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Next generation sequencing contributes to the quantitative analysis of AGEs stimulated HK-2 cell transcriptome

ABSTRACT: We sequenced the HK-2 gene expression profile stimulated by ages by high-throughput RNA analysis. Select Ctrl group and ages group, Differentially expressed genes (DEGs) were analyzed. Under the screening condition of fold change greater than or equal to 2, P < 0.05. We obtained 284 up-regulated genes and 193 down-regulated genes. It can be seen that there are obvious gene differences between Ctrl group and ages group (Fig. 3a). Gene ontology analysis (go) was completed. Through goseq software, the biological process of quantitative distribution of rich differential genes was intuitively reflected (BP), molecular function (MF) and cell composition (CC). In addition, in order to explore the impact of ages on cell pathways, we used the Kyoto Encyclopedia of biology to analyze the significantly rich metabolic pathways. There are 221 differentially expressed genes in Ctrl group and ages group. A total of 276 pathways have been established, of which 46 pathways have p < 0.05, and the first 20 pathways are shown in Figure 2C.

ORGANISM(S): Homo sapiens

PROVIDER: GSE193192 | GEO | 2022/01/10

REPOSITORIES: GEO

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Project description:Background: Around 5% of children with asthma suffer from chronic symptoms and/or severe exacerbations despite extensive treatment. The causes of severe therapy-resistant childhood asthma are poorly understood. Objectives: To define global patterns of gene expression in severe therapy-resistant vs. controlled asthma and healthy controls. Methods: Children with severe, therapy-resistant (SA, n=20) and controlled asthma (CA, n=20) were identified from a Swedish nation-wide study including extensive clinical and immunological characterisation. In addition, healthy controls were recruited (Ctrl, n=19). White blood cells were isolated and the global transcriptome profile was characterised using the Affymetrix Human Gene ST 1.0 chip. Results: 1378 genes were differentially expressed in one or several of the CA vs. Ctrl, SA vs. CA or SA vs. Ctrl contrasts. A large number could uniquely differentiate the SA group from the CA (n=351 genes) and Ctrl (n=315) groups, whereas fewer genes differentiated the CA from the Ctrl group (n=149). Several non-coding RNAs were found up-regulated in SA compared to CA or Ctrl. Three significantly enriched KEGG pathways were represented; bitter taste transduction, TAS2Rs (up-regulated mostly in SA), natural killer cell mediated cytotoxicity (up-regulated in CA) and N-Glycan biosynthesis (down-regulated in SA). An unsupervised hierarchical clustering of the 1378 genes could crudely separate the SA, CA and Ctrl individuals. Conclusion: Our data indicate a separation in gene expression patterns between children with severe, therapy-resistant asthma and controlled persistent asthma, and suggest novel pathways characterizing the severe therapy-resistant asthma phenotype. The transcriptomes of 59 subjects were assayed on the Affymetrix Human Gene ST 1.0 expression array. All samples passed pre-hybridisation quality control. After pre-processing and quality control of the post-hybridised arrays, five samples were regarded as outliers and removed (ctrl 510, MA 248, SA 141, SA 261, SA 41). The remaining sample set of 17 severe asthmatics (SA), 19 mild asthmatics (MA) and 18 controls (ctrl) were used for down-stream analysis.

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Next generation sequencing contributes to the quantitative analysis of AGEs stimulated HK-2 cell transcriptome

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