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Updated: Oct 29, 2025
Isolation of Region-specific Microglia from One Adult Mouse Brain Hemisphere for Deep Single-cell RNA Sequencing
Published on: December 3, 2019
Characterization of microglial transcriptomes in the brain and spinal cord of mice in early and late experimental
Shaona Acharjee1, Paul M K Gordon2, Benjamin H Lee1
1Hotchkiss Brain Institute, Snyder Institute for Chronic Diseases, Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada.
Abstract:
Microglia play an important role in the pathogenesis of multiple sclerosis and the mouse model of MS, experimental autoimmune encephalomyelitis (EAE). To more fully understand the role of microglia in EAE we characterized microglial transcriptomes before the onset of motor symptoms (pre-onset) and during symptomatic EAE. We compared the transcriptome in brain, where behavioral changes are initiated, and spinal cord, where damage is revealed as motor and sensory deficits. We used a RiboTag strategy to characterize ribosome-bound mRNA only in microglia without incurring possible transcriptional changes after cell isolation. Brain and spinal cord samples clustered separately at both stages of EAE, indicating regional heterogeneity. Differences in gene expression were observed in the brain and spinal cord of pre-onset and symptomatic animals with most profound effects in the spinal cord of symptomatic animals. Canonical pathway analysis revealed changes in neuroinflammatory pathways, immune functions and enhanced cell division in both pre-onset and symptomatic brain and spinal cord. We also observed a continuum of many pathways at pre-onset stage that continue into the symptomatic stage of EAE. Our results provide additional evidence of regional and temporal heterogeneity in microglial gene expression patterns that may help in understanding mechanisms underlying various symptomology in MS.
Insights
Microglia gene expression in the mouse model of multiple sclerosis (MS) shows regional and temporal differences. These changes in brain and spinal cord reveal neuroinflammation and cell division, impacting MS symptomology.
Area of Science:
- Neuroscience
- Immunology
- Genomics
Background:
- Microglia are key players in multiple sclerosis (MS) pathogenesis.
- Understanding microglial roles in the MS mouse model (EAE) is crucial.
Purpose of the Study:
- To characterize microglial transcriptomes in the EAE model.
- To investigate regional (brain vs. spinal cord) and temporal (pre-onset vs. symptomatic) differences in microglial gene expression.
Main Methods:
- Utilized the RiboTag strategy for isolating microglia-specific mRNA.
- Analyzed transcriptomes from brain and spinal cord at pre-onset and symptomatic EAE stages.
- Performed canonical pathway analysis to identify affected biological processes.
Main Results:
- Brain and spinal cord samples showed distinct clustering, indicating regional heterogeneity.
- Significant gene expression differences were observed, particularly in the spinal cord of symptomatic EAE mice.
- Key pathways affected include neuroinflammation, immune function, and cell division, with a continuum from pre-onset to symptomatic stages.
Conclusions:
- Microglial gene expression exhibits significant regional and temporal heterogeneity in the EAE model.
- These findings contribute to understanding the mechanisms behind MS symptomology.
- Highlights the dynamic nature of microglial responses throughout disease progression.
