Mechanism of Shouhui Tongbian Capsules in treating constipation based on network pharmacology and molecular docking / 中国中药杂志

To explore the mechanism of Shouhui Tongbian Capsules in treating constipation by means of network pharmacology and molecular docking approach. Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform(TCMSP) and Bioinfoematics Analysis Tool for Molecular Mechanism of Traditional Chinese Medicine(BATMAN) were applied to obtain chemical components and potential targets of eight herbs in Shouhui Tongbian Capsules according to the screening principles of oral availability(OB)≥30% and drug-like property(DL)≥0.18. Disease targets relating to constipation were screened out through GeneCards, PharmGkb and other databases, drug targets were integrated with disease targets, and intersection targets were exactly the potential action targets of Shouhui Tongbian Capsules for treating constipation; PPI network of potential targets was constructed using STRING platform, and GO(gene ontology) analysis and KEGG(Kyoto encyclopedia of genes and genomes) pathway data were obtained to conduct enrichment analysis and predict its mechanism of action. Cytoscape 3.6.1 was used to construct a network of "medicinal materials-chemical components-drug targets", and the network topology analysis was carried out on the PPI network to obtain its main components and key targets. Molecular docking between components and key targets of Shouhui Tongbian Capsules verified the accuracy of network pharmacological analysis results. The PPI network analysis showed 92 chemical components, including quercetin, stigmaste-rol, aloe-emodin, rhein, and key targets for instance AKT1, MAPK1, IL6, JUN, TNF and TP53. The enrichment analysis of KEGG screened out 157 signal pathways(P<0.01), mainly involving interleukin 17 signaling pathway, AGE-RAGE signaling pathway in diabetic complications, thyroid hormone signaling pathway. Quercetin, resveratrol and lysine with top degree value had a rational conformation in docking site of protein crystal complexes. This study preliminarily showed that various active ingredients in Shouhui Tongbian Capsules could regulate multiple signaling pathways, increase intestinal smoothness and peristalsis function, ensure smooth intestinal lumen, and play a role in treating constipation by acting on key targets, such as AKT1, MAPK1, IL6 and JUN.

Study on therapeutic mechanism of Rehmanniae Radix Praeparata- Corni Fructus in sequelae of ischemic stroke based on network pharmacology technology / 中国中药杂志

In ischemic stroke sequela phase, Rehmanniae Radix Praeparata-Corni Fructus drug pair has the effect in protecting damaged neurons, but its mechanism has not been clear. In this study, network pharmacology was used to predict the mechanism of Rehmanniae Radix Praeparata-Corni Fructus in the treatment of ischemic stroke sequela. Through database search and literature retrie-val, 40 active ingredients of Rehmanniae Radix Praeparata and Corni Fructus were obtained, and their targets were obtained through STITCH and TCMSP databases. The targets of ischemic stroke sequela were obtained through OMIM,GAD,TTD and DrugBank databases. By screening the intersections of active ingredients targets and stroke treatment targets, 21 potential targets were obtained. The DAVID database was used for GO enrichment analysis and KEGG pathway analysis of potential targets. GO enrichment analysis showed that Rehmanniae Radix Praeparata-Corni Fructus were mainly involved in regulation of blood pressure, negative regulation of extrinsic apoptotic signaling and positive regulation of angiogenesis. KEGG pathway analysis showed that Rehmanniae Radix Praeparata-Corni Fructus could inhibit inflammatory response and apoptosis signaling pathway by regulating HIF-VEGFA signaling pathway in neural stem cell proliferation, TNF signaling pathway and NF-kappaB signaling pathway. Molecular docking technique was used to verify that Rehmanniae Radix Praeparata-Corni Fructus component has a good binding activity with potential targets. The results showed that in ischemic stroke sequela phase, Rehmanniae Radix Praeparata-Corni Fructus drug pair could play an important role in recovering neural function, promoting the proliferation of neural stem cells, angiogenesis, preventing neural cells apoptosis and regulating inflammatory factors.

Differentially Expressed Genes Related to Alzheimer ’s Disease and Their Bioinformatics Analysis / 中国药房

