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Zheng S, Liang Y, Xue T, Wang W, Li S, Zhang P, Li X, Cao X, Liu Q, Qi W, Ye Y, Zao X. Application of network pharmacology in traditional Chinese medicine for the treatment of digestive system diseases. Front Pharmacol 2024; 15:1412997. [PMID: 39086391 PMCID: PMC11289720 DOI: 10.3389/fphar.2024.1412997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Accepted: 06/19/2024] [Indexed: 08/02/2024] Open
Abstract
With the general improvement in living standards in recent years, people's living habits, including their dietary habits, have changed. More people around the world do not follow a healthy diet, leading to an increase in morbidity and even mortality due to digestive system diseases, which shows an increasing trend every year. The advantage of traditional Chinese medicine (TCM) in treating digestive system diseases is evident. Consequently, the mechanisms of action of single Chinese herbs and compound Chinese medicines have become the focus of research. The research method of the network pharmacology system was highly consistent with the holistic concept of TCM, and provided a new perspective and theoretical basis for basic research on digestive system diseases. This article summarizes the common databases currently used in research on TCM. It also briefly introduces the basic methods and technologies of network pharmacology studies. It also summarizes the advancements of network pharmacology technology through a comprehensive literature search on PubMed. Based on this analysis, we further explored the role of TCM in treating digestive system diseases, including chronic gastritis, gastric cancer, ulcerative colitis, and liver cirrhosis. This study provides new ideas and references for treating digestive system diseases with TCM in the future and serves as a reference for relevant researchers.
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Affiliation(s)
- Shihao Zheng
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
- Liver Diseases Academy of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Yijun Liang
- Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing, China
| | - Tianyu Xue
- First Affiliated Hospital of Hebei University of Chinese Medicine, Shijiazhuang, China
| | - Wei Wang
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
- Liver Diseases Academy of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Size Li
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
- Liver Diseases Academy of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Peng Zhang
- Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Xiaoke Li
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
- Liver Diseases Academy of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Xu Cao
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
- Liver Diseases Academy of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Qiyao Liu
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
- Liver Diseases Academy of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
- Key Laboratory of Chinese Internal Medicine of Ministry of Education and Beijing, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Wenying Qi
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
- Liver Diseases Academy of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Yongan Ye
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
- Liver Diseases Academy of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Xiaobin Zao
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
- Liver Diseases Academy of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
- Key Laboratory of Chinese Internal Medicine of Ministry of Education and Beijing, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
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Cayratia japonica Prevents Ulcerative Colitis by Promoting M2 Macrophage Polarization through Blocking the TLR4/MAPK/NF- κB Pathway. Mediators Inflamm 2022; 2022:1108569. [PMID: 36619207 PMCID: PMC9822765 DOI: 10.1155/2022/1108569] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 11/11/2022] [Accepted: 11/24/2022] [Indexed: 12/31/2022] Open
Abstract
Background and Aims Several components of Cayratia japonica (CJ) such as rutin and quercetin have shown anti-inflammatory effect, yet its function in ulcerative colitis (UC) remains to be clarified. This study focuses on the modulatory effect of CJ on UC as well as molecular mechanism by which CJ regulates macrophage polarization in UC. Methods The targets related to CJ components and UC were, respectively, obtained through in silico analysis, and their intersection targets were selected for pathway enrichment analysis. RAW264.7 cells were stimulated with lipopolysaccharide (LPS) to induce M1 macrophages. Expression of the macrophage polarization M1 marker CD11b and M2 marker CD206 was measured to determine the phenotype of macrophages. The mouse model was treated with dextran sodium sulfate (DSS) to induce UC to observe the effects of CJ on UC in vivo. Results The in silico analysis suggested the crucial significance of TLR4 and its downstream MAPK/NF-κB pathways in the modulatory effect of CJ on UC. Furthermore, experimental data revealed that CJ could promote M2 macrophage polarization but alleviate immune inflammation and reduce colon damage in DSS-evoked UC model. Additionally, CJ can inhibit the expression of TLR4/MAPK/NF-κB signaling pathway to enhance the M2-like polarization. Conclusion Hence, CJ may exert anti-inflammatory effects and an inhibitory role in UC by inhibiting the TLR4/MAPK/NF-κB pathway and subsequent M1-like macrophage polarization.
