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Zeng Z, Hu Y, Xiang J, Su J, Tan H, Lai T, Chen X, Fang G, Li L, Luo L. Cucurbitacin B targets STAT3 to induce ferroptosis in non-small cell lung cancer. Eur J Pharmacol 2024; 978:176805. [PMID: 38950838 DOI: 10.1016/j.ejphar.2024.176805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 06/28/2024] [Accepted: 06/29/2024] [Indexed: 07/03/2024]
Abstract
Cucurbitacin B (CuB) is a compound found in plants like Cucurbitaceae that has shown promise in fighting cancer, particularly in lung cancer. However, the specific impact of CuB on ferroptosis and how it works in lung cancer cells has not been fully understood. Our research has discovered that CuB can effectively slow down the growth of non-small cell lung cancer (NSCLC) cells. Even in small amounts, it was able to inhibit the growth of various NSCLC cell lines. This inhibitory effect was reversed when ferroptosis inhibitors DFO, Lip-1 and Fer-1 were introduced. CuB was found to increase the levels of reactive oxygen species (ROS), lipid ROS, MDA, and ferrous ions within H358 lung cancer cells, leading to a decrease in GSH, mitochondrial membrane potential (MMP) and changes in ferroptosis-related proteins in a dose-dependent manner. These findings were also confirmed in A549 lung cancer cells. In A549 cells, different concentrations of CuB induced the accumulation of intracellular lipid ROS, ferrous ions and changes in ferroptosis-related indicators in a concentration-dependent manner. Meanwhile, the cytotoxic effect induced by CuB in A549 cells was counteracted by ferroptosis inhibitors DFO and Fer-1. Through network pharmacology, we identified potential targets related to ferroptosis in NSCLC cells treated with CuB, with STAT3 targets showing high scores. Further experiments using molecular docking and cell thermal shift assay (CETSA) revealed that CuB interacts with the STAT3 protein. Western blot and immunofluorescence staining demonstrated that CuB inhibits the phosphorylation of STAT3 (P-STAT3) in H358 cells. Silencing STAT3 enhanced CuB-induced accumulation of lipid ROS and iron ions, as well as the expression of ferroptosis-related proteins. On the other hand, overexpression of STAT3 reversed the effects of CuB-induced ferroptosis. The results indicate that CuB has the capability to suppress STAT3 activation, resulting in ferroptosis, and could be a promising treatment choice for NSCLC.
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Affiliation(s)
- Zeyao Zeng
- The First Clinical College, Guangdong Medical University, Zhanjiang, 524023, Guangdong, China
| | - Yingying Hu
- Department of Pathophysiology, Guangdong Medical University, Zhanjiang, 524002, Guangdong, China
| | - Jing Xiang
- The Marine Biomedical Research Institute of Guangdong Zhanjiang, School of Ocean and Tropical Medicine. Guangdong Medical University, Zhanjiang, Guangdong, 524023, China
| | - Jiating Su
- The First Clinical College, Guangdong Medical University, Zhanjiang, 524023, Guangdong, China
| | - Huiting Tan
- The First Clinical College, Guangdong Medical University, Zhanjiang, 524023, Guangdong, China
| | - Tianli Lai
- The First Clinical College, Guangdong Medical University, Zhanjiang, 524023, Guangdong, China
| | - Xinming Chen
- The First Clinical College, Guangdong Medical University, Zhanjiang, 524023, Guangdong, China
| | - Guixuan Fang
- The Marine Biomedical Research Institute of Guangdong Zhanjiang, School of Ocean and Tropical Medicine. Guangdong Medical University, Zhanjiang, Guangdong, 524023, China
| | - Li Li
- The Marine Biomedical Research Institute of Guangdong Zhanjiang, School of Ocean and Tropical Medicine. Guangdong Medical University, Zhanjiang, Guangdong, 524023, China.
| | - Lianxiang Luo
- The Marine Biomedical Research Institute of Guangdong Zhanjiang, School of Ocean and Tropical Medicine. Guangdong Medical University, Zhanjiang, Guangdong, 524023, China.
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2
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Agrawal A, Vindal V. Competing endogenous RNAs in head and neck squamous cell carcinoma: a review. Brief Funct Genomics 2024; 23:335-348. [PMID: 37941447 DOI: 10.1093/bfgp/elad049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 10/19/2023] [Accepted: 10/20/2023] [Indexed: 11/10/2023] Open
Abstract
Our understanding of RNA biology has evolved with recent advances in research from it being a non-functional product to molecules of the genome with specific regulatory functions. Competitive endogenous RNA (ceRNA), which has gained prominence over time as an essential part of post-transcriptional regulatory mechanism, is one such example. The ceRNA biology hypothesis states that coding RNA and non-coding RNA co-regulate each other using microRNA (miRNA) response elements. The ceRNA components include long non-coding RNAs, pseudogene and circular RNAs that exert their effect by interacting with miRNA and regulate the expression level of its target genes. Emerging evidence has revealed that the dysregulation of the ceRNA network is attributed to the pathogenesis of various cancers, including the head and neck squamous cell carcinoma (HNSCC). This is the most prevalent cancer developed from the mucosal epithelium in the lip, oral cavity, larynx and pharynx. Although many efforts have been made to comprehend the cause and subsequent treatment of HNSCC, the morbidity and mortality rate remains high. Hence, there is an urgent need to understand the holistic progression of HNSCC, mediated by ceRNA, that can have immense relevance in identifying novel biomarkers with a defined therapeutic intervention. In this review, we have made an effort to highlight the ceRNA biology hypothesis with a focus on its involvement in the progression of HNSCC. For the identification of such ceRNAs, we have additionally highlighted a number of databases and tools.
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Affiliation(s)
- Avantika Agrawal
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana 500046, India
| | - Vaibhav Vindal
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana 500046, India
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Chaudhary U, Banerjee S. Decoding the Non-coding: Tools and Databases Unveiling the Hidden World of "Junk" RNAs for Innovative Therapeutic Exploration. ACS Pharmacol Transl Sci 2024; 7:1901-1915. [PMID: 39022352 PMCID: PMC11249652 DOI: 10.1021/acsptsci.3c00388] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 05/15/2024] [Accepted: 05/27/2024] [Indexed: 07/20/2024]
Abstract
Non-coding RNAs are pivotal regulators of gene and protein expression, exerting crucial influences on diverse biological processes. Their dysregulation is frequently implicated in the onset and progression of diseases, notably cancer. A profound comprehension of the intricate mechanisms governing ncRNAs is imperative for devising innovative therapeutic interventions against these debilitating conditions. Significantly, nearly 80% of our genome comprises ncRNAs, underscoring their centrality in cellular processes. The elucidation of ncRNA functions is pivotal for grasping the complexities of gene regulation and its implications for human health. Modern genome sequencing techniques yield vast datasets, stored in specialized databases. To harness this wealth of information and to understand the crosstalk of non-coding RNAs, knowledge of available databases is required, and many new sophisticated computational tools have emerged. These tools play a pivotal role in the identification, prediction, and annotation of ncRNAs, thereby facilitating their experimental validation. This Review succinctly outlines the current understanding of ncRNAs, emphasizing their involvement in disease development. It also highlights the databases and tools instrumental in classifying, annotating, and evaluating ncRNAs. By extracting meaningful biological insights from seemingly "junk" data, these tools empower scientists to unravel the intricate roles of ncRNAs in shaping human health.
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Affiliation(s)
- Uma Chaudhary
- Department of Biotechnology,
School of Biosciences and Technology, Vellore
Institute of Technology (VIT), Vellore, Tamil Nadu 632014, India
| | - Satarupa Banerjee
- Department of Biotechnology,
School of Biosciences and Technology, Vellore
Institute of Technology (VIT), Vellore, Tamil Nadu 632014, India
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Zhao Y, Zhu S, Li Y, Niu X, Shang G, Zhou X, Yin J, Bao B, Cao Y, Cheng F, Li Z, Wang R, Yao W. Integrated component identification, network pharmacology, and experimental verification revealed mechanism of Dendrobium officinale Kimura et Migo against lung cancer. J Pharm Biomed Anal 2024; 243:116077. [PMID: 38460276 DOI: 10.1016/j.jpba.2024.116077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 03/11/2024]
Abstract
BACKGROUND Dendrobium officinale Kimura et Migo (DO), a valuable Chinese herbal medicine, has been reported to exhibit potential effects in the prevention and treatment of lung cancer. However, its material basis and mechanism of action have not been comprehensively analyzed. PURPOSE The objective of this study was to preliminarily elucidate the active components and pharmacological mechanisms of DO in treating lung cancer, according to UPLC-Q/TOF-MS, HPAEC-PAD, network pharmacology, molecular docking, and experimental verification. METHODS The chemical components of DO were identified via UPLC-Q/TOF-MS, while the monosaccharide composition of Dendrobium officinale polysaccharide (DOP) was determined by HPAEC-PAD. The prospective active constituents of DO as well as their respective targets were predicted in the combined database of Swiss ADME and Swiss Target Prediction. Relevant disease targets for lung cancer were searched in OMIM, TTD, and Genecards databases. Further, the active compounds and potential core targets of DO against lung cancer were found by the C-T-D network and the PPI network, respectively. The core targets were then subjected to enrichment analysis in the Metascape database. The main active compounds were molecularly docked to the core targets and visualized. Finally, the viability of A549 cells and the relative quantity of associated proteins within the major signaling pathway were detected. RESULTS 249 ingredients were identified from DO, including 39 flavonoids, 39 bibenzyls, 50 organic acids, 8 phenanthrenes, 27 phenylpropanoids, 17 alkaloids, 17 amino acids and their derivatives, 7 monosaccharides, and 45 others. Here, 50 main active compounds with high degree values were attained through the C-T-D network, mainly consisting of bibenzyls and monosaccharides. Based on the PPI network analysis, 10 core targets were further predicted, including HSP90AA1, SRC, ESR1, CREBBP, MAPK3, AKT1, PIK3R1, PIK3CA, HIF1A, and HDAC1. The results of the enrichment analysis and molecular docking indicated a close association between the therapeutic mechanism of DO and the PI3K-Akt signaling pathway. It was confirmed that the bibenzyl extract and erianin could inhibit the multiplication of A549 cells in vitro. Furthermore, erianin was found to down-regulate the relative expressions of p-AKT and p-PI3K proteins within the PI3K-Akt signaling pathway. CONCLUSIONS This study predicted that DO could treat lung cancer through various components, multiple targets, and diverse pathways. Bibenzyls from DO might exert anti-lung cancer activity by inhibiting cancer cell proliferation and modulating the PI3K-Akt signaling pathway. A fundamental reference for further studies and clinical therapy was given by the above data.
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Affiliation(s)
- Yan Zhao
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China.
| | - Shuaitao Zhu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China.
| | - Yuan Li
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China.
| | - Xuan Niu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China.
| | - Guanxiong Shang
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China.
| | - Xiaoqi Zhou
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China.
| | - Jiu Yin
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China.
| | - Beihua Bao
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China.
| | - Yudan Cao
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China.
| | - Fangfang Cheng
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China.
| | - Zhipeng Li
- Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, Jiangsu 210009, China.
| | - Ran Wang
- China Tobacco Anhui Industrial Co., Ltd., Hefei, Anhui 210088, China.
| | - Weifeng Yao
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China.
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Aggarwal S, Rosenblum C, Gould M, Ziman S, Barshir R, Zelig O, Guan-Golan Y, Iny-Stein T, Safran M, Pietrokovski S, Lancet D. Expanding and Enriching the LncRNA Gene-Disease Landscape Using the GeneCaRNA Database. Biomedicines 2024; 12:1305. [PMID: 38927512 PMCID: PMC11202217 DOI: 10.3390/biomedicines12061305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/04/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024] Open
Abstract
The GeneCaRNA human gene database is a member of the GeneCards Suite. It presents ~280,000 human non-coding RNA genes, identified algorithmically from ~690,000 RNAcentral transcripts. This expands by ~tenfold the ncRNA gene count relative to other sources. GeneCaRNA thus contains ~120,000 long non-coding RNAs (LncRNAs, >200 bases long), including ~100,000 novel genes. The latter have sparse functional information, a vast terra incognita for future research. LncRNA genes are uniformly represented on all nuclear chromosomes, with 10 genes on mitochondrial DNA. Data obtained from MalaCards, another GeneCards Suite member, finds 1547 genes associated with 1 to 50 diseases. About 15% of the associations portray experimental evidence, with cancers tending to be multigenic. Preliminary text mining within GeneCaRNA discovers interactions of lncRNA transcripts with target gene products, with 25% being ncRNAs and 75% proteins. GeneCaRNA has a biological pathways section, which at present shows 131 pathways for 38 lncRNA genes, a basis for future expansion. Finally, our GeneHancer database provides regulatory elements for ~110,000 lncRNA genes, offering pointers for co-regulated genes and genetic linkages from enhancers to diseases. We anticipate that the broad vista provided by GeneCaRNA will serve as an essential guide for further lncRNA research in disease decipherment.
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Affiliation(s)
- Shalini Aggarwal
- Department of Molecular Genetics, Weizmann Institute of Science, Herzl 234, Rehovot 7610010, Israel (S.Z.)
| | - Chana Rosenblum
- Department of Molecular Genetics, Weizmann Institute of Science, Herzl 234, Rehovot 7610010, Israel (S.Z.)
| | - Marshall Gould
- Department of Biological Sciences, University College London, Gower Street, London WC1E 6BT, UK
| | - Shahar Ziman
- Department of Molecular Genetics, Weizmann Institute of Science, Herzl 234, Rehovot 7610010, Israel (S.Z.)
| | - Ruth Barshir
- TAD Center for AI and Data Science, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Ofer Zelig
- LifeMap Sciences Inc., Alameda, CA 94501, USA
| | | | - Tsippi Iny-Stein
- Department of Molecular Genetics, Weizmann Institute of Science, Herzl 234, Rehovot 7610010, Israel (S.Z.)
| | - Marilyn Safran
- Department of Molecular Genetics, Weizmann Institute of Science, Herzl 234, Rehovot 7610010, Israel (S.Z.)
| | - Shmuel Pietrokovski
- Department of Molecular Genetics, Weizmann Institute of Science, Herzl 234, Rehovot 7610010, Israel (S.Z.)
| | - Doron Lancet
- Department of Molecular Genetics, Weizmann Institute of Science, Herzl 234, Rehovot 7610010, Israel (S.Z.)
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Wu B, Li C, Luo X, Kan H, Li Y, Zhang Y, Rao X, Zhao P, Liu Y. Identification of Key Hypolipidemic Components and Exploration of the Potential Mechanism of Total Flavonoids from Rosa sterilis Based on Network Pharmacology, Molecular Docking, and Zebrafish Experiment. Curr Issues Mol Biol 2024; 46:5131-5146. [PMID: 38920980 PMCID: PMC11201594 DOI: 10.3390/cimb46060308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/16/2024] [Accepted: 05/20/2024] [Indexed: 06/27/2024] Open
Abstract
Hyperlipidemia is a prevalent chronic metabolic disease that severely affects human health. Currently, commonly used clinical therapeutic drugs are prone to drug dependence and toxic side effects. Dietary intervention for treating chronic metabolic diseases has received widespread attention. Rosa sterilis is a characteristic fruit tree in China whose fruits are rich in flavonoids, which have been shown to have a therapeutic effect on hyperlipidemia; however, their exact molecular mechanism of action remains unclear. Therefore, this study aimed to investigate the therapeutic effects of R. sterilis total flavonoid extract (RS) on hyperlipidemia and its possible mechanisms. A hyperlipidemic zebrafish model was established using egg yolk powder and then treated with RS to observe changes in the integral optical density in the tail vessels. Network pharmacology and molecular docking were used to investigate the potential mechanism of action of RS for the treatment of hyperlipidemia. The results showed that RS exhibited favorable hypolipidemic effects on zebrafish in the concentration range of 3.0-30.0 μg/mL in a dose-dependent manner. Topological and molecular docking analyses identified HSP90AA1, PPARA, and MMP9 as key targets for hypolipidemic effects, which were exerted mainly through lipolytic regulation of adipocytes and lipids; pathway analysis revealed enrichment in atherosclerosis, chemical carcinogenic-receptor activation pathways in cancers, and proteoglycans in prostate cancer and other cancers. Mover, chinensinaphthol possessed higher content and better target binding ability, which suggested that chinensinaphthol might be an important component of RS with hypolipidemic active function. These findings provide a direction for further research on RS interventions for the treatment of hyperlipidemia.