OBJECTIVE： To provide reference for interpretation of pathogenesis， early prevention and diagnosis， and selection of therapeutic targets of Alzheimer’s disease （AD）. METHODS： The gene chip dataset GSE28146 was downloaded from the NCBI public data platform GEO， and the AD-related differentially expressed genes （DEGs） were identified by using GEO2R online analysis tool. GO analysis and KEGG enrichment pathway analysis were performed by using DAVID 6.8 bioinformatics resource database. The protein-protein interaction （PPI） network analysis was performed by using STRING database and Cytoscape 3.2.1 software. RESULTS & CONCLUSIONS： A total of 1 478 AD-related DEGs were identified， consisting of 913 up-regulated genes and 565 down-regulated genes. GO function enrichment analysis showed that DEGs mainly distributed in cytoplasm， membrane， extracellular space， and induced AD via biological processes such as positive/negative regulation of transcription， positive regulation of NF-κB activity， regulation of Rho protein signaling transduction， protein phosphorylation； via protein binding， DNA binding， transcription factor activity （sequence specific DNA binding） and other molecular functions. KEGG pathway enrichment analysis showed that DEGs was enriched in cancer pathway， pulmonary tuberculosis， osteoclast differentiation， JAK/STAT signaling pathway， FoxO signaling pathway， EB virus infection and other signaling pathways. There are 1 205 nodes and 3 931 edges in the PPI network of DEGs coding protein. Among them， the key genes are SOCS3， NEDD4 and CBLB， which may be the potential target of AD development.

Expression of MiR-455-5p in epithelial ovarian cancer and its target gene function / 实用肿瘤学杂志

Objective The aim of this study was to investigate the expression of miR-455-5p in epithelial ovarian cancer and its effect on the development of epithelial ovarian cancer. Methods The miRNA expression data of normal ovarian epithelial tis-sues and epithelial ovarian cancer tissues GSE83693 were downloaded from the GEO database. Differential expression analysis was used to obtain differential expression data of miRNAs in epithelial ovarian cancer. The expression of miR-455 -5p was analyzed whether there is difference expression between normal ovarian epithelium and epithelial ovary cancer tissues; qRT-PCR was used to verify the differential expression prediction results; bio-informatics software was used to analyze the KEGG pathway enrichment and GO gene function annotation of miR-455-5p target genes,and to explore the disorders of dyregulated miR-455-5p in the devel-opment of epithelial ovarian cancer. Results A total of 101 cases of differentially expressed miRNAs were screened,34 cases were up-regulated and 67 cases were down-regulated. Among them,miR-455-5p was down-regulated significantly(P<0. 01),and the different fulds were -2. 9019. The results of qRT-PCR showed that the expression of miR-455-5p in epithelial ovarian cancer cells(SKOV-3,OVCAR-3 and A2780)was significantly lower than that in normal ovarian epithelial cells(IOSE-80),and the dif-ferential expression was statistically significant(P<0. 05). The results of KEGG pathway enrichment analysis showed that miR-455-5p regulated target genes mainly involved in five pathways,including TGF-β signaling pathway,Hippo signaling pathway,ECM-receptor interaction,transcriptional dysregulation pathway in cancer,and chronic granule cellular leukemia,which were associated with tumors. GO functional annotation analysis showed that the target genes regulated by miR-455-5p in the above pathway was mainly involved in protein phosphorylation,promoted cell proliferation and migration,inhibited apoptosis,promoted epithelial-mesenchymal transition,regulated transcription and regulated cell cycle,etc. ,which associated with tumorigenesis. Conclusion The expression of miR-455-5p is down-regulated in epithelial ovarian cancer. The miR-455-5p target genes are involved in the pathogenesis and function of epithelial ovarian cancer,and are associated with the development of epithelial ovarian cancer.

Serum microRNA test in one Chinese early-onset familial Alzheimer's disease and preliminary analysis / 中华行为医学与脑科学杂志

Objective To determine the expression profile of serum microRNAs(miRNAs) in early-onset familial Alzheimer's disease (EO-FAD) patients. methods miRNA microarrays were performed to detect the expression profile of serum miRNAs in 2 cases of EO-FAD patients,2 cases of EO-FAD carriers and 2 cases of normal controls.Preliminary bioinformatic analysis was conducted. Result sIt was found that 21 miRNAs were up-regulated and 22 miRNAs were down-regulated in serum of EO-FAD patients,the differences were statistically significant(P<0.05).miR-5704(P=0.0002),miR-4639-3p(P=0.0195),miR-107(P=0.0204) were markedly up-regulated,miR-5572(P=0.0008),miR-204-3p(P=0.0014),miR-542-5p(P=0.0106) and miR-155-5p(P=0.0240) were markedly down-regulated.Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis suggested that the dysregulated miRNAs may be involved in the mechanism of EO-FAD by affecting neurotrophin signaling pathway.Conclusion miR-5704,miR-4639-3p,miR-107,miR-5572,miR-204-3p,miR-542-5p and miR-155-5p may be used as potential biomarkers of EO-FAD,and involved in the mechanism of EO-FAD by affecting neurotrophin signaling pathway.

