Screening and bioinformatics analysis of key autophagy-related genes in alcoholic hepatitis / 器官移植

Objective To screen key autophagy-related genes in alcoholic hepatitis (AH) and investigate potential biomarkers and therapeutic targets for AH. Methods Two AH gene chips in Gene Expression Omnibus (GEO) and autophagy-related data sets obtained from MSigDB and GeneCards databases were used, and the key genes were verified and obtained by weighted gene co-expression network analysis (WGCNA). The screened key genes were subject to gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), protein-protein interaction (PPI) and immune infiltration analyses. Messenger RNA (mRNA)- microRNA (miRNA) network was constructed to analyze the expression differences of key autophagy-related genes during different stages of AH, which were further validated by real-time fluorescence quantitative polymerase chain reaction (RT-qPCR) in the liver tissues of AH patients and mice. Results Eleven autophagy-related genes were screened in AH (EEF1A2, CFTR, SOX4, TREM2, CTHRC1, HSPB8, TUBB3, PRKAA2, RNASE1, MTCL1 and HGF), all of which were up-regulated. In the liver tissues of AH patients and mice, the relative expression levels of SOX4, TREM2, HSPB8 and PRKAA2 in the AH group were higher than those in the control group. Conclusions SOX4, TREM2, HSPB8 and PRKAA2 may be potential biomarkers and therapeutic targets for AH.

Bioinformatics analysis and validation of key genes in transformation of idiopathic membranous nephropathy to end-stage renal disease and traditional Chinese medicines for prevention and treatment / 中国中药杂志

This study used bioinformatics analysis to screen out key genes involved in the transformation of idiopathic membranous nephropathy to end-stage renal disease and to predict targeted Chinese herbs and medicines and active ingredients with preventive and curative effects. The GSE108113 microarray of idiopathic membranous nephropathy and GSE37171 microarray of were downloaded from the comprehensive gene expression database, and 8 homozygous differentially expressed genes for the transformation of idiopathic membranous nephropathy into end-stage renal disease of were screened out by R software. GraphPad Prism was used to verify the expression of homozygous differentially expressed genes in GSE115857 microarray of idiopathic membranous nephropathy and GSE66494 microarray of chronic kidney disease, and 7 key genes(FOS, OGT, CLK1, TIA1, TTC14, CHORDC1, and ANKRD36B) were finally obtained. The Gene Ontology(GO) analysis was performed. There were 209 functions of encoded proteins, mainly involved in regulation of RNA splicing, cytoplasmic stress granule, poly(A) binding, etc. Thirteen traditional Chinese medicines with the effect of preventing the transformation of idiopathic membranous nephropathy to end-stage renal disease were screened out from Coremine Medical database, including Ginseng Radix et Rhizoma, Lycopi Herba, and Gardeniae Fructus, which were included in the Chinese Pharmacopoeia(2020 edition). The active ingredient quercetin mined from Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform(TCMSP) had ability to dock with the key gene FOS-encoded protein molecule, which provided targets and research ideas for the development of new traditional Chinese medicines.

Key Prediction Genes of Nasopharyngeal Carcinoma:Screening Based on Systematic Bioinformatics and Validation by Cell Experiments / 中国医学科学院学报

Objective To screen out the potential prediction genes for nasopharyngeal carcinoma(NPC)from the gene microarray data of NPC samples and then verify the genes by cell experiments.Methods The NPC dataset was downloaded from Gene Expression Omnibus,and limma package was employed to screen out the differentially expressed genes.Weighted correlation network analysis package was used for weighted gene co-expression network analysis,and Venn diagram was drawn to find the common genes.The gene ontology annotation and Kyoto encyclopedia of genes and genomes pathway enrichment were then performed for the common genes.The biomarkers for NPC were further explored by protein-protein interaction network,LASSO regression,and non-parametric tests.Real-time quantitative PCR and Western blotting were employed to determine the mRNA and protein levels of key predictors of NPC,so as to verify the screening results.Results There were 622 up-regulated genes and 351 down-regulated genes in the GSE12452 dataset.A total of 116 common genes were obtained by limma analysis and weighted gene co-expression network analysis.The common genes were mainly involved in the biological processes of cell proliferation and regulation and regulation of intercellular adhesion.They were mainly enriched in Rap1,Ras,and tumor necrosis factor signaling pathways.Six key genes were screened out,encoding angiopoietin-2(ANGPT2),dual oxidase 2(DUOX2),coagulation factor Ⅲ(F3),interleukin-15(IL-15),lipocalin-2,and retinoic acid receptor-related orphan receptor B(RORB).Real-time quantitative PCR and Western blotting showed that the NPC cells had up-regulated mRNA and protein levels of ANGPT2 and IL-15 and down-regulated mRNA and protein levels of DUOX2,F3,and RORB,which was consistent with the results predicted by bioinformatics.Conclusion ANGPT2,DUOX2,F3,IL-15 and RORB are potential predictive molecular markers and therapeutic targets for NPC,which may be involved in Rap1,Ras,tumor necrosis factor and other signaling pathways.

