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Wang H, Quan J, Deng Y, Chen J, Zhang K, Qu Z. Utilizing network pharmacological analysis to investigate the key targets and mechanisms of kaempferol against oxaliplatin-induced neurotoxicity. Toxicol Mech Methods 2023; 33:38-46. [PMID: 35574720 DOI: 10.1080/15376516.2022.2069531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
This study investigated the pharmacological mechanism of kaempferol in the treatment of oxaliplatin-induced neuropathic pain by network pharmacological method and cells experiment. The kaempferol and disease target genes were obtained from several databases, including TCMSP, SwissTargetPrediction, GeneCards, and CTD. Then, the common target genes of drugs and diseases were obtained using Venny online tools. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional analyses were carried out to obtain the enriched molecular pathways associated with the kaempferol and disease. Finally, we constructed a neuropathic pain cell experiment to confirm the findings. 138 intersection targets were identified between targets of kaempferol and oxaliplatin-induced neurotoxicity. Enrichment analyses revealed that the IL-17 signaling pathway was associated with the therapeutic effects of kaempferol. Kaempferol down-regulated the mRNA expression levels of TNF-α, IL-6, and CCL2 in oxaliplatin-treated astrocytes. Our findings showed that kaempferol alleviated oxaliplatin-induced neurotoxicity via regulation of inflammation-related genes.
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Affiliation(s)
- Hongxing Wang
- Department of Rehabilitation, Xiangya Hospital, Central South University, Changsha Hunan, China
| | - Jing Quan
- Department of Rehabilitation, Xiangya Hospital, Central South University, Changsha Hunan, China
| | - Youming Deng
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha Hunan, China
| | - Jie Chen
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha Hunan, China
| | - Ke Zhang
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha Hunan, China
| | - Zhan Qu
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha Hunan, China
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Gao L, Li GS, Li JD, He J, Zhang Y, Zhou HF, Kong JL, Chen G. Identification of the susceptibility genes for COVID-19 in lung adenocarcinoma with global data and biological computation methods. Comput Struct Biotechnol J 2021; 19:6229-6239. [PMID: 34840672 PMCID: PMC8605816 DOI: 10.1016/j.csbj.2021.11.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 11/07/2021] [Accepted: 11/16/2021] [Indexed: 12/19/2022] Open
Abstract
Introduction The risk of infection with COVID-19 is high in lung adenocarcinoma (LUAD) patients, and there is a dearth of studies on the molecular mechanism underlying the high susceptibility of LUAD patients to COVID-19 from the perspective of the global differential expression landscape. Objectives To fill the research void on the molecular mechanism underlying the high susceptibility of LUAD patients to COVID-19 from the perspective of the global differential expression landscape. Methods Herein, we identified genes, specifically the differentially expressed genes (DEGs), correlated with the susceptibility of LUAD patients to COVID-19. These were obtained by calculating standard mean deviation (SMD) values for 49 SARS-CoV-2-infected LUAD samples and 24 non-affected LUAD samples, as well as 3931 LUAD samples and 3027 non-cancer lung samples from 40 pooled RNA-seq and microarray datasets. Hub susceptibility genes significantly related to COVID-19 were further selected by weighted gene co-expression network analysis. Then, the hub genes were further analyzed via an examination of their clinical significance in multiple datasets, a correlation analysis of the immune cell infiltration level, and their interactions with the interactome sets of the A549 cell line. Results A total of 257 susceptibility genes were identified, and these genes were associated with RNA splicing, mitochondrial functions, and proteasomes. Ten genes, MEA1, MRPL24, PPIH, EBNA1BP2, MRTO4, RABEPK, TRMT112, PFDN2, PFDN6, and NDUFS3, were confirmed to be the hub susceptibility genes for COVID-19 in LUAD patients, and the hub susceptibility genes were significantly correlated with the infiltration of multiple immune cells. Conclusion In conclusion, the susceptibility genes for COVID-19 in LUAD patients discovered in this study may increase our understanding of the high risk of COVID-19 in LUAD patients.