Study of synergistic mechanism in the combination ofberberine and evodiamine from the perspective of miRNA / 中国药理学通报

Aim To explore the mechanisms of action (MOA) of synergistic anticancer function in the combination of berberine and evodiamine.Methods We first analyzed the action of suppression in the drug combination from the cell level and validated the dose scope as well as ratio of concentration in synergistic effects of drug combination.Then, the miRNA chip of liver cancer cell BEL-7402 under different treatment was analyzed.By building the miRNA-mRNA network, the MOA of the synergistic drug combination was illustrated.Results Berberine and evodiamine used in combination could significantly synergistically suppress the proliferative ability of liver cancer cells.The special differentially expressed miRNAs (DEmiRNAs) mainly participated in some cancer proliferation-related pathways and biological processes, such as MAPK signaling pathway, endocytosis pathway and insulin signaling pathway.The special target genes influenced by the drug combination not only covered three kinds of membrane receptors, but also took part in the regulation of downstream pathways.Conclusions From the regulation of miRNAs, it is clear that berberine may play a primary role in the synergistical suppression activity of the drug combination in cancer cells.The discovery of synergistic MOA in the combination of berberine and evodiamine from the miRNA level will provide a new guidance to explore more synergistic drug combinations in the future.

miR-410 expression and bioinformatics analysis of its predicted target genes in systemic lupus erythematosus / 中国免疫学杂志

Objective:To detect expression level of miR-410 in patients with systemic lupus erythematosus (SLE),and to expose the role of miR-410 and its target genes by bioinformatics methods.Methods:Expression level of miR-410 were detected by quantitative RT-PCR in peripheral blood mononuclear cells of SLE patients,and miR-410 sequence,its target genes and Genecards database were analyzed,and analysis of GO enrichment and KEGG Pathway was further performed.Results:miR-410 expression was significantly reduced in SLE patients,and its nucleotide sequence was highly conserved among species.These genes that were predicted to be regulated by miR-410 and associated with LE pathogenesis,included FASLG,CSF2,IFNAR2,MAPK1,PLCG2,IL4 and other genes.Analysis of GO enrichment revealed that miR-410's target genes were involved in cell growth,proliferation,programmed cell death,cell differentiation,immune system development and other biological activities.Analysis of KEGG Pathway showed that the target genes of miR-410 were significantly enriched in a series of signaling pathways including pathways in cancer,cytokine-cytokine receptor interaction,glioma,melanoma,TGF-β and JAK-STAT signaling pathway.Conclusion:miR-410 maybe directly regulate its target molecules,mediate various signal pathway networks,thus participate in the occurrence and development of SLE.

Screening of specific microRNAs and bioinformatics analysis on cardiomyocytes in rat with heart failure / 中华急诊医学杂志

Objective To investigate microRNAs ( miRNAs) expression profiling of cardiomyocytes in rats with heart failure, and predict miRNAs-regulated target genes and their functions.Methods Total of 18 male SD rats weighing 200-220 g were randomly divided into 2 groups:the control group ( CON) and the heart failure group (HF).The rats in HF group were injected by adriamycin via tail vein to induce heart failure, meanwhile in CON group, rats were received an equal volume of 0.9% sodium chloride intravenously.The cardiomyocytes isolated from the rat hearts in two groups and cultured overnight.After that, total RNA was extracted and then subjected to miRNA microarray to screen differentially expressed miRNAs.The reults of microarray were further verified by quantitative real-time PCR ( qRT-PCR ) .The target genes regulated by differentially expressed miRNAs were predicted by the software of Targetscan and miRanda.Bioinformatics analysis was performed to predict the miRNAs-regulated target genes and analyze the enriched gene ontology ( GO) and signaling pathway ( KEGG Pathway) .Results The results of miRNA microarray showed that a total of 37 miRNAs were differentially expressed in HF group as compared to CON group, among which 22 miRNAs were up-regulated and 15 miRNAs were down-regulated (P<0.01, FDR<0.05).The expression of miR-133b-5p (t=14.56, P<0.01), miR-6216 (t=9.32, P<0.01) and let-7e-5p (t=13.92, P<0.01) which were detected by qRT-PCR exhibited the similar tendency of up or down regulation to those shown in microarray results.Bioinformatics analysis indicated that miRNAs-regulated target genes were significantly enriched in 31 GOs (P<0.01, FDR<0.05) and 12 signal pathways (P<0.05, FDR<0.05), among which ubiquitin-proteasome system, MAPK signaling pathway and Toll like siganling pathway exhibited a higher enrichment. Conclusion MiRNA expression profile on cardiomyocytes in rat with adriamycin-induced heart failure was significantly changed.These differentially expressed miRNAs might participate in the process of heart failing by regulating their target genes in rat cardiomyocytes.

