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The Mechanism of Ginseng and Astragalus Decoction in the Treatment of Malignant Pleural Effusion Based on Network Pharmacology and Molecular Docking Technology. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:7731402. [PMID: 35341150 PMCID: PMC8941536 DOI: 10.1155/2022/7731402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 01/31/2022] [Indexed: 11/17/2022]
Abstract
Introduction The objective of our study is to explore the potential active ingredients and activity of Ginseng and Astragalus decoction (GAD) in the treatment of malignant pleural effusion (MPE) by using network pharmacology and molecular docking technologies. Methods The active ingredients and corresponding targets of Ginseng and Astragalus were extracted from the Traditional Chinese Medicine System Pharmacology Database and Analysis Platform. The relevant targets of malignant pleural effusion (MPE) were searched in the disease databases. Overlapping targets of Ginseng and Astragalus and the corresponding targets of MPE were obtained to define the effective target of GAD for the treatment of MPE. The STRING database was applied to construct a predicted protein-protein interaction network for intersected targets. The Cytoscape software was used to screen key targets with a therapeutic potential. Using the Metascape database, we performed Gene Ontology and Kyoto Encyclopedia of Genes and Genomes functional enrichment analysis on the targets identified in the study. PyMOL and AutoDock Vina were used to molecularly dock the selected key components to their respective key targets for MPE treatment. Results The core target network revealed 22 main active ingredients, 26 main targets, and 16 signaling pathways in GAD. Molecular docking revealed 6 targets (AKT serine/threonine kinase 1, intercellular adhesion molecule, Jun proto-oncogene, peroxisome proliferator activated receptor gamma, prostaglandin-endoperoxide synthase 2, and tumor necrosis factor) that could partially dock with kaempferol, frutinone A, ginsenoside RH2, formononetin, and quercetin. Conclusions Several components, targets, and signaling pathways of GAD contribute to the treatment of MPE, which suggests a rationale for further investigation on GAD's active molecule and mechanism of action in the clinical application of MPE.
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The effects of genotype on inflammatory response in hippocampal progenitor cells: A computational approach. Brain Behav Immun Health 2021; 15:100286. [PMID: 34345870 PMCID: PMC8261829 DOI: 10.1016/j.bbih.2021.100286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 06/09/2021] [Indexed: 02/08/2023] Open
Abstract
Cell culture models are valuable tools to study biological mechanisms underlying health and disease in a controlled environment. Although their genotype influences their phenotype, subtle genetic variations in cell lines are rarely characterised and taken into account for in vitro studies. To investigate how the genetic makeup of a cell line might affect the cellular response to inflammation, we characterised the single nucleotide variants (SNPs) relevant to inflammation-related genes in an established hippocampal progenitor cell line (HPC0A07/03C) that is frequently used as an in vitro model for hippocampal neurogenesis (HN). SNPs were identified using a genotyping array, and genes associated with chronic inflammatory and neuroinflammatory response gene ontology terms were retrieved using the AmiGO application. SNPs associated with these genes were then extracted from the genotyping dataset, for which a literature search was conducted, yielding relevant research articles for a total of 17 SNPs. Of these variants, 10 were found to potentially affect hippocampal neurogenesis whereby a majority (n=7) is likely to reduce neurogenesis under inflammatory conditions. Taken together, the existing literature seems to suggest that all stages of hippocampal neurogenesis could be negatively affected due to the genetic makeup in HPC0A07/03C cells under inflammation. Additional experiments will be needed to validate these specific findings in a laboratory setting. However, this computational approach already confirms that in vitro studies in general should control for cell lines subtle genetic variations which could mask or exacerbate findings.
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Piranda DN, Abreu RBV, Freitas-Alves DR, de Carvalho MA, Vianna-Jorge R. Modulation of the prostaglandin-endoperoxide synthase 2 gene expression by variant haplotypes: influence of the 3'-untranslated region. ACTA ACUST UNITED AC 2017; 51:e6546. [PMID: 29211250 PMCID: PMC5711006 DOI: 10.1590/1414-431x20176546] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 09/19/2017] [Indexed: 12/13/2022]
Abstract
The inducible inflammatory enzyme cycloxigenase-2 is up-regulated in cancer, and favors tumor progression. Cycloxigenase-2 is encoded by the prostaglandin-endoperoxide synthase 2 (PTGS2) gene, which presents sequence variations in the promoter region (PR) and in the 3′-untranslated region (3′-UTR). Different PR (rs689465, rs689466, rs20417) and 3′-UTR (rs5275) variants were generated by site-directed mutagenesis, and combined in haplotypes to access expression levels using a reporter system (luciferase) in human cells (MCF-7 and HEK293FT). Luciferase activity did not differ significantly among PTGS2 PR constructs, except for pAAC (containing variant allele rs20417 C), with 40% less activity than pAAG (wild-type sequence) in MCF-7 cells (P<0.01). Despite the lack of individual significant differences, PTGS2 PR constructs enclosing rs689466 G (pAGG and pAGC) showed an approximate two-fold increase in luciferase activity when compared to those containing rs689466 A (pAAG, pGAC, pAAC and pGAG) in both cell lines (P<0.001 for MCF-7 and P=0.03 for HEK293FT). The effect of PTGS2 3′-UTR sequences varied between MCF-7 and HEK293FT: MCF-7 cells showed significant reduction (40–60%) in luciferase activity (at least P<0.01), whereas HEK293FT cells showed more diverse results, with an average 2-fold increase when combined constructs (PR and 3′-UTR) were compared to respective parental PR sequences. The contribution of 3′-UTR variant (rs5275) was not consistent in either cell line. Despite the modulation of the 3′-UTR, with variable effects of rs5275, the enhancing transcriptional effect of rs689466 G was still detectable (P<0.0001 in MCF-7 or P=0.03 in HEK293FT cells).
