Candidate Genes as Biomarkers in Lipopolysaccharide-Induced Acute Respiratory Distress Syndrome Based on mRNA Expression Profile by Next-Generation RNA-Seq Analysis
| Autor: | Di Wu, Qi-Quan Wan, Qi-Fa Ye |
|---|---|
| Rok vydání: | 2018 |
| Předmět: |
Lipopolysaccharides
Male 0301 basic medicine Chemokine Candidate gene Transcription Genetic Article Subject lcsh:Medicine RNA-Seq General Biochemistry Genetics and Molecular Biology Rats Sprague-Dawley 03 medical and health sciences Transcription (biology) Animals Cluster Analysis RNA Messenger Lung Gene Genetic Association Studies Respiratory Distress Syndrome General Immunology and Microbiology biology Gene Expression Profiling lcsh:R High-Throughput Nucleotide Sequencing Reproducibility of Results RNA General Medicine Molecular biology Fold change Up-Regulation Gene expression profiling Gene Ontology 030104 developmental biology biology.protein Biomarkers Research Article |
| Zdroj: | BioMed Research International, Vol 2018 (2018) BioMed Research International |
| ISSN: | 2314-6141 2314-6133 |
| DOI: | 10.1155/2018/4384797 |
| Popis: | Up until now, the regulation mechanism at the level of gene during lipopolysaccharide- (LPS-) induced acute respiratory distress syndrome (ARDS) remains unclear. The discovery of differentially expressed genes (DEGs) between LPS-induced ARDS rats and normal rats by next-generation RNA sequencing analysis is of particular interest for the current study. These DEGs may help clinical diagnosis of ARDS and facilitate the selection of the optimal treatment strategy. Randomly, 20 rats were equally divided into 2 groups, the control group and the LPS group. Three rats from each group were selected at random for RNA sequencing analysis. Sequence reads were obtained from Illumina HiSeq4000 and mapped onto the rat reference genome RN6 using Hisat2. We identified 5244 DEGs (Fold_Change > 1.5, and P<0.05) in the lung tissues from LPS-treated rats compared with normal rats, including 1413 upregulated and 3831 downregulated expressed genes. Lots of chemokine family members were among the most upregulated genes in LPS group. Gene ontology (GO) analysis revealed that almost all of the most enriched and meaningful biological process terms were mainly involved in the functions like immune-inflammation response and the pathways like cytokine-cytokine receptor interaction. We also found that, as for GO molecular function terms, the enriched terms were mainly related to chemokines and cytokines. DEGs with fold change over 100 were verified by quantitative real-time polymerase chain reaction and reanalyzed by gene-gene coexpression network, and the results elucidated central roles of chemokines in LPS-induced ARDS. Our results revealed some new biomarkers for uncovering mechanisms and processes of ARDS. |
| Databáze: | OpenAIRE |
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