Prediction of miR-199a-3p targets gene and its bioinformatics analysis / 西安交通大学学报(医学版)

Objective To provide theoretical guidance for further research on the role of miR-1 99a-3p in formation and development of bladder cancer.Methods Mature sequence of miR-1 99a-3p was analyzed;target genes and transcription factors of miRNA-1 99a-3p were predicted,and the target genes were analyzed for gene ontology (GO)enrichment and Kyoto Encyclopedia of Genes and Genome (KEGG)pathway.Then TF-miRNA-mRNA network diagram was constructed.Results Sequences of miR-1 99a-3p were highly conserved in various species.In GO analysis,the target genes of miR-1 99a-3p were enriched in many biological processes,such as regulation of cellular process,regulation of macromolecule metabolic process,and regulation of biological process (P <0.01 ).In KEGG pathway,the target genes were mainly located in bacterial invasion pathway of epithelial cells,ECM-receptor interaction pathway,PI3K-Akt signaling pathway,MAPK signaling pathway,small cell lung cancer pathway,and proteoglycans pathway in the cancer (P <0.05).According to the TF-miRNA-mRNA network diagram,the important genes that might be regulated by miR-1 99a-3p were MYC,SP1,mTOR,NFκB,and NFκB1.Conclusion miR-1 99a-3p may directly target mTOR and participate in the formation and development of bladder cancer through regulating PI3K-Akt-mTOR signaling pathway.

Microarray analysis of differentially expressed genes regulating lipid metabolism during melanoma progression.

A new hallmark of cancer involves acquisition of a lipogenic phenotype which promotes tumorigenesis. Little is known about lipid metabolism in melanomas. Therefore, we used BRB (Biometrics Research Branch) class comparison tool with multivariate analysis to identify differentially expressed genes in human cutaneous melanomas, compared with benign nevi and normal skin derived from the microarray dataset (GDS1375). The methods were validated by identifying known melanoma biomarkers (CITED1, FGFR2, PTPRF, LICAM, SPP1 and PHACTR1) in our results. Eighteen genes regulating metabolism of fatty acids, lipid second messengers and gangliosides were 2-9 fold upregulated in melanomas of GDS-1375. Out of the 18 genes, 13 were confirmed by KEGG pathway analysis and 10 were also significantly upregulated in human melanoma cell lines of NCI-60 Cell Miner database. Results showed that melanomas upregulated PPARGC1A transcription factor and its target genes regulating synthesis of fatty acids (SCD) and complex lipids (FABP3 and ACSL3). Melanoma also upregulated genes which prevented lipotoxicity (CPT2 and ACOT7) and regulated lipid second messengers, such as phosphatidic acid (AGPAT-4, PLD3) and inositol triphosphate (ITPKB, ITPR3). Genes for synthesis of pro-tumorigenic GM3 and GD3 gangliosides (UGCG, HEXA, ST3GAL5 and ST8SIA1) were also upregulated in melanoma. Overall, the microarray analysis of GDS-1375 dataset indicated that melanomas can become lipogenic by upregulating genes, leading to increase in fatty acid metabolism, metabolism of specific lipid second messengers, and ganglioside synthesis.

Spectrum construction of differently-expressed novel microRNA in SLE patients and function analysis of its target genes / 西安交通大学学报(医学版)

binding,cellular organelle membrane,and cellular metabolic process of GO enrichment.For the KEGG pathways, the target genes mainly concentrated on the focal adhesion pathway.Conclusion There is a different expression of novel microRNA between SLE and NC groups.The target genes from differently-expressed novel microRNA may play an important role in the pathogenesis of SLE and clinical symptoms and may be the unique target for further research.

Differential analysis of miRNA let-7f-1-3p in Burkitt lymphoma / 白血病·淋巴瘤

Objective To explore the differential expression of microRNAs (miRNAs) in Burkitt lymphoma (BL) and their potential use as biomarkers for BL diagnosis.Methods The different miRNAs in BL from reactive hyperplasia of lymph node cases were screened by miRNA chip.The potential targets of miRNAs were predicted using miRWALK.MAS3 program was used to determine the putative functions of potential miRNA target genes by annotation using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses.Results A total of 46 miRNAs (36 upregulated and 21 downregulated) were dysregulated in BL compared with reactive hyperplasia of lymph node.Interestingly,members of the let-7 family (let-7f-1-3p) was downregulated in BL.The target genes of let-7f-1-3p were predicted,and the GO enrichment analysis revealed their functions were mainly related with multicellular organismal development and regulation of transcription from RNA polymerase Ⅱ promote.KEGG pathway analysis was also carried out among the predicted target genes,which showed that they were mainly involved in TGF-beta signaling pathway and related with chronic myeloid leukemia.Conclusions The set of differentially expressed miRNAs identified here expands the range of potential diagnostic markers for BL.