Multiomics profiling of molecular and cellular dynamics of spinal cord injury in a rat [miRNA-seq]

Spinal cord injury (SCI) is a debilitating condition with no effective treatment. The injury triggers a complex cascade of molecular and cellular events that drive both damage and repair processes. To explore these mechanisms, we performed a comprehensive multiomics analysis in a rat compression model of SCI, focusing on the acute phase. Transcriptomic profiling revealed extensive gene dysregulation, highlighting early inflammation, neuronal death, and synaptic dysfunction, followed by the initiation of reparative processes. Cell type composition analysis showed a rapid infiltration of peripheral immune cells, activation of microglia, and loss of neurons, astrocytes, and oligodendrocytes. miRNA profiling uncovered a highly dysregulated miRNA landscape, with the miR-17~92 cluster emerging as a key regulator of neurogenesis, synaptic activity, and cell survival. Integrative miRNA-mRNA-protein analysis identified potential therapeutic targets, including miR-20a, whose inhibition in vitro supported neurogenesis and reduced apoptosis under oxidative stress. Our findings provide new insights into the molecular mechanisms of SCI and highlight miRNAs as potential targets for therapeutic intervention. Overall design: Adult male Wistar rats (n=64) were used as an experimental model. The rats were obtained from the facility's breeding center (Physiological Institute of the Academy of Sciences of the Czech Republic, Prague, Czech Republic). Animals undergoing surgery weighed 300 ± 30 g and were 10 weeks old. Animals were maintained on a 12-h light/dark cycle with ad libitum access to food and water. Rats were randomly divided into experimental groups: SCI 3 hpi (n=4), 12 hpi (n=4), 24 hpi (n=4), 3 dpi (n=4), 7 dpi (n=4), time- corresponding shame-operated groups (n=4 for each group) and an intact control group (n=4), also 8 animals were used for behavioral tests and 12 animals were used for immunohistochemical analysis.

脊髓损伤（Spinal cord injury, SCI）是一类严重致残性疾病，目前尚无有效治疗手段。损伤会触发复杂的分子与细胞级联事件，同时驱动损伤进展与修复启动两类病理过程。为探究此类机制，我们针对大鼠脊髓压迫损伤模型开展了全面的多组学分析（multiomics analysis），研究聚焦于损伤急性期。
转录组谱分析（Transcriptomic profiling）显示存在广泛的基因表达失调，明确了早期炎症反应、神经元死亡与突触功能障碍等特征，随后启动损伤修复相关进程。细胞类型组成分析结果显示，外周免疫细胞快速浸润脑组织、小胶质细胞激活，同时伴随神经元、星形胶质细胞与少突胶质细胞的丢失。
微小RNA（microRNA, miRNA）谱分析揭示了高度失调的miRNA表达图谱，其中miR-17~92簇被鉴定为神经发生、突触活动与细胞存活的关键调控因子。整合miRNA-mRNA-蛋白质组分析筛选出潜在治疗靶点，包括miR-20a；体外实验证实，抑制miR-20a可促进神经发生，并缓解氧化应激状态下的细胞凋亡。
本研究为脊髓损伤的分子病理机制提供了全新见解，并凸显微小RNA可作为脊髓损伤治疗干预的潜在靶点。
实验整体设计：本研究共使用64只成年雄性Wistar大鼠作为实验模型。大鼠购自捷克科学院生理研究所布拉格繁育中心。手术时大鼠体重为300±30克，周龄为10周。所有动物饲养于12小时光暗循环环境中，自由进食饮水。将大鼠随机分为以下组别：脊髓损伤后3小时（3 hpi，n=4）、12小时（12 hpi，n=4）、24小时（24 hpi，n=4）、3天（3 dpi，n=4）、7天（7 dpi，n=4）实验组，以及对应时间点的假手术组（sham-operated group，每组n=4）与空白对照组（intact control，n=4）。此外，另有8只大鼠用于行为学测试，12只大鼠用于免疫组织化学分析。