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Affiliation(s)
- Boxiao Wu
- Key Laboratory of State Forestry and Grassland Administration on Highly-Efficient Utilization of Forestry Biomass Resources in Southwest China, Southwest Forestry University, Kunming 650224, China; (B.W.); (C.L.); (H.K.)
| | - Churan Li
- Key Laboratory of State Forestry and Grassland Administration on Highly-Efficient Utilization of Forestry Biomass Resources in Southwest China, Southwest Forestry University, Kunming 650224, China; (B.W.); (C.L.); (H.K.)
| | - Xulu Luo
- College of Plant Protection, Yunnan Agricultural University, Kunming 650201, China; (X.L.); (Y.L.)
| | - Huan Kan
- Key Laboratory of State Forestry and Grassland Administration on Highly-Efficient Utilization of Forestry Biomass Resources in Southwest China, Southwest Forestry University, Kunming 650224, China; (B.W.); (C.L.); (H.K.)
| | - Yonghe Li
- College of Plant Protection, Yunnan Agricultural University, Kunming 650201, China; (X.L.); (Y.L.)
| | - Yingjun Zhang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China;
| | - Xiaoping Rao
- Academy of Advanced Carbon Conversion Technology, Huaqiao University, Xiamen 362021, China;
| | - Ping Zhao
- Key Laboratory of State Forestry and Grassland Administration on Highly-Efficient Utilization of Forestry Biomass Resources in Southwest China, Southwest Forestry University, Kunming 650224, China; (B.W.); (C.L.); (H.K.)
| | - Yun Liu
- Key Laboratory of State Forestry and Grassland Administration on Highly-Efficient Utilization of Forestry Biomass Resources in Southwest China, Southwest Forestry University, Kunming 650224, China; (B.W.); (C.L.); (H.K.)
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Börner K, Blood PD, Silverstein JC, Ruffalo M, Teichmann SA, Pryhuber G, Misra R, Purkerson J, Fan J, Hickey JW, Molla G, Xu C, Zhang Y, Weber G, Jain Y, Qaurooni D, Kong Y, Bueckle A, Herr BW. Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas Construction and Usage. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.27.587041. [PMID: 38826261 PMCID: PMC11142047 DOI: 10.1101/2024.03.27.587041] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
The Human BioMolecular Atlas Program (HuBMAP) aims to construct a reference 3D structural, cellular, and molecular atlas of the healthy adult human body. The HuBMAP Data Portal (https://portal.hubmapconsortium.org) serves experimental datasets and supports data processing, search, filtering, and visualization. The Human Reference Atlas (HRA) Portal (https://humanatlas.io) provides open access to atlas data, code, procedures, and instructional materials. Experts from more than 20 consortia are collaborating to construct the HRA's Common Coordinate Framework (CCF), knowledge graphs, and tools that describe the multiscale structure of the human body (from organs and tissues down to cells, genes, and biomarkers) and to use the HRA to understand changes that occur at each of these levels with aging, disease, and other perturbations. The 6th release of the HRA v2.0 covers 36 organs with 4,499 unique anatomical structures, 1,195 cell types, and 2,089 biomarkers (e.g., genes, proteins, lipids) linked to ontologies. In addition, three workflows were developed to map new experimental data into the HRA's CCF. This paper describes the HRA user stories, terminology, data formats, ontology validation, unified analysis workflows, user interfaces, instructional materials, application programming interface (APIs), flexible hybrid cloud infrastructure, and demonstrates first atlas usage applications and previews.
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Affiliation(s)
- Katy Börner
- Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, USA
- CIFAR MacMillan Multiscale Human program, CIFAR, Toronto, ON, Canada
| | - Philip D. Blood
- Pittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Jonathan C. Silverstein
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Matthew Ruffalo
- Ray and Stephanie Lane Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Sarah A. Teichmann
- CIFAR MacMillan Multiscale Human program, CIFAR, Toronto, ON, Canada
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Ravi Misra
- University of Rochester Medical Center, Rochester, NY, USA
| | | | - Jean Fan
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore MD, USA
| | - John W. Hickey
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | | | - Chuan Xu
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Yun Zhang
- J. Craig Venter Institute, La Jolla, CA, USA
| | - Griffin Weber
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Yashvardhan Jain
- Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, USA
| | - Danial Qaurooni
- Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, USA
| | - Yongxin Kong
- Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, USA
| | | | - Andreas Bueckle
- Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, USA
| | - Bruce W. Herr
- Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, USA
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8
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Pei J, Zhang J, Yu C, Luo J, Wen S, Hua Y, Wei G. Transcriptomics-based identification of TYROBP and TLR8 as novel macrophage-related biomarkers for the diagnosis of acute rejection after kidney transplantation. Biochem Biophys Res Commun 2024; 709:149790. [PMID: 38564938 DOI: 10.1016/j.bbrc.2024.149790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/06/2024] [Accepted: 03/14/2024] [Indexed: 04/04/2024]
Abstract
Macrophages play an important role in the development and progression of acute rejection after kidney transplantation. The study aims to investigate the biological role and significance of macrophage-associated genes (MAG) in acute rejection after kidney transplantation. We utilized transcriptome sequencing results from public databases related to acute rejection of kidney transplantation for comprehensive analysis and validation in animal experiments. We found that a large number of immune-related signaling pathways are activated in acute rejection. PPI protein interaction networks and machine learning were used to establish a Hub gene consisting of TYROBP and TLR8 for the diagnosis of acute rejection. The single-gene GSEA enrichment analysis and immune cell correlation analysis revealed a close correlation between the expression of Hub genes and immune-related biological pathways as well as the expression of multiple immune cells. In addition, the study of TF, miRNAs, and drugs provided a theoretical basis for regulating and treating the Hub genes in acute rejection. Finally, the animal experiments demonstrated once again that acute rejection can aggravate kidney tissue damage, apoptosis level, and increase the release of inflammatory factors. We established and validated a macrophage-associated diagnostic model for acute rejection after kidney transplantation, which can accurately diagnose the biological alterations in acute rejection after kidney transplantation.
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Affiliation(s)
- Jun Pei
- Department of Urology, Children's Hospital of Chongqing Medical University, Chongqing, China; Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China; Chongqing Key Laboratory of Children Urogenital Development and Tissue Engineering, Chongqing, China
| | - Jie Zhang
- Department of Urology, Children's Hospital of Chongqing Medical University, Chongqing, China; Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China; Chongqing Key Laboratory of Children Urogenital Development and Tissue Engineering, Chongqing, China
| | - Chengjun Yu
- Department of Urology, Children's Hospital of Chongqing Medical University, Chongqing, China; Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China; Chongqing Key Laboratory of Children Urogenital Development and Tissue Engineering, Chongqing, China
| | - Jin Luo
- Department of Urology, Children's Hospital of Chongqing Medical University, Chongqing, China; Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China; Chongqing Key Laboratory of Children Urogenital Development and Tissue Engineering, Chongqing, China
| | - Sheng Wen
- Department of Urology, Children's Hospital of Chongqing Medical University, Chongqing, China; Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China; Chongqing Key Laboratory of Children Urogenital Development and Tissue Engineering, Chongqing, China
| | - Yi Hua
- Department of Urology, Children's Hospital of Chongqing Medical University, Chongqing, China; Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China; Chongqing Key Laboratory of Children Urogenital Development and Tissue Engineering, Chongqing, China.
| | - Guanghui Wei
- Department of Urology, Children's Hospital of Chongqing Medical University, Chongqing, China; Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China; Chongqing Key Laboratory of Children Urogenital Development and Tissue Engineering, Chongqing, China.
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9
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Yang J, Jiang YH, Zhou X, Yao JQ, Wang YY, Liu JQ, Zhang PC, Tang WF, Li Z. Material basis and molecular mechanisms of Chaihuang Qingyi Huoxue Granule in the treatment of acute pancreatitis based on network pharmacology and molecular docking-based strategy. Front Immunol 2024; 15:1353695. [PMID: 38765004 PMCID: PMC11099290 DOI: 10.3389/fimmu.2024.1353695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 04/17/2024] [Indexed: 05/21/2024] Open
Abstract
Objectives This study aimed to analyze active compounds and signaling pathways of CH applying network pharmacology methods, and to additionally verify the molecular mechanism of CH in treating AP. Materials and methods Network pharmacology and molecular docking were firstly used to identify the active components of CH and its potential targets in the treatment of AP. The pancreaticobiliary duct was retrogradely injected with sodium taurocholate (3.5%) to create an acute pancreatitis (AP) model in rats. Histological examination, enzyme-linked immunosorbent assay, Western blot and TUNEL staining were used to determine the pathway and mechanism of action of CH in AP. Results Network pharmacological analysis identified 168 active compounds and 276 target proteins. In addition, there were 2060 targets associated with AP, and CH had 177 targets in common with AP. These shared targets, including STAT3, IL6, MYC, CDKN1A, AKT1, MAPK1, MAPK3, MAPK14, HSP90AA1, HIF1A, ESR1, TP53, FOS, and RELA, were recognized as core targets. Furthermore, we filtered out 5252 entries from the Gene Ontology(GO) and 186 signaling pathways from the Kyoto Encyclopedia of Genes and Genomes(KEGG). Enrichment and network analyses of protein-protein interactions predicted that CH significantly affected the PI3K/AKT signaling pathway, which played a critical role in programmed cell death. The core components and key targets showed strong binding activity based on molecular docking results. Subsequently, experimental validation demonstrated that CH inhibited the phosphorylation of PI3K and AKT in pancreatic tissues, promoted the apoptosis of pancreatic acinar cells, and further alleviated inflammation and histopathological damage to the pancreas in AP rats. Conclusion Apoptosis of pancreatic acinar cells can be enhanced and the inflammatory response can be reduced through the modulation of the PI3K/AKT signaling pathway, resulting in the amelioration of pancreatic disease.
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Affiliation(s)
- Jia Yang
- School of Integrated Traditional Chinese and Western Medicine, Southwest Medical University, Luzhou, Sichuan, China
| | - Yu-Hong Jiang
- Department of Integrated Traditional Chinese and Western Medicine, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Xin Zhou
- Department of Spleen and Stomach Diseases, Chinese Medicine Hospital Affiliated to Southwest Medical University, Luzhou, Sichuan, China
- The Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Digestive System Diseases of Luzhou city, Affiliated Traditional Medicine Hospital of Southwest Medical University, Luzhou, China
| | - Jia-Qi Yao
- Department of Integrated Traditional Chinese and Western Medicine, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Yang-Yang Wang
- School of Integrated Traditional Chinese and Western Medicine, Southwest Medical University, Luzhou, Sichuan, China
| | - Jian-Qin Liu
- Department of Spleen and Stomach Diseases, Chinese Medicine Hospital Affiliated to Southwest Medical University, Luzhou, Sichuan, China
- The Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Digestive System Diseases of Luzhou city, Affiliated Traditional Medicine Hospital of Southwest Medical University, Luzhou, China
| | - Peng-Cheng Zhang
- Department of Integrated Traditional Chinese and Western Medicine, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Wen-Fu Tang
- Department of Integrated Traditional Chinese and Western Medicine, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Zhi Li
- Department of Spleen and Stomach Diseases, Chinese Medicine Hospital Affiliated to Southwest Medical University, Luzhou, Sichuan, China
- The Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Digestive System Diseases of Luzhou city, Affiliated Traditional Medicine Hospital of Southwest Medical University, Luzhou, China
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10
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D'Antona S, Porro D, Gallivanone F, Bertoli G. Characterization of cell cycle, inflammation, and oxidative stress signaling role in non-communicable diseases: Insights into genetic variants, microRNAs and pathways. Comput Biol Med 2024; 174:108346. [PMID: 38581999 DOI: 10.1016/j.compbiomed.2024.108346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 02/16/2024] [Accepted: 03/17/2024] [Indexed: 04/08/2024]
Abstract
Non-Communicable Diseases (NCDs) significantly impact global health, contributing to over 70% of premature deaths, as reported by the World Health Organization (WHO). These diseases have complex and multifactorial origins, involving genetic, epigenetic, environmental and lifestyle factors. While Genome-Wide Association Study (GWAS) is widely recognized as a valuable tool for identifying variants associated with complex phenotypes; the multifactorial nature of NCDs necessitates a more comprehensive exploration, encompassing not only the genetic but also the epigenetic aspect. For this purpose, we employed a bioinformatics-multiomics approach to examine the genetic and epigenetic characteristics of NCDs (i.e. colorectal cancer, coronary atherosclerosis, squamous cell lung cancer, psoriasis, type 2 diabetes, and multiple sclerosis), aiming to identify novel biomarkers for diagnosis and prognosis. Leveraging GWAS summary statistics, we pinpointed Single Nucleotide Polymorphisms (SNPs) independently associated with each NCD. Subsequently, we identified genes linked to cell cycle, inflammation and oxidative stress mechanisms, revealing shared genes across multiple diseases, suggesting common functional pathways. From an epigenetic perspective, we identified microRNAs (miRNAs) with regulatory functions targeting these genes of interest. Our findings underscore critical genetic pathways implicated in these diseases. In colorectal cancer, the dysregulation of the "Cytokine Signaling in Immune System" pathway, involving LAMA5 and SMAD7, regulated by Hsa-miR-21-5p, Hsa-miR-103a-3p, and Hsa-miR-195-5p, emerged as pivotal. In coronary atherosclerosis, the pathway associated with "binding of TCF/LEF:CTNNB1 to target gene promoters" displayed noteworthy implications, with the MYC factor controlled by Hsa-miR-16-5p as a potential regulatory factor. Squamous cell lung carcinoma analysis revealed significant pathways such as "PTK6 promotes HIF1A stabilization," regulated by Hsa-let-7b-5p. In psoriasis, the "Endosomal/Vacuolar pathway," involving HLA-C and Hsa-miR-148a-3p and Hsa-miR-148b-3p, was identified as crucial. Type 2 Diabetes implicated the "Regulation of TP53 Expression" pathway, controlled by Hsa-miR-106a-5p and Hsa-miR-106b-5p. In conclusion, our study elucidates the genetic framework and molecular mechanisms underlying NCDs, offering crucial insights into potential genetic/epigenetic biomarkers for diagnosis and prognosis. The specificity of pathways and related miRNAs in different pathologies highlights promising candidates for further clinical validation, with the potential to advance personalized treatments and alleviate the global burden of NCDs.
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Affiliation(s)
- Salvatore D'Antona
- Institute of Bioimaging and Molecular Physiology, National Research Council, Via F.lli Cervi 93, 20054, Milan, Italy
| | - Danilo Porro
- Institute of Bioimaging and Molecular Physiology, National Research Council, Via F.lli Cervi 93, 20054, Milan, Italy; National Biodiversity Future Center (NBFC), Palermo, Italy
| | - Francesca Gallivanone
- Institute of Bioimaging and Molecular Physiology, National Research Council, Via F.lli Cervi 93, 20054, Milan, Italy
| | - Gloria Bertoli
- Institute of Bioimaging and Molecular Physiology, National Research Council, Via F.lli Cervi 93, 20054, Milan, Italy; National Biodiversity Future Center (NBFC), Palermo, Italy.
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11
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Uttam V, Rana MK, Sharma U, Singh K, Jain A. Circulating long non-coding RNA EWSAT1 acts as a liquid biopsy marker for esophageal squamous cell carcinoma: A pilot study. Noncoding RNA Res 2024; 9:1-11. [PMID: 38028735 PMCID: PMC10679462 DOI: 10.1016/j.ncrna.2023.10.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 10/19/2023] [Accepted: 10/19/2023] [Indexed: 12/01/2023] Open
Abstract
The widespread public health problem of esophageal squamous cell carcinoma (ESCC) is the cause of an increasing number of deaths each year due to delayed diagnosis. Therefore, we require specific and sensitive new biomarkers to manage ESCC better. The detection of diseases, such as cancer, can now be achieved through non-invasive circulating blood-based methods. Blood-based circulating non-coding RNAs, such as miRNA and lncRNA, have been extensively used as valuable markers for lung, esophageal, and breast cancer diagnostic purposes, as quoted in our previous research. Herein, we investigated the role of novel long non-coding RNA EWSAT1 as a blood-based liquid biopsy biomarker for the ESCC. Our findings indicate that EWSAT1 lncRNA has an increased tumor suppressive activity in ESCC, as it reduces by ∼2.59-fold relative to healthy controls. Moreover, we established that EWSAT1 expression can significantly distinguish between clinicopathological characteristics, including age, gender, and lifestyle choices such as smoking, alcohol consumption, and drinking hot beverages among patients with ESCC and healthy individuals. In addition, the expression levels of lncRNA EWSAT1 could distinguish between individuals with more advanced ESCC cancer and those without it, as illustrated by the ROC curve (AUC = 0.7174, 95 % confidence intervals = 0.5901 to 0.8448, p-value = 0.001). Our in-silico prediction methods demonstrated that miR-873-5p is the direct target of EWSAT1, which competes with the tumor suppressor candidate 3 (TUSC3) and EGL-9 family hypoxia-inducible factor 3 (EGLN3) mRNAs through a sponging mechanism, creating the EWSAT1/miR-873-5p/mRNA axis. We have analyzed the role of EWSAT1 in various cellular processes and signaling pathways, including mTOR, Wnt, and MAPK signaling pathways. Circulating EWSAT1 can be used as a liquid biopsy marker for diagnosis of ESCC and has the potential to serve as an effective therapeutic biomarker, according to this pilot study.
