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| 基因芯片结合生物信息学筛选辐射损伤恢复期造血相关的枢纽基因 |
| 杨悦1,2,张晶1,王寅2,张金元2,王泽剑1,沈翰林1,殷明1*,沈旭东2* |
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(1. 上海交通大学药学院神经药理组,上海 200240
2. 解放军455医院内科,上海 200052
*通信作者) |
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| 摘要: |
| 目的研究小鼠在接受亚致死剂量辐射刺激后,在损伤修复阶段小鼠骨髓全基因组表达的改变。方法以4 Gy 60Co γ 射线辐射刺激小鼠,取辐射刺激后0、3、7、11、21 d的小鼠骨髓细胞RNA样本进行基因芯片分析,通过聚类分析、功能分析和动态网络分析等生物信息学方法,全面挖掘在辐射损伤小鼠骨髓的修复阶段起关键作用的基因及其信号通路，并就筛选得到的关键基因的蛋白表达行进一步分析。结果与未经辐照组相比,辐照损伤后的骨髓组织全基因表达谱显示出1 302个显著性差异基因。通过聚类及功能分析后发现免疫反应(主要是造血作用)的相关基因在辐照损伤修复阶段的机体功能恢复中发挥重要作用。基因芯片结合生物信息学分析构建了显著性差异基因的共表达网络,最终筛选出25个枢纽基因,分别参与了免疫反应(包括造血作用)及转录调节／核小体组装两大生物学过程。重要节点CCL3在辐射后通过自发抑制及增加蛋白水解酶CtsG对其的降解而促进造血干细胞的增殖。结论基因芯片结合生物信息学分析筛选得到的25个基因可能是辐射损伤反应相关的枢纽基因；重要节点CCL3在辐射后通过自发下调及增加蛋白水解以促进造血干细胞的增殖。 |
| 关键词: 实验性辐射损伤 骨髓 造血干细胞 微阵列分析 计算生物学 |
| DOI：10.3724/SP.J.1008.2012.001293 |
| 投稿时间：2012-07-11修订日期：2012-11-20 |
| 基金项目:军队医学研究基金 (09MA027, 10MA025). |
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| Microarray combined with multiple bioinformatics for identifying hub hematopietic genes during recovery phase of irradiation injury |
| YANG Yue1,2,ZHANG Jing1,WANG Yin2,ZHANG Jin-yuan2,WANG Ze-jian1,SHEN Han-lin1,YIN Ming1*,SHEN Xu-dong2* |
(1. Group of Neuropharmacology, School of Pharmacy, Shanghai Jiaotong University, Shanghai 200240, China
2. Department of Internal Medicine, No. 455 Hospital of PLA, Shanghai 200052, China
*Corresponding authors.) |
| Abstract: |
| ObjectiveTo investigate the changes of global gene expression during bone marrow recovery period following sublethal ionizing radiation (IR) in mice. MethodsThe mice were exposed to 4 Gy of 60Co γ irradiation, and RNA samples were extracted from bone marrow cells at day 0, 3, 7, 11 and 21 after irradiation and were subjected to microarray analysis for identifying differentially expressed genes. Multiple bioinformatics analyses, including clustering analysis, gene ontology (GO) analysis, and dynamic gene network analysis, were conducted to identify key hub genes, pathways and biological processes during bone marrow recovery phase. Analysis was also made for the protein of the identified hub genes. ResultsCompared with non-IR stimulation group, 1 302 differential genes were identified by global gene expression profiling of the irradiation-damaged bone marrow. Clustering and GO analyses revealed that the immune response (especially hematopoiesis) associated genes played a critical role in the body function recovery after IR injury. Twenty-five of the differential genes were defined as the hub genes participating in two pathways including immune response and transcription/nucleosome assembly. Key node CCL3 improved the proliferation of hematopoietic stem cells (HSCs) by spontaneous down-regulation and increased degradation by CtsG. ConclusionThe 25 genes identified by microarray analysis and bioinformatics analyses may play critical roles in recovery phase after IR. Key node CCL3 may increase the proliferation of HSCs by spontaneous down-regulation and increase of protein hydrolyzation. |
| Key words: experimental radiation injuries bone marrow hematopoietic stem cells microarray analysis computational biology |
