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

CHEN Ying WANG Di NIU Xue-ying WANG Xiao-dong CHEN Xue*

doi:10.16098/j.issn.0529-1356.2017.02.002

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Acta Anatomica Sinica ›› 2017, Vol. 48 ›› Issue (2) : 128-134. DOI: 10.16098/j.issn.0529-1356.2017.02.002

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

CHEN Ying¹WANG Di³NIU Xue-ying ^1,4 WANG Xiao-dong¹CHEN Xue ^1,2*

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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

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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 https://doi.org/10.16098/j.issn.0529-1356.2017.02.002

References

［1］Dalbayrak S, Yaman O, Yilmaz T. Current and future surgery strategies for spinal cord injuries［J］. World J Orthop, 2015, 6(1): 34-41.

［2］Garcia E, Aguilar-Cevallos J, Silva-Garcia R, et al. Cytokine and growth factor activation in vivo and in vitro after spinal cord injury［J］. Mediators Inflamm, 2016, 2016:9476020.

［3］Ding L, Wendl MC, Koboldt DC, et al. Analysis of next-generation genomic data in cancer: accomplishments and challenges［J］. Hum Mol Genet, 2010, 19(R2): R188-196.

［4］Basso DM, Beattie MS, Bresnahan JC. A sensitive and reliable locomotor rating scale for open field testing in rats［J］. J Neurotrauma, 1995, 12(1): 1-21.

［5］Kabu S, Gao Y, Kwon BK, et al. Drug delivery, cell-based therapies, and tissue engineering approaches for spinal cord injury［J］. J Control Release, 2015,10(219):141-154.

［6] Liu XD,Xue ChB, Ju QQ, et al. Repair of spinal cord injury by using the tissue engineered nervegraftsconstructed by silk fibroin /filament including seed cells［J］. Acta Anatomica Sinica, 2015,46(5):596-601.(in Chinese)

刘晓东, 薛成斌, 鞠前前, 等. 含种子细胞的丝素组织工程神经移植物修复大鼠脊髓损伤［J］. 解剖学报, 2015, 46(5):596-601.

［7］Xu JW, Han Sh, Ling ShC.The expression of regeneration gene protein 2 in the spinal cord traverse injury model［J］. Acta Anatomica Sinica, 2008, 39(4):454-459.(in Chinese)

徐纪伟, 韩曙,凌树才.脊髓横断损伤后再生基因蛋白的表达［J］. 解剖学报, 2008,39(4):454-459.

［8］Zhao W, Huang X, Zhang L, et al. Penehyclidine hydrochloride pretreatment ameliorates rhabdomyolysis-induced AKI by activating the Nrf2/HO-1 pathway and allevi-ating endoplasmic reticulum stress in rats［J］. PLoS One, 2016, 11(3): e0151158.

［9］Agarwal A, Bolisetty S. Adaptive responses to tissue injury: role of heme oxygenase-1［J］. Trans Am Clin Climatol Assoc, 2013, 124(1)111-122.

［10］Agundez JA, Garcia-Martin E, Martinez C, et al. Heme oxygenase-1 and 2 common genetic variants and risk for multiple sclerosis［J］. Sci Rep, 2016, 6:20830.

［11］Hayashi G, Cortopassi G. Lymphoblast oxidative stress genes as potential biomarkers of disease severity and drug effect in friedreich’s ataxia［J］. PLoS One, 2016, 11(4): e0153574.

［12］Savchenko VL. Regulation of NADPH oxidase gene expression with PKA and cytokine IL-4 in neurons and microglia［J］. Neurotox Res, 2013, 23(3): 201-213.

［13］Riemenschneider M, Konta L, Friedrich P, et al. A functional polymorphism within plasminogen activator urokinase (PLAU) is associated with Alzheimer’s disease［J］. Hum Mol Genet, 2006, 15(16): 2446-2456.

［14］Meiri N, Masos T, Rosenblum K, et al. Overexpression of urokinase-type plasminogen activator in transgenic mice is correlated with impaired learning［J］. Proc Natl Acad Sci USA, 1994, 91(8): 3196-3200.

［15］Xu Y, Cheng X, Cui X, et al. Effects of 5-h multimodal stress on the molecules and pathways involved in dendritic morphology and cognitive function［J］. Neurobiol Learn Mem, 2015, 123:225-238.

［16］Liang Q, De Windt LJ, Witt SA, et al. The transcription factors GATA4 and GATA6 regulate cardiomyocyte hypertrophy in vitro and in vivo［J］. J Biol Chem, 2001, 276(32): 30245-30253.

［17］Kutz SM, Higgins CE, Higgins PJ. Novel combinatorial therapeutic targeting of PAI-1 (SERPINE1) gene expression in Alzheimer’s disease［J］. Mol Med Ther, 2012, 1(2): 106.

［18］Fabbro S, Schaller K, Seeds NW. Amyloid-beta levels are significantly reduced and spatial memory defects are rescued in a novel neuroserpin-deficient Alzheimer’s disease transgenic mouse model［J］.J Neurochem, 2011, 118(5): 928-938.

［19］Pelisch N, Dan T, Ichimura A, et al. Plasminogen activator inhibitor-1 antagonist TM5484 attenuates demyelination and axonal degeneration in a mice model of multiple sclerosis［J］. PLoS One, 2015, 10(4): e0124510.

［20］Ahmed Z, Bansal D, Tizzard K, et al. Decorin blocks scarring and cystic cavitation in acute and induces scar dissolution in chronic spinal cord wounds［J］. Neurobiol Dis, 2014, 64:163-176.