Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Review
. 2022 Sep 2:2022:4121910.
doi: 10.1155/2022/4121910. eCollection 2022.

Microarray and Bioinformatics Analysis of Differential Gene and lncRNA Expression during Erythropoietin Treatment of Acute Spinal Cord Injury in Rats

Haibo He  1 , Hanwen Huang  2 , Panyong Hu  3 , Zhong Chen  2
Affiliations
Review

Microarray and Bioinformatics Analysis of Differential Gene and lncRNA Expression during Erythropoietin Treatment of Acute Spinal Cord Injury in Rats

Haibo He et al. Comput Math Methods Med. .

Retraction in

Abstract

Purpose: We performed a genome-wide analysis of long noncoding RNA (lncRNA) expression to identify novel targets for the further study of recombinant human erythropoietin (rhEPO) treatment of acute spinal cord injury (SCI) in rats.

Methods: Nine rats were randomly divided into 3 groups. No operation was performed in group 1. In groups 2 and 3, a laminectomy was performed at the 10th thoracic vertebra, and a contusion injury was induced by extradural application of an aneurysm clip. Group 1 rats did not receive any treatment, group 2 rats received a single intraperitoneal injection of normal saline, and group 3 rats received rhEPO. Three days after injury, spinal cord tissues were collected for RNA-Seq, microarray, differentially expressed genes (DEGs), Gene Ontology (GO) function enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, and protein-protein interaction (PPI) analyses.

Results: Compared with group 1, 4,446 genes were found to be differentially expressed in group 2. Furthermore, 99 lncRNAs were found to be changed in the injury group. The data indicate that 2,471 mRNAs were upregulated, and 1,975 mRNAs were downregulated in group 2 as compared with group 1. In addition, 45 of the lncRNAs were upregulated, and the other 44 lncRNAs were downregulated. The top 5 upregulated and top 5 downregulated lncRNAs that were different between group 2 and group 1 are shown. The top 5 downregulated and the top 5 upregulated lncRNAs that were different between group 3 and group 2 are shown.

Conclusion: RhEPO treatment alters the expression profiles of the differentially expressed lncRNAs and genes beneficial to the development of new treatments.

PubMed Disclaimer

Conflict of interest statement

The authors declare that they have no conflict of interests.

Figures

Figure 1
Figure 1
In the volcano diagram, each point represents a gene, and the X-axis represents the logarithm of the multiple of the difference in expression of a certain gene in the two samples; the Y-axis represents the statistically significant negative logarithm of the gene expression change. The larger the absolute value of the X-axis, the greater the fold change in expression between the two samples; the larger value of Y-axis, the more significant the differential expression, and the more reliable the DEGs obtained by screening. The blue dots (fold change < −1) in the figure represent downregulated DEGs, the red dots (fold change > 1) represent upregulated DEGs, and the grey dots represent non-DEGs.
Figure 2
Figure 2
In the heatmap, the red color represents upregulated mRNAs or lncRNAs, and the blue color represents downregulated mRNAs or lncRNAs.
Figure 3
Figure 3
The qRT-PCR result was consistent with that of the microarray between group 3 and group 2, in that the first 3 mRNAs had a rising trend, while the last 3 mRNAs showed a downward trend. All 6 mRNA transcripts reached statistical significance (p < .05 for each mRNA, Student's T test), as seen in Figure 1. Verification expression levels of DEGs in qRT-PCR during EPO treatment of SCI in rats. DEGs: differentially expressed genes; SCI: spinal cord injury; EPO: erythropoietin.
Figure 4
Figure 4
GO term enrichment analysis of mRNAs in the early acute phase of SCI. (a) GO annotations of DEGs with top 15 enrichment scores between group 1 and group 2. (b) GO annotations of DEGs with top 15 enrichment scores between group 3 and group 1. The red represents BC; the green represents CC; the blue represents MF. BC: biological process; CC: cell component; MF: molecular function.
Figure 5
Figure 5
KEGG pathway analysis of DEGs in spinal cord samples in the subacute phase following SCI. (a) The top 15 KEGG analysis enrichment between group 2 and group 1. (b) The top 15 KEGG analysis enrichment between group 3 and group 2. The X-axis shows gene ratio, and the Y-axis shows the KEGG annotations. The larger the circle area, the more DEGs the pathway contains. KEGG: Kyoto Encyclopedia of Genes and Genomes.
Figure 6
Figure 6
Interaction of protein-protein network analysis of DEGs between group 2 and group 1. Nodes represent DEGs. Lines indicate interactions between DEGs.
Figure 7
Figure 7
Interaction of protein-protein network analysis of DEGs between group 3 and group 2. Nodes represent DEGs. Lines indicate interactions between DEGs.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

References

    1. Sekhon L. H. S., Fehlings M. G. Epidemiology, demographics, and pathophysiology of acute spinal cord injury. Spine . 2001;26:S2–S12. doi: 10.1097/00007632-200112151-00002. - DOI - PubMed
    1. Ahuja C. S., Nori S., Tetreault L., et al. Traumatic spinal cord injury-repair and regeneration. Neurosurgery . 2017;80(3S):S9–S22. doi: 10.1093/neuros/nyw080. - DOI - PubMed
    1. O'Shea T. M., Burda J. E., Sofroniew M. V. Cell biology of spinal cord injury and repair. The Journal of Clinical Investigation . 2017;127(9):3259–3270. doi: 10.1172/JCI90608. - DOI - PMC - PubMed
    1. Li Z., Ho I. H. T., Li X., et al. Long non-coding RNAs in the spinal cord injury: novel spotlight. Journal of Cellular and Molecular Medicine . 2019;23(8):4883–4890. doi: 10.1111/jcmm.14422. - DOI - PMC - PubMed
    1. Wenger R. H., Kurtz A. Erythropoietin. Comprehensive Physiology . 2011;1:1759–1794. doi: 10.1002/cphy.c100075. - DOI - PubMed