Abstract
To identify differentially expressed genes in sepsis and potential key role of reactive oxygen species (ROS) genes associated with sepsis. Gene expression dataset was available from GSE46599. Firstly, we screened the differentially expressed genes between sepsis and healthy samples. Then, the Database for Annotation, Visualization and Integrated Discovery (DAVID) online tools were utilized to perform gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses at the functional level. Differentially expressed genes mediating ROS levels were validated in the next investigation and analysis. We identified 1094 genes expressed differentially between normal and sepsis samples, including 655 upregulated genes and 439 downregulated genes. At the functional level, GO and KEGG pathway enrichment analysis showed that those differentially expressed genes were majorly associated with the immune response and metabolic process in sepsis. Further analysis revealed that neutrophil cytosolic factor 1(NCF1), a critical gene in the ROS system, upregulated in THP-1 cell and monocytes under lipopolysaccharides stimulation. Moreover, we identified the upregulation of NCF1 in a sepsis model. We screened the differentially expressed genes from the global level and identified NCF1 might be a critical target gene in sepsis.
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Abbreviations
- ROS:
-
reactive oxygen species
- NCF1:
-
neutrophil cytosolic factor 1
- FC:
-
fold change
- FDR:
-
false discovery rate
- BP:
-
biological processes
- MF:
-
molecular function
- CF :
-
component function
- NADPH:
-
nicotinamide adenine dinucleotide phosphate
- SIRS:
-
systemic inflammatory response syndrome
- DAVID:
-
the Database for Annotation, Visualization and Integrated Discovery
- GO:
-
gene ontology
- KEGG:
-
Kyoto Encyclopedia of Genes and Genomes pathway
- ICUs:
-
intensive care units
- GEO:
-
Gene Expression Omnibus
- PPI:
-
protein-protein interaction
- LPS:
-
lipopolysaccharides
- DEGs:
-
differentially expressed genes
- CLP:
-
cecal ligation and puncture
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Acknowledgements
The authors thank Dr Jun Zhang for the critical review and elaborate revision of this manuscript and Drs Guoming Deng and Ebun Omoyinmi for the helpful discussion with this report. In addition, they thank the subjects who agreed to participate in this genetic study.
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Table S1
137 ROS genes identified in previous study. (XLSX 10 kb)
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Chen, Df., Cui, Xz., Cao, Wm. et al. Neutrophil Cytosolic Factor 1 Contributes to the Development of Sepsis. Inflammation 42, 811–817 (2019). https://doi.org/10.1007/s10753-018-0935-z
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DOI: https://doi.org/10.1007/s10753-018-0935-z