Single-cell RNA sequencing reveals time- and sex-specific responses of spinal cord microglia to peripheral nerve injury and links ApoE to neuropathic pain

Activation of microglia in the spinal cord following peripheral nerve injury is critical for the development of long-lasting pain hypersensitivity. However, it remains unknown whether distinct microglia subpopulations or states contribute to different stages of pain development and maintenance. Here, we demonstrate, using single-cell RNA-sequencing, that microglia transcriptional states differ at early and late time points following nerve injury. Male microglia show more proliferation and distinct transcriptional changes in response to nerve injury comparing to females. Apolipoprotein E (Apoe) was the top upregulated gene in microglia at chronic time points after nerve injury in mice and polymorphisms in the APOE in humans are associated with chronic pain. Single-cell analysis of human spinal cord microglia reveals a subpopulation with a disease-related transcriptional signature. Our data provide a detailed analysis of transcriptional states of mouse and human spinal cord microglia and identify a previously unrecognized role for ApoE in neuropathic pain. Overall design: Single-cell RNA sequencing of male and female mouse microglia, before and after peripheral nerve injury (3 days, 14 days and 5 months)