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Xia M, Ai N, Pang J. Preliminary Exploration of Clinical Efficacy and Pharmacological Mechanism of Modified Danggui-Shaoyao San in the Treatment of Depression in Patients with Chronic Kidney Disease. Drug Des Devel Ther 2022; 16:3975-3989. [DOI: 10.2147/dddt.s387677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 11/06/2022] [Indexed: 11/18/2022] Open
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Zheng S, Xue T, Wang B, Guo H, Liu Q. Application of network pharmacology in the study of mechanism of Chinese medicine in the treatment of ulcerative colitis: A review. FRONTIERS IN BIOINFORMATICS 2022; 2:928116. [PMID: 36304327 PMCID: PMC9580908 DOI: 10.3389/fbinf.2022.928116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 08/23/2022] [Indexed: 11/17/2022] Open
Abstract
Network pharmacology is a research method based on a multidisciplinary holistic analysis of biological systems, which coincides with the idea of the holistic view of traditional Chinese medicine. In this review, we summarized the use of network pharmacology technology through studying Chinese medicine single medicine or Chinese medicine compound research ideas and methods for the treatment of ulcerative colitis, based on the application of the current network pharmacology in Chinese medicine research, including the important role in the mechanism of the prediction and verification, to search for new ideas for disease diagnosis and treatment, this study summarizes the application of network pharmacology in the treatment of ulcerative colitis in traditional Chinese medicine, including monotherapy and compound therapy, and considers that relevant research studies have fully demonstrated the function characteristics of the multi-component, multi-target, and multi-pathway of traditional Chinese medicine, and can also explain the connotation of “selecting appropriate treatment methods according to the differences and similarities of pathogenesis” of traditional Chinese medicine. Finally, we raised important questions about the prospects and limitations of network pharmacology, such as differences caused by different data collection methods, a considerable lag, and so on.
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Affiliation(s)
- Shihao Zheng
- Graduate School, Hebei University of Traditional Chinese Medicine, Shijiazhuang, China
| | - Tianyu Xue
- Graduate School, Hebei University of Traditional Chinese Medicine, Shijiazhuang, China
| | - Bin Wang
- Graduate School, Hebei University of Traditional Chinese Medicine, Shijiazhuang, China
| | - Haolin Guo
- Graduate School, Hebei University of Traditional Chinese Medicine, Shijiazhuang, China
| | - Qiquan Liu
- Graduate School, Hebei University of Traditional Chinese Medicine, Shijiazhuang, China
- Department of Spleen and Stomach, First Affiliated Hospital of Hebei University of Traditional Chinese Medicine, Shijiazhuang, China
- *Correspondence: Qiquan Liu,
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Network Pharmacological Study on the Mechanism of Cynanchum paniculatum (Xuchangqing) in the Treatment of Bungarus multicinctus Bites. BIOMED RESEARCH INTERNATIONAL 2022; 2022:3887072. [PMID: 35837378 PMCID: PMC9276512 DOI: 10.1155/2022/3887072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 06/17/2022] [Indexed: 12/18/2022]
Abstract
Background Bungarus multicinctus is one of the top ten venomous snakes in China. Its venom is mainly neurotoxin-based. Novel antivenom drugs need to be further researched and developed. Objective This study aimed to explore the molecular mechanism of Cynanchum paniculatum in treating Bungarus multicinctus bites based on network pharmacology. Material and methods. The potential active ingredients of Cynanchum paniculatum were screened and their SDF structures were obtained using the PubChem database and imported into the SwissTargetPrediction database, and targets were obtained for the antitoxin effects of Cynanchum paniculatum in the treatment of Bungarus multicinctus bites. The Cynanchum paniculatum-active compound-potential target network and protein-protein interaction network were constructed by using Cytoscape software, and then biological function analysis and KEGG pathway enrichment analysis were performed using the DAVID. Results Seven potential active components (cynapanoside C, cynatratoside B, tomentolide A, sitosterol, sarcostin, tomentogenin, and paeonol) and 286 drug targets were obtained, including 30 key targets for the treatment of bungarotoxin toxicity. The active components mainly acted on PIK3CA, MAPK1, MAP2K1, JAK2, FYN, ACHE, CHRNA7, CHRNA4, and CHRNB2, and they antagonized the inhibitory effect of bungarotoxin on the nervous system through cholinergic synapses and the neurotrophin signaling pathway. Conclusions Cynanchum paniculatum exerts a therapeutic effect on Bungarus multicinctus bites through multiple active components, multiple targets, and multiple pathways. The findings provide a theoretical basis for the extraction of active components of Cynanchum paniculatum and for related antivenom experiments.