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Affiliation(s)
- Vivek Uttam
- Department of Zoology, Central University of Punjab, Ghudda, 151401, Bathinda, Punjab, India
| | - Manjit Kaur Rana
- Department of Pathology/Laboratory Medicine, All India Institute of Medical Sciences, 151001, Bathinda, Punjab, India
| | - Uttam Sharma
- Department of Zoology, Central University of Punjab, Ghudda, 151401, Bathinda, Punjab, India
| | - Karuna Singh
- Department of Radiotherapy, Advanced Cancer Institute, 151001, Bathinda, Affiliated with Baba Farid University of Health Sciences, Faridkot, Punjab, India
| | - Aklank Jain
- Department of Zoology, Central University of Punjab, Ghudda, 151401, Bathinda, Punjab, India
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12
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He Y, Liu F, He M, Long F, Hu D, Chen J, Fang M, Wang Z. Molecular mechanism of resveratrol promoting differentiation of preosteoblastic MC3T3-E1 cells based on network pharmacology and experimental validation. BMC Complement Med Ther 2024; 24:108. [PMID: 38424533 PMCID: PMC10905894 DOI: 10.1186/s12906-024-04396-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 02/10/2024] [Indexed: 03/02/2024] Open
Abstract
The purpose of this study was to investigate the mechanism by which resveratrol (Res) inhibits apoptosis and promotes proliferation and differentiation of pre-osteoblastic MC3T3-E1 cells, laying the groundwork for the treatment of osteoporosis (OP). The TCMSP database was used to find the gene targets for Res. The GeneCards database acquire the gene targets for OP. After discovering the potential target genes, GO, KEGG, and Reactome enrichment analysis were conducted. Verifying the major proteins involved in apoptosis can bind to Res using molecular docking. CCK8 measured the proliferative activity of mouse pre-osteoblasts in every group following Res intervention. Alkaline phosphatase staining (ALP) and alizarin red staining to measure the ability of osteogenic differentiation. RT-qPCR to determine the expression levels of Runx2 and OPG genes for osteogenic differentiation ability of cells. Western blot to measure the degree of apoptosis-related protein activity in each group following Res intervention. The biological processes investigated for GO of Res therapeutic OP involved in cytokine-mediated signaling pathway, negative regulation of apoptotic process, Aging, extrinsic apoptotic signaling pathway in absence of ligand, according to potential therapeutic target enrichment study. Apoptosis, FoxO signaling pathway, and TNF signaling pathway are the primary KEGG signaling pathways. Recactome pathways are primarily engaged in Programmed Cell Death, Apoptosis, Intrinsic Apoptotic Pathway, and Caspase activation via extrinsic apoptotic signaling pathways. This research established a new approach for Res treatment of OP by demonstrating how Res controls the apoptosis-related proteins TNF, IL6, and CASP3 to suppress osteoblast death and increase osteoclastogenesis.
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Affiliation(s)
- Yu He
- Department of Spine Surgery, Chengdu Second People's Hospital, No.2, Huatai Road, Chenghua District, Chengdu, 610000, Sichuan, China
| | - Fei Liu
- Department of Spine Surgery, RuiKang Hospital affiliated to Guangxi University of Chinese Medicine, Nanning, 530011, Guangxi, China
- Department of orthopedics, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, No.182, Chunhui Road, Longmatan District, Luzhou, 646000, Sichuan, China
| | - Mingjuan He
- Department of Spine Surgery, Chengdu Second People's Hospital, No.2, Huatai Road, Chenghua District, Chengdu, 610000, Sichuan, China
| | - Fayu Long
- Department of Spine Surgery, Chengdu Second People's Hospital, No.2, Huatai Road, Chenghua District, Chengdu, 610000, Sichuan, China
| | - Ding Hu
- Department of Spine Surgery, Chengdu Second People's Hospital, No.2, Huatai Road, Chenghua District, Chengdu, 610000, Sichuan, China
| | - Jingwen Chen
- Department of orthopedics, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, No.182, Chunhui Road, Longmatan District, Luzhou, 646000, Sichuan, China
| | - Miao Fang
- Department of Spine Surgery, Chengdu Second People's Hospital, No.2, Huatai Road, Chenghua District, Chengdu, 610000, Sichuan, China.
| | - Zhenlong Wang
- Department of orthopedics, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, No.182, Chunhui Road, Longmatan District, Luzhou, 646000, Sichuan, China.
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Wu B, Li C, Kan H, Zhang Y, Rao X, Liu Y, Zhao P. Hypolipidemic and Antithrombotic Effect of 6'- O-Caffeoylarbutin from Vaccinium dunalianum Based on Zebrafish Model, Network Pharmacology, and Molecular Docking. Molecules 2024; 29:780. [PMID: 38398534 PMCID: PMC10893483 DOI: 10.3390/molecules29040780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/04/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
Vaccinium dunalianum leaf buds make one of the most commonly used herbal teas of the Yi people in China, which is used to treat articular rheumatism, relax tendons, and stimulates blood circulation in the body. In addition, 6'-O-caffeoylarbutin (CA) is a standardized extract of V. dunalianum, which has been found in dried leaf buds, reaching levels of up to 31.76%. Because of the uncommon phenomenon, it is suggested that CA may have a potential therapeutic role in hyperlipidemia and thrombosis. This study was designed to study the efficacy of CA on treating hyperlipidemia and thrombosis and the possible mechanisms behind these effects. Hyperlipidemia and thrombosis zebrafish models were treated with CA to observe variations of the integrated optical density within the vessels and the intensity of erythrocyte staining within the hearts. The possible mechanisms were explored using network pharmacology and molecular docking. The results demonstrate that CA exhibits an excellent hypolipidemic effect on zebrafish at concentrations ranging from 3.0 to 30.0 μg/mL and shows thrombosis inhibitory activity in zebrafish at a concentration of 30.0 μg/mL, with an inhibition rate of 44%. Moreover, network pharmacological research shows that MMP9, RELA, MMP2, PRKCA, HSP90AA1, and APP are major targets of CA for therapy of hyperlipidemia and thrombosis, and may relate to pathways in cancer, chemical carcinogenesis-receptor activation, estrogen signaling pathway, and the AGE-RAGE signaling pathway in diabetic complications.
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Affiliation(s)
- Boxiao Wu
- Key Laboratory of Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming 650224, China; (B.W.); (C.L.); (H.K.)
- Key Laboratory of State Forestry and Grassland Administration on Highly-Efficient Utilization of Forestry Biomass Resources in Southwest China, Southwest Forestry University, Kunming 650224, China
| | - Churan Li
- Key Laboratory of Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming 650224, China; (B.W.); (C.L.); (H.K.)
- Key Laboratory of State Forestry and Grassland Administration on Highly-Efficient Utilization of Forestry Biomass Resources in Southwest China, Southwest Forestry University, Kunming 650224, China
| | - Huan Kan
- Key Laboratory of Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming 650224, China; (B.W.); (C.L.); (H.K.)
| | - Yingjun Zhang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650224, China;
| | - Xiaoping Rao
- Academy of Advanced Carbon Conversion Technology, Huaqiao University, Xiamen 361021, China;
| | - Yun Liu
- Key Laboratory of Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming 650224, China; (B.W.); (C.L.); (H.K.)
- Key Laboratory of State Forestry and Grassland Administration on Highly-Efficient Utilization of Forestry Biomass Resources in Southwest China, Southwest Forestry University, Kunming 650224, China
| | - Ping Zhao
- Key Laboratory of Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming 650224, China; (B.W.); (C.L.); (H.K.)
- Key Laboratory of State Forestry and Grassland Administration on Highly-Efficient Utilization of Forestry Biomass Resources in Southwest China, Southwest Forestry University, Kunming 650224, China
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Zheng J, Jiang S, Lin X, Wang H, Liu L, Cai X, Sun Y. Comprehensive analyses of mitophagy-related genes and mitophagy-related lncRNAs for patients with ovarian cancer. BMC Womens Health 2024; 24:37. [PMID: 38218807 PMCID: PMC10788026 DOI: 10.1186/s12905-023-02864-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 12/24/2023] [Indexed: 01/15/2024] Open
Abstract
BACKGROUND Both mitophagy and long non-coding RNAs (lncRNAs) play crucial roles in ovarian cancer (OC). We sought to explore the characteristics of mitophagy-related gene (MRG) and mitophagy-related lncRNAs (MRL) to facilitate treatment and prognosis of OC. METHODS The processed data were extracted from public databases (TCGA, GTEx, GEO and GeneCards). The highly synergistic lncRNA modules and MRLs were identified using weighted gene co-expression network analysis. Using LASSO Cox regression analysis, the MRL-model was first established based on TCGA and then validated with four external GEO datasets. The independent prognostic value of the MRL-model was evaluated by Multivariate Cox regression analysis. Characteristics of functional pathways, somatic mutations, immunity features, and anti-tumor therapy related to the MRL-model were evaluated using abundant algorithms, such as GSEA, ssGSEA, GSVA, maftools, CIBERSORT, xCELL, MCPcounter, ESTIMATE, TIDE, pRRophetic and so on. RESULTS We found 52 differentially expressed MRGs and 22 prognostic MRGs in OC. Enrichment analysis revealed that MRGs were involved in mitophagy. Nine prognostic MRLs were identified and eight optimal MRLs combinations were screened to establish the MRL-model. The MRL-model stratified patients into high- and low-risk groups and remained a prognostic factor (P < 0.05) with independent value (P < 0.05) in TCGA and GEO. We observed that OC patients in the high-risk group also had the unfavorable survival in consideration of clinicopathological parameters. The Nomogram was plotted to make the prediction results more intuitive and readable. The two risk groups were enriched in discrepant functional pathways (such as Wnt signaling pathway) and immunity features. Besides, patients in the low-risk group may be more sensitive to immunotherapy (P = 0.01). Several chemotherapeutic drugs (Paclitaxel, Veliparib, Rucaparib, Axitinib, Linsitinib, Saracatinib, Motesanib, Ponatinib, Imatinib and so on) were found with variant sensitivity between the two risk groups. The established ceRNA network indicated the underlying mechanisms of MRLs. CONCLUSIONS Our study revealed the roles of MRLs and MRL-model in expression, prognosis, chemotherapy, immunotherapy, and molecular mechanism of OC. Our findings were able to stratify OC patients with high risk, unfavorable prognosis and variant treatment sensitivity, thus improving clinical outcomes for OC patients.
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Affiliation(s)
- Jianfeng Zheng
- Department of Gynecology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, 350014, China
| | - Shan Jiang
- Department of Gynecology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, 350014, China
| | - Xuefen Lin
- Department of Gynecology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, 350014, China
| | - Huihui Wang
- Department of Anesthesiology, The Central hospital of Wenzhou City, 32 Dajian Lane, Wenzhou, 325000, China
| | - Li Liu
- Department of Gynecology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, 350014, China
| | - Xintong Cai
- Department of Gynecology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, 350014, China
| | - Yang Sun
- Department of Gynecology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, 350014, China.
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Li J, Cui J, Wu L, Liu YB, Wang Q. Machine learning and molecular subtype analyses provide insights into PANoptosis-associated genes in rheumatoid arthritis. Arthritis Res Ther 2023; 25:233. [PMID: 38041172 PMCID: PMC10691119 DOI: 10.1186/s13075-023-03222-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 11/26/2023] [Indexed: 12/03/2023] Open
Abstract
BACKGROUND PANoptosis represents a newly identified form of programmed cell death that plays a significant role in the autoimmune diseases. Rheumatoid arthritis (RA) is characterized by the presence of autoantibodies. Nevertheless, the specific biomarkers and molecular mechanisms responsible for the apoptotic characteristics of RA remain largely uninvestigated. METHODS We utilized 8 synovial tissue RA datasets. We selected genes associated with PANoptosis from the GeneCard database. By employing the limma, WGCNA, and machine learning algorithms we identified core genes. We utilized consensus clustering analysis to identify distinct PANoptosis subtypes of RA. Boruta algorithm was employed to construct a PANoptosis signature score. The sensitivity of distinct subtypes to drug treatment was verified using an independent dataset. RESULTS The SPP1 emerged as the significant gene, with its elevated expression in RA patients. We identified two PANoptosis RA subtypes. Cluster 1 showed high expression of Tregs, resting dendritic cells, and resting mast cells. Cluster 2 exhibited high expression of CD4 memory T cells and follicular helper T cells. Cluster 2 exhibited a higher degree of sensitivity towards immune checkpoint therapy. Employing the Boruta algorithm, a subtype score was devised for 37 PANoptosis genes, successfully discerning the subtypes (AUC = 0.794), wherein patients with elevated scores demonstrated enhanced responsiveness to Rituximab treatment. CONCLUSION Our analysis revealed that SPP1 holds potential biomarker for the diagnosis of RA. Cluster 2 exhibited enhanced sensitivity to immune checkpoint therapy, higher PANoptosis scores, and improved responsiveness to drug treatment. This study offers potential implications in the realm of diagnosis and treatment.
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Affiliation(s)
- Jing Li
- Department of Anesthesiology, Shanxi Provincial People's Hospital (Fifth Hospital) of Shanxi Medical University, Taiyuan, China
| | - Jun Cui
- Department of Anesthesiology, The Hospital of Sinochem Second Construction Group Co, LTD, Taiyuan, China
| | - Li Wu
- Department of Anesthesiology, Shanxi Provincial People's Hospital (Fifth Hospital) of Shanxi Medical University, Taiyuan, China
- School of Basic Medical Sciences, Shanxi Medical University, Taiyuan, China
| | - Ya-Bing Liu
- Department of Anesthesiology, Shanxi Provincial People's Hospital (Fifth Hospital) of Shanxi Medical University, Taiyuan, China.
| | - Qi Wang
- School of Basic Medical Sciences, Shanxi Medical University, Taiyuan, China.
- Shanxi Key Laboratory of Big Data for Clinical Decision Research, Taiyuan, 030000, China.
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Zhu C, Zhang Z, Wang S, Sun Z. Study on the mechanism of Gastrodiae Rhizoma, Lycii Fructus, and Ziziphi Spinosae Semen in sedation and tranquillising mind. Mol Divers 2023:10.1007/s11030-023-10756-x. [PMID: 37917323 DOI: 10.1007/s11030-023-10756-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 10/22/2023] [Indexed: 11/04/2023]
Abstract
This study analysed the pharmacological mechanism of Gastrodiae Rhizoma, Lycii Fructus, and Ziziphi Spinosae Semen in sedation and tranquillising mind using network pharmacology methods. The findings of this study aimed to serve as a reference for the development of novel drugs and the clinical expansion and application of traditional Chinese medicine formulas. The chemical constituents and therapeutic targets of Gastrodiae Rhizoma, Lycii Fructus, and Ziziphi Spinosae Semen were acquired from TCMSP, HERB, and ETCM databases. Active components were identified using ADME criteria, while the primary targets associated with sedation and mental tranquillity were obtained from GENECARDS, OMIM, and DRUGBANK databases. A protein-protein interaction (PPI) network analysis was conducted using the STRING platform to investigate potential functional protein modules by the network. The METASCAPE platform was employed for the study of the "component-target" and its associated biological processes and pathways. Subsequently, the "component-target" network was constructed using Cytoscape 3.9.1 software. Finally, the validation of molecular docking was conducted through AUTODOCK. The findings revealed that Quercetin, Atropine, Dauricine, (S)-Coclaurine, and other active ingredients were identified as the core constituents of Gastrodiae Rhizoma, Lycii Fructus, and Ziziphi Spinosae Semen. Additionally, PTGS2, PTGS1, MAOB, GABRA1, SLC6A2, ADRB2, CHRM1, HTR2A, and other targets were identified as the core targets. The results of the molecular docking analysis demonstrated that Quercetin, Atropine, Dauricine, and (S)-Coclaurine exhibited binding solid affinity towards PTGS2 and PTGS1. The predominant biological pathways associated with sedation and tranquilisation primarily involved Neuroactive ligand-receptor interaction and activation of receptors involved in chemical carcinogenesis. This study provided initial findings on the multi-component, multi-target, and multi-pathway mechanism underlying the sedative and tranquillising effects of Gastrodiae Rhizoma, Lycii Fructus, and Ziziphi Spinosae Semen. These findings had the potential to serve as a foundation for the future development and utilisation of Gastrodiae Rhizoma, Lycii Fructus, and Ziziphi Spinosae Semen.
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Affiliation(s)
- Chenghao Zhu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Zhengru Zhang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Shangtao Wang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Zhirong Sun
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, China.
