Background Immune cells play crucial roles after spinal cord injury (SCI). However, incomplete knowledge of immune contributions to injury and repair hinders development of SCI therapies. We leveraged single-cell observations to describe key populations of immune cells present in the spinal cord and changes in their transcriptional profiles from uninjured to subacute and chronic stages of SCI. Methods Deep-read single-cell sequencing was performed on CD45+ cells from spinal cords of uninjured and injured Swiss-webster mice. After T9 thoracic contusion, cells were collected 3-, 7-, and 60-day post-injury (dpi). Subpopulations of CD45+ immune cells were identified informatically, and their transcriptional responses characterized with time. We compared gene expression in spinal cord microglia and B cell subpopulations with those in published models of disease and injury. Microglia were compared with Disease Associated Microglia (DAM) and Injury Responsive Microglia (IRM). B cells were compared to developmental lineage states and to an Amyotrophic Lateral Sclerosis (ALS) model. Results In uninjured and 7 dpi spinal cord, most CD45+ cells isolated were microglia while chronically B cells predominated. B cells accumulating in the spinal cord following injury included immature B to mature stages and were predominantly found in the injury zone. We defined diverse subtypes of microglia and B cells with altered gene expression with time after SCI. Spinal cord microglia gene expression indicates differences from brain microglia at rest and in inflammatory states. Expression analysis of signaling ligand–receptor partners identified microglia–B cell interactions at acute and chronic stages that may be involved in B cell recruitment, retention, and formation of ectopic lymphoid follicles. Conclusions Immune cell responses to SCI have region-specific aspects and evolve with time. Developmentally diverse populations of B cells accumulate in the spinal cord following injury. Microglia at subacute stages express B cell recruitment factors, while chronically, they express factors predicted to reduce B cell inflammatory state. In the injured spinal cord, B cells create ectopic lymphoid structures, and express secreted factors potentially acting on microglia. Our study predicts previously unidentified crosstalk between microglia and B cells post-injury at acute and chronic stages, revealing new potential targets of inflammatory responses for SCI repair warranting future functional analyses.

It is well established that immune cells play crucial roles after spinal cord injury (SCI). However, our knowledge of the contributions of various immune cells to injury progression and repair is incomplete. These gaps in understanding hamper development of SCI therapeutics. In the current study, using single-cell RNA sequencing, and transcriptomic analysis, the populations of resident and circulating CD45+ immune cells present within the uninjured and injured mouse spinal cord were identified. In the uninjured and subacutely-injured (7 day) spinal cord, most CD45+ cells were microglia while in chronic SCI (60 day) B cells predominated. Examination of microglia and B cell clusters showed subtype-specific alterations after SCI, including the presence of both immature and mature B cells chronically. Analysis of the expression of signaling partners in B cells and microglia identified injury-related microglia-B-cell interactions. This sequencing resource establishes unidentified interactions revealing new mechanisms to target inflammatory responses for SCI repair.