Acute Transcriptomic Response After Mouse Spinal Cord Injury

In order to characterize genomic response and identify molecular marker for acute neural injury, we performed RNA-sequencing 4 hours after spinal cord injury. We found a group of genes with significant differential expression (DEG) after Benjamini-Hochberg FDR multiple corrections. These DEGs mainly include early response genes, neuroinflammation, and cell injury and death. Notely, activating transcription factor 3 (ATF3) is one of the most significantly upregulated genes by 9.9 folds and is a well-recognized molecular marker for DRG sensory neuron injury in peripheral nerve injury model. Overall design: Unilateral C5 (cervical) contusion injury or laminectomy only was performed in wildtype mice (n=3 in each group). Spinal cord tissue was collected 4 hours after SCI and stored at -80 degrees. Total cellular RNA was prepared using TRIzol and RNA miniprep kit (Qiagen). RNA sequencing was performed using 1ug total RNA. Sequencing type: single-end 50bp by Illumina HiSeq 4000, Lexogen Quantseq Forward library kit with STAR_2.7.2b aligner. mm10, Ensembl mouse GRCm38.96 Alignment Genome was used.

为了表征急性神经损伤的基因组应答并鉴定其分子标志物，我们在脊髓损伤4小时后开展了RNA测序（RNA-sequencing）。经Benjamini-Hochberg错误发现率（FDR）多重校正后，我们筛选得到一批显著差异表达基因（DEG）。这些差异表达基因主要涵盖早期应答基因、神经炎症相关基因以及细胞损伤与死亡相关基因。值得注意的是，激活转录因子3（ATF3）是上调幅度最高的基因之一，其表达量上调达9.9倍，且在周围神经损伤模型中是公认的背根神经节（DRG）感觉神经元损伤的分子标志物。实验设计：对野生型小鼠实施单侧C5（颈椎）挫伤造模或仅行椎板切除术（每组n=3）。于脊髓损伤（SCI）后4小时收集脊髓组织，置于-80℃保存。采用TRIzol试剂与RNA微量制备试剂盒（Qiagen）提取总细胞RNA。取1μg总RNA进行RNA测序。测序类型为单端50bp测序，采用Illumina HiSeq 4000平台、Lexogen Quantseq Forward文库制备试剂盒，比对工具选用STAR_2.7.2b。比对基因组选用mm10、Ensembl小鼠GRCm38.96版本。