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Najafzadeh M, Naeem P, Ghaderi N, Jafarinejad S, Karimi Z, Ghaderi M, Akhbari P, Ghaderi R, Farsi P, Wright A, Anderson D. Comparing P53 expression and genome-wide transcriptome profiling to Comet assay in lymphocytes from melanoma patients and healthy controls. Sci Rep 2023; 13:18858. [PMID: 37914759 PMCID: PMC10620420 DOI: 10.1038/s41598-023-44965-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 10/13/2023] [Indexed: 11/03/2023] Open
Abstract
This study compared the expression of TP53 in lymphocytes from malignant melanoma (MM) patients with positive sentinel nodes to healthy controls (HCs) following exposure to various doses of UVA radiation. The Lymphocyte Genome Sensitivity (LGS) assay indicated significant differences in DNA damage in lymphocytes between MM patients and HCs. qPCR data demonstrated an overall 3.4-fold increase in TP53 expression in lymphocytes from MM patients compared to healthy controls, following treatment with 0.5 mW/cm2 UVA radiation. Western blotting confirmed that p53 expression was increased in MM lymphocytes following UVA exposure compared to healthy individuals. Genome transcriptome profiling data displayed differences in gene expression between UVA-treated lymphocytes from MM patients and HCs. Peripheral lymphocytes from MM patients are more susceptible to the genotoxic effects of UVA compared to healthy individuals. Our previous studies showed that UVA exposure of various intensities caused significant differences in the levels of DNA damage between lymphocytes from cancer patients compared to HCs through the LGS assay. The present study's results provide further credibility to the LGS assay as a screening test for cancer detection. Peripheral lymphocytes could be a promising blood biopsy biomarker for staging of carcinomas and prevention of carcinoma progression at early stages.
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Affiliation(s)
- Mojgan Najafzadeh
- School of Life Sciences, University of Bradford, Richmond Road, Bradford, BD7 1DP, West Yorkshire, UK.
| | - Parisa Naeem
- School of Life Sciences, University of Bradford, Richmond Road, Bradford, BD7 1DP, West Yorkshire, UK
| | - Nader Ghaderi
- Bradford Teaching Hospitals NHS Foundation Trust, St Luke's Hospital, Little Horton Lane, BD5 0NA, UK
| | - Shohreh Jafarinejad
- School of Life Sciences, University of Bradford, Richmond Road, Bradford, BD7 1DP, West Yorkshire, UK
| | - Zahra Karimi
- School of Life Sciences, University of Bradford, Richmond Road, Bradford, BD7 1DP, West Yorkshire, UK
| | - Mehran Ghaderi
- Division of Pathology F46, Department of Laboratory Medicine, Karolinska Institute, Karolinska University Hospital, Huddinge, 141 86, Stockholm, Sweden
| | - Pouria Akhbari
- Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter, Exeter, EX2 5DW, UK
| | - Rojan Ghaderi
- Department of Medicine, Imperial College London, London, SW7 2BX, UK
| | - Pedram Farsi
- Department of Clinical Pathology and Cytology, Karolinska University Hospital, 141 86, Stockholm, Sweden
| | - Andrew Wright
- Bradford Teaching Hospitals NHS Foundation Trust, St Luke's Hospital, Little Horton Lane, BD5 0NA, UK
| | - Diana Anderson
- School of Life Sciences, University of Bradford, Richmond Road, Bradford, BD7 1DP, West Yorkshire, UK
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Mirza Z, Al-Saedi DA, Saddeek S, Almowallad S, AlMassabi RF, Huwait E. Atheroprotective Effect of Fucoidan in THP-1 Macrophages by Potential Upregulation of ABCA1. Biomedicines 2023; 11:2929. [PMID: 38001931 PMCID: PMC10669811 DOI: 10.3390/biomedicines11112929] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 10/23/2023] [Accepted: 10/28/2023] [Indexed: 11/26/2023] Open
Abstract
Targeting foam cells reduces the risk and pathophysiology of atherosclerosis, of which they are one of its early hallmarks. The precise mechanism of action of fucoidan, a potential anti-atherogenic drug, is still unknown. Our objective was to assess the ability of fucoidan to regulate expression of ATP-binding cassette transporter A1 (ABCA1) in ox-LDL-induced THP-1 macrophages. Molecular docking was used to predict how fucoidan interacts with anti-foam cell markers, and further in vitro experiments were performed to evaluate the protective effect of fucoidan on modulating uptake and efflux of lipids. THP-1 macrophages were protected by 50 µg/mL of fucoidan and were then induced to form foam cells with 25 µg/mL of ox-LDL. Expression levels were assessed using RT-qPCR, and an Oil Red O stain was used to observe lipid accumulation in THP-1 macrophages. In addition, ABCA1 protein was examined by Western blot, and cellular cholesterol efflux was determined using fluorescently labeled cholesterol. Under a light microscope, decreased lipid accumulation in ox-LDL-induced-THP-1 macrophages pre-treated with fucoidan showed a significant effect, although it did not affect the expression of scavenger receptors (SR-AI and CD36). It is interesting to note that fucoidan dramatically increased the gene and protein expression of ABCA1, perhaps via the liver X receptor-α (LXR-α). Moreover, fucoidan's ability to increase and control the efflux of cholesterol from ox-LDL-induced THP-1 macrophages revealed how it may alter ABCA1's conformation and have a major effect on how it interacts with apolipoprotein A (ApoA1). In vitro results support a rationale for predicting fucoidan and its interaction with its receptor targets' predicted data, hence validating its anti-atherogenic properties and suggesting that fucoidan could be promising as an atheroprotective.
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Affiliation(s)
- Zeenat Mirza
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Dalal A. Al-Saedi
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Cell Culture Lab, Experimental Biochemistry Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Salma Saddeek
- Department of Chemistry, Faculty of Sciences, University of Hafr Al Batin, Hafr Al Batin 39511, Saudi Arabia;
| | - Sanaa Almowallad
- Department of Biochemistry, Faculty of Sciences, University of Tabuk, Tabuk 48322, Saudi Arabia (R.F.A.)
| | - Rehab F. AlMassabi
- Department of Biochemistry, Faculty of Sciences, University of Tabuk, Tabuk 48322, Saudi Arabia (R.F.A.)
| | - Etimad Huwait
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Cell Culture Lab, Experimental Biochemistry Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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19
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Li T, Li W, Guo X, Tan T, Xiang C, Ouyang Z. Unraveling the potential mechanisms of the anti-osteoporotic effects of the Achyranthes bidentata-Dipsacus asper herb pair: a network pharmacology and experimental study. Front Pharmacol 2023; 14:1242194. [PMID: 37849727 PMCID: PMC10577322 DOI: 10.3389/fphar.2023.1242194] [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: 06/18/2023] [Accepted: 09/07/2023] [Indexed: 10/19/2023] Open
Abstract
Background: Osteoporosis is a prevalent bone metabolism disease characterized by a reduction in bone density, leading to several complications that significantly affect patients' quality of life. The Achyranthes bidentata-Dipsacus asper (AB-DA) herb pair is commonly used in Traditional Chinese Medicine (TCM) to treat osteoporosis. This study aimed to investigate the therapeutic compounds and potential mechanisms of AB-DA using network pharmacology, molecular docking, molecular dynamics simulation, and experimental verification. Methods: Identified compounds of AB-DA were collected from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP), Traditional Chinese Medicine Information Database (TCM-ID), TCM@Taiwan Database, BATMAN-TCM, and relevant literature. The main bioactive ingredients were screened based on the criteria of "OB (oral bioavailability) ≥ 30, DL (drug-likeness) ≥ 0.18." Potential targets were predicted using the PharmMapper and SwissTargetPrediction websites, while disease (osteoporosis)-related targets were obtained from the GeneCards, DisGeNET, and OMIM databases. The PPI network and KEGG/GO enrichment analysis were utilized for core targets and pathway screening in the STRING and Metascape databases, respectively. A drug-compound-target-pathway-disease network was constructed using Cytoscape software to display core regulatory mechanisms. Molecular docking and dynamics simulation techniques explored the binding reliability and stability between core compounds and targets. In vitro and in vivo validation experiments were utilized to explore the anti-osteoporosis efficiency and mechanism of sitogluside. Results: A total of 31 compounds with 83 potential targets for AB-DA against osteoporosis were obtained. The PPI analysis revealed several hub targets, including AKT1, CASP3, EGFR, IGF1, MAPK1, MAPK8, and MAPK14. GO/KEGG analysis indicated that the MAPK cascade (ERK/JNK/p38) is the main pathway involved in treating osteoporosis. The D-C-T-P-T network demonstrated therapeutic compounds that mainly consisted of iridoids, steroids, and flavonoids, such as sitogluside, loganic acid, and β-ecdysterone. Molecular docking and dynamics simulation analyses confirmed strong binding affinity and stability between core compounds and targets. Additionally, the validation experiments showed preliminary evidence of antiosteoporosis effects. Conclusion: This study identified iridoids, steroids, and flavonoids as the main therapeutic compounds of AB-DA in treating osteoporosis. The underlying mechanisms may involve targeting core MAPK cascade (ERK/JNK/p38) targets, such as MAPK1, MAPK8, and MAPK14. In vivo experiments preliminarily validated the anti-osteoporosis effect of sitogluside. Further in-depth experimental studies are required to validate the therapeutic value of AB-DA for treating osteoporosis in clinical practice.
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Affiliation(s)
- Tao Li
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Wenzhao Li
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xiaoning Guo
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Tingting Tan
- Department of Immunology, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Cheng Xiang
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhengxiao Ouyang
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
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20
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He Z, Gu Y, Yang H, Fu Q, Zhao M, Xie Y, Liu Y, Du W. Identification and verification of a novel anoikis-related gene signature with prognostic significance in clear cell renal cell carcinoma. J Cancer Res Clin Oncol 2023; 149:11661-11678. [PMID: 37402968 DOI: 10.1007/s00432-023-05012-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 06/19/2023] [Indexed: 07/06/2023]
Abstract
PURPOSE Clear cell renal cell carcinomas (ccRCCs) are the most common form of renal cancer in the world. The loss of extracellular matrix (ECM) stimulates cell apoptosis, known as anoikis. A resistance to anoikis in cancer cells is believed to contribute to tumor malignancy, particularly metastasis; however, the potential influence of anoikis on the prognosis of ccRCC patients is not fully understood. METHODS In this study, anoikis-related genes (ARGs) with discrepant expression were selected from the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. The anoikis-related gene signature (ARS) was built using a combination of the univariate Cox and least absolute shrinkage and selection operator (LASSO) analyses. ARS was also evaluated for their prognostic value. We explored the tumor microenvironment and enrichment pathways between different clusters of ccRCC. We also examined differences in clinical characteristics, immune cell infiltration and drug sensitivity between the high- and low-risk sets. In addition, we utilized three external databases and quantitative real-time polymerase chain reaction (qRT-PCR) to validate the expression and prognosis of ARGs. RESULTS Eight ARGs (PLAUR, HMCN1, CDKN2A, BID, GLI2, PLG, PRKCQ and IRF6) were identified as anoikis-related prognostic factors. According to Kaplan-Meier (KM) analysis, ccRCC patients with high-risk ARGs have a worse prognosis. The risk score was found to be a significant independent prognostic indicator. According to tumor microenvironment (TME) scores, stromal score, immune score, and estimated score of the high-risk group were superior to those of the low-risk group. There were significant differences between the two groups regarding the amount of infiltrated immune cells, immune checkpoint expression as well as drug sensitivity. A nomogram was constructed using ccRCC clinical features and risk scores. The signature and the nomogram both performed well in predicting overall survival (OS) for ccRCC patients. According to a decision curve analysis (DCA), clinical treatment options for patients with ccRCC could be improved using this model. CONCLUSION The results of validation from external databases and qRT-PCR were basically agreement with findings in TCGA and GEO databases. The ARS serving as biomarkers may provide an important reference for individual therapy of ccRCC patients.
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Affiliation(s)
- Zhiqiang He
- Department of Bioinformatics, School of Life Sciences, Xuzhou Medical University, No. 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China
- Department of Biophysics, School of Life Sciences, Xuzhou Medical University, No. 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China
| | - Yufan Gu
- Department of Bioinformatics, School of Life Sciences, Xuzhou Medical University, No. 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China
- Department of Biophysics, School of Life Sciences, Xuzhou Medical University, No. 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China
| | - Huan Yang
- Department of Bioinformatics, School of Life Sciences, Xuzhou Medical University, No. 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China
- Department of Biophysics, School of Life Sciences, Xuzhou Medical University, No. 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China
| | - Qian Fu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, No. 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China
| | - Maofang Zhao
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, No. 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China
| | - Yuhan Xie
- Department of Bioinformatics, School of Life Sciences, Xuzhou Medical University, No. 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China
- Department of Biophysics, School of Life Sciences, Xuzhou Medical University, No. 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China
| | - Yi Liu
- Department of Bioinformatics, School of Life Sciences, Xuzhou Medical University, No. 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China.
- Department of Biophysics, School of Life Sciences, Xuzhou Medical University, No. 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China.
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, No. 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China.
| | - Wenlong Du
- Department of Bioinformatics, School of Life Sciences, Xuzhou Medical University, No. 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China.
- Department of Biophysics, School of Life Sciences, Xuzhou Medical University, No. 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China.
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21
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Wang L, Li Z, Lu T, Su L, Mao C, Zhang Y, Zhang X, Jiang X, Xie H, Yu X. The potential mechanism of Choulingdan mixture in improving acute lung injury based on HPLC-Q-TOF-MS, network pharmacology and in vivo experiments. Biomed Chromatogr 2023; 37:e5709. [PMID: 37533317 DOI: 10.1002/bmc.5709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 06/29/2023] [Accepted: 07/07/2023] [Indexed: 08/04/2023]
Abstract
Choulingdan mixture (CLDM) is an empirical clinical prescription for the adjuvant treatment of acute lung injury (ALI). CLDM has been used for almost 30 years in the clinic. However, its mechanism for improving ALI still needs to be investigated. In this study, high-performance liquid chromatography-quadrupole/time-of-flight mass spectrometry (HPLC-Q-TOF-MS/MS) was applied to characterize the overall chemical composition of CLDM. A total of 93 ingredients were characterized, including 25 flavonoids, 20 organic acids, 11 saponins, nine terpenoids, seven tannins and 21 other compounds. Then network pharmacology was applied to predict the potential bioactive components, target genes and signaling pathways of CLDM in improving ALI. Additionally, molecular docking was performed to demonstrate the interaction between the active ingredients and the disease targets. Finally, animal experiments further confirmed that CLDM significantly inhibits pulmonary inflammation, pulmonary edema and oxidative stress in lipopolysaccharide-induced ALI mice by inhibiting the PI3K-AKT signaling pathway. This study enhanced the amount and accuracy of compounds of CLDM and provided new insights into CLDM preventing and treating ALI.
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Affiliation(s)
- Lili Wang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Zhengyan Li
- Department of Pharmacy, Kunming Municipal Hospital of Traditional Chinese Medicine, Kunming, China
| | - Tulin Lu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Lianlin Su
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Chunqin Mao
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yiting Zhang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Xinrui Zhang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Xiaofeng Jiang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Hui Xie
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Xiaoling Yu
- Department of Pharmacy, Kunming Municipal Hospital of Traditional Chinese Medicine, Kunming, China
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22
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Hu J, Feng Y, Li B, Wang F, Qian Q, Tian W, Niu L, Wang X. Identification of quality markers for Cyanotis arachnoidea and analysis of its physiological mechanism based on chemical pattern recognition, network pharmacology, and experimental validation. PeerJ 2023; 11:e15948. [PMID: 37719108 PMCID: PMC10501370 DOI: 10.7717/peerj.15948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 08/01/2023] [Indexed: 09/19/2023] Open
Abstract
Cyanotis arachnoidea C. B. Clarke is a traditional Chinese medicinal herb that has a limited clinical use in the treatment of diabetes mellitus (DM) in minority areas of Guizhou in China. However, few prior reports are available on the quality control of Cyanotis arachnoidea, and its quality markers and hypoglycemic mechanism are still unclear. The purpose of this study is to explore the quality markers (Q-markers) of Cyanotis arachnoidea and predict its hypoglycemic mechanism. In this study, ultra-high-performance liquid chromatography (UHPLC) fingerprint combined with chemical pattern recognition were performed, and four differential components were screened out as quality markers, including 20-Hydroxyecdysone, 3-O-acetyl-20-hydroxyecdysone, Ajugasterone C, and 2-O-acetyl-20-hydroxyecdysone. Network pharmacology analysis revealed 107 therapeutic target genes of Cyanotis arachnoidea in DM treatment, and the key targets were Akt1, TNF, IL-6, MAPK3, and JUN. The hypoglycemic mode of action of Cyanotis arachnoidea may be mediated by tumor necrosis factor (TNF) signaling, cancer, insulin resistance, and JAK-STAT pathways. Molecular docking analysis disclosed that the foregoing quality markers effectively bound their key target genes. An in vitro experiment conducted on pancreatic islet β-cells indicated that the forenamed active components of Cyanotis arachnoidea had hypoglycemic efficacy by promoting PI3K/Akt and inhibiting MAPK signaling. UHPLC also accurately quantified the quality markers. The identification and analysis of quality markers for Cyanotis arachnoidea is expected to provide references for the establishment of a quality control evaluation system and clarify the material basis and hypoglycemic mechanisms of this traditional Chinese medicine (TCM).