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Affiliation(s)
- D N Piranda
- Coordenação de Pesquisa, Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brasil.,Programa de Pós-Graduação em Farmacologia e Química Medicinal, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - R B V Abreu
- Coordenação de Pesquisa, Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brasil
| | - D R Freitas-Alves
- Coordenação de Pesquisa, Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brasil.,Programa de Pós-Graduação em Saúde Pública e Meio Ambiente, Escola Nacional de Saúde Pública Sérgio Arouca, FIOCRUZ, Rio de Janeiro, RJ, Brasil
| | - M A de Carvalho
- Coordenação de Pesquisa, Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brasil.,Instituto Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - R Vianna-Jorge
- Coordenação de Pesquisa, Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brasil.,Programa de Pós-Graduação em Saúde Pública e Meio Ambiente, Escola Nacional de Saúde Pública Sérgio Arouca, FIOCRUZ, Rio de Janeiro, RJ, Brasil.,Programa de Pesquisa em Farmacologia e Inflamação, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
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Applebaum E, Nackley AG, Bair E, Maixner W, Khan AA. Genetic Variants in Cyclooxygenase-2 Contribute to Post-treatment Pain among Endodontic Patients. J Endod 2015; 41:1214-8. [PMID: 26081267 DOI: 10.1016/j.joen.2015.04.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 04/21/2015] [Accepted: 04/28/2015] [Indexed: 02/02/2023]
Abstract
INTRODUCTION Nonsteroidal anti-inflammatory drugs (NSAIDs) have a well-established analgesic efficacy for inflammatory pain. These drugs exert their effect by inhibiting the enzyme cyclooxygenase (COX) and are commonly used for the management of pain after endodontic treatment. There are 2 distinct isoforms of COX: COX-1, which is constitutively expressed, and COX-2, which is primarily induced by inflammation. Previous studies have shown that functional human genetic variants of the COX-2 gene may explain individual variations in acute pain. The present study extends this work by examining the potential contribution of the 2 COX isoforms to pain after endodontic treatment. METHODS Ninety-four patients treated by endodontic residents at the University of North Carolina School of Dentistry were enrolled into a prospective cohort study. Data on potential predictors of post-treatment pain were collected, and all patients submitted saliva samples for genetic analysis. Nonsurgical root canal therapy was performed, and participants recorded pain levels for 5 days after. RESULTS In this study, 63% of patients experienced at least mild pain after root canal therapy, and 24% experienced moderate to severe pain. The presence of pretreatment pain was correlated with higher post-treatment pain (P = .01). Elevated heart rate (P = .02) and higher diastolic blood pressure (P = .024) were also correlated with decreased post-treatment pain. Finally, we identified genetic variants in COX-2 (haplotype composed of rs2383515 G, rs5277 G, rs5275 T, and rs2206593 A) associated with post-treatment pain after endodontic treatment (P = .025). CONCLUSIONS Understanding the genetic basis of pain after endodontic treatment will advance its prevention and management.
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Affiliation(s)
- Elizabeth Applebaum
- Private Practice, School of Dentistry, University of North Carolina, Chapel Hill, North Carolina
| | - Andrea G Nackley
- Center for Pain Research and Innovation, School of Dentistry, University of North Carolina, Chapel Hill, North Carolina
| | - Eric Bair
- Center for Pain Research and Innovation, School of Dentistry, University of North Carolina, Chapel Hill, North Carolina
| | - William Maixner
- Center for Pain Research and Innovation, School of Dentistry, University of North Carolina, Chapel Hill, North Carolina
| | - Asma A Khan
- Center for Pain Research and Innovation, School of Dentistry, University of North Carolina, Chapel Hill, North Carolina.
