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Acta Histochem. 2017 Sep;119(7):663-670. doi: 10.1016/j.acthis.2017.07.007. Epub 2017 Aug 26.

Bioinformatics analyses of pathways and gene predictions in IL-1α and IL-1β knockout mice with spinal cord injury.

Author information

1
Department of Orthopedics, Affiliated Hospital of Taishan Medical University, 271000, China. Electronic address: zhucehnz@126.com.
2
Department of Orthopedics, Affiliated Hospital of Taishan Medical University, 271000, China.

Abstract

PURPOSE:

This study aimed to explore the potential genes and pathways regulated in spinal cord injury (SCI) model mice with IL-1α and IL-1β knockout (KO).

METHODS:

Gene expression profile GSE70302, which includes data from injured spinal cord of 4 IL-1α-KO mice, 4 IL-1β-KO mice and 4 C57BL with 6 mice as controls was downloaded from the Gene Expression Omnibus database. The differentially expressed genes (DEGs) of the IL-1α-KO or IL-1β-KO vs. control, and IL-1α-KO vs. IL-1β-KO groups were screened, followed by function enrichment and protein-protein interaction (PPI) analyses. Finally, miRNAs associated with SCI that may target the DEGs were predicted.

RESULTS:

A total of 579 and 992 DEGs were selected from the IL-1α-KO vs. control group and the IL-1β-KO vs. control group, respectively, and 208 genes common between the 2 comparison groups were identified. Additionally, 526 DEGs were identified from the IL-1α-KO vs. IL-1β-KO groups. These DEGs were significantly enriched in functions and pathways associated with ion transport, neuron apoptotic processes and inflammatory responses. The common genes were enriched in the pathways for cytokine-cytokine receptor interaction. DEGs of IL-1α-KO vs. IL-1β-KO were significantly enriched in the immune system, hematopoietic cell lineage and PI3K-Akt signalling pathway-associated biological processes and pathways. The PPI network consisted of 76 nodes, such as Saa2, Kcna1, Scn8a, Ccl5, Ccl28 and Pink1. A total of 94 miRNAs, including mir-17-5P and mir-30a-5p were predicted that could target the DEGs.

CONCLUSION:

IL-1α and IL-1β may play important roles in SCI by regulating ion transport, inflammation and neuron apoptotic processes and their associated genes or miRNAs. Compared with IL-1β-KO, IL-1α-KO may improve the outcome of SCI via the alteration of hematopoietic cell lineage and PI3K-Akt signalling pathways.

KEYWORDS:

Differentially expressed genes; Pathway enrichment analysis; Protein–protein interaction; Spinal cord injury; miRNA

PMID:
28851482
DOI:
10.1016/j.acthis.2017.07.007
[Indexed for MEDLINE]

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