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Yuan S, Wang Q, Li J, Xue JC, Li Y, Meng H, Hou XT, Nan JX, Zhang QG. Inflammatory bowel disease: an overview of Chinese herbal medicine formula-based treatment. Chin Med 2022; 17:74. [PMID: 35717380 PMCID: PMC9206260 DOI: 10.1186/s13020-022-00633-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/02/2022] [Indexed: 12/14/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic recurrent inflammatory disease of the intestine, including Crohn’s disease (CD) and ulcerative colitis (UC), whose etiology and pathogenesis have not been fully understood. Due to its prolonged course and chronic recurrence, IBD imposes a heavy economic burden and psychological stress on patients. Traditional Chinese Herbal Medicine has unique advantages in IBD treatment because of its symptomatic treatment. However, the advantages of the Chinese Herbal Medicine Formula (CHMF) have rarely been discussed. In recent years, many scholars have conducted fundamental studies on CHMF to delay IBD from different perspectives and found that CHMF may help maintain intestinal integrity, reduce inflammation, and decrease oxidative stress, thus playing a positive role in the treatment of IBD. Therefore, this review focuses on the mechanisms associated with CHMF in IBD treatment. CHMF has apparent advantages. In addition to the exact composition and controlled quality of modern drugs, it also has multi-component and multi-target synergistic effects. CHMF has good prospects in the treatment of IBD, but its multi-agent composition and wide range of targets exacerbate the difficulty of studying its treatment of IBD. Future research on CHMF-related mechanisms is needed to achieve better efficacy.
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Affiliation(s)
- Shuo Yuan
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, College of Pharmacy, Yanbian University, Yanji, 133002, Jilin, China.,Chronic Disease Research Center, Medical College, Dalian University, Dalian, 116622, Liaoning, China
| | - Qi Wang
- Chronic Disease Research Center, Medical College, Dalian University, Dalian, 116622, Liaoning, China
| | - Jiao Li
- Chronic Disease Research Center, Medical College, Dalian University, Dalian, 116622, Liaoning, China.,Department of Immunology and Pathogenic Biology, Yanbian University College of Basic Medicine, Yanji, 133002, Jilin, China
| | - Jia-Chen Xue
- Chronic Disease Research Center, Medical College, Dalian University, Dalian, 116622, Liaoning, China.,Department of Immunology and Pathogenic Biology, Yanbian University College of Basic Medicine, Yanji, 133002, Jilin, China
| | - You Li
- Chronic Disease Research Center, Medical College, Dalian University, Dalian, 116622, Liaoning, China
| | - Huan Meng
- Chronic Disease Research Center, Medical College, Dalian University, Dalian, 116622, Liaoning, China
| | - Xiao-Ting Hou
- Chronic Disease Research Center, Medical College, Dalian University, Dalian, 116622, Liaoning, China
| | - Ji-Xing Nan
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, College of Pharmacy, Yanbian University, Yanji, 133002, Jilin, China.
| | - Qing-Gao Zhang
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, College of Pharmacy, Yanbian University, Yanji, 133002, Jilin, China. .,Chronic Disease Research Center, Medical College, Dalian University, Dalian, 116622, Liaoning, China. .,Department of Immunology and Pathogenic Biology, Yanbian University College of Basic Medicine, Yanji, 133002, Jilin, China.
