High Throughput Bioinformatics-based Prediction of the targets for BushenjieduDecoction in preventing relapse of acute leukemia

Abstract Leukemia is a lethal myeloproliferative disorder, its’ relapse following chemotherapy is the major concern in clinical practice. For a long time, we found that traditional Chinese medicines such as Bushenjiedudecoction (BSJD) have significant effects on delaying relapse. However, the underlying mechanisms are not clear, which limits the clinical application of BSJD decoction. Therefore, we tried to make some explorations in this study. We isolated mesenchymal stem cells (MSC) after treated them with BSJD for proteomic analysis. And then 109 targets were screened out through analysis of the shared proteins of that affected by BSJD and those related to leukemia. Subsequently, the data were analyzed by GO functions, KEGG pathways, PPI network and topological analysis, and then some nodes were selected for animal experiment. As a result, we demonstrated the effective targets of BSJD on MSC through bioinformatics analysis and explored the potential mechanism of BSJD from its influence on niches.

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Bioinformatics-based Prediction of the mechanism and targets for BushenjieduDecoction in preventing relapse of acute leukemia

10.21203/rs.3.rs-47500/v1 ◽

2020 ◽

Author(s):

Weilong Sun ◽

Fujun Yang ◽

Weipeng Shi ◽

Xia Tao ◽

Zhiwei Xi ◽

...

Keyword(s):

Bioinformatics Analysis ◽

Topological Analysis ◽

Traditional Chinese Medicines ◽

Potential Mechanism ◽

Ppi Network ◽

Chinese Medicines ◽

Kegg Pathways ◽

Long Time ◽

Underlying Mechanisms

Abstract Background: Leukemia is a lethal myeloproliferative disorder, its’ relapse following chemotherapy is the major concern in clinical practice. For a long time, we found that traditional Chinese medicines such as Bushenjiedudecoction (BSJD) have significant effects on delaying relapse. However, the underlying mechanisms are not clear, which limits the clinical application of BSJD decoction. Methods: Therefore, we tried to make some explorations in this study. We isolated mesenchymal stem cells (MSC) after treated them with BSJD for proteomic analysis. And then 109 targets were screened out through analysis of the shared proteins of that affected by BSJD and those related to leukemia. Subsequently, the data were analyzed by GO functions, KEGG pathways, PPI network and topological analysis, and then some nodes were selected for animal experiment. Results: As a result, we demonstrated the effective targets of BSJD on MSC through bioinformatics analysis and explored the potential mechanism of BSJD from its influence on niches.These targets contains Hspb1、Dnmt1、Mmp2、Thbs1、Crebbp、Hmgb1、Acta2、Cdkn1b、Atg7、Tsc2 and Icam1. Afterwards, we confirmed BSJD reduced the gene expression of ICAM-1 through cultured MSC in vitro.Conclusions: We screened the potential targets of BSJD on MSC through proteomics and bioinformatics analysis, and selected some genes for experimental verification. These studies demonstrated the effect of BSJD on MSC. We hope that this research method could provide a new way of systematically studying the effects of traditional Chinese medicine on diseases.

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Bioinformatics Analysis for the Antirheumatic Effects of Huang-Lian-Jie-Du-Tang from a Network Perspective

Evidence-based Complementary and Alternative Medicine ◽

10.1155/2013/245357 ◽

2013 ◽

Vol 2013 ◽

pp. 1-11 ◽

Cited By ~ 9

Author(s):

Haiyang Fang ◽

Yichuan Wang ◽

Tinghong Yang ◽

Yang Ga ◽

Yi Zhang ◽

...

Keyword(s):

Therapeutic Effect ◽

Bioinformatics Analysis ◽

Topological Analysis ◽

Ppi Network ◽

New Approach ◽

Target Proteins ◽

Multiple Components ◽

Main Pathway ◽

Tcm Theory ◽

Therapeutic Mechanisms

Huang-Lian-Jie-Du-Tang (HLJDT) is a classic TCM formula to clear “heat” and “poison” that exhibits antirheumatic activity. Here we investigated the therapeutic mechanisms of HLJDT at protein network level using bioinformatics approach. It was found that HLJDT shares 5 target proteins with 3 types of anti-RA drugs, and several pathways in immune system and bone formation are significantly regulated by HLJDT’s components, suggesting the therapeutic effect of HLJDT on RA. By defining an antirheumatic effect score to quantitatively measure the therapeutic effect, we found that the score of each HLJDT’s component is very low, while the whole HLJDT achieves a much higher effect score, suggesting a synergistic effect of HLJDT achieved by its multiple components acting on multiple targets. At last, topological analysis on the RA-associated PPI network was conducted to illustrate key roles of HLJDT’s target proteins on this network. Integrating our findings with TCM theory suggests that HLJDT targets on hub nodes and main pathway in the Hot ZENG network, and thus it could be applied as adjuvant treatment for Hot-ZENG-related RA. This study may facilitate our understanding of antirheumatic effect of HLJDT and it may suggest new approach for the study of TCM pharmacology.

