目的 幽门螺杆菌NCTC11637菌株Hp1501基因进行序列测定，并运用生物信息学软件对其进行分析。 方法 用聚合酶链反应方法从幽门螺杆菌 NCTC11637菌株基因组DNA扩增Hp1501基因，T-A克隆，鉴定后测序，将基因序列向GeneBank提交并申请登录号，用生物信息学软件分析其生物学特性。 结果 成功获取幽门螺杆菌 NCTC11637株Hp1501基因序列，获得GeneBank登录号JF820815。软件分析表明，序列全长为1 164 bp，与幽门螺杆菌国际标准株26695和J99的基因序列一致性为96%～97%，氨基酸序列一致性为97%～98%；软件预测其编码的前59个氨基酸为信号肽，其编码的核心肽为幽门螺杆菌外膜蛋白。 结论 成功测定幽门螺杆菌 NCTC11637菌株Hp1501基因序列并预测出其生物学特性，为进一步研究其功能，阐明其致病机制奠定了基础。Objective To determine the sequence of Hp1501 gene from H. pylori NCTC11637 and analyze the sequence with bioinformatics software. Methods Polymerase chain reaction (PCR) was used to amplify the Hp1501 gene from chromosomal DNA of H. pylori NCTC11637. After T-A clone, the amplified DNA sequence was determined and the gene sequence was sent to GeneBank for analysis with bioinformatics software. Results Hp1501 gene from H. pylori NCTC11637 was successfully attained, and the logging number for GeneBank was JF820815. The analysis showed that the gene sequence was 1164 bp in length, 96%-97% identical in DNA sequence and 97%-98% identical in amino acid sequence compared with standard strain 26695 and J99. The forward 59 amino acids were signal peptide and the core peptide was outer membrane protein of H. pylori based on the software prediction. Conclusions The sequence and bionomics of Hp1501 gene from H. pylori NCTC11637 has been determined successfully. It provides a solid base for the further research of the biological function and pathogenicity mechanism of H. pylori.
ObjectiveTo analyze the expression and clinical significance of cyclin-dependent kinase 1 (CDK1) in lung adenocarcinoma by bioinformatics.MethodsBased on the gene expression data of lung adenocarcinoma patients in The Cancer Genome Atlas (TCGA), the differential expression of CDK1 in lung adenocarcinoma tissues and normal lung tissues was analyzed. The expression of CDK1 gene in lung adenocarcinoma was analyzed by UALCAN at different angles. Survival analysis of different levels of CDK1 gene expression in lung adenocarcinoma was performed using Kaplan-Meier Plotter. Correlation Cox analysis of CDK1 expression and overall survival was based on clinical data of lung adenocarcinoma in TCGA. Gene set enrichment analysis was performed on gene sequences related to CDK1 expression in clinical cases. The protein interaction network of CDK1 from Homo sapiens was obtained by STRING. CDK1-related gene proteins were obtained and analyzed by the web server Gene Expression Profiling Interactive Analysis (GEPIA).ResultsBased on the analysis of TCGA gene expression data, CDK1 expression in lung adenocarcinoma was higher than that in normal lung tissues. UALCAN analysis showed that high CDK1 expression may be associated with smoking. Survival analysis indicated that when CDK1 gene was highly expressed, patients with lung adenocarcinoma had a poor prognosis. Univariate and multivariate Cox regression analysis of CDK1 expression and overall survival showed that high CDK1 expression was an independent risk factor for survival of patients with lung adenocarcinoma. Gene set enrichment analysis revealed that high CDK1 expression was closely related to DNA replication, cell cycle, cancer pathway and p53 signaling pathway.ConclusionCDK1 may be a potential molecular marker for prognosis of lung adenocarcinoma. In addition, CDK1 regulation may play an important role in DNA replication, cell cycle, cancer pathway and p53 signaling pathway in lung adenocarcinoma.
