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Updated: Jan 29, 2026
Analysis of Microglia and Monocyte-derived Macrophages from the Central Nervous System by Flow Cytometry
Published on: June 22, 2017
Comprehensive gene expression meta-analysis identifies signature genes that distinguish microglia from peripheral
Verena Haage1, Marcus Semtner1, Ramon Oliveira Vidal1
1Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
Abstract:
Monocytes/macrophages have begun to emerge as key cellular modulators of brain homeostasis and central nervous system (CNS) disease. In the healthy brain, resident microglia are the predominant macrophage cell population; however, under conditions of blood-brain barrier leakage, peripheral monocytes/macrophages can infiltrate the brain and participate in CNS disease pathogenesis. Distinguishing these two populations is often challenging, owing to a paucity of universally accepted and reliable markers. To identify discriminatory marker sets for microglia and peripheral monocytes/macrophages, we employed a large meta-analytic approach using five published murine transcriptional datasets. Following hierarchical clustering, we filtered the top differentially expressed genes (DEGs) through a brain cell type-specific sequencing database, which led to the identification of eight microglia and eight peripheral monocyte/macrophage markers. We then validated their differential expression, leveraging a published single cell RNA sequencing dataset and quantitative RT-PCR using freshly isolated microglia and peripheral monocytes/macrophages from two different mouse strains. We further verified the translation of these DEGs at the protein level. As top microglia DEGs, we identified P2ry12, Tmem119, Slc2a5 and Fcrls, whereas Emilin2, Gda, Hp and Sell emerged as the best DEGs for identifying peripheral monocytes/macrophages. Lastly, we evaluated their utility in discriminating monocyte/macrophage populations in the setting of brain pathology (glioma), and found that these DEG sets distinguished glioma-associated microglia from macrophages in both RCAS and GL261 mouse models of glioblastoma. Taken together, this unbiased bioinformatic approach facilitated the discovery of a robust set of microglia and peripheral monocyte/macrophage expression markers to discriminate these monocyte populations in both health and disease.
Insights
Researchers identified key gene markers to distinguish between brain-resident microglia and infiltrating peripheral monocytes/macrophages, crucial for understanding central nervous system (CNS) health and disease.
Area of Science:
- Neuroimmunology
- Cellular Biology
- Genomics
Background:
- Monocytes and macrophages are key regulators of brain homeostasis and central nervous system (CNS) diseases.
- Distinguishing resident microglia from infiltrating peripheral monocytes/macrophages in the CNS is challenging due to a lack of reliable markers.
Purpose of the Study:
- To identify and validate a robust set of gene expression markers that can reliably discriminate between microglia and peripheral monocytes/macrophages in the brain.
- To assess the utility of these markers in distinguishing these cell populations during CNS pathology, specifically glioma.
Main Methods:
- A meta-analytic approach using five murine transcriptional datasets to identify differentially expressed genes (DEGs) between microglia and peripheral monocytes/macrophages.
- Hierarchical clustering and filtering of DEGs using a brain cell type-specific sequencing database.
- Validation of identified markers using single-cell RNA sequencing, quantitative RT-PCR, and protein-level verification in mouse models.
Main Results:
- Eight specific gene markers were identified for microglia (e.g., P2ry12, Tmem119) and eight for peripheral monocytes/macrophages (e.g., Emilin2, Hp).
- Validated differential expression at both RNA and protein levels.
- Demonstrated the utility of these marker sets in discriminating glioma-associated microglia from infiltrating macrophages in mouse glioblastoma models.
Conclusions:
- This study provides a validated set of molecular markers for distinguishing microglia from peripheral monocyte/macrophage populations in the CNS.
- These markers are valuable tools for research in neuroimmunology, aiding in the study of CNS homeostasis and diseases like glioma.
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