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Yao Z, Fu S, Ren B, Ma L, Sun D. Based on Network Pharmacology and Gut Microbiota Analysis to Investigate the Mechanism of the Laxative Effect of Pterostilbene on Loperamide-Induced Slow Transit Constipation in Mice. Front Pharmacol 2022; 13:913420. [PMID: 35652049 PMCID: PMC9148975 DOI: 10.3389/fphar.2022.913420] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/02/2022] [Indexed: 12/19/2022] Open
Abstract
Background: Pterostilbene (PTE) is a natural polyphenol compound that has been proven to improve intestinal inflammation, but its laxative effect on slow transit constipation (STC) has never been studied. This study aims to investigate the laxative effect of PTE on loperamide (LOP)-induced STC mice and its influence on intestinal microbes through a combination of network pharmacological analysis and experimental verification.Material and Methods: PTE was used to treat LOP-exposed mice, and the laxative effect of PTE was evaluated by the total intestinal transit time and stool parameters. The apoptosis of Cajal interstitial cells (ICCs) was detected by immunofluorescence. The mechanism of PTE’s laxative effect was predicted by network pharmacology analysis. We used western blot technology to verify the predicted hub genes and pathways. Malondialdehyde (MDA) and GSH-Px were tested to reflect oxidative stress levels and the changes of gut microbiota were detected by 16S rDNA high-throughput sequencing.Results: PTE treatment could significantly improve the intestinal motility disorder caused by LOP. Apoptosis of ICCs increased in the STC group, but decreased significantly in the PTE intervention group. Through network pharmacological analysis, PTE might reduce the apoptosis of ICCs by enhancing PI3K/AKT and Nrf2/HO-1 signaling, and improve constipation caused by LOP. In colon tissues, PTE improved the Nrf2/HO-1 pathway and upregulated the phosphorylation of AKT. The level of MDA increased and GSH-Px decreased in the STC group, while the level of oxidative stress was significantly reduced in the PTE treatment groups. PTE also promoted the secretion of intestinal hormone and restored the microbial diversity caused by LOP.Conclusion: Pterostilbene ameliorated the intestinal motility disorder induced by LOP, this effect might be achieved by inhibiting oxidative stress-induced apoptosis of ICCs through the PI3K/AKT/Nrf2 signaling pathway.