ObjectiveTo screen differential expression of genes in hepatocellular carcinoma (HCC) by bioinformatics method, and analyze its clinical significance and its possible molecular mechanism in HCC.MethodsThe HCC gene expression profile GSE101728 was picked out to analyze the differential expression genes. The hub genes were identified by STRING and Cytoscape. GO and KEGG analysis were carried out by using DAVID and PPI network were constructed by STRING. The relationship among the hub genes were analyzed by using GEPIA.ResultsA total of 1 082 DEGs were captured (354 up-regulated genes and 728 down-regulated genes). Meantime, 10 hub genes ［cyclin dependent kinase 1 (CDK1), cyclin B1 (CCNB1), cyclin A2 (CCNA2), polo-like kinase 1 (PLK1), laser kinase B (AURKB), cyclin of cell division 20 (CDC20), centromere protein A (CENPA), mitotic arrest defective protein 2 (MAD2L1), cyclin B2 (CCNB2), and kinesin family 2C (KIF2C)］ were identified, and its expression and clinical significance were verified by GEPIA. GO and KEGG analysis showed 10 hub genes were mainly enriched in cell division and cell cycle. Expressions of AURKB, CCNB1, and MAD2L1 were obviously positively correlated (P<0.05).ConclusionThis study analyzes the hub genes in the development of HCC by bioinformatics methods and provides valuable information for further research on the mechanism of HCC.
ObjectiveTo explore the clinical significance and possible potential mechanism of hepatocellular carcinoma through the screening of key genes in hepatocellular carcinoma.MethodsHepatocellular carcinoma gene chip was obtained from GEO database, differentially expressed genes (DEGs) were screened by GEO2R online tools and Venn map, GO analysis and KEGG pathway analysis were performed in DAVID database, core genes were screened by STRING and Cytscape software, core genes were analyzed in Kaplan-Meier Plotter for survival analysis, and expression was analyzed by GEPIA database. The core genes related to prognosis and highly expressed in hepatocellular carcinoma were analyzed by Metascape online tool for function and pathway enrichment analysis. Finally, the key genes were verified in hepatocellular carcinoma and paracancerous tissues.ResultsA total of 94 DEGs were screened from three gene chips GSE14520, GSE60502, and GSE102079, obtained from GEO. After the selected DEGs was analyzed by GO function analysis, KEGG pathway enrichment analysis, STRING and Cytscape software by DAVID, 19 core DEGs were screened. After 19 core DEGs were analyzed by Kaplan-Meier Plotter website, 9 genes [ribonucleotide reductase M2 (RRM2), polycomb repressive complex 1 (PRC1), topoisomerase Ⅱ alpha (TOP2A), aurora kinase A (AURKA), nucleolar spindle-associated protein 1 (NUSAP1), Rac-GTPase activating protein 1 (RACGAP1), abnormal spindle-like microcephaly-associated (ASPM), cyclin dependent kinase 1 (CDK1) and GINS complex subunit 1 (GINS1)] were found to be associated with the prognosis of hepatocellular carcinoma. The expressions of these 9 genes were analyzed by GEPIA, and the results showed that all 9 genes were highly expressed in hepatocellular carcinoma tissues. The functions and pathways of 9 highly expressed genes were analyzed by metascape website. Finally, RRM2 was selected for verification in hepatocellular carcinoma tissues and adjacent tissues, and it was found that the staining score of RRM2 in hepatocellular carcinoma tissues was (10.9±1.5) points, which was significantly higher than its staining score in adjacent tissues [(4.5±1.2) points], P<0.001.ConclusionThe nine genes identified by bioinformatics analysis may be the key genes in the occurrence and development of hepatocellular carcinoma, which can provide reference for further study on the pathogenesis, diagnosis and treatment of hepatocellular carcinoma.
