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Gayathri K, Abhinand P, Gayathri V, Prasanna Lakshmi V, Chamundeeswari D, Jiang L, Tian Z, Malathi N. Computational analysis of phytocompounds in Centella asiatica for its antifibrotic and drug-likeness properties - Herb to drug study. Heliyon 2024; 10:e33762. [PMID: 39027607 PMCID: PMC11255509 DOI: 10.1016/j.heliyon.2024.e33762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 06/24/2024] [Accepted: 06/26/2024] [Indexed: 07/20/2024] Open
Abstract
Oral submucous fibrosis (OSMF) is a potentially malignant disorder with no permanent cure that affects the quality of life due to trismus. Computational pharmacology has accelerated the discovery of drug candidates for the treatment of incurable diseases. The present study aimed to screen the compounds of the miracle herb Centella asiatica with drug-likeness properties based on the absorption, distribution, metabolism, and excretion (ADME) properties. The pharmacological actions of these screened compounds against OSMF were identified by network pharmacology, gene ontology, pathway enrichment analysis, molecular docking, and simulation. Fifteen drug-like ligands were identified after virtual screening viz; asiatic acid, kaempferol, quercetin, luteolin, apigenin, bayogenin, gallic acid, isothankunic acid, madecassic acid, madasiatic acid, arjunolic acid, terminolic acid, catechin, epicatechin, and nobiletin. 850 potential targets were predicted for the ligands, which were analyzed against 354 proteins associated with OSMF. Compound pathway analysis and disease pathway analysis identified 53 common proteins. The GO enrichment analysis identified 472 biological process terms, 76 molecular function terms, and 44 cellular component terms. Pathway enrichment analysis predicted 142 KEGG pathways, 35 Biocarta pathways, and 236 Reactome pathways for the target proteins. The analysis revealed that the herb targets crucial events of fibrosis such as inflammation, oxidative stress, apoptosis, collagen deposition, and epithelial-mesenchymal transition. The common 53 proteins were used for protein-protein interaction (PPI) network analysis, which revealed 4 key proteins interacting with the phytocompounds viz; transforming growth factor-β1 (TGF-β1), mothers against decapentaplegic-3 (SMAD-3), mitogen-activated protein kinase-1 (MAPK-1) and proto-oncogene tyrosine-protein kinase (SRC). Molecular docking revealed that all ligands had a good binding affinity to the target proteins. Bayogenin had the highest binding affinity towards MAPK-1 (-9.7 kcal/mol), followed by isothankunic acid towards SRC protein (-9.3 kcal/mol). Madasiatic acid had the highest binding affinity to SMAD-3 (-7.6 kcal/mol) and TGF-β1 (-7.1 kcal/mol). Molecular dynamics simulation demonstrated stable ligand protein interactions of bayogenin and MAPK complex, isothankunic acid and SRC complex. This in silico study is the first to identify potential phytochemicals present in Centella asiatica and their target molecules, which might be responsible for reversing OSMF.
