Bioinformatics based analysis of key genes underlying the development of nonalcoholic fatty liver disease / 中华内分泌代谢杂志

Objective:To identify key genes and their potential biological mechanisms in the progression of non-alcoholic fatty liver disease (NAFLD) using bioinformatics technology.Methods:Genes differentially expressed in simple non-alcoholic fatty liver disease (NAFL) and non-alcoholic steatohepatitis (NASH) were analyzed by integrating NAFLD-related sequencing datasets GSE135251 and GSE167523 from the Gene Expression Omnibus (GEO) datebase. Gene Ontology (GO) functional enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) and Reactome signaling pathway analysis were performed. Key genes were identified by STRING database and Cytoscape3.7.2 software, and the expression of key genes under different fibrosis grades and activity scores was observed. In addition, the expression of key genes in different cell clusters was observed based on the single-cell RNA-seq dataset of NAFLD mice.Results:Bioinformatics methods were used to obtain 97 common differential genes in NAFLD from two datasets. GO functional enrichment analysis was mainly performed in Extracellular Matrix (ECM) tissues. The main signaling pathway is ECM-receptor interaction. Five key genes were identified based on PPI network and Cytoscape software: COL1A1, THBS2, CXCL8, THY1 and LOXL1. The expression of key genes was significantly positively correlated with fibrosis grade and activity score, indicating that they were closely related to the progression of NAFLD. These key genes are highly expressed in hepatic stellate cells (HSCs) and natural killer/T cells (NK/T cells).Conclusion:In this study, bioinformatics technology was used to identify five key genes that may be involved in the NAFL-NASH transformation, suggesting that the ECM-receptor interaction signaling pathway may be a key molecular mechanism of NAFLD disease progression.

Key Genes of Peripheral Blood Mononuclear Cells in Hepatocellular Carcinoma and Effective Chinese Herbs： A Bioinformatics Analysis and Systematic Review / 中国实验方剂学杂志

Objective:To explore the key gens of peripheral blood mononuclear cells in hepatocellular carcinoma（HCC-PBMC） and potentially effective Chinese herbs based on bioinformatics， and to verify the clinical efficacy of these Chinese herbs via a systematic review. Method:The chips GSE58208 and GSE36076 of HCC-PBMC were downloaded from the Gene Expression Omnibus （GEO）， followed by the identification of differentially expressed genes （DEGs） using RStudio. After protein-protein interaction （PPI） analysis by STRING， the DAVID was employed for gene ontology （GO） and Kyoto Encyclopedia of Genes and Genomes （KEGG） enrichment analysis. The DEGs of HCC-PBMC were visualized by Cytoscape. The key genes of HCC-PBMC were calculated by CytoHubba plug-in and mapped with those in Coremine Medical for screening out the potential Chinese herbs for the treatment of HCC， which were then included for subsequent systematic review. Result:A total of 203 DEGs were obtained （194 up-regulated and nine down-regulated）. As revealed by DAVID analysis， the DEGs were mainly enriched in such biological processes and signaling pathways as transcriptional regulation of DNA template， hydrolysis of ribonucleic acid phosphodiester bond， positive regulation of intranuclear mitosis and division， skeletal muscle fiber development， activation of mitogen-activated protein kinase（MAPK）activity， Fanconi anemia pathway， and metabolic pathway. The key genes of HCC-PBMC were calculated by Cytoscape to be<italic> </italic>GTPase IMAP family member 1 （GIMAP1）， GTPase IMAP family member 4 （GIMAP4）， GTPase IMAP family member 6 （GIMAP6）， GTPase IMAP family member 7 （GIMAP7）， GTPase IMAP family member 8 （GIMAP8）， interleukin-1<italic>β </italic>（IL-1<italic>β）</italic>， CX3C chemokine receptor 1 （CX3CR1）， C-C chemokine receptor type 2 （CCR2）， Toll-like receptor 7（TLR7）， and epidermal growth factor（EGF）. Through Coremine Medical analysis， it was concluded that Ginseng Radix et Rhizoma， Curcumae Longae Rhizoma， Centellae Herba， and Hedyotidis Herba were closely related to the key genes. Ginseng Radix et Rhizoma has the effects of tonifying and benefiting lung and spleen and enhancing strength， suitable for the liver depression and spleen deficiency syndrome or Qi-Yin deficiency syndrome of HCC. Hence， Si Junzitang with Ginseng Radix et Rhizoma as the sovereign medicinal was included for systematic review. It has been confirmed that Ginseng Radix Et Rhizoma was superior to western medicine alone in improving the overall clinical efficacy， alleviating TCM syndrome， elevating serum CD4⁺and CD4⁺/CD8⁺levels， and reducing the serum CD8⁺and TBIL levels （<italic>P</italic><0.01）， with high safety. Conclusion:This study conducted at the gene level has provided new ideas for clinical diagnosis and treatment of HCC. The systematic review of Ginseng Radix Et Rhizoma against HCC provides a basis for the clinical prevention and treatment of HCC with TCM.

