Spatial transcriptomics reveals acute white matter pathology consistent with increased risk of chronic neurodegenerative outcomes with a single, focal cortical contusion injury in mice

Abstract Text: The degree of axonal injury in the brain white matter (WM) correlates with symptom severity and inversely with prognosis in patients with a traumatic brain injury (TBI). Preclinical data indicates secondary axonal pathology is reversible: acute axonal pathology can be genetically dissociated from irreversible axonal damage and axons that maintain connectivity remain capable of remyelination following TBI. These findings are significant in that they reveal a window for therapeutic intervention after the initial trauma to limit axonal demyelination and fragmentation. To investigate how TBI may alter the molecular signatures of the WM, we utilized a well-characterized focal controlled cortical impact (CCI) model of TBI in mice and spatially mapped gene expression changes in WM tracts at 2 and 7 days post-injury (PI) utilizing Visium Spatial Gene Expression (10X Genomics). We hypothesized focal contusion injury would result in differentially expressed genes (DEGs) associated with damage/disease-associated molecular (DAM) cell states in vulnerable WM post-injury. We compared DEGs in the WM tracts closest to the site of impact, the corpus callosum and external capsule (CC-EC), versus the more distal WM tract of the anterior commissure (AC). CC-EC and AC gene signatures were compared within and between CCI and sham groups. This comparative analysis allowed us to detect discrete, spatially-dependent molecular responses PI consistent with the presence of DAM oligodendrocyte, astrocyte and microglia cell states in the EC-CC. DAM gene signatures were detected during the acute post-injury period, at both 2 and 7 days PI, and were associated with robust neuroinflammatory and myeloid cell gene signatures in the damaged CC-EC. Our data indicates a single, focal brain injury induces a temporal and spatially-dependent, acute transcriptional response in vulnerable WM tracts linked to chronic activation of the immune system and long-term risk of neurodegeneration.

Keywords: mice, controlled cortical impact, spatial gene expression, white matter, corpus callosum, external capsule, anterior commissure, damage/disease-associated molecular cell states