ObjectiveTo predict as well as bioinformatically analyze the target genes of has-miR-451. MethodsmiRBase, miRanda, TargetScan and PicTar were used to predict the target genes of hsa-miRNA-451. The functions of the target genes were demonstrated by Gene Ontology and pathway enrichment analysis. P < 0.05 was set as statistically significant. Results18 target spots of hsa-miRNA-451 were predicted by 3 databases or prediction software at least. The functions of the target genes were enriched in proliferation and development of epithelial cells and regulation of kinase activity (P < 0.05). Pathway analysis showed that transforming growth factor-beta signaling pathway, mitogen-activated protein kinase signaling pathway, epidermal growth factor signaling pathway, Wnt signaling pathway and mammalian target of rapamycin signaling pathway were significantly enriched (P < 0.05). Conclusionhsa-miRNA-451 might be involved in various signaling pathways related to proliferation and development of epithelial cells.
ObjectiveTo screen compounds or drugs can affect the hypoxia induced-gene expression of retinal vascular endothelial cell based on gene expression microarrays and connectivity map (CMAP) technology. MethodsTotally 326 up-regulated and down-regulated genes of hypoxic human embryonic retinal microvascular endothelial cells minduced by cobalt chloride in the previous study were converted into query signature format documents. Gene profile of the disease characteristics was then compared with that of control in CMAP website database, positive and negative compounds related to retinopathy of prematurity (ROP) were finally screened out. Results44 and 18 compounds or drugs have positive and negative relationship with ROP respectively by searching CMAP database with differentially expressed genes. Ciclopirox, cobalt chloride, gossypol and withaferin A have positive relationship with ROP. Cyclic adenosine monophosphate, harmalol, naringin and probenecid have a negative effect on ROP. ConclusionsCiclopirox, cobalt chloride, gossypol and withaferin A have a positive effect on ROP. However, cyclic adenosine monophosphate, harmalol, naringin and probenecid have a negative effect.
ObjectiveTo analyze the early changes of gene expression levels and signaling pathways in 661W cell line under hypoxic conditions and to find potential functional target genes.MethodsThe cultured mouse 661W cells were divided into hypoxia treatment group and normoxia control group. Cells in the hypoxia treatment group were cultured in a three-gas incubator with volume fraction of 1% and 5% CO2 at 37 ℃. Cells in the normoxia control group were cultured in an incubator at 37 ℃ with volume fraction of 5% CO2. High-throughput sequencing technology was used to sequence the transcriptome of 661W cell treated with hypoxia and normoxia for 4 hours to screen for differentially expressed genes (DEG). Clustering heat map analysis, gene ontology (GO) functional enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis and protein-protein interaction network (PPI) analysis were performed. The reverse transcription-polymerase chain reaction (RT-PCR) was used to verify the accuracy of the sequencing results.ResultsA total of 506 differentially expressed genes were screened, including 459 up-regulated genes and 47 down-regulated genes. GO functional enrichment analysis showed that the main biological processes of DEG were the cell's response to hypoxia, glycolysis, negative regulation of cell proliferation and apoptosis. hypoxia inducible factor (HIF)-1α pathway, glycolysis, Forkhead box O (FoxO) pathway, Insulin signaling pathway and Adenosine 5'-monophosphate-activated protein kinase (AMPK) pathway were involved in the above process. PPI analysis results showed that hub genes related to hypoxia were Aldoa, Aldoc, Gpi1, Hk2, Hk1, Pfkl, Pfkp, Vhl, Fbxo10 and Fbxo27. The RT-PCR results showed that the relative expression levels of 15 DEG mRNA in the hypoxic treatment group were higher than that of the normoxic control group, and the difference was statistically significant (P＜0.05). The mRNA expression levels of N-myc downstream-regulated gene-1 (Ndrg1), Mt1, and vascular endothelial growth factor A (VEGFA) were time-dependent on hypoxia.ConclusionsUnder hypoxia, DEG is mainly related to glucose metabolism, cell response to hypoxia, regulation of proliferation and apoptosis. HIF-1α pathway, glycolysis, FoxO pathway and AMPK pathway are involved in the early changes of 661W cells under hypoxia. Aldoa, Aldoc, Gpi1, Hk2, Hk1, Pfkl, Pfkp, Vhl, Fbxo10, Fbxo27 may play key roles in the response of 661W cells to hypoxia. Ndrg1, Mt1 and VEGFA could be potential functional target genes for the study of ischemia and hypoxia-related fundus diseases.
Objective To explore the role of high endothelial venule (HEV) in chronic obstructive pulmonary disease (COPD) at the single cell level. Methods A total of 219257 cells from the lung tissues of 18 COPD patients and 28 healthy controls in the GEO public database (GSE136831) were used to analyze the relationship between HEV with T lymphocytes, B lymphocytes, and dendritic cells. Results Endothelial cells were extracted using single cell analysis technique, and sorting out venous endothelium, CCL14, IGFBP7, POSTN were used as marker genes for HEV endothelial cells. The ratio of HEV endothelial cells was also identified as up-regulated expression in COPD. The function of the differential genes of HEV endothelial cells was analyzed, suggesting the presence of immune regulation. By trajectory analysis, it was suggested that the differential genes of HEV endothelial cells were enriched for extracellular matrix deposition in late development. Finally, by receptor-ligand pairing, it was suggested that HEV endothelial cells was recruited through a series of ligands with T lymphocytes, B lymphocytes, and dendritic cells. Conclusions HEV endothelial cells are elevated in COPD and have an immunomodulatory role by secreting a series of ligands after recruiting T lymphocytes, B lymphocytes as well as dendritic cells for immune action. HEV may be a potential target for the study of COPD therapy.
ObjectiveTo explore the functional heterogeneity of T lymphocytes in various organs after SARS-CoV-2 infection. Methods Using the public database GEO data (GSE171668, GSE159812, GSE159556, GSE167747) and the analysis method of single-cell technology, the functional differences of T lymphocytes in various organs of patients after infection with SARS-CoV-2 were analyzed. Results Through single-cell data extraction of 16 livers, 19 hearts,2 spleens, 6 brains, 58 lungs, 21 kidneys and 5 pancreases from SARS-CoV-2 infected patients, invasion genes were relatively highly expressed in T lymphocytes of the lung and pancreas. The lung had a special ability to express the interferon signaling pathway, while the expression of other organs was relatively low; at the same time, the T lymphocytes of the lung also highly expressed fatty acid binding sites. Conclusion After SARS-CoV-2 infection, compared with other organs, the lung has a special interferon-activated signaling pathway and fatty acid binding site.