Microglia subtype transcriptomes differ between Alzheimer Disease and control human postmortem brain samples

Abstract

Background Microglia‐mediated neuroinflammation is hypothesized to contribute to disease progression in neurodegenerative diseases such as Alzheimer’s Disease (AD). Microglia subtypes are complex, with beneficial and harmful phenotypes. Understanding the gene expression networks which define the spectrum of microglia phenotypes is critical to identifying specific targets for neuroinflammation modulating therapies. Method Our study utilized post‐mortem brain tissue from 22 total (7 male) participants; 12 (3 male) had significant AD neuropathic change. Nuclei isolated from prefrontal cortex were sorted for the myeloid marker PU.1 using fluorescence activated nucleus sorting (FANS). The FANS approach yields larger numbers of nuclei annotated as microglia with high quality sequence from each individual. We performed single‐nucleus RNA‐seq using the 10X Genomics Chromium platform. Results We isolated more than 120,000 microglia nuclei, facilitating group comparisons based on disease state. Unbiased clustering revealed 10 microglia clusters and improved resolution of microglia heterogeneity compared to standard single‐cell approaches. We identify clusters of microglia enriched for biological pathways implicating defined myeloid roles including interferon‐stimulated, endo/lysosomal, neurodegenerative with a “disease‐associated microglia” (DAM) signature, as well as a metabolically active and autophagic cluster. Interestingly, the cluster proportionately enriched for AD individuals’ nuclei is not the DAM cluster but instead one of the clusters in which endo/lysosomal genes are highly upregulated. Furthermore, many of the genes in known AD risk loci are strongly differentially regulated in this AD associated cluster. We also identify a cluster of microglia that is proportionately enriched for control samples with upregulated cell cycle and proliferation genes. Trajectory analysis suggests that the paths AD and control nuclei take from unactivated “homeostatic” to various phenotypic states are also distinct. Conclusion Using human AD tissue collected with uniform protocols we characterize the transcriptomic profiles of microglia subtypes in human brain. By enriching for myeloid cells prior to analysis we can resolve microglia subtypes revealing the diversity of microglia which are “inflammatory” as well as other microglia subtypes responding with induction of metabolic and lysosomal pathways. Our data identifies subtypes of microglia that are unique to AD and control individuals. These results support the possibility of pharmacological targeting of specific subtypes of microglia to alter AD progression.

Microglia activation linking amyloid-β drive tau spatial propagation in Alzheimer's disease

“…However, early results from transgenic mouse and autopsy studies have shown that the increased TSPO density in the AD brain co-localizes to microglia rather than astrocytes (Venneti et al, 2008;Gulyas et al, 2009). Beyond that, microglial activation is a complex process that produces multiple phenotypes (Prater et al, 2021;Wang, 2021), while TSPO PET tracers cannot robustly distinguish between these distinct phenotypes. Thus, caution must be used when interpreting TSPO PET imaging in animals or patients.…”