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Affiliation(s)
- K. Gayathri
- Faculty of Biomedical Sciences, Sri Ramachandra Institute of Higher Education and Research, Porur, Chennai, 600116, India
- Department of Oral Pathology and Microbiology, Sri Ramachandra Dental College, Sri Ramachandra Institute of Higher Education and Research, Porur, Chennai, 600116, India
| | - P.A. Abhinand
- Department of Bioinformatics, Faculty of Engineering and Technology, Sri Ramachandra Institute of Higher Education & Research, Porur, Chennai, 600116, India
| | - V. Gayathri
- Centre for Toxicology and Developmental Research, Sri Ramachandra Institute of Higher Education and Research, Porur, Chennai, 600116, India
| | - V. Prasanna Lakshmi
- Department of Bioinformatics, Faculty of Engineering and Technology, Sri Ramachandra Institute of Higher Education & Research, Porur, Chennai, 600116, India
| | - D. Chamundeeswari
- Faculty of Pharmacy, Meenakshi Academy of Higher Education and Research, Chennai, India
| | - Li Jiang
- Department of Oral Pathology, The Ninth People's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Zhen Tian
- Department of Oral Pathology, The Ninth People's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - N. Malathi
- Department of Oral Pathology and Microbiology, Sri Ramachandra Dental College, Sri Ramachandra Institute of Higher Education and Research, Porur, Chennai, 600116, India
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Molecular pathways of oral submucous fibrosis and its progression to malignancy. Arch Oral Biol 2023; 148:105644. [PMID: 36804642 DOI: 10.1016/j.archoralbio.2023.105644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 02/01/2023] [Accepted: 02/03/2023] [Indexed: 02/09/2023]
Abstract
OBJECTIVE The review aims to comprehend various factors engaged in the alteration of molecular events resulting in Oral submucous fibrosis (OSMF) and its malignant transformation. DESIGN Literature pertinent to pathways involved in OSMF were explored in databases such as PubMed, Scopus and Google Scholar. The relevant literature was reviewed and critically appraised in this narrative review. RESULTS Areca nut components influence myriad of cellular molecules such as cytokines, growth factors, myofibroblasts, non-coding RNAs and alter their expression. These aberrantly expressed molecules drive the progression of OSMF from localized inflammation to fibrosis of buccal mucosa. The oral tissue suffers from oxidative stress, hypoxia, autophagy, aberration of cell cycle and DNA damage. Apoptosis of epithelial layer results in its atrophy facilitating deeper penetration of areca nut elements. With the advance of disease, epithelial-mesenchymal transition eventuates and promotes dysplasia. The jeopardized expression of various cellular molecules, suppressed apoptosis, along with increased genetic alterations and neovascularization favors the malignant transformation. CONCLUSION OSMF is a progressive disorder with complex mechanism of pathogenesis initiated by inflammation of oral mucosa. Continuous habit of areca nut chewing and the resulting insult to the tissues prevents healing process and is destined to debilitating disease which affects the quality of life with a higher probability of progression to malignancy.
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Arsenic, Oxidative Stress and Reproductive System. J Xenobiot 2022; 12:214-222. [PMID: 35893266 PMCID: PMC9326564 DOI: 10.3390/jox12030016] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 06/25/2022] [Accepted: 07/12/2022] [Indexed: 11/17/2022] Open
Abstract
Infertility is a severe medical problem and is considered a serious global public health issue affecting a large proportion of humanity. Oxidative stress is one of the most crucial factors involved in infertility. Recent studies indicate that the overproduction of reactive oxygen species (ROS) or reactive nitrogen species (RNS) may cause damage to the male and female reproductive systems leading to infertility. Low amounts of ROS and RNS are essential for the normal functioning of the male and female reproductive systems, such as sperm motility, acrosome reaction, interactions with oocytes, ovulation, and the maturation of follicles. Environmental factors such as heavy metals can cause reproductive dysfunction in men and women through the overproduction of ROS and RNS. It is suggested that oxidative stress caused by arsenic is associated with male and female reproductive disorders such as through the alteration in sperm counts and motility, decreased sex hormones, dysfunction of the testis and ovary, as well as damage to the processes of spermatogenesis and oogenesis. This review paper highlights the relationship between arsenic-induced oxidative stress and the prevalence of infertility, with detailed explanations of potential underlying mechanisms.