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Key Words
- CI, confidence interval
- COVID-19
- COVID-19, coronavirus disease 2019
- DEG
- DEG, differentially expressed genes
- FC, fold change
- FPKM, fragments per kilobase per million
- GTEx, Genotype-tissue Expression
- HPA, human protein atlas
- IHC, immunohistochemistry
- Immune infiltration
- LUAD
- LUAD, lung adenocarcinoma
- PPI, protein-to-protein interaction
- SARS-CoV-2, severe acute respiratory syndrome coronavirus 2
- SMD, standard mean difference
- SROC, summarized receiver’s operating characteristics
- Susceptibility
- TF, transcription factor
- TPM, transcripts per million reads
- WGCNA
- WGCNA, weighted gene co-expression network analysis
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Affiliation(s)
- Li Gao
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, No. 6 Shuangyong Rd, Nanning, Guangxi Zhuang Autonomous Region 530021, PR China
| | - Guo-Sheng Li
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, No. 6 Shuangyong Rd, Nanning, Guangxi Zhuang Autonomous Region 530021, PR China
| | - Jian-Di Li
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, No. 6 Shuangyong Rd, Nanning, Guangxi Zhuang Autonomous Region 530021, PR China
| | - Juan He
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, No. 6 Shuangyong Rd, Nanning, Guangxi Zhuang Autonomous Region 530021, PR China
| | - Yu Zhang
- Department of Pathology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, No. 324. Jingwu Rd, Jinan, Shandong 250021, PR China
| | - Hua-Fu Zhou
- Department of Cardio-Thoracic Surgery, The First Affiliated Hospital of Guangxi Medical University, No. 6 Shuangyong Rd, Nanning, Guangxi Zhuang Autonomous Region 530021, PR China
| | - Jin-Liang Kong
- Ward of Pulmonary and Critical Care Medicine, Department of Respiratory Medicine, The First Affiliated Hospital of Guangxi Medical University, No. 6 Shuangyong Rd, Nanning, Guangxi Zhuang Autonomous Region 530021, PR China
| | - Gang Chen
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, No. 6 Shuangyong Rd, Nanning, Guangxi Zhuang Autonomous Region 530021, PR China
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Abdelhamid L, Cabana-Puig X, Swartwout B, Lee J, Li S, Sun S, Li Y, Ross AC, Cecere TE, LeRoith T, Werre SR, Wang H, Reilly CM, Luo XM. Retinoic Acid Exerts Disease Stage-Dependent Effects on Pristane-Induced Lupus. Front Immunol 2020; 11:408. [PMID: 32265909 PMCID: PMC7103630 DOI: 10.3389/fimmu.2020.00408] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 02/21/2020] [Indexed: 12/17/2022] Open
Abstract
We previously showed that all-trans-retinoic acid (tRA), an active metabolite of vitamin A, exacerbated pre-existing autoimmunity in lupus; however, its effects before the development of autoimmunity are unknown. Here, using a pristane-induced model, we show that tRA exerts differential effects when given at the initiation vs. continuation phase of lupus. Unlike tRA treatment during active disease, pre-pristane treatment with tRA aggravated glomerulonephritis through increasing renal expression of pro-fibrotic protein laminin β1, activating bone marrow conventional dendritic cells (cDCs), and upregulating the interaction of ICAM-1 and LFA-1 in the spleen, indicating an active process of leukocyte activation and trafficking. Transcriptomic analysis revealed that prior to lupus induction, tRA significantly upregulated the expression of genes associated with cDC activation and migration. Post-pristane tRA treatment, on the other hand, did not significantly alter the severity of glomerulonephritis; rather, it exerted immunosuppressive functions of decreasing circulatory and renal deposition of autoantibodies as well as suppressing the renal expression of proinflammatory cytokines and chemokines. Together, these findings suggest that tRA differentially modulate lupus-associated kidney inflammation depending on the time of administration. Interestingly, both pre- and post-pristane treatments with tRA reversed pristane-induced leaky gut and modulated the gut microbiota in a similar fashion, suggesting a gut microbiota-independent mechanism by which tRA affects the initiation vs. continuation phase of lupus.