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A Survival Association Study of 102 Polymorphisms Previously Associated with Survival Outcomes in Colorectal Cancer. BIOMED RESEARCH INTERNATIONAL 2015; 2015:968743. [PMID: 26064972 PMCID: PMC4443940 DOI: 10.1155/2015/968743] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 04/06/2015] [Indexed: 12/31/2022]
Abstract
Several published studies identified associations of a number of polymorphisms with a variety of survival outcomes in colorectal cancer. In this study, we aimed to explore 102 previously reported common genetic polymorphisms and their associations with overall survival (OS) and disease-free survival (DFS) in a colorectal cancer patient cohort from Newfoundland (n = 505). Genotypes were obtained using a genomewide SNP genotyping platform. For each polymorphism, the best possible genetic model was estimated for both overall survival and disease-free survival using a previously published approach. These SNPs were then analyzed under their genetic models by Cox regression method. Correction for multiple comparisons was performed by the False Discovery Rate (FDR) method. Univariate analysis results showed that RRM1-rs12806698, IFNGR1-rs1327474, DDX20-rs197412, and PTGS2-rs5275 polymorphisms were nominally associated with OS or DFS (p < 0.01). In stage-adjusted analysis, the nominal associations of DDX20-rs197412, PTGS2-rs5275, and HSPA5-rs391957 with DFS were detected. However, after FDR correction none of these polymorphisms remained significantly associated with the survival outcomes. We conclude that polymorphisms investigated in this study are not associated with OS or DFS in our colorectal cancer patient cohort.
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Agúndez JAG, Blanca M, Cornejo-García JA, García-Martín E. Pharmacogenomics of cyclooxygenases. Pharmacogenomics 2015; 16:501-22. [DOI: 10.2217/pgs.15.6] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Cyclooxygenases (COX-1 and COX-2) are key enzymes in several physiopathological processes. Many adverse drugs reactions to NSAIDs are attributable to COX-inhibition. The genes coding for these enzymes (PTGS1 and PTGS2) are highly variable, and variations in these genes may underlie the risk of developing, or the clinical evolution of, several diseases and adverse drug reactions. We analyze major variations in the PTGS1 and PTGS2 genes, allele frequencies, functional consequences and population genetics. The most salient clinical associations of PTGS gene variations are related to colorectal cancer and stroke. In many studies, the SNPs interact with NSAIDs use, dietary or environmental factors. We provide an up-to-date catalog of PTGS clinical associations based on case–control studies and genome-wide association studies, and future research suggestions.
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Affiliation(s)
- José AG Agúndez
- Department of Pharmacology, University of Extremadura, Cáceres, Spain
- Red de Investigación de Reacciones Adversas a Alergenos y Fármacos, Spain
| | - Miguel Blanca
- Red de Investigación de Reacciones Adversas a Alergenos y Fármacos, Spain
- Allergy Service, Carlos Haya Hospital, Málaga, Spain
| | - José A Cornejo-García
- Red de Investigación de Reacciones Adversas a Alergenos y Fármacos, Spain
- Allergy Service, Carlos Haya Hospital, Málaga, Spain
| | - Elena García-Martín
- Red de Investigación de Reacciones Adversas a Alergenos y Fármacos, Spain
- Department of Biochemistry & Molecular Biology, University of Extremadura, Cáceres, Spain
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Tang Q, Zhong H, Xie F, Xie J, Chen H, Yao G. Expression of miR-106b-25 induced by salvianolic acid B inhibits epithelial-to-mesenchymal transition in HK-2 cells. Eur J Pharmacol 2014; 741:97-103. [PMID: 25094038 DOI: 10.1016/j.ejphar.2014.07.051] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 07/22/2014] [Accepted: 07/23/2014] [Indexed: 12/12/2022]
Abstract
Epithelial-to-mesenchymal transition (EMT) is a highly conserved physiological program involved in renal fibrosis. Previous studies have shown that transforming growth factor (TGF)-β1 induces EMT in human kidney proximal tubular epithelial cells (HK-2 cells), whereas salvianolic acid B (Sal B) has a protective effect against EMT. The molecular pathogenesis of such processes is currently not well understood. In this study, a miRCURYTM LNA Array was used to screen HK-2 cells for expression changes of microRNAs (miRNAs) implicated in EMT. After validation by real-time PCR, all three members of the miR-106b-25 cluster (miR-106b, miR-93, and miR-25) were found to be markedly down-regulated during EMT in response to TGF-β1, whereas these miRNAs were up-regulated by Sal B treatment in a dose-dependent manner. Moreover, enhanced expression of miR-106b attenuated EMT by retaining the epithelial morphology of HK-2 cells, reducing the levels of α-smooth muscle actin (α-SMA), and increasing the levels of E-cadherin. To explore the molecular basis underlying the inhibitive effect of the miR-106b-25 cluster against EMT, bioinformatics analysis revealed that TGF-β type II receptor, a regulator of TGF-β signaling, might be a direct target of the miR-106b-25 cluster. In turn, low levels of TGF-β type II receptor in EMT of HK-2 cells were shown under the increase of miR-106b. In conclusion, our data suggest that the miR-106b-25 cluster may contribute to EMT in the kidney, and is involved in the protective effect of Sal B. Targeting of specific miRNAs may be a novel therapeutic approach to treat renal fibrosis.
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Affiliation(s)
- Qiong Tang
- Department of Nephrology, Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, PR China
| | - Haizhen Zhong
- Department of Nephrology, Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, PR China
| | - Fengyan Xie
- Department of Nephrology, Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, PR China
| | - Jiayong Xie
- Department of Nephrology, Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, PR China
| | - Huimei Chen
- Jiangsu Key Laboratory of Molecular Medicine, School of Medicine, Nanjing University, Nanjing 210093, PR China.
| | - Gang Yao
- Department of Nephrology, Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, PR China.
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