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Affiliation(s)
- Jingnan Hu
- Hebei University of Chinese Medicine, Shijiazhuang, China
| | - Yu Feng
- Hebei University of Chinese Medicine, Shijiazhuang, China
| | - Baolin Li
- Hebei University of Chinese Medicine, Shijiazhuang, China
| | - Fengxia Wang
- Hebei University of Chinese Medicine, Shijiazhuang, China
| | - Qi Qian
- Hebei University of Chinese Medicine, Shijiazhuang, China
- Hebei Traditional Chinese Medicine Formula Granule Engineering & Technology Innovate Center, Shijiazhuang, China
- Quality Evaluation & Standardization Hebei Province Engineering Research Center of Traditional Chinese Medicine, Shijiazhuang, China
| | - Wei Tian
- Hebei University of Chinese Medicine, Shijiazhuang, China
- Hebei Traditional Chinese Medicine Formula Granule Engineering & Technology Innovate Center, Shijiazhuang, China
- Quality Evaluation & Standardization Hebei Province Engineering Research Center of Traditional Chinese Medicine, Shijiazhuang, China
| | - Liying Niu
- Hebei University of Chinese Medicine, Shijiazhuang, China
- Hebei Traditional Chinese Medicine Formula Granule Engineering & Technology Innovate Center, Shijiazhuang, China
- Quality Evaluation & Standardization Hebei Province Engineering Research Center of Traditional Chinese Medicine, Shijiazhuang, China
| | - Xinguo Wang
- Hebei University of Chinese Medicine, Shijiazhuang, China
- Hebei Traditional Chinese Medicine Formula Granule Engineering & Technology Innovate Center, Shijiazhuang, China
- Quality Evaluation & Standardization Hebei Province Engineering Research Center of Traditional Chinese Medicine, Shijiazhuang, China
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23
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Green JR, Mahalingaiah PKS, Gopalakrishnan SM, Liguori MJ, Mittelstadt SW, Blomme EAG, Van Vleet TR. Off-target pharmacological activity at various kinases: Potential functional and pathological side effects. J Pharmacol Toxicol Methods 2023; 123:107468. [PMID: 37553032 DOI: 10.1016/j.vascn.2023.107468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/16/2023] [Accepted: 08/01/2023] [Indexed: 08/10/2023]
Abstract
In drug discovery, during the lead optimization and candidate characterization stages, novel small molecules are frequently evaluated in a battery of in vitro pharmacology assays to identify potential unintended, off-target interactions with various receptors, transporters, ion channels, and enzymes, including kinases. Furthermore, these screening panels may also provide utility at later stages of development to provide a mechanistic understanding of unexpected safety findings. Here, we present a compendium of the most likely functional and pathological outcomes associated with interaction(s) to a panel of 95 kinases based on an extensive curation of the scientific literature. This panel of kinases was designed by AbbVie based on safety-related data extracted from the literature, as well as from over 20 years of institutional knowledge generated from discovery efforts. For each kinase, the scientific literature was reviewed using online databases and the most often reported functional and pathological effects were summarized. This work should serve as a practical guide for small molecule drug discovery scientists and clinical investigators to predict and/or interpret adverse effects related to pharmacological interactions with these kinases.
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Affiliation(s)
- Jonathon R Green
- Departments of Preclinical Safety, AbbVie, 1 North Waukegan Road, North Chicago, IL 60064, United States.
| | | | - Sujatha M Gopalakrishnan
- Drug Discovery Science and Technology, AbbVie, 1 North Waukegan Road, North Chicago, IL 60064, United States
| | - Michael J Liguori
- Departments of Preclinical Safety, AbbVie, 1 North Waukegan Road, North Chicago, IL 60064, United States
| | - Scott W Mittelstadt
- Departments of Preclinical Safety, AbbVie, 1 North Waukegan Road, North Chicago, IL 60064, United States
| | - Eric A G Blomme
- Departments of Preclinical Safety, AbbVie, 1 North Waukegan Road, North Chicago, IL 60064, United States
| | - Terry R Van Vleet
- Departments of Preclinical Safety, AbbVie, 1 North Waukegan Road, North Chicago, IL 60064, United States
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24
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Triantaphyllopoulos KA. Long Non-Coding RNAs and Their "Discrete" Contribution to IBD and Johne's Disease-What Stands out in the Current Picture? A Comprehensive Review. Int J Mol Sci 2023; 24:13566. [PMID: 37686376 PMCID: PMC10487966 DOI: 10.3390/ijms241713566] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/23/2023] [Accepted: 08/27/2023] [Indexed: 09/10/2023] Open
Abstract
Non-coding RNAs (ncRNA) have paved the way to new perspectives on the regulation of gene expression, not only in biology and medicine, but also in associated fields and technologies, ensuring advances in diagnostic means and therapeutic modalities. Critical in this multistep approach are the associations of long non-coding RNA (lncRNA) with diseases and their causal genes in their networks of interactions, gene enrichment and expression analysis, associated pathways, the monitoring of the involved genes and their functional roles during disease progression from one stage to another. Studies have shown that Johne's Disease (JD), caused by Mycobacterium avium subspecies partuberculosis (MAP), shares common lncRNAs, clinical findings, and other molecular entities with Crohn's Disease (CD). This has been a subject of vigorous investigation owing to the zoonotic nature of this condition, although results are still inconclusive. In this review, on one hand, the current knowledge of lncRNAs in cells is presented, focusing on the pathogenesis of gastrointestinal-related pathologies and MAP-related infections and, on the other hand, we attempt to dissect the associated genes and pathways involved. Furthermore, the recently characterized and novel lncRNAs share common pathologies with IBD and JD, including the expression, molecular networks, and dataset analysis results. These are also presented in an attempt to identify potential biomarkers pertinent to cattle and human disease phenotypes.
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Affiliation(s)
- Kostas A Triantaphyllopoulos
- Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos St., 11855 Athens, Greece
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25
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Wang N, Li Q. Simultaneous Extraction and Analysis of Seven Major Saikosaponins from Bupleuri Radix and the Exploration of Antioxidant Activity and Its Mechanism. Molecules 2023; 28:5872. [PMID: 37570843 PMCID: PMC10420870 DOI: 10.3390/molecules28155872] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 07/24/2023] [Accepted: 08/02/2023] [Indexed: 08/13/2023] Open
Abstract
Saikosaponins (SS) are the main active components of Bupleuri Radix. In this study, the yields of SS a, b1, b2, c, d, e, and f were simultaneously determined using the HPLC-DAD dual wavelength method, and the ultrasound-assisted extraction process of saikosaponins was optimized using the response surface methodology. The antioxidant effect of saikosaponins was investigated using the scavenging rate of 1, 1-diphenyl-2-picrylhydrazyl (DPPH), 2, 2-diazo-bis (3-ethyl-benzothiazole-6-sulfonic acid) diammonium salt (ABTS), and hydroxyl (-OH) groups, and the mechanism was clarified via network pharmacological analysis. The results showed that the optimal extraction process of SS was a 5% ammonia-methanol solution as an extraction solvent, a material-liquid ratio of 1:40, a temperature of 46.66 °C, an extraction time of 65.07 min, and an ultrasonic power of 345.56 W. The total content of the seven saikosaponins under this condition was up to 6.32%, which was close to the model's predicted value of 6.56%, where the yields of the seven saikosaponins a, b1, b2, c, d, e, and f were 1.18%, 0.11%, 0.26%, 1.02%, 3.02%, 0.38%, and 0.44%, respectively. The saikosaponins have an obvious scavenging ability for DPPH, ABTS, and -OH radicals. The interactions of seven saikosaponins with antioxidant targets were studied, and a database was used to collate the core of saikosaponins and antioxidants through network pharmacology. The mechanisms of the antioxidant effects of the saikosaponins were derived via GO enrichment analysis and KEGG pathway analysis. Finally, the binding energy of the saikosaponins to the antioxidant targets was found to be less than -5.0 kcal·mol-1 via molecular docking, indicating that the antioxidant capacity of the saikosaponins are good. Therefore, this study developed a rapid and efficient method for the extraction of saikosaponins, which provides a theoretical basis for an in-depth understanding of the rational utilization of saikosaponins and the development of their medicinal value.
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Affiliation(s)
| | - Qian Li
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China;
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Larson J, Ozen MO, Kohli M, Akin D, Demirci U. Systematic Analysis of Tissue-Derived and Biofluid Extracellular Vesicle miRNAs Associated with Prostate Cancer. Adv Biol (Weinh) 2023:e2200327. [PMID: 37300338 DOI: 10.1002/adbi.202200327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 04/15/2023] [Indexed: 06/12/2023]
Abstract
Extracellular vesicles (EVs) are emerging as biomarker candidates for early detection of prostate cancer. Studies compare EV-microRNA (miRNA) expression in individuals with prostate cancer (PCa) with cancer-free samples for diagnostic purposes. The aim of this study is to review miRNA signatures to investigate the overlap between miRNAs enriched in PCa tissue and miRNAs enriched in EVs isolated from subjects with PCa biofluids (i.e., urine, serum, and plasma). Signatures dysregulated in EVs from PCa biofluids and tissue are potentially associated with the primary tumor site and might be more indicative of PCa at an early stage. A systematic review of EV-derived miRNAs and a reanalysis of PCa tissue miRNA sequencing data for comparison is presented. Articles in the literature are screened for validated miRNA dysregulation in PCa and compared with TCGA primary PCa tumor data using DESeq2. This resulted in 190 dysregulated miRNAs being identified. Thirty-one eligible studies are identified, indicating 39 dysregulated EV-derived miRNAs. The top ten markers identified as significantly dysregulated in the PCa tissue dataset TCGA (e.g., miR-30b-3p, miR-210-3p, miR-126-3p, and miR-196a-5p) have a significant expression change in EVs with the same directionality in one or several statistically significant results. This analysis highlights several less frequently studied miRNAs in PCa literature.
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Affiliation(s)
- Jeevan Larson
- Department of Radiology, Canary Center for Cancer Early Detection, Bioacoustic MEMS in Medicine (BAMM) Labs, Stanford University, 94305, Stanford, USA
| | - Mehmet Ozgun Ozen
- Department of Radiology, Canary Center for Cancer Early Detection, Bioacoustic MEMS in Medicine (BAMM) Labs, Stanford University, 94305, Stanford, USA
| | - Manish Kohli
- Huntsman Cancer Institute, University of Utah, 84112, Salt Lake City, USA
| | - Demir Akin
- Department of Radiology, Canary Center for Cancer Early Detection, Bioacoustic MEMS in Medicine (BAMM) Labs, Stanford University, 94305, Stanford, USA
| | - Utkan Demirci
- Department of Radiology, Canary Center for Cancer Early Detection, Bioacoustic MEMS in Medicine (BAMM) Labs, Stanford University, 94305, Stanford, USA
- Department of Electrical Engineering (by courtesy), Stanford University, 94305, Stanford, USA
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Hong Z, Lu Y, Liu B, Ran C, Lei X, Wang M, Wu S, Yang Y, Wu H. Glycolysis, a new mechanism of oleuropein against liver tumor. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023; 114:154770. [PMID: 36963367 DOI: 10.1016/j.phymed.2023.154770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 01/10/2023] [Accepted: 03/13/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Benign and malignant liver tumors are prevalent worldwide. However, there is no effective and comprehensive treatment option for many patients with malignant tumors. Thus, it is critical to prevent benign tumors from worsening, increasing the number of treatment options and effective medications against malignant liver tumors. Oleuropein is a natural and non-toxic product and inhibits tumor growth in various ways. METHODS We employed bioinformatics analysis and molecular docking to identify potential targets of oleuropein. Surface plasmon resonance (SPR) was used to determine the direct binding strength of the target and compounds. Essential functionalities of the targets were analyzed using gene interference approaches. Transcriptomic studies were performed to observe the global genomic alterations occurring inside cells. Changes in glycolytic metabolites and gene and protein expressions were also detected. The anti-tumor benefits of oleuropein in vivo were determined using a tumor-bearing mouse model. RESULTS Glucose-6-phosphate isomerase (GPI) was found to be a direct target of oleuropein. GPI discontinuation in liver tumor cells altered the expression of many genes, causing glycogenolysis. GPI interference was associated with PYGM and PFKFB4 inhibitors to inhibit glycolysis in liver tumors. Oleuropein inhibited glycolysis and showed good anti-tumor activity in vivo without adverse side effects. CONCLUSIONS GPI is a crucial enzyme in glycolysis and the immediate target of oleuropein. GPI expression inside tumor cells affects different physiological functions and signal transduction. Oleuropein has depicted anti-tumor action in vivo without harmful side effects. Moreover, it can control tumor glycolysis through GPI.
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Affiliation(s)
- Zongchao Hong
- Faculty of Pharmacy, Hubei University of Chinese Medicine, No. 16, Huangjiahu West Road, Hongshan District, Wuhan, Hubei 430065, China
| | - Yi Lu
- Faculty of Pharmacy, Hubei University of Chinese Medicine, No. 16, Huangjiahu West Road, Hongshan District, Wuhan, Hubei 430065, China
| | - Bo Liu
- Faculty of Pharmacy, Hubei University of Chinese Medicine, No. 16, Huangjiahu West Road, Hongshan District, Wuhan, Hubei 430065, China
| | - Chongwang Ran
- Faculty of Pharmacy, Hubei University of Chinese Medicine, No. 16, Huangjiahu West Road, Hongshan District, Wuhan, Hubei 430065, China
| | - Xia Lei
- Faculty of Pharmacy, Hubei University of Chinese Medicine, No. 16, Huangjiahu West Road, Hongshan District, Wuhan, Hubei 430065, China
| | - Mengfan Wang
- Faculty of Pharmacy, Hubei University of Chinese Medicine, No. 16, Huangjiahu West Road, Hongshan District, Wuhan, Hubei 430065, China
| | - Songtao Wu
- Faculty of Pharmacy, Hubei University of Chinese Medicine, No. 16, Huangjiahu West Road, Hongshan District, Wuhan, Hubei 430065, China.
| | - Yanfang Yang
- Faculty of Pharmacy, Hubei University of Chinese Medicine, No. 16, Huangjiahu West Road, Hongshan District, Wuhan, Hubei 430065, China; Key Laboratory of Traditional Chinese Medicine Resources and Chemistry of Hubei Province, Wuhan, China.
| | - Hezhen Wu
- Faculty of Pharmacy, Hubei University of Chinese Medicine, No. 16, Huangjiahu West Road, Hongshan District, Wuhan, Hubei 430065, China; Key Laboratory of Traditional Chinese Medicine Resources and Chemistry of Hubei Province, Wuhan, China; Modern Engineering Research Center of Traditional Chinese Medicine and Ethnic Medicine of Hubei Province, Wuhan, 430065, China.
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Wang Y, Yan H, Zhao L, He XL, Bao TRG, Sun XD, Yang YC, Zhu SY, Gao XX, Wang AH, Jia JM. An integrated network pharmacology approach reveals that Darutigenol reduces inflammation and cartilage degradation in a mouse collagen-induced arthritis model by inhibiting the JAK-STAT3 pathway. JOURNAL OF ETHNOPHARMACOLOGY 2023; 314:116574. [PMID: 37160212 DOI: 10.1016/j.jep.2023.116574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 04/27/2023] [Accepted: 05/01/2023] [Indexed: 05/11/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Darutigenol (DL) is a natural active product derived from the Chinese herbal medicine Sigesbeckia glabrescens (Makino) Makino. It is administered as a traditional Chinese medicine (TCM) to dispel rheumatism, benefit the joints, and detoxify. However, its potential mechanism in the treatment of rheumatoid arthritis (RA) remains unknown. AIMS OF THE STUDY The objectives of this research were to determine the effects and elucidate the modes of action of DL on RA-related joint inflammation. MATERIALS AND METHODS Network pharmacology and molecular docking were used to screen and validate candidate DL targets for RA treatment, respectively. A DBA/1 mouse rheumatoid arthritis model was induced with bovine type II collagen. Intragastric DL administration was followed by the calculation of the clinical arthritis index. A section of the ankle joint was excised and stained and the pathological changes in it were observed. Enzyme-linked immunosorbent assays (ELISA) and western blotting (WB) were used to clarify the mechanisms of DL in RA treatment. RESULTS DL effectively attenuated the inflammation, mitigated the articular cartilage degradation, and bone erosion, and alleviated the inflammatory joints associated with RA. Network pharmacology screened six key targets of DL while molecular docking revealed that it docked well with its protein targets. The DL treatment group presented with significantly less ankle joint redness and swelling, a lower arthritis index scores and serum and bone marrow supernatant IL-6 levels, more complete ankle joint surfaces, and less synovial inflammation, cartilage degradation, and bone erosion than the collagen-induced arthritis (CIA) group. The DL treatment also substantially downregulated the Janus kinase (JAK)1, JAK3, matrix metalloproteinase (MMP)2, MMP9, and phospho-signal transducer and activator of transcription (p-STAT)3 proteins in the joints. CONCLUSIONS To the best of our knowledge, the present work was the first to demonstrate that DL has significant anti-inflammatory efficacy and reduces cartilage degradation and bone erosion. It also demonstrated that the anti-RA effect of DL may be explained by its ability to inhibit joint inflammation and reduce articular cartilage degradation through the interleukin (IL)-6/JAK1,3/STAT3 axis and downregulate MMP2 and MMP9. Hence, DL might play a therapeutic role in a mouse RA model.
