Single-cell transcriptome analysis reveals the immune heterogeneity and the repopulation of microglia by Hif1α in mice after spinal cord injury

Neuroinflammation is regarded as a vital pathological process in spinal cord injury (SCI), which removes damaged tissue, secretes cytokines, and facilitates regeneration. Repopulation of microglia has been shown to favor recovery from SCI. However, the origin and regulatory factors of microglia repopulation after SCI remain unknown. Here, we used single-cell RNA sequencing to portray the dynamic transcriptional landscape of immune cells during the early and late phases of SCI in mice. B cells and migDCs, located in the meninges under physiological conditions, are involved in immune surveillance. Microglia quickly reduced, and peripheral myeloid cells infiltrated three days-post-injury (dpi). At 14 dpi, microglia repopulated, myeloid cells were reduced, and lymphocytes infiltrated. Importantly, genetic lineage tracing of nestin(+) and Cx3cr1(+) cells in vivo showed that the repopulation of microglia was derived from residual microglia after SCI. We found that residual microglia regress to a developmental growth state in the early stages after SCI. Hif1 alpha promotes microglial proliferation. Conditional ablation of Hif1 alpha in microglia causes larger lesion sizes, fewer axon fibers, and impaired functional recovery in the late stages after SCI. Our results mapped the immune heterogeneity in SCI and raised the possibility that targeting Hif1 alpha may help in axon regeneration and functional recovery after SCI.

Automated summary

Neuroinflammation is an important pathological process in spinal cord injury (SCI), and repopulation of microglia has been shown to aid in recovery. However, the origin and regulatory factors of microglia repopulation after SCI are still unknown. In this study, researchers used single-cell RNA sequencing to study the immune cells during different phases of SCI in mice. They found that residual microglia were the source of repopulated microglia after SCI, and Hif1 alpha played a role in their proliferation. These findings provide new insights into the immune heterogeneity in SCI and suggest that targeting Hif1 alpha may promote axon regeneration and functional recovery.