Microglial Cells — Cell Type Hierarchy

Microglial Cells — Cell Type Hierarchy

Overview

<table class="infobox infobox-cell">
<tr>
<th class="infobox-header" colspan="2">Microglial Cells — Cell Type Hierarchy</th>
</tr>
<tr>
<td class="label">Cell Ontology ID</td>
<td>Cell Type</td>
</tr>
<tr>
<td class="label">[CL:0000129](https://www.ebi.ac.uk/ols4/ontologies/cl/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FCL_0000129)</td>
<td>microglial cell</td>
</tr>
<tr>
<td class="label">[CL:0002628](https://www.ebi.ac.uk/ols4/ontologies/cl/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FCL_0002628)</td>
<td>immature microglial cell</td>
</tr>
<tr>
<td class="label">[CL:4307132](https://www.ebi.ac.uk/ols4/ontologies/cl/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FCL_4307132)</td>
<td>microglial cell (Mmus)</td>
</tr>
<tr>
<td class="label">Marker</td>
<td>Gene</td>
</tr>
<tr>
<td class="label">IBA1</td>
<td>AIF1</td>
</tr>
<tr>
<td class="label">TMEM119</td>
<td>TMEM119</td>
</tr>
<tr>
<td class="label">P2RY12</td>
<td>P2RY12</td>
</tr>
<tr>
<td class="label">CX3CR1</td>
<td>CX3CR1</td>
</tr>
<tr>
<td class="label">TREM2</td>
<td>TREM2</td>
</tr>
<tr>
<td class="label">CD68</td>
<td>CD68</td>
</tr>
<tr>
<td class="label">CD14</td>
<td>CD14</td>
</tr>
<tr>
<td class="label">Strategy</td>
<td>Target</td>
</tr>
<tr>
<td class="label">CSF1R inhibition</td>
<td>Proliferation</td>
</tr>
<tr>
<td class="labe

Microglial Cells — Cell Type Hierarchy

Overview

<table class="infobox infobox-cell">
<tr>
<th class="infobox-header" colspan="2">Microglial Cells — Cell Type Hierarchy</th>
</tr>
<tr>
<td class="label">Cell Ontology ID</td>
<td>Cell Type</td>
</tr>
<tr>
<td class="label">[CL:0000129](https://www.ebi.ac.uk/ols4/ontologies/cl/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FCL_0000129)</td>
<td>microglial cell</td>
</tr>
<tr>
<td class="label">[CL:0002628](https://www.ebi.ac.uk/ols4/ontologies/cl/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FCL_0002628)</td>
<td>immature microglial cell</td>
</tr>
<tr>
<td class="label">[CL:4307132](https://www.ebi.ac.uk/ols4/ontologies/cl/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FCL_4307132)</td>
<td>microglial cell (Mmus)</td>
</tr>
<tr>
<td class="label">Marker</td>
<td>Gene</td>
</tr>
<tr>
<td class="label">IBA1</td>
<td>AIF1</td>
</tr>
<tr>
<td class="label">TMEM119</td>
<td>TMEM119</td>
</tr>
<tr>
<td class="label">P2RY12</td>
<td>P2RY12</td>
</tr>
<tr>
<td class="label">CX3CR1</td>
<td>CX3CR1</td>
</tr>
<tr>
<td class="label">TREM2</td>
<td>TREM2</td>
</tr>
<tr>
<td class="label">CD68</td>
<td>CD68</td>
</tr>
<tr>
<td class="label">CD14</td>
<td>CD14</td>
</tr>
<tr>
<td class="label">Strategy</td>
<td>Target</td>
</tr>
<tr>
<td class="label">CSF1R inhibition</td>
<td>Proliferation</td>
</tr>
<tr>
<td class="label">TREM2 activation</td>
<td>Phagocytosis</td>
</tr>
<tr>
<td class="label">Anti-inflammatory</td>
<td>Cytokines</td>
</tr>
<tr>
<td class="label">Complement inhibition</td>
<td>Synaptic pruning</td>
</tr>
<tr>
<td class="label">CX3CR1 modulation</td>
<td>Neuron-microglia signaling</td>
</tr>
<tr>
<td class="label">State</td>
<td>Morphology</td>
</tr>
<tr>
<td class="label">Ramified</td>
<td>Highly branched, small cell body</td>
</tr>
<tr>
<td class="label">Primed</td>
<td>Intermediate branching</td>
</tr>
<tr>
<td class="label">Reactive (AM)</td>
<td>Enlarged cell body, retracted processes</td>
</tr>
<tr>
<td class="label">Dystrophic</td>
<td>Beaded, fragmented processes</td>
</tr>
<tr>
<td class="label">Model</td>
<td>Application</td>
</tr>
<tr>
<td class="label">CX3CR1-GFP</td>
<td>Live imaging</td>
</tr>
<tr>
<td class="label">CCR2-RFP</td>
<td>Monocyte tracking</td>
</tr>
<tr>
<td class="label">PLX3397</td>
<td>Depletion</td>
</tr>
<tr>
<td class="label">TREM2 knockout</td>
<td>Functional studies</td>
</tr>
<tr>
<td class="label">Agent</td>
<td>Target</td>
</tr>
<tr>
<td class="label">AL002</td>
<td>TREM2</td>
</tr>
<tr>
<td class="label">AL003</td>
<td>TREM2</td>
</tr>
<tr>
<td class="label">JNJ-40356527</td>
<td>CSF1R</td>
</tr>
<tr>
<td class="label">Peptide 6</td>
<td>CSF1R</td>
</tr>
<tr>
<td class="label">Avid 105</td>
<td>CD33</td>
</tr>
</table>

