Adrian Funk

Background: Alzheimer’s disease (AD) is a neurodegenerative disorder that is classically characterized by varying types of cognitive decline, extracellular β-amyloid plaques, intracellular tau neurofibrillary tangles, synaptic loss, and neuroinflammation. Although microglia initially function as protective immune cells by clearing neuroinflammatory cellular debris and reducing AD-associated plaque toxicity, continued exposure to AD pathology can alter microglia toward dysfunctional states that promote neurodegeneration. Recent studies have identified “dark microglia” as a stress-associated microglial phenotype found near β-amyloid plaques and dystrophic neurites.¹˒² These dysregulated microglial cells display signs of chronic cellular stress and degeneration, suggesting that AD-associated microglial dysfunction may involve more than a generalized inflammation pathway. A suggested mechanism linking microglial stress to neuronal injury is activation of the integrated stress response (ISR) pathway, primarily through eIF2α phosphorylation, leading to downstream ATF4 signaling.¹ This review highlights how ISR activation in dark microglia may promote toxic lipid secretion and impaired plaque clearance, leading to downstream synaptic injury and the progressive neurodegeneration seen in AD.

Objective: This review examines whether ISR activation in dark microglia represents initiation of toxic lipid-mediated neurodegeneration in Alzheimer’s disease and if this pathway provides a more specific therapeutic target for AD neurodegeneration treatment than the current established therapy.

Search Methods: An online literature search was conducted using the PubMed database for articles published from 2016 to 2026. Search terms included “Alzheimer disease,” “dark microglia,” “integrated stress response,” “eIF2α,” “ATF4,” “microglial lipid metabolism,” “toxic lipid secretion,” “β-amyloid,” “tau,” and “neurodegeneration.”

Results: Dark microglia are enriched in regions adjacent to plaques of AD mouse models and human postmortem hippocampal tissue, with quantitative electron microscopy showing that roughly 40–50% of microglia near plaques in aged AD mouse models exhibit dark-microglia features.² These findings support the hypothesis that dark microglia is a disease-associated phenotype rather than a nonspecific structural finding. A recent study demonstrated that ISR-positive microglia overlap with dark microglia and accumulate near AD-associated amyloid plaques and tau proteins.¹ ISR activation of microglia increased dark microglia abundance, amyloid plaque burden, axonal disruption, tau aggregation, and synaptic loss, but inhibition of microglial ISR signaling reduced tau accumulation and preserved synapses.¹ ISR activation also altered microglial lipid secretion, resulting in the release of toxic long-chain oxidized lipid species that reduced neuronal survival.¹ Additional lipid-metabolism studies support this model by showing that amyloidosis-associated lipid dysfunction includes microglia-dependent lysosomal lipid accumulation and microglial lipid-droplet formation.³˒⁴ Plaque-associated lipid-excreting microglia exhibit impaired β-amyloid phagocytosis, while reduction of microglial lipid excretion improves Aβ uptake and plaque clearance in AD mouse models.⁴

Conclusion: Recent studies support an AD progression model in which AD pathology promotes the accumulation of ISR-positive dark microglia, leading to dysfunctional lipid metabolism, toxic lipid secretion, impaired plaque clearance, synaptic injury, and neuronal degeneration. These findings suggest that microglial dysfunction in AD is not simply inflammatory, but also stress-mediated and metabolically activated. Targeting microglial ISR activation or downstream toxic lipid pathways may assist generalized inflammation-directed therapies by limiting the cellular response that converts plaque-associated stress into progressive neurodegeneration. Future studies should determine which ISR components can be safely targeted in humans and whether toxic lipid species may serve as biomarkers or therapeutic targets in AD.

Works Cited

1. Flury A, Aljayousi L, Park HJ, et al. A neurodegenerative cellular stress response linked to dark microglia and toxic lipid secretion. Neuron. 2025;113(4):554-571.e14. doi:10.1016/j.neuron.2024.11.018
2. St-Pierre MK, Carrier M, González Ibáñez F, et al. Ultrastructural characterization of dark microglia during aging in a mouse model of Alzheimer’s disease pathology and in human post-mortem brain samples. J Neuroinflammation. 2022;19:235. doi:10.1186/s12974-022-02595-8
3. Xu Z, Kiani Shabestari S, Barannikov S, et al. Microglia-specific regulation of lipid metabolism in Alzheimer’s disease revealed by microglial depletion in 5xFAD mice. Nat Commun. 2025;16:9156. doi:10.1038/s41467-025-64161-z
4. Wu X, Miller JA, Lee BTK, et al. Reducing microglial lipid load enhances β amyloid phagocytosis in an Alzheimer’s disease mouse model. Sci Adv. 2025;11(6):eadq6038. doi:10.1126/sciadv.adq6038