Time-resolved single-cell RNAseq profiling identifies a novel Fabp5-expressing subpopulation of inflammatory myeloid cells in chronic spinal cord injury

Traumatic spinal cord injury (SCI) is a debilitating central nervous system (CNS) pathology that lacks effective restorative treatments. The mechanisms of tissue recovery after SCI are dysregulated in comparison to normal wound healing, leading to a chronic wound state, rather than a return to homeostasis. While this state is characterized by persistent inflammation driven by CNS resident microglia (MG) and infiltrating myeloid cells, the precise roles of myeloid cell subsets after SCI remains unclear. In particular, upon crossing the blood-brain barrier, tissue infiltrating monocyte-derived macrophages (MCd) take on the morphology of MG, and upregulate canonical MG markers2, making the two populations practically indistinguishable. Here, we first employed a Cx3cr1-CreERT2 mouse model to label Cx3cr1+ cells for FACS isolation. Then we utilized fate-mapping approach (see methods) to investigate the ontology and temporal dynamics of Cx3cr1+ spinal cord MG (RFP+/YFP+) and Cx3cr1+ infiltrating myeloid cells (RFP-/YFP+) via FACS isolation and single-cell RNA sequencing (scRNAseq) in a mouse model of thoracic contusion SCI. Useful Links: Github repository (https://github.com/regan-hamel/SCI_2020) Overall design: 30,958 cells isolated via FACS from the lesion epicentre. Collected at 1, 3, 10, and 21 days post-SCI and laminectomy-only controls. Each sample comprises tissue from 1-3 mice.