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Zhang Q, Yang J, Yang C, Yang X, Chen Y. Eucommia ulmoides Oliver- Tribulus terrestris L. Drug Pair Regulates Ferroptosis by Mediating the Neurovascular-Related Ligand-Receptor Interaction Pathway- A Potential Drug Pair for Treatment Hypertension and Prevention Ischemic Stroke. Front Neurol 2022; 13:833922. [PMID: 35345408 PMCID: PMC8957098 DOI: 10.3389/fneur.2022.833922] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 02/08/2022] [Indexed: 01/04/2023] Open
Abstract
Background In this study, we used the network pharmacology approach to explore the potential disease targets of the Eucommia ulmoides Oliver (EUO)-Tribulus terrestris L. (TT) drug pair in the treatment of hypertension-associated neurovascular lesions and IS via the ferroptosis pathway. Methods We used the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform to search for the key active compounds and targets of the drug pair. Based on the GeneCards database, the relevant targets for the drug pair were obtained. Then, we performed the molecular docking of the screened core active ingredients and proteins using the DAVID database and the R AutoDock Vina software. Based on the GSE22255 dataset, these screened target proteins were used to build random forest (RF) and support vector machine (SVM) models. Finally, a new IS nomogram prediction model was constructed and evaluated. Results There were 36 active compounds in the EUO-TT drug pair. CHRM1, NR3C1, ADRB2, and OPRD1 proteins of the neuroactive ligand-receptor interaction pathway interacted with the proteins related to the ferroptosis pathway. Molecular docking experiments identified 12 active ingredients of the drug pair that may tightly bind to those target proteins. We constructed a visual IS nomogram prediction model using four genes (CHRM1, NR3C1, ADRB2, and OPRD1). The calibration curve, DCA, and clinical impact curves all indicated that the nomogram model is clinically applicable and diagnostically capable. CHRM1, NR3C1, ADRB2, and OPRD1, the target genes of the four effective components of the EUO-TT drug pair, were considered as risk markers for IS. Conclusions The active ingredients of EUO-TT drug pair may act on proteins associated with the neuroactive ligand-receptor interaction pathway to regulate ferroptosis in vascular neurons cells, ultimately affecting the onset and progression of hypertension.
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Affiliation(s)
- Qian Zhang
- Department of Science and Technology Office, The Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Jie Yang
- Department of Cardiology, The Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Chuanhua Yang
- Department of Cardiology, The Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Xuesong Yang
- Department of Vascular Surgery, The Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yongzhi Chen
- Department of Cardiology, The Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
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Exploring the Mechanism of Yiqi Qingre Ziyin Method in Regulating Neuropeptide Expression for the Treatment of Atrophic Rhinitis. DISEASE MARKERS 2022; 2022:4416637. [PMID: 35299869 PMCID: PMC8923799 DOI: 10.1155/2022/4416637] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/29/2022] [Accepted: 02/09/2022] [Indexed: 01/18/2023]
Abstract
Atrophic rhinitis (AR) is a chronic disease that causes severe structural changes to the nasal mucosa leading to squamous epithelial metaplasia. However, treatment regarding AR remains a major challenge. We used network pharmacology and molecular docking methods to explore the potential mechanisms of the Yiqi Qingre Ziyin method to modulate neuropeptides in the treatment of AR. The active ingredients of the Yiqi Qingre Ziyin method and their targets of action were obtained from the Traditional Chinese Medicine Systematic Pharmacology Database Analysis Platform (TCMSP). Disease targets for AR were obtained from four databases: GeneCards, PharmGKB, DrugBank, and Online Mendelian Inheritance in Man (OMIM). A total of 59 active ingredients, 39 potential targets, and 76 relevant neuropeptides were obtained after deduplication. We constructed target interaction networks with the STRING database. Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed on the 14 potential target proteins. We used Cytoscape software to construct the “drug-active ingredient-potential target” and “ingredient-target-pathway” networks of the Yiqi Qingre Ziyin method for treating AR. Molecular docking results suggest that dipeptidyl peptidase 4 (DPP4), opioid receptor gene d1 (OPRD1), and opioid receptor m1 (OPRM1) are key targets for the Yiqi Qingre Ziyin method. Therefore, this study proposed a potential mechanism for the treatment of AR by affecting the expression of neuropeptide-related genes (including DPP4, OPRD1, and OPRM1), which may potentially improve the immune microenvironment of the nasal mucosa.