The expression of GSTM5 in prostate cancer and its potential mechanism for the progress of prostate cancer / 西安交通大学学报(医学版)

【Objective】 To explore the differentially expressed genes in normal prostate and prostate cancer (PCa) tissues based on bioinformatics and screen out potential biomarkers for PCa, so as to provide scientific basis for later clinical medicine. 【Methods】 Three gene chip datasets of GSE55945, GSE46602 and GSE69223 were downloaded from GEO database, and differentially expressed genes (DEGs) were screened by the OmicStudio tools, and protein-protein interaction network (PPI) of DEGs was constructed by STRING. After Cytoscape was imported, CytoHubba plug-in was used to screen the top 30 genes in MCC score as key genes (Hub gene). DAVID was used for GO and KEGG enrichment analysis of Hub gene, and GraphPad Prism software was used to draw ROC curve. GEPIA database was used to verify the key genes, and survival analysis was further carried out. UALCAN was used to verify the correlation between the expression of key genes and Gleason grade of PCa. 【Results】 Three data sets (GSE55945, GSE46602 and GSE69223) obtained 428, 727 and 1285 differentially expressed genes, respectively. The Venn diagram shows that the three datasets contain 105 DEGs. Among 105 PPI networks corresponding to DEGs, the top 30 genes with MCC score were selected as Hub genes. The biological processes involved mainly include the positive regulation of protein kinase B signal, cell differentiation, positive regulation of transcription, negative regulation of transforming growth factor β receptor signaling pathway, positive regulation of cell migration, etc. The pathways involved are adhesion plaque, estrogen signaling pathway, etc. ROC curve results showed that the diagnostic ability of 9 genes in 3 data sets was statistically significant, and 9 Hub genes were CAV1, KDR, CAV2, TGFBR1, SLC7A11, GSTM2, GSTM3, GSTM5 and MYO6. Nine Hub genes were verified by GEPIA website, among which CAV1, KDR, CAV2, TGFBR1, GSTM2, GSTM3 and GSTM5 showed low expression in PCa, while SLC7A11 and MYO6 showed high expression in PCa. Survival analysis suggested that high GSTM5 expression prolonged OS in PCa patients. UALCAN results showed that the expression of GSTM5 gene was significantly correlated with Gleason grade, and the expression of GSTM5 gene decreased with the increase of Gleason score. 【Conclusion】 Hub genes CAV1, KDR, CAV2, TGFBR1, GSTM2, GSTM3 and GSTM5 are low expression in PCa, while SLC7A11 and MYO6 are high expression in PCa. GSTM5 gene is related to the survival rate of PCa. The expression of GSTM5 decreased with the increase of Gleason score, which indicated that GSTM5 may be a potential biomarker for PCa.

Identification of key genes in nonarteritic anteriorischemic optic neuropathy through weighted gene co-expression network analysis / 国际眼科杂志(Guoji Yanke Zazhi)