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Affiliation(s)
- Yong Wang
- Teaching and Research Department of Chinese Materia Medica Resources, College of Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Hui Yan
- Teaching and Research Department of Chinese Materia Medica Resources, College of Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Long Zhao
- Teaching and Research Department of Chinese Materia Medica Resources, College of Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Xue-Lai He
- School of Pharmaceutical Sciences, Hubei University of Medicine, Shiyan, 442000, People's Republic of China; Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Shiyan, 442000, People's Republic of China
| | - Te-Ri-Gen Bao
- Teaching and Research Department of Chinese Materia Medica Resources, College of Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Xian-Duo Sun
- Teaching and Research Department of Chinese Materia Medica Resources, College of Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Yong-Cheng Yang
- Teaching and Research Department of Chinese Materia Medica Resources, College of Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Shu-Yi Zhu
- Teaching and Research Department of Chinese Materia Medica Resources, College of Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Xiao-Xu Gao
- Teaching and Research Department of Chinese Materia Medica Resources, College of Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - An-Hua Wang
- Teaching and Research Department of Chinese Materia Medica Resources, College of Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China.
| | - Jing-Ming Jia
- Teaching and Research Department of Chinese Materia Medica Resources, College of Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China.
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Azarova I, Polonikov A, Klyosova E. Molecular Genetics of Abnormal Redox Homeostasis in Type 2 Diabetes Mellitus. Int J Mol Sci 2023; 24:ijms24054738. [PMID: 36902173 PMCID: PMC10003739 DOI: 10.3390/ijms24054738] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/20/2023] [Accepted: 02/24/2023] [Indexed: 03/05/2023] Open
Abstract
Numerous studies have shown that oxidative stress resulting from an imbalance between the production of free radicals and their neutralization by antioxidant enzymes is one of the major pathological disorders underlying the development and progression of type 2 diabetes (T2D). The present review summarizes the current state of the art advances in understanding the role of abnormal redox homeostasis in the molecular mechanisms of T2D and provides comprehensive information on the characteristics and biological functions of antioxidant and oxidative enzymes, as well as discusses genetic studies conducted so far in order to investigate the contribution of polymorphisms in genes encoding redox state-regulating enzymes to the disease pathogenesis.
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Affiliation(s)
- Iuliia Azarova
- Department of Biological Chemistry, Kursk State Medical University, 3 Karl Marx Street, 305041 Kursk, Russia
- Laboratory of Biochemical Genetics and Metabolomics, Research Institute for Genetic and Molecular Epidemiology, Kursk State Medical University, 18 Yamskaya Street, 305041 Kursk, Russia
| | - Alexey Polonikov
- Laboratory of Statistical Genetics and Bioinformatics, Research Institute for Genetic and Molecular Epidemiology, Kursk State Medical University, 18 Yamskaya Street, 305041 Kursk, Russia
- Department of Biology, Medical Genetics and Ecology, Kursk State Medical University, 3 Karl Marx Street, 305041 Kursk, Russia
- Correspondence:
| | - Elena Klyosova
- Laboratory of Biochemical Genetics and Metabolomics, Research Institute for Genetic and Molecular Epidemiology, Kursk State Medical University, 18 Yamskaya Street, 305041 Kursk, Russia
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Eldosoky MA, Hammad R, Elmadbouly AA, Aglan RB, Abdel-Hamid SG, Alboraie M, Hassan DA, Shaheen MA, Rushdi A, Ahmed RM, Abdelbadea A, Abdelmageed NA, Elshafei A, Ali E, Abo-Elkheir OI, Zaky S, Hamdy NM, Lambert C. Diagnostic Significance of hsa-miR-21-5p, hsa-miR-192-5p, hsa-miR-155-5p, hsa-miR-199a-5p Panel and Ratios in Hepatocellular Carcinoma on Top of Liver Cirrhosis in HCV-Infected Patients. Int J Mol Sci 2023; 24:ijms24043157. [PMID: 36834570 PMCID: PMC9962339 DOI: 10.3390/ijms24043157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 02/09/2023] Open
Abstract
Early hepatocellular carcinoma (HCC) diagnosis is challenging. Moreover, for patients with alpha-fetoprotein (AFP)-negative HCC, this challenge is augmented. MicroRNAs (miRs) profiles may serve as potential HCC molecular markers. We aimed to assess plasma homo sapiens-(hsa)-miR-21-5p, hsa-miR-155-5p, hsa-miR-192-5p, and hsa-miR-199a-5p-expression levels as a panel of biomarkers for HCC in chronic hepatitis C virus (CHCV) patients with liver cirrhosis (LC), especially AFP-negative HCC cases, as a step toward non-protein coding (nc) RNA precision medicine. SUBJECTS AND METHODS 79 patients enrolled with CHCV infection with LC, subclassified into an LC group without HCC (n = 40) and LC with HCC (n = 39). Real-time quantitative PCR was used to measure plasma hsa-miR-21-5p, hsa-miR-155-5p, hsa-miR-192-5p, and hsa-miR-199a-5p. RESULTS Plasma hsa-miR-21-5p and hsa-miR-155-5p demonstrated significant upregulation, while hsa-miR-199a-5p demonstrated significant downregulation in the HCC group (n = 39) when compared to the LC group (n = 40). hsa-miR-21-5p expression was positively correlated with serum AFP, insulin, and insulin resistance (r = 0.5, p < 0.001, r = 0.334, p = 0.01, and r = 0.303, p = 0.02, respectively). According to the ROC curves, for differentiating HCC from LC, combining AFP with each of hsa-miR-21-5p, hsa-miR-155-5p, and miR199a-5p improved the diagnostic sensitivity to 87%, 82%, and 84%, respectively, vs. 69% for AFP alone, with acceptable specificities of 77.5%, 77.5%, and 80%, respectively, and AUC = 0.89, 0.85, and 0.90, respectively vs. 0.85 for AFP alone. hsa-miR-21-5p/hsa-miR-199a-5p and hsa-miR-155-5p/hsa-miR-199a-5p ratios discriminated HCC from LC at AUC = 0.76 and 0.71, respectively, with sensitivities = 94% and 92% and specificities = 48% and 53%, respectively. Upregulation of plasma hsa-miR-21-5p was considered as an independent risk factor for HCC development [OR = 1.198(1.063-1.329), p = 0.002]. CONCLUSIONS Combining each of hsa-miR-21-5p, hsa-miR-155-5p, and hsa-miR-199a-5p with AFP made it possible to identify HCC development in the LC patients' cohort with higher sensitivity than using AFP alone. hsa-miR-21-5p/hsa-miR-199a-5p and hsa-miR-155-5p/hsa-miR-199a-5p ratios are potential HCC molecular markers for AFP-negative HCC patients. hsa-miR-21-5p was linked, clinically and via in silico proof, to insulin metabolism, inflammation, dyslipidemia, and tumorigenesis in the HCC patients' group as well as for an upregulated independent risk factor for the emergence of HCC from LC in the CHCV patients.
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Affiliation(s)
- Mona A. Eldosoky
- Clinical Pathology Department, Faculty of Medicine (for Girls), Al-Azhar University, Nasr City 11884, Egypt
| | - Reham Hammad
- Clinical Pathology Department, Faculty of Medicine (for Girls), Al-Azhar University, Nasr City 11884, Egypt
| | - Asmaa A. Elmadbouly
- Clinical Pathology Department, Faculty of Medicine (for Girls), Al-Azhar University, Nasr City 11884, Egypt
| | - Reda Badr Aglan
- Hepatology and Gastroenterology Department, National Liver Institute, Menoufia University, Shibin El-Kom 32514, Egypt
| | | | - Mohamed Alboraie
- Department of Internal Medicine, Al-Azhar University, Cairo 11884, Egypt
| | - Donia Ahmed Hassan
- Clinical Pathology Department, Faculty of Medicine (for Girls), Al-Azhar University, Nasr City 11884, Egypt
| | - Mohamed A. Shaheen
- Clinical Pathology Department, Faculty of Medicine (for Boys), Al-Azhar University, Cairo 11884, Egypt
| | - Areej Rushdi
- Microbiology and Immunology Department, Faculty of Medicine for Girls, Al-Azhar University, Cairo 11884, Egypt
| | - Reem M. Ahmed
- Medical Biochemistry and Molecular Biology, Faculty of Medicine for Girls, Al-Azhar University, Cairo 11884, Egypt
| | - Alzahra Abdelbadea
- Medical Biochemistry and Molecular Biology, Faculty of Medicine for Girls, Al-Azhar University, Cairo 11884, Egypt
| | - Neamat A. Abdelmageed
- Hepatology, Gastroenterology and Infectious Diseases Department, Faculty of Medicine (for Girls), Al-Azhar University, Cairo 11884, Egypt
| | - Ahmed Elshafei
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt
| | - Elham Ali
- Molecular Biology, Zoology and Entomology Department, Faculty of Science (for Girls), Al-Azhar University, Cairo 11884, Egypt
| | - Omaima I. Abo-Elkheir
- Community Medicine and Public Health, Faculty of Medicine, Al-Azhar University, Cairo 11884, Egypt
| | - Samy Zaky
- Hepatology, Gastroenterology and Infectious Diseases Department, Faculty of Medicine (for Girls), Al-Azhar University, Cairo 11884, Egypt
| | - Nadia M. Hamdy
- Biochemistry Department, Faculty of Pharmacy, Ain Shams University, Cairo 11566, Egypt
- Correspondence:
| | - Claude Lambert
- Cytometry Unit, Immunology Laboratory, Saint-Etienne University Hospital, 42100 Saint-Etienne, France
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Vijh D, Imam MA, Haque MMU, Das S, Islam A, Malik MZ. Network pharmacology and bioinformatics approach reveals the therapeutic mechanism of action of curcumin in Alzheimer disease. Metab Brain Dis 2023; 38:1205-1220. [PMID: 36652025 DOI: 10.1007/s11011-023-01160-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 01/04/2023] [Indexed: 01/19/2023]
Abstract
Curcumin is a natural anti-inflammatory and antioxidant substance which plays a major role in reducing the amyloid plaques formation, which is the major cause of Alzheimer's disease (AD). Consequently, a methodical approach was used to select the potential protein targets of curcumin in AD through network pharmacology. In this study, through integrative methods, AD targets of curcumin through SwissTargetPrediction database, STITCH database, BindingDB, PharmMapper, Therapeutic Target Database (TTD), Online Mendelian Inheritance in Man (OMIM) database were predicted followed by gene enrichment analysis, network construction, network topology, and docking studies. Gene ontology analysis facilitated identification of a list of possible AD targets of curcumin (74 targets genes). The correlation of the obtained targets with AD was analysed by using gene ontology (GO) pathway enrichment analyses and Kyoto Encyclopaedia of Genes and Genomes (KEGG). We have incorporated the applied network pharmacological approach to identify key genes. Furthermore, we have performed molecular docking for analysing the mechanism of curcumin. In order to validate the temporospatial expression of key genes in human central nervous system (CNS), we searched the Human Brain Transcriptome (HBT) dataset. We identified top five key genes namely, PPARγ, MAPK1, STAT3, KDR and APP. Further validated the expression profiling of these key genes in publicly available brain data expression profile databases. In context to a valuable addition in the treatment of AD, this study is concluded with novel insights into the therapeutic mechanisms of curcumin, will ease the treatment of AD with the clinical application of curcumin.
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Affiliation(s)
- Deepanshi Vijh
- Agriculture Plant Biotechnology Lab (ARL-316), University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector 16-C, Dwarka, New Delhi, 110078, India
| | - Md Ali Imam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India
| | | | - Subhajit Das
- National Centre for Cell Science, Pune, Maharashtra, India, 411007
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Md Zubbair Malik
- Department of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India.
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, P.O. Box 1180, 15462, Dasman, Kuwait.
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Network Pharmacology and Molecular Docking Analysis of Shufeiya Recipe in the Treatment of Pulmonary Hypertension. BIOMED RESEARCH INTERNATIONAL 2022; 2022:7864976. [PMID: 36756383 PMCID: PMC9900250 DOI: 10.1155/2022/7864976] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 11/16/2022] [Accepted: 12/05/2022] [Indexed: 12/30/2022]
Abstract
Objective This study is aimed at exploring the molecular mechanism of Shufeiya recipe in the treatment of pulmonary hypertension (PH) using network pharmacology and molecular docking analysis. Methods Active components and their target proteins in the recipe were screened using the TCMSP database. PH-related core proteins were screened using GeneCards, STRING database, and Cytoscape-v3.8.2. Common proteins were obtained by intersection of the target proteins of these recipe active components and pH-related core proteins. Rx64 4.0.2 software was used to perform GO functional enrichment analysis and KEGG pathway enrichment analysis on the common proteins to obtain pathway-enriched proteins, and then core enriched proteins were further screened. We analyzed the relationship between the active components and pathway-enriched proteins using Cytoscape-v3.8.2. AutoDock Vina was used to dock their core proteins into the components. Results Shufeiya recipe contained 67 active components. 61 common proteins of the target proteins of the active components and PH-related core proteins were obtained. The treatment involved both functional and pathway regulations. The core pathway-enriched proteins were prostaglandin G/H synthase 2 (PTGS2), epidermal growth factor receptor (EGFR), and RAC-alpha serine/threonine-protein kinase (AKT1), and their binding energies to the corresponding components were all less than -5 kJ•mol-1. Conclusion It was found that the main mechanism might be the active components acting on the core pathway-enriched proteins to regulate related signaling pathways, thereby playing roles in anticoagulation, vasodilation, anti-PASMC proliferation, promotion of PAECs apoptosis, inhibition of oxidative stress, and anti-inflammatory effects.
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Hydroxysafflor Yellow A Exerts Neuroprotective Effects via HIF-1α/BNIP3 Pathway to Activate Neuronal Autophagy after OGD/R. Cells 2022; 11:cells11233726. [PMID: 36496986 PMCID: PMC9736542 DOI: 10.3390/cells11233726] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/12/2022] [Accepted: 11/19/2022] [Indexed: 11/24/2022] Open
Abstract
In the process of ischemic stroke (IS), cellular macroautophagy/autophagy and apoptosis play a vital role in neuroprotection against it. Therefore, regulating their balance is a potential therapeutic strategy. It has been proved that hydroxysafflor yellow A (HSYA) has anti-inflammatory and antioxidant effects, which can both protect neurons. By exploring bioinformatics combined with network pharmacology, we found that HIF1A and CASP3, key factors regulating autophagy and apoptosis, may be important targets of HSYA for neuroprotection in an oxygen glucose deprivation and reperfusion (OGD/R) model. In this study, we explored a possible new mechanism of HSYA neuroprotection in the OGD/R model. The results showed that OGD/R increased the expression of HIF1A and CASP3 in SH-SY5Y cells and induced autophagy and apoptosis, while HSYA intervention further promoted the expression of HIF1A and inhibited the level of CASP3, accompanied by an increase in autophagy and a decrease in apoptosis in SH-SY5Y cells. The inhibition of HIF1A diminished the activation of autophagy induced with HSYA, while the inhibition of autophagy increased cell apoptosis and blocked the neuroprotective effect of HSYA, suggesting that the neuroprotective effect of HSYA should be mediated by activating the HIF1A/BNIP3 signaling pathway to induce autophagy. These results demonstrate that HSYA may be a promising agent for treating IS.