ObjectiveTo investigate differentially expressed genes (DEGs) and potential molecular mechanisms between hepatitis C-related hepatocellular carcinoma (HCV-HCC) and hepatitis B-related HCC (HBV-HCC). MethodsThe data of HCV-HCC and HBV-HCC gene expressions were downloaded and integrated from the public gene expression database, and the limma package was used to investigate the DEGs between the HCV-HCC and HBV-HCC samples. The gene set enrichment analysis (GSEA) was used to explore the differences in suppressed or activated gene sets between the HCV-HCC and HBV-HCC samples, and the MCODE was used to explore the key molecular modules, and then the potential biological processes and molecular pathways of the key molecular modules were analyzed. The effect of key genes on survival of the HCC patients was analyzed by the Kaplan-Meier-Plotter database.ResultsIn this study, 119 HBV-HCC samples and 163 HCV-HCC samples were obtained, and the 199 DEGs were screened out. Compared with HBV-HCC, the activated gene sets of HCV-HCC were mainly enriched in the gene sets of inflammation, complement, up-regulation of genes in response to interferon, up-regulation of genes in response to KRAS, genes regulated by the nuclear factor- κB-tumor necrosis factor pathway, and apoptosis. However, the cell cycle-related gene sets were obviously suppressed. Eight key molecular modules enriched by DEGs were found, which included 18 key genes (IFI27, DDX60, MX1, IRF9, OAS3, OAS1, RSAD2, GBP4, HERC6, ISG15, IFIT1, CMPK2, EPSTI1, IFI44, IFI44L, HERC5, IFITM1, CXCL10). GO analysis showed that the biological process was mainly concentrated in the body response related to virus infection, the molecular component was mainly in the host cells, and the molecular function was mainly enriched in the biological combination. KEGG analysis showed that the key genes were mainly involved in the molecular signaling pathway related to virus infection. The survival analysis showed that the 9 key genes (CXCL10, HERC6, DDX60, IFITM1, IFI27, GBP4, IFI44L, IFI44, MX1) were closely related to better prognosis of patients with HCC (HR<1, P<0.05). ConclusionsThere is an essential difference between HBV-HCC and HCV-HCC. Occurrence of HCV-HCC is mainly related to virus infection and immune response induced by the virus. Therefore, for HCV infection, active antiviral treatment is necessary for avoiding hepatitis turning into chronic viral infection and preventing or blocking HCV infection converting to HCC.
Objective To explore the pathogenesis of acute respiratory disease syndrome (ARDS) by bioinformatics analysis of neutrophil gene expression profile in order to find new therapeutic targets. Methods The gene expression chips include ARDS patients and healthy volunteers were screened from the Gene Expression Omnibus (GEO) database. The differentially expressed genes were carried out through GEO2R, OmicsBean, STRING, and Cytoscape, then enrichment analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Gene and Genomes (KEGG) pathways was conducted to investigate the biological processes involved in ARDS via DAVID website. Results Bioinformatics analysis showed 86 differential genes achieved through the GEO2R website. Eighty-one genes were included in the STRING website for protein interaction analysis. The results of the interaction were further analyzed by Cytoscape software to obtain 11 hub genes: AHSP, ALAS2, CD177, CLEC4D, EPB42, GPR84, HBD, HVCN1, KLF1, SLC4A1, and STOM. GO analysis showed that the differential gene was enriched in the cellular component, especially the integrity of the plasma membrane. KEGG analysis showed that multiple pathways especially the cytokine receptor pathway involved in the pathogenesis of ARDS. Conclusions A variety of genes and pathways have been involved in the pathogenesis of ARDS. Eleven hub genes are screened, which may be involved in the pathogenesis of ARDS and can be used in subsequent studies.
ObjectiveTo explore the mechanism of dihydrouridine synthase 4-like (DUS4L) on the development of lung adenocarcinoma (LUAD).MethodsThe RNA-seq expression data of LUAD was downloaded from The Cancer Genome Atlas (TCGA), and the relationship between its clinical pathological characteristics and DUS4L mRNA expression was evaluated. The effect of DUS4L knockdown on the proliferation of A549 cells was detected by EDU proliferation assay. The gene expression profile of lung adenocarcinoma A549 cells in the DUS4L knockdown group (KD group) and control group (NC group) was detected by transcriptome sequencing technique. The differential genes were screened by DESeq2. ClusterProfiler was used to perform GO functional enrichment analysis of differential genes.ResultsThe expression of DUS4L mRNA in LUAD tissues was higher than that in normal tissues, and the up-regulation of DUS4L was related to the clinical pathological characteristics of LUAD patients. EDU proliferation assay suggested that knocking down DUS4L could inhibit the proliferation of A549 cells. A total of 456 differential genes were screened, including 289 up-regulated genes and 167 down-regulated genes [|log2(fold change)|>1 and Padj<0.05]. STC2 and TRIB3 were significantly down-regulated (P<0.05). Differential genes were mainly involved in the production of interleukin-8, angiogenesis, vascular endothelial cell proliferation and other biological pathways.ConclusionDUS4L can widely regulate the gene expression of LUAD cells, which provides a new idea for further studying the function and role of DUS4L in the occurrence and development of LUAD and finding new therapeutic targets for LUAD.
