Single-cell sequencing of cortical cells following murine traumatic brain injury [scRNA-seq]

Traumatic brain injury (TBI) can lead to significant neuropsychiatric problemsand neurodegenerative pathologies, which develop and persist years after injury. Neuroinflammatory processes evolve over this same period. Cortical mRNA analysis showed a robust contribution of microglia to neuroinflammatory pathways that persisted over time post-injury. These data also indicate that inflammation persists in the subacute and chronic time points after TBI, which may affect surrounding neurons, oligodendrocytes and astrocytes. To investigate this hypothesis, a single-cell sequencing approach was used to determine cell-type specific gene expression within the cortex 7 dpi with and without microglial depletion. Overall design: Mice were subjected to midline fluid percussion injury (TBI) or kept as naïve controls. Half of the mice were fed PLX5622 (colony stimulating factor 1-receptor antagonist) in the chow prior to injury and up until the 7 dpi endpoint; the other half were fed AIN-7 vehicle chow. PLX5622 and CSF1R antagonism were used to deplete microglia. Therefore there were four experimental groups: Control, Control+PLX5622, TBI, and TBI+PLX5622. Cortex was dissociated and single cell suspensions from 3 mice per group were pooled into a single sample. This experiment was completed in two replicates (6 mice per group total; 2 experimental replicates per group).