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Role of Calcium Signaling Pathway-Related Gene Regulatory Networks in Ischemic Stroke Based on Multiple WGCNA and Single-Cell Analysis. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2021:8060477. [PMID: 34987704 PMCID: PMC8720592 DOI: 10.1155/2021/8060477] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 11/20/2021] [Accepted: 11/27/2021] [Indexed: 01/28/2023]
Abstract
Background This study is aimed at investigating the changes in relevant pathways and the differential expression of related gene expression after ischemic stroke (IS) at the single-cell level using multiple weighted gene coexpression network analysis (WGCNA) and single-cell analysis. Methods The transcriptome expression datasets of IS samples and single-cell RNA sequencing (scRNA-seq) profiles of cerebrovascular tissues were obtained by searching the Gene Expression Omnibus (GEO) database. First, gene pathway scoring was calculated via gene set variation analysis (GSVA) and was imported into multiple WGCNA to acquire key pathways and pathway-related hub genes. Furthermore, SCENIC was used to identify transcription factors (TFs) regulating these core genes using scRNA-seq data. Finally, the pseudotemporal trajectory analysis was used to analyse the role of these TFs on various cell types under hypoxic and normoxic conditions. Results The scores of 186 KEGG pathways were obtained via GSVA using microarray expression profiles of 40 specimens. WGCNA of the KEGG pathways revealed the two following pathways: calcium signaling pathway and neuroactive ligand-receptor interaction pathways. Subsequently, WGCNA of the gene expression matrix of the samples revealed the calcium signaling pathway-related genes (AC079305.10, BCL10, BCL2A1, BRE-AS1, DYNLL2, EREG, and PTGS2) that were identified as core genes via correlation analysis. Furthermore, SCENIC and pseudotemporal analysis revealed JUN, IRF9, ETV5, and PPARA score gene-related TFs. Jun was found to be associated with hypoxia in endothelial cells, whereas Irf9 and Etv5 were identified as astrocyte-specific TFs associated with oxygen concentration in the mouse cerebral cortex. Conclusions Calcium signaling pathway-related genes (AC079305.10, BCL10, BCL2A1, BRE-AS1, DYNLL2, EREG, and PTGS2) and TFs (JUN, IRF9, ETV5, and PPARA) were identified to play a key role in IS. This study provides a new perspective and basis for investigating the pathogenesis of IS and developing new therapeutic approaches.
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Chen Y, Sun Y, Xu Y, Lin WW, Luo Z, Han Z, Liu S, Qi B, Sun C, Go K, Kang XR, Chen J. Single-Cell Integration Analysis of Heterotopic Ossification and Fibrocartilage Developmental Lineage: Endoplasmic Reticulum Stress Effector Xbp1 Transcriptionally Regulates the Notch Signaling Pathway to Mediate Fibrocartilage Differentiation. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2021; 2021:7663366. [PMID: 34737845 PMCID: PMC8563124 DOI: 10.1155/2021/7663366] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/21/2021] [Accepted: 10/01/2021] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Regeneration of fibrochondrocytes is essential for the healing of the tendon-bone interface (TBI), which is similar to the formation of neurogenic heterotopic ossification (HO). Through single-cell integrative analysis, this study explored the homogeneity of HO cells and fibrochondrocytes. METHODS This study integrated six datasets, namely, GSE94683, GSE144306, GSE168153, GSE138515, GSE102929, and GSE110993. The differentiation trajectory and key transcription factors (TFs) for HO occurrence were systematically analyzed by integrating single-cell RNA (scRNA) sequencing, bulk RNA sequencing, and assay of transposase accessible chromatin seq. The differential expression and enrichment pathways of TFs in heterotopically ossified tissues were identified. RESULTS HO that mimicked pathological cells was classified into HO1 and HO2 cell subsets. Results of the pseudo-temporal sequence analysis suggested that HO2 is a differentiated precursor cell of HO1. The analysis of integrated scRNA data revealed that ectopically ossified cells have similar transcriptional characteristics to cells in the fibrocartilaginous zone of tendons. The modified SCENIC method was used to identify specific transcriptional regulators associated with ectopic ossification. Xbp1 was defined as a common key transcriptional regulator of ectopically ossified tissues and the fibrocartilaginous zone of tendons. Subsequently, the CellPhoneDB database was completed for the cellular ligand-receptor analysis. With further pathway screening, this study is the first to propose that Xbp1 may upregulate the Notch signaling pathway through Jag1 transcription. Twenty-four microRNAs were screened and were found to be potentially associated with upregulation of XBP1 expression after acute ischemic stroke. CONCLUSION A systematic analysis of the differentiation landscape and cellular homogeneity facilitated a molecular understanding of the phenotypic similarities between cells in the fibrocartilaginous region of tendon and HO cells. Furthermore, by identifying Xbp1 as a hub regulator and by conducting a ligand-receptor analysis, we propose a potential Xbp1/Jag1/Notch signaling pathway.
