Mouse and human microglial phenotypes in Alzheimer’s disease are controlled by amyloid plaque phagocytosis through Hif1α

Abstract

The important role of microglia, the brain’s resident immune cells, in Alzheimer’s disease (AD) is now well recognized, however their molecular and functional diversity and underlying mechanisms still remain controversial. To transcriptionally and functionally characterize the diversity of microglia in AD and aging, we isolated the amyloid plaque-containing (XO4+) and non-containing (XO4−) microglia from an AD mouse model. Transcriptomics analysis unveiled independent transcriptional trajectories in ageing and AD. XO4+ microglial transcriptomes linked plaque phagocytosis to altered expression of bona fide late onset AD genetic risk factors. We further revealed that the XO4+ transcriptional program is present in a subset of human microglia from AD patients and is a direct and reversible consequence of Aβ plaque phagocytosis. Conversely, XO4− microglia in AD displayed an accelerated ageing signature and contained more intracellular post synaptic material than plaque-containing microglia, despite reduced active synaptosome phagocytosis. Mechanistically, we predicted HIF1α as a core regulator of the XO4−/XO4+ axis, and further validated the mechanism in vitro using human stem cell-derived microglia like cells and primary human microglia. Together these findings unveiled the molecular mechanism underpinning the functional diversity of microglia in AD, providing opportunities to develop treatments targeted at subset specific manipulation of the microglial niche.

A Consensus Proteomic Analysis of Alzheimer’s Disease Brain and Cerebrospinal Fluid Reveals Early Changes in Energy Metabolism Associated with Microglia and Astrocyte Activation

“…The majority of these markers were from microglia (Supplementary Table 5). To further validate these findings, we analyzed whether these markers were increased at both the transcript and protein levels in acutely isolated microglia from AD mouse models 48,49 . The top 30 most differentially abundant microglial transcripts corresponding to proteins in the M4 module were found to be heavily biased toward an anti-inflammatory phenotype (Figure 6D, Supplementary Table 5).…”

“…The top 30 most differentially abundant microglial transcripts corresponding to proteins in the M4 module were found to be heavily biased toward an anti-inflammatory phenotype (Figure 6D, Supplementary Table 5). Furthermore, many of the disease-associated M4 microglial protein markers were found to be increased in microglia undergoing active amyloid plaque phagocytosis ( Supplementary Figure 7, Supplementary Table 5) 49 . In summary, we found that the M4 astrocyte/microglial metabolism module was enriched in AD genetic risk factors, and that microglia cell type markers within M4 appeared to be biased towards a protective anti-inflammatory, rather than a deleterious proinflammatory, microglial phenotype.…”

“…WGCNA collapseRows function was used to handle multiple probe mappings to any gene, with probe selection method="maxRowVariance". Grubman et al 49 peptide-level total peak area data for XO4 + (amyloid-β plaque phagocytosing) and XO4 -(amyloid-β plaque non-phagocytosing) acutely purified microglia from AD and WT mice, respectively, were summed and log 2 -transformed to achieve protein-level data for 94 gene product proteins. Grubman et al mRNA-level measurements were obtained directly and used without further processing.…”

The Physiology, Pathology, and Potential Therapeutic Applications of the TREM2 Signaling Pathway

“…Activation of the DAM program, which is TREM2 dependent, has been predicted computationally to rely on four transcription factors: basichelix-loop-helix family member E40 (BHLHE40), RXR gamma (RXRG), hypoxia-inducible factor 1-alpha (HIF1a), and microphthalmia-associated transcription factor (MITF). Among these, HIF1a expression is increased in DAMs in a TREM2-dependent manner in a 5xFAD AD mouse model (Keren-Shaul et al, 2017;Ulland et al, 2017), and a recent preprint showed that HIF1a controls microglial ability to engulf plaques, which entails induction of the DAM phenotype in an AD mouse model (Grubman et al, 2019b). Further experiments with human embryonic stem cell (ESC)-derived microglia-like cells in vitro showed that HIF1a promotes this transition via myeloid differentiation primary response 88 (MyD88) and mTor (Grubman et al, 2019b).…”

Reprogramming roadmap reveals route to human induced trophoblast stem cells

“…For the bulk RNAseq of the iTSC and iTSC-differentiated cells, RNA-seq was performed with a multiplexing approach, using an 8 bp sample index 48 and a 10 bp unique molecular identifier (UMI) were added during initial poly(A) priming and pooled samples were amplified using a templateswitching oligonucleotide. The Illumina P5 (5' AAT GAT ACG GCG ACC ACC GA 3') and P7 (5' CAA GCA GAA GAC GGC ATA CGA GAT 3') sequences were added by PCR and Nextera transposase, respectively.…”