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Nagesh R, Kiran Kumar K, Naveen Kumar M, Patil RH, Sharma SC. Regulation of Jun and Fos AP-1 transcription factors by JNK MAPKs signaling cascade in areca nut extract treated KB cells. Biochem Biophys Rep 2021; 27:101090. [PMID: 34401529 PMCID: PMC8350022 DOI: 10.1016/j.bbrep.2021.101090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 07/20/2021] [Accepted: 07/23/2021] [Indexed: 11/13/2022] Open
Abstract
The edible endosperm of Areca catechu is recognized as a potent carcinogenic agent either consumed alone or in combination with tobacco. Habitual chewing of areca nut leads to orally potential malignant disorders which are highly effective in malignant transformation and thereby lead to oral carcinogenesis. Human buccal epithelial KB carcinoma cells were used as an experimental cell system to inspect the mechanistic act of aqueous extract of areca nut on biochemical status and their implications on transcriptional activation of cancer signaling cascade that could possibly trigger numerous oncogenic players and finally decides the cells fate. Extract treated cells showed reduced viability with altered balance between oxidants and antioxidants which lead to redox status and which is known to distort various biological processes within the cell system. Results of RT-PCR demonstrated decreased expression of BCl2, cell cycle regulators along with Activator Protein -1 (AP-1) components. While Bax, p16 and p21 mRNAs showed increased expression in extract treated KB cells. Likewise, the translational levels of proliferation cell nuclear antigen (PCNA), tumor suppressor p53, retinoblastoma (Rb) and cyclin dependent kinase 4 (CDK4) were decreased along with AP-1 subunits (c-Jun/c-Fos) with increased protein levels of p21 in extract treated KB cells. Further, the downstream activation and regulation of AP-1 transcription factors could be through stress activated c-Jun - N terminal Kinase (JNK) Mitogen Activated Protein Kinases (MAPKs) which downregulated both Jun and Fos mRNA transcripts in areca nut extract exposed KB cells. Thus, outcome of the study provides insights into mechanistic path of pathogenesis of areca related disorders. Further, it could aid in designing new therapeutic modalities that specific targets these oncogenic players and help in disease management.
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Affiliation(s)
- Rashmi Nagesh
- Department of Microbiology and Biotechnology, Bangalore University, Jnana Bharathi, Bengaluru, 560 056, Karnataka, India
- Department of Biotechnology and Genetics, M S Ramaiah College of Arts Science and Commerce, Bengaluru, 560 054, Karnataka, India
| | - K.M. Kiran Kumar
- Department of Biotechnology, The Oxford College of Science, Bengaluru, 560 102, Karnataka, India
| | - M. Naveen Kumar
- Department of Biotechnology and Genetics, M S Ramaiah College of Arts Science and Commerce, Bengaluru, 560 054, Karnataka, India
| | - Rajeshwari H. Patil
- Department of Molecular Reproduction Development and Genetics, Indian Institute of Science, Bengaluru, 560 012, Karnataka, India
| | - S. Chidananda Sharma
- Department of Microbiology and Biotechnology, Bangalore University, Jnana Bharathi, Bengaluru, 560 056, Karnataka, India
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L-Tryptophan activates the aryl hydrocarbon receptor and induces cell cycle arrest in porcine trophectoderm cells. Theriogenology 2021; 171:137-146. [PMID: 34058506 DOI: 10.1016/j.theriogenology.2021.05.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 05/10/2021] [Accepted: 05/12/2021] [Indexed: 12/21/2022]
Abstract
During implantation, the proliferation of trophectoderm cells (the outer epithelium of blastocysts) is related to conceptus elongation and placenta formation. Tryptophan (Trp) is a key regulator of embryogenesis and embryonic implantation during pregnancy. We sought to determine whether different concentrations of Trp alters porcine trophectoderm (pTr) cell proliferation. pTr cells were cultured in medium containing 40, 500, or 1000 μM Trp. The cell proliferation rate and the progression of the cells through the cell cycle were determined. To identify differentially expressed genes (DEGs) in the pTr cells, we compared mRNA transcriptomes by RNA-Seq after cell treatment with different concentrations of Trp. Some candidate DEGs were identified by quantitative reverse transcription PCR (qPCR). High L-Trp levels (500 and 1000 μM) inhibited cell proliferation and induced cell cycle arrest. We identified 19 DEGs between the 500 μM L-Trp and 40 μM L-Trp groups and 168 DEGs between the 1000 μM L-Trp and 40 μM L-Trp groups and subsequently used qPCR to validate some genes that were upregulated or downregulated. The functional gene networks in which the DEGs were most enriched included those associated with regulating DNA replication and the cell cycle, and the majority of the DEGs in both of these functional pathways was downregulated. The results showed that the addition of 500 and 1000 μM Trp significantly increased the abundance of proteins in the Aryl Hydrocarbon Receptor (AHR) signaling pathway. Collectively, these results indicate a novel and important role for Trp in mediating the proliferation of porcine placental cells largely via the AHR signaling pathway. Additionally, these findings help to explain the side effects of excessive Trp supplementation on placenta development and embryo growth in mammals.
