Transcriptome profile of rat genes in injured spinal cord at different stages by RNA-sequencing.
Transcriptome profile of rat genes in injured spinal cord at different stages by RNA-sequencing.
复制标题
通过RNA测序分析不同阶段大鼠脊髓损伤基因的转录组谱
DOI：
10.1186/s12864-017-3532-x
复制
发表时间：
2017-02-15
期刊：
影响因子：
4.4
通讯作者：
Lü HZ
中科院分区：
文献类型：
--
作者：
Shi LL;Zhang N;Xie XM;Chen YJ;Wang R;Shen L;Zhou JS;Hu JG;Lü HZ
脊髓损伤（SCI）会导致致命损害，目前没有有效的治疗方法。 RNA - 序列（RNA-seq）是系统的，以识别与SCI病理学有关的关键基因和途径。
从急性，亚急性和慢性阶段在损伤后的急性，亚急性和慢性阶段中从假手术大鼠和大鼠的脊髓收获的总RNA（分别为1天，6天和28天； n = 3中；每n = 3分别，每种n = 3）与假控制组相比，急性期不同表达的基因的数量为1797（1223个更新和574个下调），在亚急性阶段（3460次更新，下调3130），在慢性阶段进行了3499（1866年更新（1866年）和1633年），通过DESEQ进行了调整的P值<0.05。核糖体，离子门控通道活性的一致性，较小的GTPase介导的信号转移以及细胞因子和/或趋化因子活性。 ，轴突引导，多巴胺能突触，谷氨酸能突触，GABA能突触，TNF，HIF-1，Toll-Kappa B，NF-KAPPA B，NOD-KAPPA B，NOD样受体，cAMP，钙，钙，氧毒素，Oxytocin，Rap1，B细胞受体和趋化因子和趋化因子信号通道。
这项研究不仅表征了通过大鼠SCI进展的各个阶段的全局基因表达的变化，而且还系统地确定了SCI病理学中的关键基因和信号传导途径。为将来研究脊髓组织损伤和修复提供了基础。
这项研究的序列数据已沉积到序列读取存档中（http://www.ncbi.nlm.nih.gov/sra；登录号PRJNA318311）。
本文的在线版本（doi：10.1186/s12864-017-3532-x）包含补充材料，可供授权用户使用。
BackgroundSpinal cord injury (SCI) results in fatal damage and currently has no effective treatment. The pathological mechanisms of SCI remain unclear. In this study, genome-wide transcriptional profiling of spinal cord samples from injured rats at different time points after SCI was performed by RNA-Sequencing (RNA-Seq). The transcriptomes were systematically characterized to identify the critical genes and pathways that are involved in SCI pathology.ResultsRNA-Seq results were obtained from total RNA harvested from the spinal cords of sham control rats and rats in the acute, subacute, and chronic phases of SCI (1 day, 6 days and 28 days after injury, respectively;n= 3 in every group). Compared with the sham-control group, the number of differentially expressed genes was 1797 in the acute phase (1223 upregulated and 574 downregulated), 6590 in the subacute phase (3460 upregulated and 3130 downregulated), and 3499 in the chronic phase (1866 upregulated and 1633 downregulated), with an adjustedP-value <0.05 by DESeq. Gene ontology (GO) enrichment analysis showed that differentially expressed genes were most enriched in immune response, MHC protein complex, antigen processing and presentation, translation-related genes, structural constituent of ribosome, ion gated channel activity, small GTPase mediated signal transduction and cytokine and/or chemokine activity. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that the most enriched pathways included ribosome, antigen processing and presentation, retrograde endocannabinoid signaling, axon guidance, dopaminergic synapses, glutamatergic synapses, GABAergic synapses, TNF, HIF-1, Toll-like receptor, NF-kappa B, NOD-like receptor, cAMP, calcium, oxytocin, Rap1, B cell receptor and chemokine signaling pathway.ConclusionsThis study has not only characterized changes in global gene expression through various stages of SCI progression in rats, but has also systematically identified the critical genes and signaling pathways in SCI pathology. These results will expand our understanding of the complex molecular mechanisms involved in SCI and provide a foundation for future studies of spinal cord tissue damage and repair.The sequence data from this study have been deposited into Sequence Read Archive ( http://www.ncbi.nlm.nih.gov/sra ; accession number PRJNA318311).