Background
Traumatic spinal cord injury (SCI) elicits a complex cascade of immune cell activation and recruitment. Although critical for normal wound healing, the inflammatory response in SCI typically does not resolve, leading to protracted immune cell activity at the damaged site. Why there is no timely resolution of the inflammatory phase of wound healing in SCI remains poorly understood, and a deep understanding of the specific subsets/states of immune cells at the lesion site is also missing. To address this, we have used single-cell and spatial RNA sequencing to characterise the spatio-temporal evolution of the inflammatory infiltrate in SCI.
Methods and Results
We have curated an atlas of >35,000 immune cells from the lesion site over the first week of SCI through single-cell RNASeq. We identified seven broad immune cell types: microglia, neutrophils, monocytes, macrophages, dendritic cells (DCs), B cells, and NKT cells. Each cell category was revealed to be highly heterogeneous and dynamic, with further reclustering and deep annotation splitting them into 39 different immune cell subtypes and/or transcriptional states. We then mapped the location of cell subtypes in space using Visium spatial transcriptomics, finding that the different cell subtypes localised to particular anatomical microdomains within the lesion site. These spatial differences were associated with changes in cell crosstalk, as revealed by spatially-guided cell-cell interaction analysis.
Conclusion
By integrating data from independent yet complementary spatial and single-cell technologies, we were able to build a comprehensive spatial atlas of inflammation in acute SCI. We reveal unprecedented diversity of infiltrating immune cells, have mapped their activity to anatomical context, and profiled how these cells communicate with one another through complex cytokine and chemokine networks, dependent on their spatio-temporal locations. We are now using this information to dissect the role of inflammation in local spinal cord wound healing responses.