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Zhou K, Sun M, Xia Y, Xie Y, Shu R. LPS stimulates gingival fibroblasts to express PD-L1 via the p38 pathway under periodontal inflammatory conditions. Arch Oral Biol 2021; 129:105161. [PMID: 34090065 DOI: 10.1016/j.archoralbio.2021.105161] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/12/2021] [Accepted: 05/17/2021] [Indexed: 02/04/2023]
Abstract
OBJECTIVE The overall aim of this research was to investigate the differences in the expression of programmed death ligand 1 (PD-L1) in human gingival fibroblasts (HGFs) between a periodontal healthy group and a periodontal inflammatory group. and explore the possible mechanism involved. METHODS Differences in PD-L1 mRNA and protein expression in HGFs from a periodontal healthy group and a periodontal inflammatory group were examined by qPCR and western blotting, respectively, and were further tested after lipopolysaccharide (LPS) stimulation in both groups. The effects of a p38 pathway inhibitor on the changes in p38 phosphorylation levels and PD-L1 expression after LPS stimulation were investigated in both groups. RESULTS PD-L1 mRNA and protein levels in HGFs in the periodontal inflammatory group were significantly higher than those in the periodontal healthy group (p < 0.05). After 10 μg/mL LPS stimulation, PD-L1 mRNA levels in HGFs from both groups increased significantly (p < 0.05), peaking at 4 h, and the peak was significantly higher in the periodontal inflammatory group than in the periodontal healthy group (p < 0.05). However, PD-L1 protein expression was upregulated only in the inflammatory group (p < 0.05). Inhibition of the p38 pathway in HGFs decreased p38 phosphorylation in both groups (p < 0.05) but this treatment reversed the LPS-induced increase in PD-L1 mRNA and protein levels only in the inflammatory group (p < 0.05). CONCLUSION In the periodontal inflammatory state, the expression of PD-L1 in HGFs is more easily activated, and may be influenced by the p38 pathway.
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Affiliation(s)
- Kecong Zhou
- Department of Periodontology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; College of Stomatology, Shanghai Jiao Tong University, Shanghai, China; National Center for Stomatology, Shanghai, China; National Clinical Research Center for Oral Diseases, Shanghai, China; Shanghai Key Laboratory of Stomatology, Shanghai, China; Laboratory of Oral Microbiota and Systemic Diseases, Shanghai Ninth People's Hospital Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Mengjun Sun
- Department of Periodontology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; College of Stomatology, Shanghai Jiao Tong University, Shanghai, China; National Center for Stomatology, Shanghai, China; National Clinical Research Center for Oral Diseases, Shanghai, China; Shanghai Key Laboratory of Stomatology, Shanghai, China; Laboratory of Oral Microbiota and Systemic Diseases, Shanghai Ninth People's Hospital Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Yiru Xia
- Department of Periodontology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; College of Stomatology, Shanghai Jiao Tong University, Shanghai, China; National Center for Stomatology, Shanghai, China; National Clinical Research Center for Oral Diseases, Shanghai, China; Shanghai Key Laboratory of Stomatology, Shanghai, China; Laboratory of Oral Microbiota and Systemic Diseases, Shanghai Ninth People's Hospital Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Yufeng Xie
- Department of Periodontology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; College of Stomatology, Shanghai Jiao Tong University, Shanghai, China; National Center for Stomatology, Shanghai, China; National Clinical Research Center for Oral Diseases, Shanghai, China; Shanghai Key Laboratory of Stomatology, Shanghai, China; Laboratory of Oral Microbiota and Systemic Diseases, Shanghai Ninth People's Hospital Research Center, Shanghai Jiao Tong University, Shanghai, China.
| | - Rong Shu
- Department of Periodontology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; College of Stomatology, Shanghai Jiao Tong University, Shanghai, China; National Center for Stomatology, Shanghai, China; National Clinical Research Center for Oral Diseases, Shanghai, China; Shanghai Key Laboratory of Stomatology, Shanghai, China; Laboratory of Oral Microbiota and Systemic Diseases, Shanghai Ninth People's Hospital Research Center, Shanghai Jiao Tong University, Shanghai, China.