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Liao Y, Ding Y, Yu L, Xiang C, Yang M. Exploring the mechanism of Alisma orientale for the treatment of pregnancy induced hypertension and potential hepato-nephrotoxicity by using network pharmacology, network toxicology, molecular docking and molecular dynamics simulation. Front Pharmacol 2022; 13:1027112. [PMID: 36457705 PMCID: PMC9705790 DOI: 10.3389/fphar.2022.1027112] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 10/18/2022] [Indexed: 10/28/2023] Open
Abstract
Background: Pregnancy-induced Hypertension (PIH) is a disease that causes serious maternal and fetal morbidity and mortality. Alisma Orientale (AO) has a long history of use as traditional Chinese medicine therapy for PIH. This study explores its potential mechanism and biosafety based on network pharmacology, network toxicology, molecular docking and molecular dynamics simulation. Methods: Compounds of AO were screened in TCMSP, TCM-ID, TCM@Taiwan, BATMAN, TOXNET and CTD database; PharmMapper and SwissTargetPrediction, GeneCards, DisGeNET and OMIM databases were used to predict the targets of AO anti-PIH. The protein-protein interaction analysis and the KEGG/GO enrichment analysis were applied by STRING and Metascape databases, respectively. Then, we constructed the "herb-compound-target-pathway-disease" map in Cytoscape software to show the core regulatory network. Finally, molecular docking and molecular dynamics simulation were applied to analyze binding affinity and reliability. The same procedure was conducted for network toxicology to illustrate the mechanisms of AO hepatotoxicity and nephrotoxicity. Results: 29 compounds with 78 potential targets associated with the therapeutic effect of AO on PIH, 10 compounds with 117 and 111 targets associated with AO induced hepatotoxicity and nephrotoxicity were obtained, respectively. The PPI network analysis showed that core therapeutic targets were IGF, MAPK1, AKT1 and EGFR, while PPARG and TNF were toxicity-related targets. Besides, GO/KEGG enrichment analysis showed that AO might modulate the PI3K-AKT and MAPK pathways in treating PIH and mainly interfere with the lipid and atherosclerosis pathways to induce liver and kidney injury. The "herb-compound-target-pathway-disease" network showed that triterpenoids were the main therapeutic compounds, such as Alisol B 23-Acetate and Alisol C, while emodin was the main toxic compounds. The results of molecular docking and molecular dynamics simulation also showed good binding affinity between core compounds and targets. Conclusion: This research illustrated the mechanism underlying the therapeutic effects of AO against PIH and AO induced hepato-nephrotoxicity. However, further experimental verification is warranted for optimal use of AO during clinical practice.
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Affiliation(s)
- Yilin Liao
- Department of Obstetrics and Gynecology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Yiling Ding
- Department of Obstetrics and Gynecology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Ling Yu
- Department of Obstetrics and Gynecology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Cheng Xiang
- Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Mengyuan Yang
- Department of Obstetrics and Gynecology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
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Du G, Qu X, Hu J, Zhang Y, Cai Y. Identification of Taohong Siwu Decoction in Treating Chronic Glomerulonephritis Using Network Pharmacology and Molecular Docking. Nat Prod Commun 2022; 17:1934578X2211399. [DOI: 10.1177/1934578x221139966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Background: Based on network pharmacology and molecular docking technology, the pharmacological mechanism of Taohong Siwu Decoction (THSWD) in the treatment of chronic glomerulonephritis (CGN) was analyzed to provide a theoretical basis for the subsequent development of new drugs and the clinical application of Traditional Chinese Medicine (TCM). Methods: Active ingredients of drugs and disease target genes were obtained from Traditional Chinese Medicine Database and Analysis Platform (TCMSP) database and GeneCards database. The “drug component target” network of THSWD was constructed using Cytoscape version 3.8.2 software. The protein interaction was analyzed using STRING platform, the protein–protein interaction (PPI) network was constructed, and the potential protein function modules in the network were mined. Metascape platform was used to analyze “drug component target” and its biological processes and pathways. The clusterProfiler R package was called to perform kyoto encyclopedia of genes and genomes (KEGG) pathway and gene ontology (GO) function enrichment analysis on CGN-related targets regulated by THSWD. Molecular docking verification was performed by AutoDock Vina software. Results: THSWD has 205 target genes and 45 active components, 104 of which are cross with the CGN inflammatory gene. Its main active ingredients, stigmasterol, kaempferol, and sitosterol, have positive relationships with the inflammatory targets of CGN, tumor necrosis factor (TNF), IL-6, AKT1, and MAPK14. THSWD modulates the biological pathway of CGN and mainly acts on TNF-α signal pathway, interleukin-17 signal pathway, etc., whose main functions are response to lipid sugar, heme binding, G protein-coupled amine receptor activity, etc. The results of molecular docking showed that the main active compounds could bind to the core targets and showed good affinity. Conclusion: The molecular mechanism of THSWD in the treatment of CGN from the perspective of network pharmacology are components such as beta-sitosterol, kaempferol, and quercetin and key action targets such as TNF, IL-6, AKT1 protein kinase, and MAPK14 protein kinase play a synergistic role in autoimmune, infection, and inflammatory response-related pathways.
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Affiliation(s)
- Guoxia Du
- School of Public Health, Guangdong Pharmaceutical University, Guangzhou, China
| | - Xiaohan Qu
- School of Public Health, Guangdong Pharmaceutical University, Guangzhou, China
| | - Jing Hu
- School of Public Health, Guangdong Pharmaceutical University, Guangzhou, China
| | - Yuzhen Zhang
- College of Medical Information and Engineering,Guangdong Pharmaceutical University, Guangzhou, China
| | - Yongming Cai
- College of Medical Information and Engineering,Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong Provincial Traditional Chinese Medicine Precision Medicine Big Data Engineering Technology Research Center, Guangdong Pharmaceutical University, Guangzhou, China
- Key Specialty of Clinical Pharmacy, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
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Zhang Q, Guo Y, Zhang B, Liu H, Peng Y, Wang D, Zhang D. Identification of hub biomarkers of myocardial infarction by single-cell sequencing, bioinformatics, and machine learning. Front Cardiovasc Med 2022; 9:939972. [PMID: 35958412 PMCID: PMC9357907 DOI: 10.3389/fcvm.2022.939972] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/05/2022] [Indexed: 12/11/2022] Open
Abstract
Background Myocardial infarction (MI) is one of the first cardiovascular diseases endangering human health. Inflammatory response plays a significant role in the pathophysiological process of MI. Messenger RNA (mRNA) has been proven to play a key role in cardiovascular diseases. Single-cell sequencing (SCS) technology is a new technology for high-throughput sequencing analysis of genome, transcriptome, and epigenome at the single-cell level, and it also plays an important role in the diagnosis and treatment of cardiovascular diseases. Machine learning algorithms have a wide scope of utilization in biomedicine and have demonstrated superior efficiency in clinical trials. However, few studies integrate these three methods to investigate the role of mRNA in MI. The aim of this study was to screen the expression of mRNA, investigate the function of mRNA, and provide an underlying scientific basis for the diagnosis of MI. Methods In total, four RNA microarray datasets of MI, namely, GSE66360, GSE97320, GSE60993, and GSE48060, were downloaded from the Gene Expression Omnibus database. The function analysis was carried out by Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Disease Ontology (DO) enrichment analysis. At the same time, inflammation-related genes (IRGs) were acquired from the GeneCards database. Then, 52 co-DEGs were acquired from differentially expressed genes (DEGs) in differential analysis, IRGs, and genes from SCS, and they were used to construct a protein-protein interaction (PPI) network. Two machine learning algorithms, namely, (1) least absolute shrinkage and selection operator and (2) support vector machine recursive feature elimination, were used to filter the co-DEGs. Gene set enrichment analysis (GSEA) was performed to screen the hub-modulating signaling pathways associated with the hub genes. The results were validated in GSE97320, GSE60993, and GSE48060 datasets. The CIBERSORT algorithm was used to analyze 22 infiltrating immune cells in the MI and healthy control (CON) groups and to analyze the correlation between these immune cells. The Pymol software was used for molecular docking of hub DEGs and for potential treatment of MI drugs acquired from the COREMINE. Results A total of 126 DEGs were in the MI and CON groups. After screening two machine learning algorithms and key co-DEGs from a PPI network, two hub DEGs (i.e., IL1B and TLR2) were obtained. The diagnostic efficiency of IL1B, TLR2, and IL1B + TLR2 showed good discrimination in the four cohorts. GSEA showed that KEGG enriched by DEGs were mainly related to inflammation-mediated signaling pathways, and GO biological processes enriched by DEGs were linked to biological effects of various inflammatory cells. Immune analysis indicated that IL1B and TLR2 were correlated with various immune cells. Dan shen, san qi, feng mi, yuan can e, can sha, san qi ye, san qi hua, and cha shu gen were identified as the potential traditional Chinese medicine (TCM) for the treatment of MI. 7-hydroxyflavone (HF) had stable combinations with IL1B and TLR2, respectively. Conclusion This study identified two hub DEGs (IL1B and TLR2) and illustrated its potential role in the diagnosis of MI to enhance our knowledge of the underlying molecular mechanism. Infiltrating immune cells played an important role in MI. TCM, especially HF, was a potential drug for the treatment of MI.
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Affiliation(s)
- Qunhui Zhang
- Research Center for High Altitude Medicine, Key Laboratory of High-Altitude Medicine (Ministry of Education), Key Laboratory of Application and Foundation for High Altitude Medicine Research in Qinghai Province (Qinghai-Utah Joint Research Key Lab for High Altitude Medicine), Qinghai University, Xining, China.,College of Eco-Environmental Engineering, Qinghai University, Xining, China
| | - Yang Guo
- Research Center for High Altitude Medicine, Key Laboratory of High-Altitude Medicine (Ministry of Education), Key Laboratory of Application and Foundation for High Altitude Medicine Research in Qinghai Province (Qinghai-Utah Joint Research Key Lab for High Altitude Medicine), Qinghai University, Xining, China.,College of Eco-Environmental Engineering, Qinghai University, Xining, China
| | - Benyin Zhang
- College of Eco-Environmental Engineering, Qinghai University, Xining, China
| | - Hairui Liu
- College of Eco-Environmental Engineering, Qinghai University, Xining, China
| | - Yanfeng Peng
- College of Eco-Environmental Engineering, Qinghai University, Xining, China
| | - Di Wang
- College of Eco-Environmental Engineering, Qinghai University, Xining, China
| | - Dejun Zhang
- Research Center for High Altitude Medicine, Key Laboratory of High-Altitude Medicine (Ministry of Education), Key Laboratory of Application and Foundation for High Altitude Medicine Research in Qinghai Province (Qinghai-Utah Joint Research Key Lab for High Altitude Medicine), Qinghai University, Xining, China.,College of Eco-Environmental Engineering, Qinghai University, Xining, China
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Network Pharmacology Analysis and Experimental Validation to Explore the Anti-inflammatory Mechanism of Asiatic Acid on Alcoholic Steatohepatitis. Mediators Inflamm 2022; 2022:1708030. [PMID: 36262544 PMCID: PMC9576410 DOI: 10.1155/2022/1708030] [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: 04/02/2022] [Revised: 06/26/2022] [Accepted: 07/20/2022] [Indexed: 11/18/2022] Open
Abstract
Objective The mechanism of action of asiatic acid (AA) on alcoholic steatohepatitis (ASH) was investigated using network pharmacology and experiments. Methods Through data retrieval, network construction, and enrichment analysis, the potential mechanism of AA in the treatment of alcoholic steatohepatitis was explored. Animal and cell models were established in this study. Animal Model. The mouse model was divided into six groups: normal group; model group; low, medium, and high AA group; and silibinin-positive group. Cell Model. An in vitro inflammatory model of RAW264.7 cells was established by alcohol stimulation. Results Compared with the model group, the low, medium, and high AA group showed decreased serum aspartate aminotransferase (AST), alanine aminotransferase (ALT), triglyceride (TG), and total cholesterol (T-CHO). The inflammatory factor tumor necrosis factor alpha (TNF-α), interleukin 1 beta (IL-1β), and interleukin 6 (IL-6) in a dose-dependent manner were decreased. In addition, hematoxylin-eosin staining showed that liver tissue damage and inflammatory cell infiltration in mice were significantly reduced with increasing doses. Further, oil red staining showed that lipid accumulation in hepatocytes in the low, medium, and high AA group was significantly reduced, with increasing dose. In addition, in the cellular model, real-time reverse transcriptase-polymerase chain reaction (Real-Time RT-PCR) and enzyme-linked immunosorbent assay (ELISA) results showed that AA could alleviate alcohol-induced cellular inflammation, while western blot and immunofluorescence results showed that AA might alleviate alcohol-induced cellular inflammation by inhibiting the nuclear factor-κB (NF-κB) pathway. Conclusion This study provides multiple lines of evidence that asiatic acid may alleviate alcoholic hepatitis in mice by modulating the NF-κB pathway.
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Prediction of the Active Components and Mechanism of Forsythia suspensa Leaf against Respiratory Syncytial Virus Based on Network Pharmacology. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:5643345. [PMID: 35911158 PMCID: PMC9328944 DOI: 10.1155/2022/5643345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/20/2022] [Accepted: 05/31/2022] [Indexed: 11/18/2022]
Abstract
Objective Forsythia suspensa leaf (FSL) has been used as a health tea in China for centuries. Previous experiments have proved that FSL extract has a good effect on the antirespiratory syncytial virus (RSV) in vitro, but its exact mechanism is not clear. Therefore, this study aims to determine the active components and targets of FSL and further explore its anti-RSV mechanism. Methods UPLC-Q-Exactive-MS was used to analyze the main chemical components of FSL. The compound disease target network, PPI, GO, and KEGG were used to obtain key targets and potential ways. Then, the molecular docking was verified by Schrödinger Maestro software. Next, the cell model of RSV infection was established, and the inhibitory effect of each drug on RSV was detected. Finally, western blotting was used to detect the effect of the active components of FSL on the expression of PI3K/AKT signaling pathway-related protein. Results UPLC-Q-Exactive-MS analysis showed that there were 67 main chemical constituents in FSL, while network pharmacological analysis showed that there were 169 anti-RSV targets of the active components in FSL, involving 177 signal pathways, among which PI3K/AKT signal pathway played an important role in the anti-RSV process of FSL. The results of molecular docking showed that cryptochlorogenic acid, phillyrin, phillygenin, rutin, and rosmarinic acid had higher binding activities to TP53, STAT3, MAPK1, AKT1, and MAPK3, respectively. In vitro experiments showed that phillyrin and rosmarinic acid could effectively improve the survival rate of RSV-infected cells, increase the expression level of PI3K, and decrease the expression level of AKT. Conclusion The active ingredients of FSL, phillyrin, and rosmarinic acid can play an anti-RSV role by inhibiting PI3K/AKT signaling pathway. This study provides reliable theoretical and experimental support for the anti-RSV treatment of FSL.
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Hao J, Bei J, Li Z, Han M, Ma B, Ma P, Zhou X. Qing`e Pill Inhibits Osteoblast Ferroptosis via ATM Serine/Threonine Kinase (ATM) and the PI3K/AKT Pathway in Primary Osteoporosis. Front Pharmacol 2022; 13:902102. [PMID: 35865965 PMCID: PMC9294279 DOI: 10.3389/fphar.2022.902102] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 05/23/2022] [Indexed: 12/24/2022] Open
Abstract
Osteoporosis (OP) is an aging-related disease that is the main etiology of fragility fracture. Qing’e Pill (QEP) is a mixture of traditional Chinese medicine (TCM) consisting of Eucommia ulmoides Oliv., Psoralea corylifolia L., Juglans regia L., and Allium sativum L. QEP has an anti-osteoporosis function, but the underlying mechanism remains unclear. In this study, online databases were employed to determine the chemical compounds of QEP and potential target genes in osteoporosis. Potential pathways associated with genes were defined by Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) databases. A compound–target–disease network was constructed. Hub genes screened through Cytoscape were intersected with the FerrDB database. The potential key genes were validated in HFOB 1.19 cells, and rat models were ovariectomized through Western blot, RT-qPCR, ELISA, HE staining, immunohistochemistry, and immunofluorescence analyses. The intersection targets of QEP and osteoporosis contained 121 proteins, whereas the target–pathway network included 156 pathways. We filtered five genes that stood out in the network analysis for experimental verification. The experiments validated that QEP exerted therapeutic effects on osteoporosis by inhibiting ferroptosis and promoting cell survival via the PI3K/AKT pathway and ATM. In conclusion, combining the application of network analysis and experimental verification may provide an efficient method to validate the molecular mechanism of QEP on osteoporosis.
