Brainstem control of transcription after spinal cord injury (SCI)

The spinal cord after injury shows altered transcription in numerous genes. We tested in a pilot study whether the nucleus raphé magnus, a descending serotonergic brainstem region whose stimulation improves recovery after incomplete spinal cord injury, can influence these transcriptional changes. Rats received 2 hours of low-frequency electrical stimulation in the raphé magnus three days after an impact contusion at segment T8. Comparison groups lacked injuries or activated stimulators or both. Immediately following stimulation, spinal cords were extracted, their RNA transcriptome sequenced, and differential gene expression quantified. Confirming many previous studies, injury primarily increased inflammatory and immune transcripts and decreased those related to lipid and cholesterol synthesis and neuronal signaling. Stimulation plus injury, contrasted with injury alone, caused significant changes in 43 transcripts (39 increases, 4 decreases), all protein-coding. Injury itself decreased only four of these 43 transcripts, all reversed by stimulation, and increased none of them. The non-specific 5-HT7 receptor antagonist pimozide reversed 25 of the 43 changes. Stimulation in intact rats principally caused decreases in transcripts related to oxidative phosphorylation, none of which were altered by stimulation in injury. Gene ontology (biological process) annotations comparing stimulation with either no stimulation or pimozide treatment in injured rats highlighted defense responses to lipopolysaccharides and microorganisms, and also erythrocyte development and oxygen transport (possibly yielding cellular oxidant detoxification). Connectivity maps of human orthologous genes generated in the CLUE database of perturbagen-response transcriptional signatures showed that drug classes whose effects in injured rats most closely resembled stimulation without pimozide include peroxisome proliferator-activated receptor agonists and angiotensin receptor blockers, which are reportedly beneficial in spinal cord injury. Thus, the initial transcriptional response of injured spinal cord to raphé magnus stimulation is upregulation of genes that in various ways are mostly protective, some probably located in recently arrived myeloid cells.损伤后的脊髓在众多基因中均出现转录水平改变。本研究通过预实验探究了中缝大核（nucleus raphé magnus）——一种可通过刺激改善不完全性脊髓损伤后恢复的下行性5-羟色胺能脑干核团——是否能够调控此类转录变化。实验中，大鼠在T8节段遭受撞击性挫伤后的第3天，接受了2小时的中缝大核低频电刺激；对照组分别设置为无脊髓损伤组、未启动刺激组，以及既无脊髓损伤也未启动刺激的空白组。刺激结束后立即提取脊髓组织，对其RNA转录组进行测序，并定量分析差异基因表达情况。与既往多项研究结果一致，脊髓损伤主要上调了炎症与免疫相关转录本，而下调了脂质、胆固醇合成及神经元信号传导相关转录本。与单纯损伤组相比，联合刺激与损伤组的43个转录本出现显著变化（其中39个上调、4个下调），且所有转录本均为蛋白编码型。单纯损伤仅下调了上述43个转录本中的4个，且所有此类下调均被刺激逆转，而单纯损伤未上调任何一个该类转录本。非特异性5-羟色胺7（5-HT7）受体拮抗剂匹莫齐特可逆转43个转录本中的25个变化。对未受损伤的正常大鼠施加刺激，主要下调了氧化磷酸化相关转录本，而此类转录本在脊髓损伤大鼠的刺激组中未出现显著变化。对脊髓损伤大鼠中刺激组与无刺激组/匹莫齐特处理组进行基因本体论（Gene ontology, GO）生物过程注释分析，结果显示富集的生物学过程包括脂多糖与微生物防御反应，以及红细胞发育与氧气运输——该过程可能有助于细胞氧化解毒。基于CLUE扰动应答转录特征数据库生成的人类同源基因连接图谱显示，在脊髓损伤大鼠中，效应与未使用匹莫齐特的刺激组最为相似的药物类别包括过氧化物酶体增殖物激活受体（peroxisome proliferator-activated receptor, PPAR）激动剂与血管紧张素受体阻滞剂，此类药物据报道对脊髓损伤具有治疗益处。综上，损伤脊髓对中缝大核刺激的初始转录应答为上调多数具有保护作用的基因，其中部分基因可能来源于新近浸润的髓系细胞。