Genetic context alters central nervous system compartment dependent responses to lipopolysaccharide

Systemic inflammation drives neurodegeneration, yet its differential effects across neural tissues and genetic backgrounds remain poorly understood. We performed RNA-sequencing on brain, optic nerve head (ONH), and retina from four genetically diverse mouse strains (B6, CAST, NZO, WSB) following lipopolysaccharide (LPS)-induced systemic inflammation. The ONH mounted the largest response to LPS (9510 DEGs), followed by retina (5152) and brain (4586). A conserved core of 1444 DEGs across all tissues was enriched for innate immune and acute-phase pathways. Tissue-specific responses were apparent; the retina downregulated phototransduction and visual perception genes; ONH exhibited bidirectional remodeling with upregulated proteasome and ribosome biogenesis and suppressed lipid metabolism and lysosomal function; yet the brain displayed no significant pathway level enrichment. Genetic background strongly modulated the LPS response across the three tissues; the retina exhibited the greatest strain-dependent divergence. Interestingly, differing genetic context affected the ONH response to LPS the least despite its markedly larger response to LPS overall. In totality, both genetic and physical context dictate the neuroinflammatory response to LPS.