Single-nucleus transcriptomics reveals a distinct microglial state and increased MSR1-mediated phagocytosis as common features across dementia subtypes

Abstract

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.

Keywords: Alzheimer’s disease; Dementia with Lewy bodies; Macrophage scavenger receptor 1 (MSR1); Microglia; Myelin; Parkinson’s disease dementia; Phagocytosis; Single-nucleus RNA-sequencing.

Fig. 1

SnRNA-seq revealed an increase in microglial proportion in AD, DLB, and PDD. a Schematic diagram of experimental design. b Unbiased UMAP projection of 90,733 single nuclei, showing 8 major cell clusters. Each dot represents a single nucleus, colour-coded by cell type. c Dot plot showing the expression of specific marker genes for the 8 cell clusters. Dot size reflects the percentage of cells expressing each gene within the cluster, while colour represents average log-normalised gene expression. Marker genes were ordered to highlight the differences between cell types. d Unsupervised hierarchical clustering of samples (nuclei number > 200) based on cell type proportions. e Box plots showing microglial composition among NCI, AD, DLB and PDD groups

Fig. 2

Cell type-specific transcriptomic profiling demonstrated shared DEGs between microglia and oligodendrocytes across dementia subtypes. a Heatmap and bar plot displaying the number of upregulated (right panel) and downregulated (left panel) DEGs (log₂ FC > 1, FDR < 0.01) across the eight major cell types in AD, DLB, and PDD. The colour intensity within each cell type represents the abundance of DEGs identified in that specific cell type when comparing dementia subtypes to NCI. b Venn diagrams illustrating the overlap of DEGs shared among the three dementia subtypes compared to NCI, as well as the unique DEGs specific to each subtype. c Heatmap showing the log₂ FC of the most significantly upregulated (red) or downregulated (blue) DEGs shared across the three dementia subtypes for each cell type. d Heatmaps showing hierarchical clustering of samples based on the expression of DEGs across selected cell types when comparing AD, DLB, or PDD to NCI. Each column represents a DEG identified in a specific cell type, and each row corresponds to a sample. Only cell types with significant DEGs are shown. The clustering highlights the separation between disease and control samples based on cell type-specific transcriptional changes. Cell type annotations are indicated by the colour bar below each heatmap. e Clustering of shared pathway enrichments using the DEGs identified from each cell type in DLB and PDD through Gene Ontology (GO) term analysis

Fig. 3

Transcriptional profiling revealed shared and distinct transcriptional signatures in DLB and PDD. a Heatmap illustrating transcriptional changes among NCI, AD, and LBD (consisting of DLB and PDD). b Heatmap comparing transcriptional changes between DLB and PDD. c Pathway enrichment analysis of microglial DEGs in PDD and DLB

Fig. 4

A distinct microglial state was enriched across dementia subtypes. a UMAP projection illustrating the re-clustered microglial and oligodendrocyte populations. The microglial cluster is highlighted in red, the oligodendrocyte cluster in orange, and the distinct microglia in blue. b Diffusion maps and density plots based on the signature scores per cell for microglial and oligodendrocyte clusters. c Violin plots showing the expression of oligodendrocyte markers (orange), microglial markers (red), and co-expressed markers indicative of distinct microglia (blue). d Box plot quantifying the percentage of the distinct microglia across dementia subtypes. e,f Bar plots demonstrating the count and weight of interactions between microglial and oligodendrocyte clusters across dementia subtypes. g Pathway analysis of upregulated DEGs in DLB microglia compared to NCI microglia. h Violin plot showing significantly elevated MSR1 expression in microglia from individuals with AD, DLB, and PDD compared to those from NCI. i Violin plots displaying increased HSPA1A expression in oligodendrocytes from AD, DLB, and PDD compared to those from NCI

Fig. 5

RNAscope supported potential interactions between microglia and oligodendrocytes in PDD. Representative RNAscope images showing the expression of microglial markers (PTPRC, green; ITGAM, red), oligodendrocyte markers (MBP, cyan; PLP1, grey), and nuclei (DAPI, blue) in the white matter and grey matter of human cortical tissues from NCI and PDD cases. ITGAM colocalised with PTPRC, and PLP1 colocalised with MBP. Higher-magnification images illustrate that microglia (nuclei circled with dotted lines) and oligodendrocytes (nuclei circled with solid lines) were in closer proximity, suggesting potential interactions. Dashed lines in the overview panels indicate the boundary between white matter (W) and grey matter (G). Scale bars: left panel, 50 μm; right panel, 20 μm

Fig. 6

Elevated expression of MSR1 and myelin-associated genes in microglia revealed myelin dysregulation in dementia. a MSR1 mRNA expression in postmortem prefrontal cortex from 20 individuals with NCI, AD, DLB, and PDD. b Representative western blot and quantification of MSR1 protein levels in cortical tissues from LRRK2-G2019S PD mice and non-transgenic (NTg) mice. c mRNA expression of MSR1, MBP, MOBP, and PLP1 in CD11b-positive primary microglia isolated from PD and NTg mice. d mRNA expression of MOBP, MAG, and MBP in postmortem prefrontal cortex from NCI, AD, DLB, and PDD individuals. e,f mRNA expression of MSR1, MOBP, MOG, and MBP in cortical tissues from PD and NTg mice. Data are presented as mean ± SEM, 3 mice per group, aged 15–17 months. *p < 0.05, **p < 0.01, and ***p < 0.001 by Student’s t test for two-group comparisons or one-way ANOVA with Tukey’s post hoc test for multiple comparisons

Fig. 7

Microglial MSR1 contributes to myelin phagocytosis in dementia