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Affiliation(s)
- Leila Abdelhamid
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Xavier Cabana-Puig
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Brianna Swartwout
- Translational Biology, Medicine and Health Graduate Program, Virginia Polytechnic Institute and State University, Roanoke, VA, United States
| | - Jiyoung Lee
- Department of Crop and Soil Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Song Li
- Department of Crop and Soil Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Sha Sun
- Department of Development and Cell Biology, University of California, Irvine, Irvine, CA, United States
| | - Yaqi Li
- Department of Nutritional Sciences, Pennsylvania State University, University Park, PA, United States
| | - A Catharine Ross
- Department of Nutritional Sciences, Pennsylvania State University, University Park, PA, United States
| | - Thomas E Cecere
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Tanya LeRoith
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Stephen R Werre
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Haifeng Wang
- College of Animal Science, Key Laboratory of Molecular Animal Nutrition, Zhejiang University, Hangzhou, China
| | - Christopher M Reilly
- Department of Cell Biology and Physiology, Edward via College of Osteopathic Medicine, Blacksburg, VA, United States
| | - Xin M Luo
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
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Yu JW, Yuan HW, Bao LD, Si LG. Interaction between piperine and genes associated with sciatica and its mechanism based on molecular docking technology and network pharmacology. Mol Divers 2020; 25:233-248. [PMID: 32130644 PMCID: PMC7870775 DOI: 10.1007/s11030-020-10055-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 02/17/2020] [Indexed: 12/15/2022]
Abstract
Abstract Piperine is the main active component of Piper longum L., which is also the main component of anti-sciatica Mongolian medicine Naru Sanwei pill. It has many pharmacological activities such as anti-inflammatory and immune regulation.
This paper aims to preliminarily explore the potential mechanism of piperine in the treatment of sciatica through network pharmacology and molecular docking. TCMSP, ETCM database and literature mining were used to collect the active compounds of Piper longum L. Swiss TargetPrediction and SuperPred server were used to find the targets of compounds. At the same time, CTD database was used to collect the targets of sciatica. Then the above targets were compared and analyzed to select the targets of anti-sciatica in Piper longum L. The Go (gene ontology) annotation and KEGG pathway of the targets were enriched and analyzed by Metascape database platform. The molecular docking between the effective components and the targets was verified by Autodock. After that, the sciatica model of rats was established and treated with piperine. The expression level of inflammatory factors and proteins in the serum and tissues of rat sciatic nerve were detected by ELISA and Western blot. HE staining and immunohistochemistry were carried out on the sciatica tissues of rats. The results showed that Piper longum L. can regulate the development of sciatica and affect the expressions of PPARG and NF-kB1 through its active ingredient piperine, and there is endogenous interaction between PPARG and NF-kB1. Graphic abstract ![]()
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Affiliation(s)
- Jiu-Wang Yu
- Department of Pharmacy, Affiliated Hospital of Inner Mongolia Medical University, Hohhot, 010059, Inner Mongolia, People's Republic of China
| | - Hong-Wei Yuan
- Department of Pathology, Affiliated Hospital of Inner Mongolia Medical University, Hohhot, 010059, Inner Mongolia, People's Republic of China
| | - Li-Dao Bao
- Department of Pharmacy, Affiliated Hospital of Inner Mongolia Medical University, Hohhot, 010059, Inner Mongolia, People's Republic of China.
| | - Leng-Ge Si
- Mongolia Medical School, Inner Mongolia Medical University, Hohhot, 010110, Inner Mongolia, People's Republic of China
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