Bioinformatics analysis of key genes and its biofunction of aldosterone producing adenoma / 中华内分泌代谢杂志

Objective:To explore the key genes and its biological functions of aldosterone producing adenoma (APA) using bioinformatics analysis.Methods:Differentially expressed genes of APA were identified from two training datasets GSE60042 and GSE64957 in GEO database. Function and pathway enrichment analyses for differentially expressed genes were performed and transcriptional regulation network among these genes were determined. Hub genes were extracted by node analysis from the protein-protein interaction (PPI) network. The expression of key genes was verified by a testing dataset GSE8514. Receiver operating characteristic(ROC) curve analysis was applied to assess the diagnostic efficiency of key genes in APA. The biofunction of each key gene were determined by gene set enrichment analysis (GSEA).Results:A total of 68 differentially expressed genes, including 33 up-regulated genes and 35 down-regulated genes, were detected from the training datasets. These genes were mainly enriched in aldosterone biosynthetic process, calcium signaling pathway, serotonin receptor signaling pathway, transcriptional activator activity, and regulation of transcription. JUN and VDR were at the center of the transcriptional factor-gene network. Furthermore, we identified nine Hub genes from the PPI network. In testing dataset, CYP11B2 and VDR showed the higher expression, while JUN, NFKBIZ, EGR3, and KLF6 showed lower expression in APA (all P<0.05), and the value of area under ROC curve analysis was 0.936, 0.833, 0.953, 0.854, 0.868, and 0.929, respectively. GSEA indicated the alter of key genes in APA led to up-regulation of the steroid biosynthesis, cell adhesion molecules, immune cells signaling pathway, and complement and coagulation cascades [all normalized enrichment score (NES)>1.5, P<0.05], but down-regulation of the DNA replication, ribosome, and autophagy (all NES<-1.5, P<0.05). Conclusion:Results of bioinformatics indicate that JUN and VDR are key transcriptional factors, and CYP11B2, NFKBIZ, EGR3, and KLF6 are the key genes for APA, which are involved in the steroid biosynthesis, cell adhesion molecules, immune cells signaling pathway in APA.

Mining genes associated with furanocoumarin biosynthesis in an endangered medicinal plant, Glehnia littoralis