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Ma Y, Li G, Yu M, Cao K, Li Q, Sun X, Yang G, Wang X. Anti-Lung Cancer Targets of Radix Paeoniae Rubra and Biological Molecular Mechanism: Network Pharmacological Analyses and Experimental Validation. Onco Targets Ther 2021; 14:1925-1936. [PMID: 33758512 PMCID: PMC7981145 DOI: 10.2147/ott.s261071] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 02/23/2021] [Indexed: 12/24/2022] Open
Abstract
Objective To systematically explore the pharmacological mechanism of Radix Paeoniae Rubra (RPR) against lung cancer (LC). Methods A network pharmacology approach, which involves active ingredients and target forecast, network construction, gene ontology and pathway enrichment, was employed in this research. In addition, the effect of Baicalein (BAI) in RPR on A549 cells was researched in vitro and in vivo. Results A total of 159 targets of the 29 active components in RPR were procured by pharmacokinetic parameters. The network analysis showed that β-sitosterol, baicalein, (+)-catechin, ellagic acid, stigmasterol, (2R, 3R)-4-methoxyl-distylin were the main ingredients and JUN, VEGFA, BCL2 were the hub targets of RPR in the treatment of LC. The functional enrichment analysis showed that RPR likely was useful to LC by regulating numerous pathways including Pathways in cancer, MAPK signaling pathway and so on. MTT results showed that 100μM, 200μM, 400μM of BAI had a time and dose-dependent inhibitory effect on A549 cells proliferation; Wound healing and transwell assays showed that 100μM, 200μM, 400μM of BAI could significantly restrain the migration and invasion of A549 cells; Flow cytometry assay results showed that 100μM, 200μM, 400μM of BAI could induce apoptosis of A549 cells. In vivo, BAI (50, 100 mg/kg) significantly inhibited tumor growth and promoted apoptosis of tumor cells compared with the control group. Conclusion BAI in RPR may exert anti-tumor effects by inhibiting the proliferation, migration and invasion of LC cells, and inducing the apoptosis of LC cells.
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Affiliation(s)
- Yunfei Ma
- Department of Oncology, Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, People's Republic of China
| | - Guangda Li
- School of Graduates, Beijing University of Chinese Medicine, Beijing, People's Republic of China
| | - Mingwei Yu
- Department of Oncology, Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, People's Republic of China
| | - Kexin Cao
- Department of Oncology, Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, People's Republic of China
| | - Qiwei Li
- Department of Oncology, Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, People's Republic of China
| | - Xu Sun
- Department of Integrated Chinese and Western Medicine, The Tumor Hospital Affiliated to Zhengzhou University, Zhengzhou, People's Republic of China
| | - Guowang Yang
- Department of Oncology, Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, People's Republic of China
| | - Xiaomin Wang
- Department of Oncology, Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, People's Republic of China
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A novel protective role of sacubitril/valsartan in cyclophosphamide induced lung injury in rats: impact of miRNA-150-3p on NF-κB/MAPK signaling trajectories. Sci Rep 2020; 10:13045. [PMID: 32747644 PMCID: PMC7400763 DOI: 10.1038/s41598-020-69810-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 06/30/2020] [Indexed: 12/12/2022] Open
Abstract
Cyclophosphamide (CP) is a chemotherapeutic agent that induces oxidative stress causing multiple organ damage. Sacubitril/valsartan, is a combined formulation of neprilysin inhibitor (sacubitril) and angiotensin II receptor blocker (valsartan), that induces the protective effect of brain natriuretic peptide. The aim of the current study is to investigate the prophylactic impacts of sacubitril/valsartan versus valsartan against CP-induced lung toxicity in rats. Rats were assigned randomly into 6 groups; control; received corn oil (2 ml/kg/day; p.o. for 6 days), sacubitril/valsartan (30 mg/kg; p.o. for 6 days), valsartan (15 mg/kg; p.o. for 6 days), CP (200 mg/kg; i.p. on day 5), sacubitril/valsartan + CP (30 mg/kg; p.o. for 6 days, 200 mg/kg; i.p. single dose on day 5, respectively), valsartan + CP (15 mg/kg; p.o. for 6 days, 200 mg/kg; i.p. single dose on day 5, respectively). Both sacubitril/valsartan and valsartan produced a significant decrease in the inflammation and fibrosis markers in the BALF, in comparison with the CP group. Both sacubitril/valsartan and valsartan produced an apparent decrease in the relative genes expression of miR-150-3p and NF-κB, as well as a significant decrease in the relative expression of P38 and ERK1/2 MAPKs and an increase in the relative gene expression of Nrf-2, compared to CP group. Intriguingly, sacubitril/valsartan , showed subtle superiority in almost all investigated parameters, compared to valsartan. In conclusion, sacubitril/valsartan effectively abrogated the CP induced lung inflammation and fibrosis, providing a potential promising protection that could be linked to their ability to inhibit miR-150-3p via inhibition of NF-κB and MAPK signaling pathways.
