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Identification of EML4 as a key hub gene for endometriosis and its molecular mechanism and potential drug prediction based on the GEO database

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生物细胞(英文) 2023年第9期47卷 2059-2068页

作者： XIANBAO FANG MINGYAN TANG ZIYANG YU JIAQI DING CHONG CUI HONG ZHANG Reproductive Medicine Center The Second Affiliated Hospital of Soochow UniversitySuzhou215002China Imaging Diagnosis Department The Second Affiliated Hospital of Soochow UniversitySuzhou215002China

Objective:Key genes were screened to analyze molecular mechanisms and their drug targets of endometriosis by applying a bioinformatics ***:Gene expression profiles of endometriosis and healthy controls were obtained from the Gene Expression Omnibus *** differentially expressed genes were screened using the limma *** pathways were screened by Spearman correlation analysis on the echinoderm microtubule-associated protein-like 4(EML4)and enrichment in endometriosis pathways and estimated by the GSVA *** characteristics were assessed by the“ESTIMATE”R *** regulatory pathways were determined by enrichment *** SWISS-MODE website was used in homology modeling with EML4 and EML4 protein activity was *** was employed in molecular docking for screening potential compound inhibitors targeting ***:Ten endometriosis and 10 normal samples were ***4 was significantly upregulated in endometriosis(p<0.05).Thirty significantly correlated pathways involving 18 positive and 12 negative correlations,including GLYCOSAMINOGLYCAN_BIOSYNTHESIS_HEPARAN_SULFATE and GLYCOSPHINGOLIPID_BIOSYNTHESIS_GANGLIO_SERIES were screened between EML4 and *** analysis showed a significant difference in immune-related pathways in endometriosis and normal samples(p<0.05).In endometriosis,EML4 was associated with T-cell CD4 resting memory,activated mast cells,plasma cells,activated NK cells,M2 macrophages,and follicular helper T cells(p<0.05).Molecular docking identified five potential inhibitors of EML4,and compound DB05104(asimadoline)bound well to EML4 protein to exert its physiological ***:Differential gene expression and immune correlation analyses revealed that EML4 may affect endometriosis through multiple targets and pathways,the mechanism of which involved immune cell activation and *** docking and dynamics simulation ve

关键词： Endometriosis EML4 Immune drug prediction

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Key genes and regulatory networks for diabetic retinopathy based on hypoxia-related genes:a bioinformatics analysis

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International Journal of Ophthalmology(English edition) 2024年第8期17卷 1411-1417页

作者： Cai-Han Yu Cai-Xia Wu Dai Li Lan-Lan Gong Xu-Dong Lyu Jie Yang Department of Ophthalmology Xianning Central HospitalThe First Affiliated Hospital of Hubei University of Science and TechnologyXianning 437100Hubei ProvinceChina School of Pharmacy Xianning Medical CollegeHubei University of Science and TechnologyXianning 437100Hubei ProvinceChina School of Optometry Hubei University of Science and TechnologyXianning 430071Hubei ProvinceChina

AIM:To prevent neovascularization in diabetic retinopathy(DR)patients and partially control disease ***:Hypoxia-related differentially expressed genes(DEGs)were identified from the GSE60436 and GSE102485 datasets,followed by gene ontology(GO)functional annotation and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment *** candidate drugs were screened using the CMap ***,a protein-protein interaction(PPI)network was constructed to identify hypoxia-related hub genes.A nomogram was generated using the rms R package,and the correlation of hub genes was analyzed using the Hmisc R *** clinical significance of hub genes was validated by comparing their expression levels between disease and normal groups and constructing receiver operating characteristic curve(ROC)***,a hypoxia-related miRNA-transcription factor(TF)-Hub gene network was constructed using the NetworkAnalyst online ***:Totally 48 hypoxia-related DEGs and screened 10 potential candidate drugs with interaction relationships to upregulated hypoxia-related genes were identified,such as ruxolitinib,meprylcaine,and *** addition,8 hub genes were also identified:glycogen phosphorylase muscle associated(PYGM),glyceraldehyde-3-phosphate dehydrogenase spermatogenic(GAPDHS),enolase 3(ENO3),aldolase fructose-bisphosphate C(ALDOC),phosphoglucomutase 2(PGM2),enolase 2(ENO2),phosphoglycerate mutase 2(PGAM2),and 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3(PFKFB3).Based on hub gene predictions,the miRNA-TF-Hub gene network revealed complex interactions between 163 miRNAs,77 TFs,and hub *** results of ROC showed that the except for GAPDHS,the area under curve(AUC)values of the other 7 hub genes were greater than 0.758,indicating their favorable diagnostic ***:PYGM,GAPDHS,ENO3,ALDOC,PGM2,ENO2,PGAM2,and PFKFB3 are hub genes in DR,and hypoxia-related hub genes exhibited favorable diagnostic perform

