, the top 5 significant pathway of SA targets include phosphatidylinositol 3 kinase/Akt (PI3K/Akt) signaling, prostate cancer signaling, macrophage migration inhibitory factor (MIF) regulation of innate immunity, Guanosine-binding protein coupled receptor (GPCR) signaling, and ataxia telangiectasia mutated protein (ATM) signaling. Disease and bio-function network analysis indicated that mitogen activated protein kinase 1 (MAPK1), MAPK3, p65 nuclear factor κB (RELA), nuclear factor of κB inhibitor alpha (NFκBIA), interleukin 1β(IL-1β), prostaglandin G/H synthase 2 (PTGS2) and tumor protein 53 (TP53) were the critical targets in various diseases treated by SA.@*CONCLUSION@#In the different view of target, pathway, disease and bio-function, inflammation was found to be a central theme in many chronic conditions. SA could be used not only as an anti-inflammatory agent, but also for the treatment of cancers, neurological diseases, psychological disorders and metabolic diseases.
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Humans , Computational Biology , Methods , Disease , Molecular Targeted Therapy , Proteins , Metabolism , Signal Transduction , Sinomenium , ChemistryABSTRACT
Objective: To research endogenous metabolites changes of model group on human umbilical vein endothelial cells (HUVECs) injury induced by advanced glycation end products (AGEs) and the accommodation mechanism of morroniside (active components in Cornus officinalis) on the abnormal metabolism. To find potential biomarkers which morroniside protected the injured HUVECs, and to explore mechanisms of morroniside in treatment of HUVECs injury induced by AGEs. Methods: HUVECs were cultivated in vitro, HUVECs injury model was established by the induction of AGEs. Cells were divided into three groups, control group, model group, and treatment group. Cell samples of three groups were determined with UPLC-Q-TOF/MS. Pattern recognition methods including PCA, PLS-DA, and OPLS-DA were applied to analyze multivariate data, and t-test was used in significant statistical analysis. It was used to find out potential biomarkers. Metabolomic feature network graphs were constructed ingenuity pathway analysis (IPA). Results: In pattern recognition, control group, model group, and treatment group could be distinguished better from each other. According to VIP values, 30 ions which had a significant contribution to the classification were screened further, 10 potential metabolic biomarkers were identified qualitatively. These endogenous substances of the cells in treatment group in vivo had varying degrees of recovery. Five metabolic pathways were identified, and a metabolomic feature network of morroniside to protect against HUVECs injury induced by AGEs was constructed. Conclusion: Changed metabolities on HUVECs injury induced by AGEs can be certainly recovered by morroniside, and the treatment effect of morroniside can be connected with the regulation of five related metabolic pathways.
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To investigate the effect of Salvianolate Lyophilized Injection (SLI) combined with Xueshuantong Injection (XST) on expression of astrocytes and microglia in cerebral ischemia-reperfusion injury rats. Methods The Wistar rats (250-300 g, male) were randomly divided into six groups: control group, model group, Edaravone group (6 mg/kg, EDI), SLI group (21 mg/kg), XST group (100 mg/kg), and SLI+XST group (1X1S, 21 mg/kg and 100 mg/kg). Rat model of cerebral ischemia-reperfusion injury was created by the middle cerebral artery occlusion (MCAO) by longa method. Drugs were administered tail intravenous injection once a day for 3 d starting from 24 h after reperfusion. The body weight, neurological deficit scores and survival percentage were observed in 3 d after the cerebral ischemia. The expression of GFAP and IBA-1 was determined at 3 d by immunofluorescence. The complicated compound-target-stroke network of SLI and XST was constructed and analyzed by IPA. Results Compared with the model group, 1X1S could significantly improve the neurological dysfunction, increase the body weight, and inhibit the expression of GFAP and IBA-1 in ischemic penumbra (P < 0.01), IPA reveals the molecular mechanism of SLI and XST in the active ingredient and related targets. Conclusion 1X1S has significant protection on cerebral ischemia reperfusion injury in rats, which may be related to the inhibition of the expression of GFAP and IBA-1 and high mobility group box-1 signaling and Interleukine-8 signaling.