Microglial Checkpoint Regulation: TIM-3 Blockade Releases Protective Microglial States in Alzheimer’s Disease

Alzheimer’s disease research is increasingly recognizing the central role of microglia, the brain’s resident immune cells, in shaping disease progression. In our recent Nature publication, we investigated how the immune checkpoint molecule TIM-3 (HAVCR2) regulates microglial function and constrains their ability to combat amyloid pathology.

A major conceptual insight from this study is that blocking TIM-3 releases microglia from a homeostatic state, enabling them to enter a neuroprotective, plaque-clearing phenotype that slows Alzheimer’s pathology.

I contributed to the single-cell RNA-seq, bulk RNA-seq processing, and transcriptomic analysis that uncovered the gene-expression programs underlying this shift.

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TIM-3 as a Microglial Checkpoint

TIM-3 is well known for driving T-cell exhaustion, but its function in microglia has been poorly understood. Using biochemical and transcriptomic analyses
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• TGFβ signalling induces TIM-3 expression in microglia.
• TIM-3 binds TGFBR2 and SMAD2, enhancing SMAD2 phosphorylation.
• This interaction stabilizes a homeostatic microglial identity.

When TIM-3 is present, microglia remain in a restrained state, limiting their ability to respond to pathological cues such as amyloid-β (Aβ).

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Releasing Microglia from Homeostasis Improves Alzheimer’s Pathology

When Havcr2 (TIM-3) is selectively deleted in microglia:

• Microglia shift into a MGnD/DAM-like activation state with increased phagocytic gene expression
• Pro-inflammatory signalling programs (TNF, IFNα, cGAS–STING) are decoupled from phagocytosis
• Amyloid plaque burden decreases significantly
• Cognitive performance improves in 5×FAD Alzheimer’s mouse models
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This demonstrates that TIM-3 acts as a molecular brake preventing microglia from entering a protective activation state. Its removal unleashes microglia to engage plaques more effectively and mitigate neurodegeneration.

Importantly, TIM-3 expression is elevated in APOE4 carriers, particularly women, correlating with impaired MGnD activation—suggesting strong translational relevance.

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Transcriptomic Profiling Reveals the Mechanism

Using single-nucleus RNA-seq, single-cell RNA-seq, and bulk RNA-seq, we profiled how TIM-3 blockade remodels microglial states
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• Phagosome and lysosomal pathways were upregulated across microglial clusters
• Neuroprotective signalling (PI3K–AKT–mTOR) increased
• Homeostatic marker genes like P2ry12, Csf1r, and Siglech were downregulated
• MGnD gene signatures were strongly enhanced
• Hypoxia signatures—associated with dysfunctional AD microglia—were reduced

These multi-omics findings support a model in which TIM-3 normally maintains homeostasis via TGFβ signalling. Removing TIM-3 releases microglia into a protective, anti-inflammatory, pro-phagocytic state that is unusually effective at controlling plaque accumulation.

My role: I contributed to the computational analysis of both single-cell and bulk transcriptomic datasets, including quality control, differential gene expression, cluster-level scoring, and visualization of microglial state transitions.

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Therapeutic Implications

Because HAVCR2 is expressed specifically in microglia within the CNS, targeting TIM-3 may allow:

• selective microglial reprogramming
• enhanced plaque clearance
• reduced inflammatory toxicity
• minimal systemic immune side effects

This positions TIM-3 as an attractive therapeutic target—especially for patient subgroups with impaired microglial activation, such as APOE4 carriers.

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Read the Full Publication

Immune checkpoint TIM-3 regulates microglia and Alzheimer’s disease
Nature (2025)
https://www.nature.com/articles/s41586-025-08852-z

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