关键词： diabetic retinopathy hypoxia-related genes hub genes miRNA-TF-Hub gene drug prediction

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Liver tissue microbiota in nonalcoholic liver disease:a change in the paradigm of host-bacterial interactions

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Hepatobiliary Surgery and Nutrition 2021年第3期10卷 337-349页

作者： Silvia Sookoian Carlos J.Pirola School of Medicine Institute of Medical Research A LanariUniversity of Buenos AiresCiudad Autónoma de Buenos AiresArgentina Department of Clinical and Molecular Hepatology Institute of Medical Research(IDIM)National Scientific and Technical Research Council(CONICET)University of Buenos AiresCiudad Autónoma de Buenos AiresArgentina Department of Molecular Genetics and Biology of Complex Diseases Institute of Medical Research(IDIM)National Scientific and Technical Research Council(CONICET)University of Buenos AiresCiudad Autónoma de Buenos AiresArgentina

Nonalcoholic fatty liver disease(NAFLD)pathogenesis is explained by the complex relationship among diet and lifestyle-predisposing factors,the genetic variance of the nuclear and mitochondrial genome,associated phenotypic traits,and the yet not fully explored interactions with epigenetic and other environmental factors,including the *** the wealth of knowledge gained from molecular and genome-wide investigations in patients with NAFLD,the precise mechanisms that explain the variability of the histological phenotypes are not fully *** studies of the gut microbiota in patients with NAFLD and nonalcoholic steatohepatitis(NASH)provided clues on the role of the fecal microbiome in the disease ***,the composition of the gut microbiota does not fully explain tissue-specific mechanisms associated with the degree of disease severity,including liver inflammation,ballooning of hepatocytes,and *** liver acts as a key filtration system of the whole body by receiving blood from the hepatic artery and the portal ***,not only microbes would become entrapped in the complex liver anatomy but,more importantly,bacterial derived products that are likely to be potentially powerful stimuli for initiating the inflammatory ***,the study of liver tissue microbiota offers the opportunity of changing the paradigm of host-NAFLD-microbial interactions from a“gut-centric”to a“liver-centric”***,we highlight the evidence on the role of liver tissue bacterial DNA in the biology of NAFLD and ***,we provide evidence of metagenomic findings that can serve as the seed of further hypothesis-raising studies as well as can be leveraged to discover novel therapeutic targets.

关键词： Nonalcoholic fatty liver disease(NAFLD) nonalcoholic steatohepatitis(NASH) HSD17B13 microbiota microbiome proteobacteria lipopolysaccharide(LPS) drug prediction

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Bioinformatics analysis of SARS-CoV-2 infectionassociated immune injury and therapeutic prediction for COVID-19

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Emergency and Critical Care Medicine 2021年第1期1卷 20-28页

作者： Haomin Zhang Haoran Chen Jundong Zhang Ximeng Chen Bin Guo Peng Zhi Zhuoyang Li Geliang Liu Bo Yang Xiaohua Chi Yixing Wang Feng Cao Jun Ren Xuechun Lu Department of Hematology the Second Medical Center of the China PLA General Hospital&National Center for Clinical Medicine of Geriatric DiseasesBeijingChina Management School Shanxi Medical UniversityTaiyuanChina Chinese Journal of Hepatobiliary Surgery BeijingChina Department of Personnel Cardiovascular Disease Hospital of Shanxi ProvinceTaiyuanChina Department of Pharmacy China PLA Special Medical CenterBeijingChina Department of Internal Medicine of Traditional Chinese Medicine Shanghai East HospitalTongji University School of MedicineShanghaiChina Department of Cardiology the Second Medical Center of the China PLA General HospitalBeijingChina School of Pharmacy University of Wyoming College of Health SciencesLaramieWYUSA

Background:Severe acute respiratory syndrome coronavirus 2 is a highly contagious viral infection,without any available targeted *** high mortality rate of COVID-19 is speculated to be related to immune ***:In this study,clinical bioinformatics analysis was conducted on transcriptome data of coronavirus ***:Bioinformatics analysis revealed that the complex immune injury induced by coronavirus infection provoked dysfunction of numerous immune-related molecules and signaling pathways,including immune cells and toll-like receptor *** of numerous cytokines through the Th17 signaling pathway led to elevation in plasma levels of cytokines(including IL6,NF-kB,and TNF-a)followed by concurrent inflammatory storm,which mediates the autoimmune *** novel medications seemed to display therapeutic effects on immune damage associated with coronavirus ***:This study provided insights for further large-scale studies on the target therapy on reconciliation of immunological damage associated with COVID-19.

关键词： Bioinformatics Coronavirus COVID-19 drug prediction Immune injury

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