Monocytes/macrophages have begun to emerge as key cellular modulators of brain homeostasis and central\nnervous system (CNS) disease. In the healthy brain, resident microglia are the predominant macrophage cell\npopulation; however, under conditions of blood-brain barrier leakage, peripheral monocytes/macrophages can\ninfiltrate the brain and participate in CNS disease pathogenesis. Distinguishing these two populations is often\nchallenging, owing to a paucity of universally accepted and reliable markers. To identify discriminatory marker sets\nfor microglia and peripheral monocytes/macrophages, we employed a large meta-analytic approach using five\npublished murine transcriptional datasets. Following hierarchical clustering, we filtered the top differentially\nexpressed genes (DEGs) through a brain cell type-specific sequencing database, which led to the identification of\neight microglia and eight peripheral monocyte/macrophage markers. We then validated their differential\nexpression, leveraging a published single cell RNA sequencing dataset and quantitative RT-PCR using freshly\nisolated microglia and peripheral monocytes/macrophages from two different mouse strains. We further verified the\ntranslation of these DEGs at the protein level. As top microglia DEGs, we identified P2ry12, Tmem119, Slc2a5 and\nFcrls, whereas Emilin2, Gda, Hp and Sell emerged as the best DEGs for identifying peripheral monocytes/\nmacrophages. Lastly, we evaluated their utility in discriminating monocyte/macrophage populations in the setting\nof brain pathology (glioma), and found that these DEG sets distinguished glioma-associated microglia from\nmacrophages in both RCAS and GL261 mouse models of glioblastoma. Taken together, this unbiased bioinformatic\napproach facilitated the discovery of a robust set of microglia and peripheral monocyte/macrophage expression\nmarkers to discriminate these monocyte populations in both health and disease.
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