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Affiliation(s)
- Yisheng Chen
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai 200080, China
- Department of Sports Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Yaying Sun
- Department of Sports Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Yuzhen Xu
- Department of Rehabilitation, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong Province 271000, China
| | - Wei-Wei Lin
- Department of Neurosurgery, Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, 88 Jiefang Road, Hangzhou, 310009 Zhejiang, China
| | - Zhiwen Luo
- Department of Sports Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Zhihua Han
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai 200080, China
| | - Shaohua Liu
- Department of Sports Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Beijie Qi
- Department of Sports Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Chenyu Sun
- Internal Medicine, AMITA Health Saint Joseph Hospital Chicago, 2900 N. Lake Shore Drive, Chicago, 60657 Illinois, USA
| | - Ken Go
- Department of Clinical Training Centre, St. Marianna Hospital, Tokyo, Japan
| | - x.-R. Kang
- Shanghai Jiao Tong University, Shanghai 200080, China
| | - Jiwu Chen
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai 200080, China
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Wang B, Liu Y, Sun J, Zhang N, Zheng X, Liu Q. Exploring the Potential Mechanism of Xiaokui Jiedu Decoction for Ulcerative Colitis Based on Network Pharmacology and Molecular Docking. JOURNAL OF HEALTHCARE ENGINEERING 2021; 2021:1536337. [PMID: 34733451 PMCID: PMC8560263 DOI: 10.1155/2021/1536337] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 09/08/2021] [Accepted: 10/09/2021] [Indexed: 12/30/2022]
Abstract
Introduction Network pharmacology is in line with the holistic characteristics of TCM and can be used to elucidate the complex network of interactions between disease-specific genes and compounds in TCM herbal medicines. Here, we investigate the pharmacological mechanism of Xiaokui Jiedu decoction (XJD) for the treatment of ulcerative colitis (UC). Methods The Computational Systems Biology Laboratory Platform (TCMSP) database was searched and screened for the active ingredients of all drugs in XJD. The Uniport database was used to retrieve possible gene targets for the therapeutic effects of XJD. GeneCards, PharmGKB, TTD, and OMIM databases were used to retrieve XJD-related gene targets. A herb-compound-protein network and a protein-protein interaction (PPI) network were constructed, and hub genes were screened for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Finally, molecular docking was performed to validate the interrelationship between disease target proteins and active drug components. Results A total of 135 XJD potential action targets, 5097 UC-related gene targets, and 103 XJD-UC intersection gene targets were screened. The hub gene targets of XJD that exert therapeutic effects on UC are RB1, MAPK1, TP53, JUN, NR3C1, MAPK3, and ESR1. GO enrichment analysis showed 741 biofunctional enrichments, and KEGG enrichment analysis showed 124 related pathway enrichments. Molecular docking showed that the active components of XJD (β-sitosterol, kaempferol, formononetin, quercetin, and luteolin) showed good binding activities to five of the six hub gene targets. Discussion. The active ingredients of XJD (β-sitosterol, kaempferol, formononetin, quercetin, and luteolin) may regulate the inflammatory and oxidative stress-related pathways of colon cells during the course of UC by binding to the hub gene targets. This may be a potential mechanism of XJD in the treatment of UC.