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Identification of Genes and Pathways of Nonsteroidal Anti-inflammatory Drugs acting on Synovia from Women with Knee Osteoarthritis by Bioinformatics Analysis

10.21203/rs.3.rs-407139/v1 ◽

2021 ◽

Author(s):

Chao Zhao ◽

Han Wang ◽

Conglei Dong ◽

Huijun Kang ◽

Fei Wang

Keyword(s):

Gene Expression ◽

Knee Osteoarthritis ◽

Bioinformatics Analysis ◽

Gene Expression Omnibus ◽

Control Group ◽

Ppi Network ◽

Kegg Pathways ◽

Inflammatory Drugs ◽

Anti Inflammatory ◽

R Programming

Abstract Objective: Through the bioinformatics analysis, to identify the genes and pathways of nonsteroidal anti-inflammatory drugs(NSARDs) acting on synovia from women with knee osteoarthritis (KOA), and to provide reference for clinical application. Methods: We downloaded the gene microarray datasets with the accession number of GSE55457 and GSE55584 from the Gene Expression Omnibus (GEO; https://www.ncbi.nlm.nih.gov/geo/) database, including 5 untreated KOA patients, 9 NSARDs treated KOA patients and 2 patients without KOA The samples in the untreated KOA group and the NSARDs treated KOA group were used for main analysis. The samples in the untreated KOA group and the normal control group were used for cooperative analysis. Then we performed robust multi-array (RMA) normalization with affy R programming package. After that, differential expression genes (DEGs) in main analysis and cooperative analysis were identified based on limma package separately. Screening the common DEGs from main analysis and cooperative analysis. Enriched gene ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of DEGs were obtained through the Database for Annotation, Visualization and Integrated Discovery (DAVID). What's more, protein-protein interaction (PPI) network was constructed, and we identified modules of PPI network through Cytoscape to screen valuable targets. The value of gene expression fold change (FC) ≥1.4 or ≤1/1.4, and P <0.05 were used as the screening conditions. P <0.05 and Associated genes count>5 were used as the screening conditions.Results: There were 338 DEGs in main analysis. Among them, 211 genes were up-regulated and 127 genes were down-regulated. There were 7005 DEGs in cooperative analysis. Among them, 6952 genes were up-regulated and 53 genes were down-regulated. A total of 129 common DEGs were identified between main analysis and cooperative analysis. There are 2 biological processes, 3 cell components and 2 molecular functions for the enrichment of differentially expressed genes.Conclusion: NSARDs may play a certain role in synovia from women with KOA by regulating the mRNA expressions of il-6, TNFRSF11A and CSF1R, which may become one of the indicators for monitoring the efficacy of NSAIDs.

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Traditional Chinese medicine Dingkun Pill facilitates uterine receptivity for implantation in mice†

Biology of Reproduction ◽

10.1093/biolre/ioz141 ◽

2019 ◽

Vol 101 (4) ◽

pp. 695-703

Author(s):

Lin Huang ◽

Lemeng Wang ◽

Haili Bao ◽

Yingchun Xu ◽

Meiqing Meng ◽

...

Keyword(s):

Target Genes ◽

Embryo Implantation ◽

Differential Regulation ◽

Human Reproduction ◽

Traditional Chinese Medicines ◽

Uterine Receptivity ◽

Chinese Medicines ◽

Beneficial Effects ◽

Gynecological Diseases ◽

Underlying Mechanisms

Abstract Dingkun Pill (DK) is one of the representative traditional Chinese medicines, which has been used in the treatment of gynecological diseases for hundreds of years. Accumulative observations and evidence have shown the beneficial effects of DK, including enhancing the function of hypothalamic-pituitary-ovarian axis. However, the underlying mechanisms remain elusive. In this study, the effects of DK on uterine receptivity and implantation were explored by a series of studies with different mouse models. The results showed that DK can advance the time of implantation by influencing the expression of estrogen target genes to facilitate embryo implantation. DK was efficient to activate embryo implantation at the presence of suboptimal estrogen in delayed implantation mouse model. Our further study revealed that the improvement of DK on receptivity establishment is attributed to the differential regulation of DK on implantation-associated genes. This study provides previously unappreciated molecular mechanism of DK in embryo implantation and benefits the potential clinical application of DK in human reproduction improvement.