AIM: We sought to identify key genes related to nonarteritic anterior ischemic optic neuropathy(NAION)and provide bioinformatics support for elucidating the pathogenesis of NAION.METHODS: Based on rat GSE43671 dataset, which was acquired from GEO, we identified modular genes with highly correlated clinical phenotype by WGCNA package in the R language. Then Gene Ontology(GO)and Kyoto encyclopedia of genes and genomes(KEGG)analysis were performed with ClusterProfiler package. In addition, Cytoscape was used to screen potential key genes and establish miRNA-key genes network.RESULTS: There were 22 modules identified from the GSE43671 dataset by the WGCNA method, among which the blue module has the highest correlation coefficient. GO enrichment analysis suggested that the genes in the module mainly manifest in the epithelial tube morphogenesis and other biological processes, receptor complex and other cell components, and structural constituent of eye lens and other molecular functions. KEGG suggested that the genes in the module mainly relate to signaling pathways including neuroactive ligand-receptor interaction, human papillomavirus, MAPK and PI3K/Akt. There were 10 key genes screened by PPI network and Cytoscape including Psmb9, Psma7, Map3k14, Psme1, Nfkb1, Rela, Psma5, Relb, Psmb4 and Nfkb2, and 6 miRNA were predicted as miR-383-5p, miR-9a-5p, miR-155-5p, miR-223-3p, miR-495 and miR-325-3p.CONCLUSION: Using the WGCNA method to screen out the relevant pathways, key genes, and microRNA for NAION, it provides a theoretical basis for exploring pathogenesis and treatment methods of NAION, however, more animal and cell experiments are needed to further validate.

Transcriptomics analysis of key genes and signaling pathways in sepsis-related exogenous acute respiratory distress syndrome / 中华危重病急救医学

Objective:To analyze the differentially expressed gene (DEG) in rats with sepsis-induced exogenous acute respiratory distress syndrome (ARDS) and explore the early diagnosis and protective mechanism of sepsis-induced ARDS at the transcriptome level.Methods:Twelve 6 to 8 weeks old male Sprague-Dawley (SD) rats were randomly divided into lipopolysaccharide (LPS) induced sepsis-induced ARDS model group (model group, intraperitoneal injection of LPS 15 mg/kg) and control group (intraperitoneal injection of the same volume of normal saline), with 6 rats in each group. RNA was extracted from the left lung tissue of the two groups, and the paired-end sequencing mode of the illumina Hiseq sequencing platform was used for high-throughput sequencing. The DESeq2 software was used to screen DEG with | log 2 (fold change, FC) | ≥ 3 and P < 0.001. Gene ontology (GO) function enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed on DEG. STRING and CytoScape software were used to construct a protein-protein interaction (PPI) network and screen key genes. The peripheral blood mononuclear cell (PBMC) of 20 septic patients admitted to the emergency and critical care medical department of Lianyungang First People's Hospital from March to November 2021 and 20 age-matched healthy people in the same period were isolated and extracted, and the key genes were verified by real-time fluorescent quantitative polymerase chain reaction (RT-qPCR). Results:A total of 286 DEG were screened, including 202 up-regulated genes and 84 down-regulated genes. GO enrichment analysis showed that DEG was mainly involved in biological processes such as neutrophil chemotaxis migration, antibacterial humoral response, host immune response, and humoral immune response. KEGG analysis showed that DEG mainly played a biological role through interleukin-17 (IL-17) signaling pathway, tumor necrosis factor (TNF) signaling pathway, and chemokine signaling pathway. In PPI analysis, a total of 262 node proteins were screened, and the interaction relationship was 852 edges. The first 15 key genes were IL-6, TNF, IL-10, IL-1β, chemokine ligand 1 (CXCL1), CXCL10, chemokine receptor 3 (CXCR3), CXCR2, CXCL9, chemokine ligand 7 (CCL7), CXCL11, CCL1, CXCL13, CCL12, and CCL22. Five representative key genes were performed on PBMC of blood samples from septic ARDS patients and healthy controls by RT-qPCR. The results showed that their expression was significantly higher than that in the healthy controls [IL-6 mRNA (2 -ΔΔCt): 2.803±1.081 vs. 0.951±0.359, TNF mRNA (2 -ΔΔCt): 2.376±0.799 vs. 1.150±0.504, CXCL10 mRNA (2 -ΔΔCt): 2.500±0.815 vs. 1.107±0.515, CXCR3 mRNA (2 -ΔΔCt): 1.655±0.628 vs. 0.720±0.388, CCL22 mRNA (2 -ΔΔCt): 1.804±0.878 vs. 1.010±0.850, all P < 0.05], and the trends were consistent with the RNA-Seq results. Conclusion:Biological processes such as chemotactic migration and degranulation of inflammatory cells, cytokine immune response, and signal pathways such as CXCL10/CXCR3 and IL-17 play important roles in the occurrence and development of sepsis-related exogenous ARDS, which would provide new ideas and targets for further study of lung injury mechanisms and clinical prevention and treatment.