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Affiliation(s)
- Bin Wang
- Department of Spleen and Stomach Diseases, The First Affiliated Hospital of Hebei College of Traditional Chinese Medicine, Shijiazhuang, China
| | - Yang Liu
- Department of Spleen and Stomach Diseases, The First Affiliated Hospital of Hebei College of Traditional Chinese Medicine, Shijiazhuang, China
| | - Jianhui Sun
- Department of Spleen and Stomach Diseases, The First Affiliated Hospital of Hebei College of Traditional Chinese Medicine, Shijiazhuang, China
| | - Nailin Zhang
- Department of Spleen and Stomach Diseases, The First Affiliated Hospital of Hebei College of Traditional Chinese Medicine, Shijiazhuang, China
| | - Xiaojia Zheng
- Department of Spleen and Stomach Diseases, The First Affiliated Hospital of Hebei College of Traditional Chinese Medicine, Shijiazhuang, China
| | - Qiquan Liu
- Department of Spleen and Stomach Diseases, The First Affiliated Hospital of Hebei College of Traditional Chinese Medicine, Shijiazhuang, China
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Zhou C, Zhou H, Zhang F, Hao L, Guo J. Active Ingredients and Potential Mechanisms of the Gan Jiang-Huang Qin-Huang Lian-Ren Shen Decoction against Ulcerative Colitis: A Network Pharmacology and Molecular Docking-Based Study. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2021; 2021:1925718. [PMID: 34539797 PMCID: PMC8445727 DOI: 10.1155/2021/1925718] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 08/01/2021] [Accepted: 08/31/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND Ulcerative colitis (UC), a chronic and nonspecific inflammatory bowel disease, seriously affects the quality of patients' life. Han Re Bing Yong Fa (treating diseases with both cool- and warm-natured herbs) is a classical therapeutic principle of traditional Chinese medicine (TCM), which is often used to treat chronic diseases, including UC. The Gan Jiang-Huang Qin-Huang Lian-Ren Shen decoction (GJHQHLRSD), a representative of Han Re Bing Yong Fa, is effective in alleviating inflammatory symptoms in UC. However, the pharmacological mechanism underlying its anti-inflammatory effect remains unclear. METHODS A network pharmacology strategy, including the construction and analysis of the drug-disease network, was used to explore the complex mechanism of GJHQHLRSD treatment of UC. In addition, molecular docking technology was used to preliminarily examine the binding ability of the potential active components and core therapeutic targets of GJHQHLRSD. RESULTS The network pharmacology results revealed 140 targets of GJHQHLRSD which are involved in UC. The PPI network analysis identified seven target genes: BCL2L1, NR3C1, ALOX5, S1PR5, NR1I2, CYP2D6, and LPAR6. The molecular docking results revealed that the following displayed strongest combined effects: EGFR with kaempferol, ERK1 with worenine, STAT3 with Palmidin A, BCL2L1 with diop and VEGFA with ginsenoside Rg3. The KEGG and gene ontology enrichment analyses results indicated that GJHQHLRSD functions by regulating the EGFR signaling pathway in UC treatment. Other effective biological processes involved in UC treatment included cancer-related as well as inflammation and viral infection signaling pathways, such as the "MicroRNAs in cancer," "TNF signaling pathway," and "JAK-STAT signaling pathway." CONCLUSIONS This study reflects the multicomponent, multitarget, and multipathway characteristics of the action mechanism of GJHQHLRSD in treating UC. Furthermore, it helps better understand the TCM therapeutic principle of Han Re Bing Yong Fa and explore novel candidate drug targets for UC treatment.
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Affiliation(s)
- Ce Zhou
- Department of Proctology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu 610072, China
| | - Hang Zhou
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 610072, China
| | - Furong Zhang
- College of Health Preservation and Rehabilitation, Chengdu University of Traditional Chinese Medicine, Chengdu 610072, China
| | - Liangliang Hao
- Department of Proctology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu 610072, China
| | - Jing Guo
- School of Clinical Medicine, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu 610072, China
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