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Zhang D, Cao Y, Zuo Y, Wang Z, Mi X, Tang W. Integrated bioinformatics analysis reveals novel hub genes closely associated with pathological mechanisms of immunoglobulin A nephropathy. Exp Ther Med 2019; 18:1235-1245. [PMID: 31316619 PMCID: PMC6601137 DOI: 10.3892/etm.2019.7686] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 05/09/2019] [Indexed: 02/06/2023] Open
Abstract
Immunoglobulin A (IgA) nephropathy (IgAN) is the most common glomerular disease. The major pathological changes associated with it affect cell proliferation, fibrosis, apoptosis, inflammation and extracellular matrix (ECM) organization. However, the molecular events underlying IgAN remain to be fully elucidated. In the present study, an integrated bioinformatics analysis was applied to further explore novel potential gene targets for IgAN. The mRNA expression profile datasets GSE93798 and GSE37460 were downloaded from the Gene Expression Omnibus database. After data preprocessing, differentially expressed genes (DEGs) were identified. Gene Ontology (GO) enrichment analysis of DEGs was performed. Protein-protein interaction (PPI) networks of the DEGs were built with the STRING online search tool and visualized by using Cytoscape, and hub genes were identified through the degree of connectivity in the PPI. The hub genes were subjected to Kyoto Encyclopedia of Genes and Genomes pathway analysis, and co-expression analysis was performed. A total of 298 DEGs between IgAN and control groups were identified, and 148 and 150 of these DEGs were upregulated and downregulated, respectively. The DEGs were enriched in distinct GO terms for Biological Process, including cell growth, epithelial cell proliferation, ERK1 and ERK2 cascades, regulation of apoptotic signaling pathway and ECM organization. The top 10 hub genes were then screened from the PPI network by Cytoscape. As novel hub genes, Fos proto-oncogene, AP-1 transcription factor subunit and early growth response 1 were determined to be closely associated with apoptosis and cell proliferation in IgAN. Tumor protein 53, integrin subunit β2 and fibronectin 1 may also be involved in the occurrence and development of IgAN. Co-expression analysis suggested that these hub genes were closely linked with each other. In conclusion, the present integrated bioinformatics analysis provided novel insight into the molecular events and novel candidate gene targets of IgAN.
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Affiliation(s)
- Dongmei Zhang
- Department of Nephrology, West China Hospital, Sichuan University, Chengdu, Sichuan 610000, P.R. China
| | - Yiling Cao
- Department of Nephrology, West China Hospital, Sichuan University, Chengdu, Sichuan 610000, P.R. China
| | - Yongdi Zuo
- Department of Nephrology, West China Hospital, Sichuan University, Chengdu, Sichuan 610000, P.R. China
| | - Zheng Wang
- Department of Nephrology, West China Hospital, Sichuan University, Chengdu, Sichuan 610000, P.R. China
| | - Xuhua Mi
- Department of Nephrology, West China Hospital, Sichuan University, Chengdu, Sichuan 610000, P.R. China
| | - Wanxin Tang
- Department of Nephrology, West China Hospital, Sichuan University, Chengdu, Sichuan 610000, P.R. China
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