Analysis of sepsis-related genes through weighted gene co-expression network / 中华危重病急救医学

Objective:To identify the Key genes in the development of sepsis through weighted gene co-expression network analysis (WGCNA).Methods:The gene expression dataset GSE154918 was downloaded from the public database Gene Expression Omnibus (GEO) database, which containes data from 105 microarrays of 40 control cases, 12 cases of asymptomatic infection, 39 cases of sepsis, and 14 cases of follow-up sepsis. The R software was used to screen out differentially expressed genes (DEG) in sepsis, and the distributed access view integrated database (DAVID), search tool for retrieval of interacting neighbouring genes (STRING) and visualization software Cytoscape were used to perform gene function and pathway enrichment analysis, Protein-protein interaction (PPI) network analysis and key gene analysis to screen out the key genes in the development of sepsis.Results:Forty-six candidate genes were obtained by WGCNA and combined with DEG expression analysis, and these 46 genes were analyzed by gene ontology (GO) and Kyoto City Encyclopedia of Genes and Genomes (KEGG) pathway enrichment to obtain gene functions and involved signaling pathways. The PPI network was further constructed using the STRING database, and 5 key genes were selected by the PPI network visualization software Cytoscape, including the mast cell expressed membrane protein 1 gene (MCEMP1), the S100 calcium-binding protein A12 gene (S100A12), the adipokine resistance factor gene (RETN), the c-type lectin structural domain family 4 member gene (CLEC4D), and peroxisome proliferator-activated receptor gene (PPARG), and differential expression analysis of each of these 5 genes showed that the expression levels of the above 5 genes were significantly upregulated in sepsis patients compared with healthy controls.Conclusion:In this study, 5 key genes related to sepsis were screened by constructing WGCNA method, which may be potential candidate targets related to sepsis diagnosis and treatment.

Biosynthesis of Steroidal Saponins in Herbs / 中国实验方剂学杂志

Steroidal saponins are efficacious substances wildly existed in the herbs，and consist of glycosyl and steroid sapogenin. The biosynthesis pathways of steroidal saponins mainly include the cytosolic mevalonate （MVA） pathway and the plastidial methylerythritol 4-phosphate （MEP） pathway，with the MVA pathway as the main pathway. The key enzymes are involved in the biosynthetic pathway, including 3-hydroxy-3-methyl glutaryl coenzyme A reductase（HMGR），1-deoxy-D-xylulose 5-phosphate synthase（DXS），1-deoxy-D-xylulose-5-phosphatereduetoisomerase（DXR），farnesyl pyrophosphate synthase（FPS），squalene synthase（SS），squalene epoxidase（SE），cycloartenol synthase（CAS），cytochrome P450（CYP450），and steroidalglycosyltransferase（SGTase）. In the paper，the biosynthesis roadmap of steroidal saponins was optimized based on previous studies. According to a comprehensive analysis on studies of key enzymes for the past five years, genes, like HMGR，SS，CYP450 and UGT，were studied more，while other genes，like FPS，SE，CAS，were known less. In conclusion， current studies still focus on the primary stage，but lack direct evidence for the roles of key enzymes. This paper would provide a reference and theoretical support for subsequent studies.

Quantitative effect of the expression level of key genes in naringenin synthesis on the accumulation level of target products / 生物工程学报

Naringenin is a natural flavonoid compound with anti-inflammatory, anti-oxidation, anti-viral, anti-atherosclerosis and other pharmacological activities. It is also an important precursor of other flavonoid synthesis and with great value of application. At present, the production of flavonoids such as naringenin by microbial methods has a low yield due to imbalance of metabolic pathways, which greatly limits its industrial application. In this study, a naringenin-producing strain of Saccharomyces cerevisiae Y-01 was used in the research object. The expression levels of 4-coumaric acid: CoA ligase (4CL), chalcone synthase (CHS) and chalcone isomerase (CHI) were controlled by promoter and copy numbers to investigate the quantitative effect of key enzyme expression level on the accumulation level of target products. The results showed that the correlation between naringenin production and 4CL or CHI expression was not significant while there was a positive correlation with the expression level of CHS. Strain Y-04 with high yield of naringenin was obtained by regulating the expression level of chs gene, and the yield was increased by 4.1-folds compared with the original strain Y-01. This study indicated that CHS is a key regulatory target of naringenin synthesis. Rational regulation of CHS expression can significantly promote the accumulation of naringenin. The related results provide an important theoretical reference for the use of metabolic engineering to strengthen microbial synthesis of important flavonoids such as naringenin.

