Screening the differentially expressed genes after spinal cord injury by RNA-Seq and subsequent functional analysis for partial candidate genes

doi:10.16098/j.issn.0529-1356.2017.02.002

Abstract

Abstract:

Objective We apply RNA-Seq technology to characterize the temporal changes in global gene expression after spinal cord injury (SCI) in rats. Methods Spinal cord contusion injury was produced with the Infinite Horizon Device. A total of 48 rats were randomly divided into sham control, and contusion injury for 1 day, 4 days and 7days. RNA-Seq technology was carried out to screen the differentially expressed genes (DE genes) after SCI. We also performed expression pattern and pathway analysis for the DE genes, and selected the candidates to further expression variation validation. Results Compared with sham group, there were 944DE genes at the first day, 1362 DE genes at the 4th day and 1421 DE genes at the 7th day. The expression variation patterns were roughly divided into 8 kinds of forms.In addition, Real-time PCR results showed that the expression patterns of heme-oxygenases 1（Hmox1）, Plau, Serpine1 and Ncf2 were consistent with RNA-seq analysis. The result of immunohistochemistry showed that Hmox1 was highly expressed in spinal cord neurons after injury. Conclusion RNA-Seq analysis is useful to screen the DE genes after SCI, and the validated genes could partially explain the molecular mechanism of SCI.

Key words: Spinal cord injury, Heme-oxygenase 1, RNA-Seq, Real-time PCR, Immunofluoresence, Rat

CHEN Ying WANG Di NIU Xue-ying WANG Xiao-dong CHEN Xue. Screening the differentially expressed genes after spinal cord injury by RNA-Seq and subsequent functional analysis for partial candidate genes[J]. Acta Anatomica Sinica, 2017, 48(2): 128-134.

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