ObjectiveTo analyze the expression of cold-induced RNA-binding protein (CIRBP) in lung adenocarcinoma and its clinical significance based on bioinformatics, in order to provide a new direction for the study of therapeutic targets for lung adenocarcinoma.MethodsThe CIRBP gene expression data and patient clinical information data in lung adenocarcinoma tissues and adjacent tissues were downloaded from The Cancer Genome Atlas and Gene Expression Omnibus databases. The expression of CIRBP in lung adenocarcinoma was analyzed. Furthermore, its relationship with clinicopathological features and prognosis in patients with lung adenocarcinoma was analyzed. GO and KEGG enrichment analysis were carried out for the screened genes. The CIRBP protein interaction network was constructed by STRING, and the correlation analysis was carried out using the GEPIA online website.ResultsThe expression level of CIRBP gene in lung adenocarcinoma tissues was significantly lower than that in adjacent tissues (P<0.01), and its expression level was correlated with T stage and N stage in clinicopathological features. The prognosis of patients with high CIRBP expression in lung adenocarcinoma was significantly better than that with low CIRBP expression. Univariate and multivariate Cox regression analysis showed that CIRBP was an independent prognostic factor in patients with lung adenocarcinoma. GO functional annotation showed its enrichment in organelle fission, nuclear fission, chromosome separation, and DNA replication, etc. KEGG analysis showed that it was mainly involved in cell cycle and DNA replication. Protein interaction network and GEPIA online analysis showed that the expression level of CIRBP was negatively correlated with the expression level of cyclin B2.ConclusionCIRBP gene is down-regulated in lung adenocarcinoma tissues, and its expression level is closely related to patient prognosis. CIRBP gene may be a potential therapeutic target and prognostic marker for lung adenocarcinoma.
Objective To explore the aberrantly expressed genes in hepatocellular carcinoma (HCC) and their relationship with prognosis of HCC through bioinformatics analysis. Methods Five datasets related to HCC were selected from the GeneExpression Omnibus database to explore differentially expressed genes (DEGs), followed by further gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. The co-upregulated genes CNIH4 and TOMM40 were selected to explore the differences in their expressions in HCC tissues and normal tissues, and to explore the relationship between their expressions and the 5-year survival of patients by using TCGA database. Tissues and paraneoplastic tissues of eight cases of HCC who underwent surgery at the Guangdong Second Provincial General Hospital were collected to verify the expression differences of CNIH4 and TOMM40L mRNA. Results A total of 25 up-regulated genes and 21 down-regulated genes were identified in this study. The results of GO analysis and KEGG analysis indicated that DEGs were mainly related to catabolism, cell division, DNA replication and repair. The results of TCGA database analysis showed that the expression of up-regulated genes CNIH4 mRNA and TOMM40L mRNA were up-regulated in HCC tissues as compared with normal tissues (P<0.05) and that the 5-year survival of patients in the high expression group was worse than that in the low expression group (P<0.05). The results of clinical samples showed that CNIH4 mRNA and TOMM40L mRNA were up-regulated in HCC tissues as compared with paraneoplastic tissues. Conclusion CNIH4 and TOMM40L genes are up-regulated in HCC tissues, and their high expressions are associated with poor prognosis, and may be potential biomarkers and prognostic indicators for HCC.
ObjectiveTo evaluate the changes in the expression and significance of serum exosomal miRNAs in patients with DeBakey typeⅠacute aortic dissection (AAD). MethodsTwelve male patients with AAD and six healthy male medical examiners from our hospital were retrospectively included in this study. According to the time of chest pain, the AAD patients were divided into an AAD group within 24 h of chest pain onset, aged 47.00±8.79 years and an AAD group within 48 h of chest pain onset, aged 50.17±9.99 years. The healthy males were allocated to a control group, aged 49.17±4.26 years. Serum exosomal miRNAs were isolated, identified and quantified, and then differentially expressed exosomal miRNAs were screened. The bioinformatic analyses such as GO and KEGG were performed on the differentially expressed exosomal miRNAs. ResultsHigh-throughput screening results revealed differential expression of AAD serum exosomal miRNAs. The upregulated miRNAs of AAD groups was hsa-miR-574-5p (P<0.05), and downregulated miRNAs were hsa-miR-223-3p, hsa-miR-146b-5p, hsa-miR-15b-5p, and hsa-miR-155-5p (P<0.05). Further bioinformatic analysis of the above miRNAs revealed that they were mainly enriched in signaling pathways such as transforming growth factor-β, cell cycle and endoplasmic reticulum protein synthesis. ConclusionDifferential expressions of serum exosomal miRNAs in AAD patients may be related to the pathogenesis of AAD, providing new ideas and clues for further exploration of AAD diagnostic markers and pathogenesis.