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A Song of Ice and Fire: Cold and Hot Properties of Traditional Chinese Medicines

Frontiers in Pharmacology ◽

10.3389/fphar.2020.598744 ◽

2021 ◽

Vol 11 ◽

Author(s):

Juan Liu ◽

Wuwen Feng ◽

Cheng Peng

Keyword(s):

Clinical Application ◽

Basic Theory ◽

Human Diseases ◽

Traditional Chinese Medicines ◽

Research Strategies ◽

Research Directions ◽

Antipyretic Effect ◽

Chinese Medicines ◽

Long Time ◽

Classification And Treatment

The theory of cold and hot properties is the basic theory of traditional Chinese medicines (TCMs) and has been successfully applied to combat human diseases for thousands of years. Although the theory of cold and hot is very important to guide the clinical application of TCMs, this ancient theory remains an enigma for a long time. In recent years, more and more researchers have tried to uncover this ancient theory with the help of modern techniques, and the cold and hot properties of a myriad of TCMs have been studied. However, there is no review of cold and hot properties. In this review, we first briefly introduced the basic theories about cold and hot properties, including how to distinguish between the cold and hot properties of TCMs and the classification and treatment of cold and hot syndromes. Then, focusing on the application of cold and hot properties, we take several important TCMs with cold or hot property as examples to summarize their traditional usage, phytochemistry, and pharmacology. In addition, the mechanisms of thermogenesis and antipyretic effect of these important TCMs, which are related to the cold and hot properties, were summarized. At the end of this review, the perspectives on research strategies and research directions of hot and cold properties were also offered.

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Identification of Genes and Pathways of Nonsteroidal Anti-Inflammatory Drugs Acting on Synovia from Women with Knee Osteoarthritis by Bioinformatics Analysis

10.21203/rs.3.rs-407139/v2 ◽

2021 ◽

Author(s):

Chao Zhao ◽

Han Wang ◽

Conglei Dong ◽

Huijun Kang ◽

Fei Wang

Keyword(s):

Gene Expression ◽

Knee Osteoarthritis ◽

Bioinformatics Analysis ◽

Gene Expression Omnibus ◽

Control Group ◽

Ppi Network ◽

Kegg Pathways ◽

Inflammatory Drugs ◽

Anti Inflammatory ◽

R Programming

Abstract Purpose: Through the bioinformatics analysis, to identify the genes and pathways of nonsteroidal anti-inflammatory drugs(NSAIDs) acting on synovia from women with knee osteoarthritis (KOA), and to provide reference for clinical application. Methods: We downloaded the gene microarray datasets with the accession number of GSE55457 and GSE55584 from the Gene Expression Omnibus (GEO; https://www.ncbi.nlm.nih.gov/geo/) database, including 5 untreated KOA patients, 9 NSAIDs treated KOA patients and 2 patients without KOA The samples in the untreated KOA group and the NSAIDs treated KOA group were used for main analysis. The samples in the untreated KOA group and the normal control group were used for cooperative analysis. Then we performed robust multi-array (RMA) normalization with affy R programming package. After that, differential expression genes (DEGs) in main analysis and cooperative analysis were identified based on limma package separately. Screening the common DEGs from main analysis and cooperative analysis. Enriched gene ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of DEGs were obtained through the Database for Annotation, Visualization and Integrated Discovery (DAVID). What's more, protein-protein interaction (PPI) network was constructed, and we identified modules of PPI network through Cytoscape to screen valuable targets. The value of gene expression fold change (FC) ≥1.4 or ≤1/1.4, and P <0.05 were used as the screening conditions. P <0.05 and Associated genes count>5 were used as the screening conditions. Results: There were 338 DEGs in main analysis. Among them, 211 genes were up-regulated and 127 genes were down-regulated. There were 7005 DEGs in cooperative analysis. Among them, 6952 genes were up-regulated and 53 genes were down-regulated. A total of 129 common DEGs were identified between main analysis and cooperative analysis. There are 2 biological processes, 3 cell components and 2 molecular functions for the enrichment of differentially expressed genes. Conclusion: NSAIDs may play a certain role in synovia from women with KOA by regulating the mRNA expressions of il-6, TNFRSF11A and CSF1R, which may become one of the indicators for monitoring the efficacy of NSAIDs.

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