Gene expression patterns following unilateral traumatic brain injury reveals a local pro-inflammatory and remote anti-inflammatory response

Abstract Background Traumatic brain injury (TBI) results in irreversible damage at the site of impact and initiates cellular and molecular processes that lead to secondary neural injury in the surrounding tissue. We used microarray analysis to determine which genes, pathways and networks were significantly altered using a rat model of TBI. Adult rats received a unilateral controlled cortical impact (CCI) and were sacrificed 24h post-injury. The ipsilateral hemi-brain tissue at the site of the injury, the corresponding contralateral hemi-brain tissue, and naïve (control) brain tissue were used for microarray analysis. Ingenuity Pathway Analysis (IPA) software was used to identify molecular pathways and networks that were associated with the altered gene expression in brain tissues following TBI. Results Inspection of the top fifteen biological functions in IPA associated with TBI in the ipsilateral tissues revealed that all had an inflammatory component. IPA analysis also indicated that inflammatory genes were altered on the contralateral side, but many of the genes were inversely expressed compared to the ipsilateral side. The contralateral gene expression pattern suggests a remote anti-inflammatory molecular response. We created a network of the inversely expressed common (i.e., same gene changed on both sides of the brain) inflammatory response (IR) genes and those IR genes included in pathways and networks identified by IPA that changed on only one side. We ranked the genes by the number of direct connections each had in the network, creating a gene interaction hierarchy (GIH). Two well characterized signaling pathways, toll-like receptor/NF-kappaB signaling and JAK/STAT signaling, were prominent in our GIH. Conclusions Bioinformatic analysis of microarray data following TBI identified key molecular pathways and networks associated with neural injury following TBI. The GIH created here provides a starting point for investigating therapeutic targets in a ranked order that is somewhat different than what has been presented previously. In addition to being a vehicle for identifying potential targets for post-TBI therapeutic strategies, our findings can also provide a context for evaluating the potential of therapeutic agents currently in development.摘要 背景 创伤性脑损伤（Traumatic brain injury, TBI）会在撞击部位造成不可逆损伤，并启动细胞与分子进程，导致周围组织发生继发性神经损伤。本研究借助微阵列分析（microarray analysis），基于创伤性脑损伤大鼠模型，筛选发生显著改变的基因、通路及网络。成年大鼠接受单侧可控皮层撞击（unilateral controlled cortical impact, CCI）造模，并于损伤后24小时处死。分别采集损伤侧同侧半脑组织、对应对侧半脑组织及未处理对照（naïve, control）脑组织，用于微阵列分析。使用Ingenuity通路分析（Ingenuity Pathway Analysis, IPA）软件，识别创伤性脑损伤后脑组织基因表达异常相关的分子通路与网络。 结果 对IPA分析中与损伤侧脑组织创伤性脑损伤相关的前15项生物学功能进行检视，发现所有功能均存在炎症相关组分。IPA分析同时显示，对侧脑组织中炎症基因亦发生表达改变，但多数基因的表达趋势与损伤侧呈反向。该对侧基因表达模式提示存在远端抗炎分子应答。我们构建了反向表达的共有炎症反应（inflammatory response, IR）基因网络——即双侧脑组织均发生表达改变的基因，同时纳入IPA鉴定出的仅单侧发生改变的炎症反应基因。基于各基因在网络中的直接连接数量对其进行排序，构建得到基因互作层级（gene interaction hierarchy, GIH）。在该层级中，两条已得到充分研究的信号通路：toll样受体/NF-κB信号通路与JAK/STAT信号通路，占据显著地位。 结论 本研究对创伤性脑损伤后微阵列数据开展生物信息学分析，筛选得到与创伤性脑损伤后神经损伤相关的关键分子通路与网络。本研究构建的基因互作层级，为按排序优先级探究创伤性脑损伤后治疗靶点提供了起点，其排序逻辑与既往研究存在一定差异。本研究结果不仅可用于筛选创伤性脑损伤后治疗策略的潜在靶点，还可为评估当前在研治疗药物的潜力提供参考框架。