Microglial cells are the resident immune cells of the central nervous system (CNS), representing the brain's primary defense mechanism against pathogens, injury, and disease PMID: 39833308. As the CNS equivalent of peripheral macrophages, microglia arise from embryonic yolk sac progenitors distinct from other myeloid lineages, establishing themselves in the brain early in development and persisting throughout life through self-renewal [@ginhoux2010] PMID: 17882014.

In neurodegenerative diseases such as Alzheimer's disease (AD) and Parkinson's disease (PD), microglia adopt complex activation states that can be both protective and pathogenic PMID: 34107264. Understanding microglial heterogeneity—through Cell Ontology classifications and disease-associated molecular signatures—is essential for developing targeted therapeutic interventions.

Microglial Ontology and Classification

Cell Ontology Hierarchy

This page provides a navigable hierarchy of microglial cell (CL:0000129) from the [Cell Ontology](https://obofoundry.org/ontology/cl.html), cross-referenced with NeuroWiki cell type pages.

Coverage: 1/3 types have NeuroWiki pages (33%)

Hierarchy Diagram

> Green nodes link to existing NeuroWiki pages. Blue nodes represent microglial functional states in disease.

Microglial Origin and Development

Embryonic Origin

Microglia originate from primitive macrophages in the embryonic yolk sac, distinct from bone marrow-derived monocytes that enter the brain only under pathological conditions [@ginhoux2010]. This embryonic origin establishes microglia as a self-renewing population maintained independently of hematopoietic stem cells throughout life.

Key developmental features:

• Y sac progenitors: Arise from c-Myb-independent primitive macrophages at embryonic day 7.5
• Brain colonization: Enter the developing CNS around embryonic day 9.5-10.5
• Self-renewal: Maintain population through local proliferation, not turnover from blood monocytes
• Territorial maintenance: Each microglia occupies a defined territory, extending and retracting processes to survey the surrounding tissue

Adult Homeostasis

Under normal conditions, microglia exist in a "surveillance" or "resting" state characterized by:

• Small cell bodies with highly ramified, dynamic processes
• Continuous scanning of the extracellular environment
• Rapid process extension toward sites of injury or infection
• Limited proliferative capacity under homeostasis

Molecular Markers

Canonical Microglial Markers

Disease-Associated Markers

Microglia in neurodegenerative diseases upregulate distinct gene modules:

DAM signature (Disease-Associated Microglia):

• TREM2: Triggering receptor expressed on myeloid cells 2 — lipid sensing and phagocytosis [@wang2016]
• APOE: Apolipoprotein E — lipid transport and neuroinflammation
• TGFβ: Transforming growth factor beta — immunomodulation
• CST3: Cystatin C — protease inhibition

• IL1β: Interleukin-1 beta — pro-inflammatory cytokine
• TNFα: Tumor necrosis factor alpha — inflammation amplification
• IL6: Interleukin-6 — acute phase response
• NOS2: Inducible nitric oxide synthase — oxidative stress

Microglial Activation States

Classical M1 vs. Alternative M2 Paradigm

The traditional M1/M2 classification system, borrowed from peripheral macrophage polarization, has been largely superseded by recognition of diverse microglial activation states [@ransohoff2016]:

• M1 (Classical activation): Pro-inflammatory, driven by IFN-γ and LPS; produces nitric oxide and pro-inflammatory cytokines
• M2 (Alternative activation): Anti-inflammatory, driven by IL-4 and IL-13; promotes tissue repair

Disease-Associated Microglia (DAM)

The landmark study by Keren-Shaul et al. (2017) identified a unique microglia type in Alzheimer's disease models—termed disease-associated microglia (DAM)—characterized by a distinct transcriptional program [@keren-shaul2017]:

Stage 1 DAM:

• Triggered by TREM2-independent signals
• Upregulates genes involved in lipid metabolism (Apoe, Trigpl1)
• Represents early compensatory response

• TREM2-dependent activation
• Upregulates phagocytic genes (Tyrobp, Fcgr2b)
• Associates with amyloid plaques
• Emerges in the presence of neurodegeneration

Surveillance-Associated Microglia (SAM)

A contrasting microglial state associated with aging and cognitive decline characterized by:

• Upregulation of complement system components (C1q, C3)
• Enhanced synaptic pruning capability
• Pro-inflammatory priming
• Reduced surveillance capacity

Role in Neurodegenerative Diseases

Alzheimer's Disease

Microglia in AD exhibit both protective and pathogenic roles [@hansen2018]:

Protective functions:

• Phagocytic clearance of amyloid-beta plaques
• Production of neurotrophic factors
• Support of neuronal health through CX3CR1 signaling
• Formation of protective barriers around plaques

• Chronic production of pro-inflammatory cytokines (IL-1β, TNF-α)
• Amplification of neuroinflammation
• Synaptic pruning leading to cognitive decline
• Promotion of tau pathology spread

• TREM2 loss-of-function variants increase AD risk 3-4x [@deczkowska2018]
• CD33 overexpression impairs microglial phagocytosis
• ABI3 variants affect microglial motility

Parkinson's Disease

Microglial activation in PD contributes to dopaminergic neuron death:

Mechanisms:

• α-Synuclein-triggered inflammation
• NADPH oxidase-mediated oxidative stress
• NLRP3 inflammasome activation
• Pro-inflammatory cytokine release

• CSF1R antagonists reduce microglial proliferation
• TREM2 agonists enhance phagocytosis
• Anti-inflammatory compounds (e.g., minocycline)

Multiple Sclerosis

Microglia play complex roles in MS pathogenesis:

• Attack myelin and axons in active lesions
• Present antigens to T cells
• Produce neurotrophic factors that promote remyelination
• The inflammatory phenotype can be modulated by drugs like glatiramer acetate

Therapeutic Implications

Targeting Microglia in Neurodegeneration

CSF1R Signaling

Colony-stimulating factor 1 receptor (CSF1R) signaling is essential for microglial survival, proliferation, and function. Inhibition via CSF1R antagonists (e.g., PLX3397, PLX5622) leads to microglial depletion and has shown promise in:

• Reducing amyloid pathology in AD models
• Decreasing neuroinflammation
• Improving cognitive performance

TREM2 as Therapeutic Target

TREM2 represents one of the most promising microglial targets in neurodegeneration [@deczkowska2018]:

Rationale:

• Rare coding variants cause early-onset dementia (Nasu-Hakola disease)
• Common variants alter AD risk 3-4 fold
• TREM2 mediates lipid sensing and phagocytosis
• DAM formation requires TREM2 signaling

• Agonists: Enhance TREM2 signaling to boost phagocytosis
• Antagonists: Prevent hyperactivation in some contexts
• Gene therapy: Deliver functional TREM2 to the brain

Related NeuroWiki Pages

Disease-Specific Microglia

• [Alzheimer's Disease Microglia](/cell-types/alzheimers-microglia) — Comprehensive AD microglial coverage
• [Parkinson's Disease Microglia](/cell-types/microglia-pd) — PD-specific microglial changes
• [Disease-Associated Microglia (DAM)disease-associated-microglia) — DAM pathway
• [TREM2-Expressing Microglia](/cell-types/trem2-expressing-microglia) — TREM2+ subset

Microglial States

• [M1 Microglia](/cell-types/m1-microglia) — Classical activation
• [Amyloid-Responsive Microglia](/cell-types/amyloid-responsive-microglia) — Early responders to Aβ
• [Primed Microglia](/cell-types/microglia-primed) — Preconditioned inflammatory state

Related Cell Types

• [Astrocytes](/cell-types/astrocytes) — Neuroimmune interactions
• [Oligodendrocytes](/cell-types/oligodendrocytes) — Myelin biology
• [Neurons](/cell-types/neurons) — Microglial-neuronal crosstalk

References

• PMID: 17882014 Distinct types of microglial activation in white and grey matter of rat lumbosacral cord after mid-thoracic spinal transection. (2007; J Neuropathol Exp Neurol)
• PMID: 34107264 Sublayer- and cell-type-specific neurodegenerative transcriptional trajectories in hippocampal sclerosis. (2021; Cell Rep)
• PMID: 39833308 Mapping the cellular etiology of schizophrenia and complex brain phenotypes. (2025; Nat Neurosci)