Microglia Transcriptional States and Their Functional Significance: Context Drives Diversity

Neurology Life Sciences Medicine Immunology Cell Biology Biochemistry
microglia transcriptional states single-cell sequencing brain microenvironment functional diversity

Academic Background

Microglia are the only resident macrophages in the central nervous system (CNS) and play critical roles in development, homeostasis, and disease. Traditionally, microglia were viewed as homogeneous “resting” or “activated” states, but the advent of single-cell sequencing technologies has revealed their remarkable transcriptional heterogeneity. However, the functional significance of this heterogeneity, its driving factors, and cross-species differences (e.g., between mice and humans) remain unclear.
This review, authored by Beth Stevens’ team, systematically synthesizes the diversity of microglial transcriptional states across contexts (e.g., development, aging, neurodegenerative diseases), explores the relationship between states and functions, and analyzes challenges and strategies in human microglia research, providing a theoretical framework for microglia-targeting therapies.

Source of the Paper

  • Authors: Constanze Depp, Jordan L. Doman et al. (co-first authors), Beth Stevens (corresponding author)
  • Institutions: Boston Children’s Hospital, Broad Institute of MIT and Harvard, among others
  • Journal: Immunity (published May 13, 2025)
  • DOI: 10.1016/j.immuni.2025.04.009

Key Arguments and Evidence

1. Dynamicity and Context-Dependence of Microglial States

Core Argument: Microglial transcriptional states are highly dependent on their microenvironment, exhibiting specificity across developmental stages, brain regions, and pathological conditions.
- Development: Embryonic microglia highly express genes related to brain colonization (e.g., Ms4a cluster). Postnatally, “axonal tract microglia” (ATMs) or “proliferative region-associated microglia” (PAMs) emerge, marked by Clec7a, Fabp5, etc., and participate in myelination and oligodendrocyte clearance.
- Adult Homeostasis: Single-cell sequencing shows low heterogeneity in adult microglia, but spatial transcriptomics (e.g., MERFISH) suggests subtle laminar differences in the cortex.
- Disease and Aging: In Alzheimer’s disease (AD) models, microglia near amyloid plaques adopt a “disease-associated microglia” (DAM) state, characterized by Trem2-dependent upregulation of Apoe and Gpnmb. Aging induces “white matter-associated microglia” (WAM), which preferentially engulf degenerating myelin.

Supporting Evidence:
- Single-cell RNA sequencing (scRNA-seq) data (e.g., Matcovitch-Natan et al., 2016) reveal gene expression changes across developmental time points.
- Spatial transcriptomics shows DAM states are localized near amyloid plaques (Keren-Shaul et al., 2017).

2. Conservation and Disease-Specific Modifications of DAM States

Core Argument: DAM states across diseases share a “core signature” (e.g., Apoe, Lpl upregulation) but exhibit disease-specific modifications.
- Conserved Core: AD, ALS, and aging all induce Gpnmb, Cst7, etc., reflecting phagocytic and lipid metabolism activation.
- Disease-Specific Features:
- ALS models show marked upregulation of Ms4a cluster genes and Abca1 (cholesterol transporter), absent in AD models.
- Combined myelin damage and amyloid pathology leads microglia to preferentially associate with myelin debris over plaques (Safaiyan et al., 2021).

Supporting Evidence:
- Integrated scRNA-seq analysis across disease models (AD, ALS, aging) (Hammond et al., 2019).
- Knockout experiments confirm Trem2 loss impedes DAM transition (Zhou et al., 2020).

3. Linking Transcriptional States to Function

Core Argument: Transcriptional changes may reflect functional adaptations but require experimental validation.
- Development: PAMs clear excess oligodendrocytes via high phagocytic activity (Li et al., 2019).
- Disease:
- DAM states may enhance sustained phagocytosis, but overactivation can lead to “exhaustion” (e.g., reduced phagocytosis near plaques in 5xFAD models).
- Trem2-dependent plaque “corralling” limits neurite damage (Wang et al., 2020).

Controversies:
- Some studies associate DAM states with enhanced phagocytosis (Grubman et al.), while others report reduced capacity (Ulrich et al.), possibly due to disease stages or methodological differences (e.g., ex vivo phagocytosis assay artifacts).

4. Human Microglia Uniqueness and Modeling Challenges

Core Argument: Human microglia differ significantly from murine counterparts, necessitating novel models.
- Transcriptional Differences: Human microglia highly express complement and antigen presentation genes (e.g., HLA-DRB), while mice rely on TGF-β signaling for homeostasis.
- Technical Challenges:
- Postmortem tissue processing may introduce activation signatures (e.g., FOS, JUN upregulation).
- iPSC-derived microglia (iMGs) lack homeostatic markers (e.g., TMEM119) in vitro but partially regain in vivo features when transplanted into mouse brains (xMGs) (Mancuso et al.).

Supporting Tools:
- CRISPR screening platforms (e.g., iTF-microglia by Drager et al.) for high-throughput functional gene identification.
- Spatial transcriptomics (Slide-seq) to resolve human brain region-specific microenvironments.

5. Therapeutic Potential and Future Directions

Core Argument: Targeting specific microglial states may yield therapies for neurodegenerative diseases.
- Intervention Targets:
- Trem2 agonists or LXRs (liver X receptors) modulators may enhance lipid metabolism and phagocytosis.
- Epigenetic editing (e.g., HDAC inhibitors) could reverse aging-associated states.
- Cell Therapy: iMG transplantation shows promise in CSF1R-related leukoencephalopathy models (Dorman et al.).

Significance and Impact

  1. Theoretical Contribution: Systematically integrates single-cell data on microglial heterogeneity, proposing an “environment-driven states” framework beyond traditional “M1/M2” polarization.
  2. Technical Guidance: Emphasizes cross-species comparisons and human-specific models, advancing standardization of iMGs and spatial omics.
  3. Clinical Translation: Provides a molecular basis for drugs targeting DAM or WAM states, e.g., Trem2- or lipid metabolism-focused therapies.

Highlights:
- First comprehensive comparison of microglial state evolution across development, aging, and disease.
- Introduces “core DAM signature” to distinguish conserved vs. disease-specific features.
- Integrates CRISPR screens, organoids, and chimeric models to advance human microglia research.