The microglial reaction signature revealed by RNAseq from individual mice

Expression profiling by high throughput sequencing Microglial cells have a double life as the immune cells of the brain in times of stress but have also specific physiological functions in homeostatic conditions. In pathological contexts, microglia undergo a phenotypic switch called “reaction” ’that promotes the initiation and the propagation of neuro-inflammation. Reaction is complex, molecularly heterogeneous and still poorly characterized, leading to the concept that microglial reactivity might be too diverse to be molecularly defined. However, it remains unknown whether reactive microglia from different pathological contexts share a common molecular signature. Using improved flow cytometry and RNAseq approaches we studied, with higher statistical power, the remodeling of microglia transcriptome in a mouse model of sepsis. Through bioinformatic comparison of our results with published datasets, we defined the microglial reactome as a set of genes discriminating reactive from homeostatic microglia. Ultimately, we identified a subset of 86 genes deregulated in both acute and neurodegenerative conditions. Our data provide a new comprehensive resource that includes functional analysis and specific molecular makers of microglial reaction which represent new tools for its unambiguous characterization. Whole transcriptome RNA sequencing was performed on acutely isolated microglia from 2-3 months old female CX3CR1+/egfp mice(C57BL6/J bacground) which received either intraperitoneal LPS (4 mg/kg; LPS group) or saline solution injection (control group). The mice were eutanized 24h after the injection. 5 LPS and 5 control biological replicates were sequenced, each replicate corresponds to a single mouse.