Translational Profiling Of Microglia Reveals Artifacts Of Cell Sorting

Microglia are the resident innate immune population of the central nervous system that constantly survey and influence their local environment. Transcriptomic profiling has led to significant advances in our understanding of microglia in several disease states, but tissue dissociation and purification of microglia is known to lead to cellular activation. Here we use RiboTag translational RNAseq profiling to demonstrate that commonly used cell sorting methods lead to a fundamental alteration of the microglial transcriptome, with several transcripts that can be used to mark artifacts of isolation. Microglial RiboTag RNAseq profiling after peripheral immune challenge with lipopolysaccharide demonstrates unique transcriptional targets that are not evident using cell sorting methodology. Finally, we applied our technique to reveal novel shared and distinct pathways when comparing microglial transcriptomes after peripheral challenge with bacterial or viral mimetics. This study has broad implications for approaches that examine microglial transcriptomes in normal and pathological states.