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Updated: Sep 11, 2025
Isolation of Region-specific Microglia from One Adult Mouse Brain Hemisphere for Deep Single-cell RNA Sequencing
Published on: December 3, 2019
Single-nucleus transcriptomics reveals a distinct microglial state and increased MSR1-mediated phagocytosis as common
Sook-Yoong Chia1, Mengwei Li2, Zhihong Li1,3
1Neural Stem Cell Research Lab, Research Department, National Neuroscience Institute, Singapore, 308433, Singapore.
Background:
Alzheimer's disease (AD), dementia with Lewy bodies (DLB), and Parkinson's disease dementia (PDD) collectively represent the majority of dementia cases worldwide. While these subtypes share clinical, genetic, and pathological features, their transcriptomic similarities and differences remain poorly understood.
Methods:
We applied single-nucleus RNA-sequencing (snRNA-seq) to prefrontal cortex samples from individuals with non-cognitive impairment control (NCI), and dementia subtypes (AD, DLB, and PDD) to investigate cell type-specific gene expression patterns and pathways underlying pathological similarities and differences across dementia subtypes. SnRNA-seq findings were validated through RNAscope, immunohistochemistry, and additional biochemical analyses in human tissues and cellular models.
Results:
SnRNA-seq analysis revealed elevated microglial proportions across all dementia subtypes compared to NCI. Further analysis of cell type-specific transcriptomes identified overlapping differentially expressed genes (DEGs) between microglia and oligodendrocytes across all dementia subtypes. While AD showed molecular similarities to NCI, PDD and DLB were clustered more closely together, sharing a greater number of DEGs and related pathways, predominantly associated with microglia. Investigation of interactions between microglia and oligodendrocytes revealed a distinct microglial state in all dementia subtypes. MSR1, a gene encoding a scavenger receptor, was upregulated in microglia across all dementia subtypes, along with its associated gene HSPA1A in oligodendrocytes. RNAscope supported the potential interaction between microglia and oligodendrocytes, where these cells were in closer proximity to each other in human cortical tissues of PDD compared to NCI. MSR1 expression was significantly increased in cortical primary microglia from PD mice compared with non-transgenic (NTg) mice. Additionally, the expression of myelin-associated genes (MBP, MOBP, and PLP1) was significantly upregulated in PD microglia compared to NTg, supporting the presence of the distinct microglia. Furthermore, MSR1-positive microglia colocalised with MBP in cortical tissue of PDD patients, suggesting a functional role of MSR1 in myelin debris clearance. Overexpression of MSR1 in microglial cells enhanced their phagocytic activity toward myelin, and reciprocally, myelin treatment upregulated MSR1 protein levels, indicating enhanced MSR1-mediated myelin phagocytosis.
Conclusions:
Our findings provide novel insights into the cell type-specific role of microglial MSR1 in AD, DLB, and PDD, linking its increased phagocytic capacity to myelin defects as a common feature of neurodegenerative dementias.
Insights
Microglial MSR1 plays a key role in Alzheimer's disease (AD), dementia with Lewy bodies (DLB), and Parkinson's disease dementia (PDD). This scavenger receptor
Area of Science:
- Neuroscience and Neurodegenerative Diseases
- Molecular Biology and Genetics
- Cellular Biology and Pathology
Background:
- Alzheimer's disease (AD), dementia with Lewy bodies (DLB), and Parkinson's disease dementia (PDD) are major causes of dementia, sharing overlapping features.
- Transcriptomic differences and similarities across these dementia subtypes are not well understood.
- Investigating cell type-specific gene expression is crucial for understanding dementia pathogenesis.
Purpose of the Study:
- To investigate cell type-specific gene expression patterns in the prefrontal cortex of individuals with non-cognitive impairment (NCI), AD, DLB, and PDD.
- To identify transcriptomic similarities and differences underlying pathological features across dementia subtypes.
- To elucidate the role of microglia and oligodendrocytes in the pathogenesis of AD, DLB, and PDD.
Main Methods:
- Single-nucleus RNA sequencing (snRNA-seq) was performed on prefrontal cortex samples from NCI, AD, DLB, and PDD individuals.
- Differential gene expression analysis and pathway analysis were conducted to identify cell type-specific changes.
- Validation of snRNA-seq findings using RNAscope, immunohistochemistry, and biochemical analyses in human tissues and cellular models.
Main Results:
- Microglial proportions were elevated across all dementia subtypes (AD, DLB, PDD) compared to NCI.
- Overlapping differentially expressed genes (DEGs) were identified in microglia and oligodendrocytes across dementia subtypes, with PDD and DLB clustering together.
- Upregulation of microglial scavenger receptor MSR1 and oligodendrocyte HSPA1A was observed in all dementia subtypes, linked to myelin defects and enhanced microglial phagocytosis of myelin debris.
Conclusions:
- Microglial MSR1 plays a significant cell type-specific role in AD, DLB, and PDD.
- Increased MSR1-mediated phagocytic capacity in microglia is associated with myelin defects, a common feature in neurodegenerative dementias.
- Findings highlight a conserved microglial pathway involved in myelin debris clearance across different dementia subtypes.
