Single-nuclei sequencing reveals a robust corticospinal response to nearby axotomy but overall insensitivity to spinal injury

The ability of neurons to sense and respond to damage is crucial for maintaining homeostasis and facilitating nervous system repair. For some cell types, notably dorsal root ganglia (DRG) and retinal ganglion cells (RGCs), extensive profiling has uncovered a significant transcriptional response to axon injury, which influences survival and regenerative outcomes. In contrast, the injury responses of most supraspinal cell types, which display limited regeneration after spinal damage, remain mostly unknown. In this study, we used single-nuclei sequencing in adult male and female mice to profile the transcriptional responses of diverse supraspinal cell types to spinal injury. Surprisingly, thoracic spinal injury induced only modest changes in gene expression across all populations, including corticospinal tract (CST) neurons. Additionally, CST neurons exhibited minimal response to cervical injury but showed much stronger reaction to intracortical axotomy, with upregulation of numerous regeneration and apoptosis-related transcripts shared with injured DRG and RGC neurons. Thus, the muted response of CST neuron to spinal injury is linked to the injury's distal location, rather than intrinsic cellular characteristics. More broadly, these findings indicate that a central challenge for enhancing regeneration after a spinal injury is the limited detection of distant injuries and the subsequent modest baseline neuronal response.Significance statement The inability of axons to regenerate after spinal injury limits functional recovery. Efforts to improve regeneration rely on a precise understanding of the baseline transcriptional response to spinal injury. Through single-nuclei sequencing of diverse descending cell types, we find that spinal injury causes only modest changes in gene expression, whereas axon damage close to cell bodies elicits a much larger response. These findings highlight the muted detection of distant injury, and the subsequent failure to initiate widespread gene expression changes, as major obstacles to axon regeneration after spinal injury.