Mechanism of Modified Taohe Chengqitang in Treating Diabetic Nephropathy Based on Network Pharmacology / 中国实验方剂学杂志

Objective: To study the mechanism of modified Taohe Chengqitang in preventing and treating diabetic nephropathy by means of network pharmacology. Method: Target genes of modified Taohe Chengqitang were obtained from BAT-MAN database, while target genes of diabetic nephropathy were obtained from CTD database. The target genes of disease-drug protein were obtained by crossing two groups of genes. STRING was used to build the protein-protein interaction network and visualize the results. The key genes were screened out through the computational analysis algorithm of network structure and weighted relatedness between nodes. With DAVID online tools, gene ontology (GO) analysis of Disease-Drug Intersection Target Genes and enrichment analysis of kyoto encyclopedia of genes and genomes(KEGG) pathway were conducted. Finally, CTD database and literature study were used to obtain the key genes in the treatment of diabetic nephropathy. Result: Among 621 compounds in modified Taohe Chengqitang, 581 of them were related to diabetic nephropathy. NOS3, OAT, NT5C2, ACACB, AGXT, PDE3B and other key genes mainly regulated nerve tissue transmission, cholinergic synaptic pathway, calcium channel, metabolic pathway, purine metabolic pathway, angiotensin-neurosynaptic pathway, cyclic guanosine monophosphate/cGMP-dependent protein kinase G (cGMP/PKG) signaling pathway and cyclic adenosine phosphate signaling pathway, with effect in molecular reactions, such as plasma membrane, postsynaptic membrane and mitochondria. Conclusion: The network pharmacology predicts the key targets of modified Taohe Chengqitang in the prevention and treatment of diabetic nephropathy and the related pathways involved, suggesting a multi-target, multi-channel and multi-choice complex mechanism, and which is mostly related to anti-inflammation, oxidative phosphorylation and purine metabolism.

Interference of DEHP on the key genes of glucose and lipid metabolism in HepG2 cells / 中国职业医学

OBJECTIVE: To investigate the effects of di-( 2-ethylhexyl) phthalate( DEHP) on the expression of the key genes involved in glucose and lipid metabolism,and explore the toxicity of DEHP on the glucose and lipid metabolism in HepG2 cells cultured in vitro. METHODS: HepG2 cells in logarithmic growth phase were divided into DEHP exposure group and control group. The exposure group was exposed to DEHP with different final concentrations( 5,10,50,100,500 and1 000 μmol / L),and the control group was exposed to dimethyl sulfoxide of corresponding concentrations. After 24 hours of DEHP exposure,real-time fluorescence quantitative polymerase chain reaction( Q-PCR) was applied to detect the level of mRNA transcription of peroxisome proliferators-activated receptor α( PPARα), which is an endogenous marker indicating the success of DEHP exposure. In addition,the level of mRNA transcription of key genes involved in glucose and lipid metabolism were also measured by Q-PCR,including glucose-6-phosphatase( G-6-Pase),phosphoenolpyruvate carboxykinase( PEPCK),stearoyl-coenzyme A desaturase 1( SCD1),fatty acid synthase,sterol regulatory elementbinding protein 1c and acetyl Co A carboxylase 1. P ≤0. 008 was considered as statistical significance. RESULTS: After DEHP exposure,the mRNA transcription level of PPARα was significantly elevated in all exposure groups( P < 0. 008)except for 5 μmol / L DEHP exposure group,which indicated the successful establishment of DEHP exposure model. The mRNA transcription level of G-6-Pase was significantly increased in 100 and 500 μmol / L DEHP exposure groups( P ≤0. 008) when compared with the controls; the PEPCK mRNA transcription level of showed no significant differences between the 6 DEHP exposure groups and their corresponding control groups( P > 0. 008). The mRNA transcription level of SCD1 was significantly down-regulated in 100 μmol / L DEHP exposure group( P < 0. 008) when compared with its control. The mRNA transcription level of other key genes involved in the lipid metabolism were not significantly altered after DEHP exposure( P > 0. 008). CONCLUSION: The effect of DEHP on glucose metabolism was mainly manifested by promoting G-6-Pase gene expression,which is the rate-limiting enzyme for gluconeogenesis. The effect of DEHP on the lipid metabolism of HepG2 cells was limited.