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Affiliation(s)
- Jian Hao
- Orthopedics Department, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, China
- *Correspondence: Jian Hao, ; Xianhu Zhou,
| | - Jiaxin Bei
- Laboratory of Interventional Radiology, Department of Minimally Invasive Interventional Radiology and Department of Radiology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhenhan Li
- School of Clinical, Wannan Medical College, Wuhu, China
| | - Mingyuan Han
- Orthopedics Department, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, China
| | - Boyuan Ma
- Orthopedics Department, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, China
| | - Pengyi Ma
- Department of Orthopaedic, Graduate School, Tianjin Medical University, Tianjin, China
| | - Xianhu Zhou
- Orthopedics Department, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, China
- *Correspondence: Jian Hao, ; Xianhu Zhou,
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Zhang T, Chen L, Li R, Liu N, Huang X, Wong G. PIWI-interacting RNAs in human diseases: databases and computational models. Brief Bioinform 2022; 23:6603448. [PMID: 35667080 DOI: 10.1093/bib/bbac217] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/24/2022] [Accepted: 05/09/2022] [Indexed: 11/12/2022] Open
Abstract
PIWI-interacting RNAs (piRNAs) are short 21-35 nucleotide molecules that comprise the largest class of non-coding RNAs and found in a large diversity of species including yeast, worms, flies, plants and mammals including humans. The most well-understood function of piRNAs is to monitor and protect the genome from transposons particularly in germline cells. Recent data suggest that piRNAs may have additional functions in somatic cells although they are expressed there in far lower abundance. Compared with microRNAs (miRNAs), piRNAs have more limited bioinformatics resources available. This review collates 39 piRNA specific and non-specific databases and bioinformatics resources, describes and compares their utility and attributes and provides an overview of their place in the field. In addition, we review 33 computational models based upon function: piRNA prediction, transposon element and mRNA-related piRNA prediction, cluster prediction, signature detection, target prediction and disease association. Based on the collection of databases and computational models, we identify trends and potential gaps in tool development. We further analyze the breadth and depth of piRNA data available in public sources, their contribution to specific human diseases, particularly in cancer and neurodegenerative conditions, and highlight a few specific piRNAs that appear to be associated with these diseases. This briefing presents the most recent and comprehensive mapping of piRNA bioinformatics resources including databases, models and tools for disease associations to date. Such a mapping should facilitate and stimulate further research on piRNAs.
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Affiliation(s)
- Tianjiao Zhang
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R. 999078, China
| | - Liang Chen
- Department of Computer Science, School of Engineering, Shantou University, Shantou, China
| | - Rongzhen Li
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R. 999078, China
| | - Ning Liu
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R. 999078, China
| | - Xiaobing Huang
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R. 999078, China
| | - Garry Wong
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R. 999078, China
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Huang J, Liu D, Zhang J, Xiao H. A Network Pharmacology Study: Reveal the Mechanisms of Palovarotene Against Heterotopic Ossification. Front Med (Lausanne) 2022; 9:897392. [PMID: 35646981 PMCID: PMC9136101 DOI: 10.3389/fmed.2022.897392] [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: 03/16/2022] [Accepted: 04/14/2022] [Indexed: 11/30/2022] Open
Abstract
Heterotopic ossification (HO) occurs when bone forms within non-ossifying tissues, such as in muscle. Palovarotene, an activator of retinoic acid receptor γ (RAR-γ), has been shown to inhibit the formation of ectopic bone in HO model mice, but its specific mechanism of action remains unclear. This study will explore the target and molecular mechanism of Palovarotene's action on HO by network pharmacology study. We collected the relevant targets of Palovarotene and HO from the database, obtained the potential targets of Palovarotene acting on HO through Venn analysis, and constructed the protein-protein interaction (PPI) network. Then, Gene Ontology (GO) and KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment Analysis and Module-based Network Analysis were performed for potential targets, and in addition, PPI Network Topology Analysis and Gene-Phenotype Correlation Analysis were performed. The results suggested that MAPK1, MDM2, and other targets as well as P53 signaling pathway and PI3K–Akt signaling pathway may be closely related to Palovarotene treatment of HO. We carried out verification experiments to confirm our finding, alkaline phosphatase and alizarin red staining in vitro and Micro-CT as well as hematoxylin-eosin staining in vivo were performed to verify treatment for HO of Palovarotene, reverse transcription polymerase chain reaction was also used to explore the transcription changes of MAPK1, MDM2, and osteogenic genes. This study systematically elucidated the possible mechanism of Palovarotene in the treatment of HO through network pharmacology study, revealing a new direction for the further application of Palovarotene in the treatment of HO.
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Affiliation(s)
- Junchao Huang
- Department of Orthopedics, Shanghai Fenxian District Central Hospital/Anhui University of Science and Technology Affiliated Fengxian Hospital, Shanghai, China
| | - Dachuan Liu
- Department of Orthopaedic Surgery, Orthopaedic Institute, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jingwei Zhang
- Department of Orthopedics, Shanghai Fenxian District Central Hospital/Anhui University of Science and Technology Affiliated Fengxian Hospital, Shanghai, China
| | - Haijun Xiao
- Department of Orthopedics, Shanghai Fenxian District Central Hospital/Anhui University of Science and Technology Affiliated Fengxian Hospital, Shanghai, China
- *Correspondence: Haijun Xiao
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Liu XY, Zhang TQ, Zhang Q, Guo J, Zhang P, Mao T, Tian ZB, Zhang CP, Li XY. Differential Long Non-Coding RNA Expression Analysis in Chronic Non-Atrophic Gastritis, Gastric Mucosal Intraepithelial Neoplasia, and Gastric Cancer Tissues. Front Genet 2022; 13:833857. [PMID: 35571069 PMCID: PMC9091194 DOI: 10.3389/fgene.2022.833857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 03/25/2022] [Indexed: 11/13/2022] Open
Abstract
Gastric cancer (GC) has a high incidence worldwide, and when detected, the majority of patients have already progressed to advanced stages. Long non-coding RNAs (lncRNAs) have a wide range of biological functions and affect tumor occurrence and development. However, the potential role of lncRNAs in GC diagnosis remains unclear. We selected five high-quality samples from each group of chronic non-atrophic gastritis, gastric mucosal intraepithelial neoplasia, and GC tissues for analysis. RNA-seq was used to screen the differentially expressed lncRNAs, and we identified 666 differentially expressed lncRNAs between the chronic non-atrophic gastritis and GC groups, 13 differentially expressed lncRNAs between the gastric mucosal intraepithelial neoplasia and GC groups, and 507 differentially expressed lncRNAs between the chronic non-atrophic gastritis and gastric mucosal intraepithelial neoplasia groups. We also identified six lncRNAs (lncRNA H19, LINC00895, lnc-SRGAP2C-16, lnc-HLA-C-2, lnc-APOC1-1, and lnc-B3GALT2-1) which not only differentially expressed between the chronic non-atrophic gastritis and GC groups, but also differentially expressed between the gastric mucosal intraepithelial neoplasia and GC groups. Furthermore, RT-qPCR was used to verify the differentially co-expressed lncRNAs. LncSEA was used to conduct a functional analysis of differentially expressed lncRNAs. We also predicted the target mRNAs of the differentially expressed lncRNAs through bioinformatics analysis and analyzed targeting correlations between three differentially co-expressed lncRNAs and mRNAs (lncRNA H19, LINC00895, and lnc-SRGAP2C-16). Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases were used to explore the functions of target mRNAs of differentially expressed lncRNAs. In conclusion, our study provides a novel perspective on the potential functions of differentially expressed lncRNAs in GC occurrence and development, indicating that the differentially expressed lncRNAs might be new biomarkers for early GC diagnosis.
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Affiliation(s)
- Xin-Yuan Liu
- Department of Gastroenterology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Tian-Qi Zhang
- Department of Gastroenterology, Qingdao Women and Children’s Hospital, Qingdao, China
| | - Qi Zhang
- Department of Gastroenterology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Jing Guo
- Department of Gastroenterology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Peng Zhang
- Department of Gastroenterology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Tao Mao
- Department of Gastroenterology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Zi-Bin Tian
- Department of Gastroenterology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Cui-Ping Zhang
- Department of Gastroenterology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xiao-Yu Li
- Department of Gastroenterology, The Affiliated Hospital of Qingdao University, Qingdao, China
- *Correspondence: Xiao-Yu Li,
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Wu Z, Cai Z, Shi H, Huang X, Cai M, Yuan K, Huang P, Shi G, Yan T, Li Z. Effective biomarkers and therapeutic targets of nerve-immunity interaction in the treatment of depression: an integrated investigation of the miRNA-mRNA regulatory networks. Aging (Albany NY) 2022; 14:3569-3596. [PMID: 35468096 PMCID: PMC9085226 DOI: 10.18632/aging.204030] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 04/11/2022] [Indexed: 11/25/2022]
Abstract
Background: Major depressive disorder (MDD) is an emotional condition that interferes with sufferers’ work and daily life. Numerous studies have found that miRNAs play a significant role in the development of MDD and can be utilized as a biomarker for its diagnosis and therapy. However, there have been few studies on nerve-immunity interaction treatment for the brains of MMD patients. Methods: The work is performed on microarray data. We analyzed the differences of miRNAs (GSE58105, GSE81152, GSE152267, and GSE182194) and mRNA (GSE19738, GSE32280, GSE44593, GSE53987, and GSE98793) in MDD and healthy samples from GEO datasets. FunRich was used to predict the transcription factors and target genes of the miRNAs, and TF and GO enrichment analyses were performed. Then, by comparing the differential expression of the anticipated target genes and five mRNAs, intersecting mRNAs were discovered. The intersecting genes were submitted to GO and KEGG analyses to determine their functions. These intersecting potential genes and pathways that linked to MDD in neurological and immunological aspects have been identified for future investigation. Results: We discovered five hub genes: KCND2, MYT1L, GJA1, CHL1, and SNAP25, which were all up-regulated genes. However, in MMD, the equivalent miRNAs, hsa-miR-206 and hsa-miR-338-3p, were both down-regulated. These miRNAs can activate or inhibit the T cell receptor signal pathway, JAK-STAT and other signal pathways, govern immune-inflammatory response, neuronal remodeling, and mediate the onset and development of MMD Conclusions: The results of a thorough bioinformatics investigation of miRNAs and mRNAs in MDD showed that miR-338-3P and miR-206 might be effective biomarkers and possible therapeutic targets for the treatment of MDD via nerve-immunity interaction.
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Affiliation(s)
- Zixuan Wu
- Guangzhou University of Chinese Medicine, Guangzhou 510006, Guangdong Province, China
| | - Zhixiang Cai
- Guangzhou University of Chinese Medicine, Guangzhou 510006, Guangdong Province, China
| | - Hongshuo Shi
- Shandong University of Traditional Chinese Medicine, Jinan 250355, Shandong Province, China
| | - Xuyan Huang
- Guangzhou University of Chinese Medicine, Guangzhou 510006, Guangdong Province, China
| | - Minjie Cai
- Guangzhou University of Chinese Medicine, Guangzhou 510006, Guangdong Province, China.,Shantou Health School, Shantou 515061, Guangdong Province, China
| | - Kai Yuan
- Yunnan University of Chinese Medicine, Kunming 650500, Yunnan Province, China
| | - Peidong Huang
- Yunnan University of Chinese Medicine, Kunming 650500, Yunnan Province, China
| | - Guoqi Shi
- Guangzhou University of Chinese Medicine, Guangzhou 510006, Guangdong Province, China
| | - Tao Yan
- Guangzhou University of Chinese Medicine, Guangzhou 510006, Guangdong Province, China.,Department of Cardiovascular Surgery, General Hospital of Southern Theater Command, PLA 510010, Guangdong Province, China
| | - Zhichao Li
- The Second Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan 250355, Shandong Province, China
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Xu A, Kouznetsova VL, Tsigelny IF. Alzheimer's Disease Diagnostics Using miRNA Biomarkers and Machine Learning. J Alzheimers Dis 2022; 86:841-859. [PMID: 35147545 DOI: 10.3233/jad-215502] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND The current standard for Alzheimer's disease (AD) diagnosis is often imprecise, as with memory tests, and invasive or expensive, as with brain scans. However, the dysregulation patterns of miRNA in blood hold potential as useful biomarkers for the non-invasive diagnosis and even treatment of AD. OBJECTIVE The goal of this research is to elucidate new miRNA biomarkers and create a machine-learning (ML) model for the diagnosis of AD. METHODS We utilized pathways and target gene networks related to confirmed miRNA biomarkers in AD diagnosis and created multiple models to use for diagnostics based on the significant differences among miRNA expression between blood profiles (serum and plasma). RESULTS The best performing serum-based ML model, trained on filtered disease-specific miRNA datasets, was able to identify miRNA biomarkers with 92.0% accuracy and the best performing plasma-based ML model, trained on filtered disease-specific miRNA datasets, was able to identify miRNA biomarkers with 90.9% accuracy. Through analysis of AD implicated miRNA, thousands of descriptors reliant on target gene and pathways were created which can then be used to identify novel biomarkers and strengthen disease diagnosis. CONCLUSION Development of a ML model including miRNA and their genomic and pathway descriptors made it possible to achieve considerable accuracy for the prediction of AD.
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Affiliation(s)
- Amy Xu
- IUL Science Internship Program, San Diego, CA, USA
| | - Valentina L Kouznetsova
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, USA.,BiAna, San Diego, CA, USA
| | - Igor F Tsigelny
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, USA.,BiAna, San Diego, CA, USA.,Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
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Du L, Xiao Y, Xu Y, Chen F, Chu X, Cao Y, Zhang X. The Potential Bioactive Components of Nine TCM Prescriptions Against COVID-19 in Lung Cancer Were Explored Based on Network Pharmacology and Molecular Docking. Front Med (Lausanne) 2022; 8:813119. [PMID: 35127768 PMCID: PMC8811133 DOI: 10.3389/fmed.2021.813119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 12/13/2021] [Indexed: 01/08/2023] Open
Abstract
Objective The purpose of this study was to screen active components and molecular targets of nine prescriptions recommended by the National Health Commission (NHC) of China by network pharmacology, and to explore the potential mechanism of the core active components against COVID-19 with molecular docking. Methods Differentially expressed genes of lung adenocarcinoma (LUAD) screened by edgeR analysis were overlapped with immune-related genes in MMPORT and COVID-19-related genes in GeneCards. The overlapped genes were also COVID-19 immune-related genes in LUAD. TCMSP platform was used to identify active ingredients of the prescription, potential targets were identified by the UniProt database, and the cross genes with COVID-19 immune-related genes in LUAD were used to construct a Chinese Medicine-Logy-immune target network. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed on the target genes of each prescription. Finally, the key active components were selected for molecular docking simulation with ACE2. Results We obtained 15 overlapping immunization target genes from FPQXZ, HSYFZ, HSZFZ, and QFPDT, 16 overlapping immunization target genes from QYLFZ, SDYFZ, SRYFZ, and YDBFZ, and 17 overlapping immunization target genes from QYLXZ. ADRB2, FOS, HMOX1, ICAM1, IL6, JUN, NFKBIA, and STAT1 also had the highest-ranked therapeutic targets for 9 prescriptions, and their expressions were positively correlated with TME-related stromal score, immune score, and ESTIMATE score. Among 9 compounds with the highest frequency of occurrence in the 9 prescriptions, baicalein had the highest ACE2 binding affinity and can be well-combined into the active pocket of ACE2 It is stabilized by forming hydrogen bonds with ASN290 and ILE291 in ACE2 and hydrophobic interaction with PHE438, ILE291, and PRO415. Conclusion The nine Chinese medicine prescriptions may play an anti-SARS-CoV-2 role via regulating viral transcription and immune function through multi-component, multi-target, and multi-pathway.
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Affiliation(s)
- Lin Du
- Department of Thoracic Surgery, Tianjin Chest Hospital, Tianjin, China
| | - Yajie Xiao
- Department of Clinical Translational Medicine, YuceBio Technology Co., Ltd., Shenzhen, China
| | - Yijun Xu
- Department of Thoracic Surgery, Tianjin Chest Hospital, Tianjin, China
| | - Feng Chen
- Department of Thoracic Surgery, Tianjin Chest Hospital, Tianjin, China
| | - Xianghui Chu
- Department of Thoracic Surgery, Tianjin Chest Hospital, Tianjin, China
| | - Yuqi Cao
- Department of Thoracic Surgery, Tianjin Chest Hospital, Tianjin, China
| | - Xun Zhang
- Department of Thoracic Surgery, Tianjin Chest Hospital, Tianjin, China
- *Correspondence: Xun Zhang
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Casadio R, Lenhard B, Sternberg MJE. Computational Resources for Molecular Biology 2021. J Mol Biol 2021; 433:166962. [PMID: 33774035 DOI: 10.1016/j.jmb.2021.166962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Rita Casadio
- Biocomputing Group, FABIT-University of Bologna, Italy
| | - Boris Lenhard
- Institute of Clinical Sciences, Faculty of Medicine. Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, UK; Computational Regulatory Genomics, MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK
| | - Michael J E Sternberg
- Structural Bioinformatics Group, Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK.
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