The endangered medicinal plant Glehnia littoralis is one of the important natural source of furanocoumarin, which has been used as mucolytic, antitussive, antitumour and antibacterial. However, the genetic information of furanocoumarin biosynthesis in G. littoralis is scarce at present. The objective of this study was to mine the putative candidate genes involved in the biosynthesis pathway of furanocoumarin and provide references for gene identification, and functional genomics of G. littoralis. We carried out the transcriptome analysis of leaves and roots in G. littoralis, which provided a dataset for gene mining. Psoralen, imperatorin and isoimperatorin were detected in G. littoralis by high performance liquid chromatography analysis. Candidate key genes were mined based on the annotations and local BLAST with homologous sequences using BioEdit software. The relative expression of genes was analysed using quantitative real-time polymerase chain reaction. Further, the CYP450 genes were mined using phylogenetic analyses using MEGA 6.0 software. A total of 156,949 unigenes were generated, of which 9021 were differentially-expressed between leaves and roots. A total of 82 unigenes encoding eight enzymes in furanocoumarin biosynthetic pathway were first obtained. Seven genes that encoded key enzymes in the downstream furanocoumarin biosynthetic pathway and expressed more in roots than leaves were screened. Twenty-six candidate CYP450 unigenes expressed abundantly in roots and were chiefly concentrated in CYP71, CYP85 and CYP72 clans. Finally, we filtered 102 differentially expressed transcription factors (TFs) unigenes. The transcriptome of G. littoralis was characterized which would help to elucidate the furanocoumarin biosynthetic pathway in G. littoralis and provide an invaluable resource for further study of furanocoumarin.

Bioinformatics analysis and systematic review of key genes and therapeutic traditional Chinese medicine of ulcerative colitis active stage / 中国中药杂志

Data GSE75214 and GSE48959 that contained ulcerative colitis(UC) in the active stage was download from GEO database. Differential genes of UC in the active phase were obtained by using adjusted P<0.05 and |log_2 FC|≥1.5, which was the screening criteria. PPI analysis was performed in the STRING database, and GO and KEGG pathway analysis was performed in DAVID database. Cytoscape was used to visualize differential genes, and calculate key genes in the active phase. Coremine Medical was used to analyze and systematically evaluate traditional Chinese medicines for treating key genes. Finally, 139 differentially expressed genes in the active phase were screened out, which included the 109 up-regulated genes and 30 down-regulated genes. DAVID analyzed that the biology and pathways of these differential genes were mainly concentrated in inflammatory response, immune response, chemokine activity, TNF pathway, NF-κB pathway, and Toll-like receptor pathway. Cytoscape software calculated that IL-6, CXCL8, IL-1β, MMP9, CXCL1, ICAM1, CXCL10, TIMP1, PTGS2 and CXCL9 were the key genes of UC in the active phase. According to Coremine Medical analysis, traditional Chinese medicines for UC in the active stage included Curcumae Longae Rhizoma, Scutellariae Radix, Curcumae Radix had clearing heat clearing damp, reducing fire and detoxifying effects, which was in line with the pathogenesis of UC active stage, and was often used in clinical treatment of dampness-heat diarrhea. Therefore, Huangqin Decoction, which Scutellariae Radix was the principal drug, was selected for systematic evaluation. The evaluation showed that Scutellariae Radix was superior to Western medicine in terms of improving clinical efficiency, reducing inflammatory factors and immunoglobulin levels, with statistically significant differences and fewer adverse reactions. This study provided a new idea for further research on the pathogenesis of UC in the active phase by analyzing the genes and their mechanism of action, and the systematic evaluation of Chinese medicine for the treatment of UC active stage provided a basis for the clinical prevention and treatment of UC by Chinese medicine.

Research progress on Nisin biosynthesis and breeding of high-yield strains / 中国生化药物杂志

Nisin, produced by several strains in the growth process of Lactococcus lactis, is a natural antimicrobial polypeptide.Now, Nisin has served as an effective and safe food additive extensively used in food industry in many countries and regions because of its excellent antimicrobial activity.However, the current production of Nisin is largely fermented by lactobacillus and its industrialized production still can not meet enormous market needs, therefore establishing reasonably high-yield Nisin strains is of great significance.This review mainly summarizes the development pathway of molecule based on the functional expression of Nisin biosynthetic genes and regulation of gene expression, and also the study status on high Nisin-producing strains which provides practical foundation for further study on expected strains as well as some useful guidance for large-scale industrialized production of Nisin.