Effect of sensory deprivation on the transcriptome of adult murine brain microglia

Microglia, the CNS’s resident macrophages, are involved in brain homeostasis, synapse formation, plasticity, and cognition. Their response to neuronal activity changes remains unclear, though sensory deprivation in young mice alters microglial morphology and increases neuronal phagocytosis. However, the molecular mechanisms driving these changes are unknown. This study investigated microglial responses to altered neuronal activity in the adult mouse visual cortex using a monocular deprivation (MD) model. We hypothesized that MD alters microglial function, reflected in specific signaling pathways. Using RNA-Seq, we analyzed the microglial transcriptome at 12h, 24h, 5d, and 10d post-MD in 3-month-old male and female Cx3cr1CreERT2/+;Rpl22HA/+ (RiboTag) mice. The RiboTag approach enabled the isolation of ribosome-bound mRNA, providing insights into microglial activity. We optimized the protocol to ensure high-quality RNA and used qPCR to assess plasticity-related genes. Microglia in the contralateral visual cortex (VL) showed stronger and earlier responses than in the ipsilateral cortex (VR), with the highest number of altered genes at 12h and 24h. Microglia upregulated G protein-coupled receptors and downregulated transcription factors regulating the cytoskeleton. We identified Sptbn4, Actn1, and Mical2 as novel players in microglial responses to sensory deprivation. Prolonged MD (5–10d) increased immediate early gene and plasticity-related gene expression, suggesting a homeostatic response. The VR showed minimal early changes, though some genes exhibited a conserved systemic response. Neuronal gene analysis revealed delayed Arc and Egr1 upregulation in the VR at 10d, suggesting late strengthening of the non-deprived cortex. In conclusion, microglia rapidly respond to sensory deprivation in the VL, with minimal VR changes. This study identifies novel pathways in microglial adaptation, offering targets for future research.