A core transcriptional signature of human microglia: derivation and utility in describing region-dependent alterations associated with Alzheimer’s disease
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Abstract
Growing recognition of the pivotal role microglia play in neurodegenerative and neuroinflammatory disorders has accentuated the need to characterize their function in health and disease. Studies in mouse have applied transcriptome‐wide profiling of microglia to reveal key features of microglial ontogeny, functional profile, and phenotypic diversity. While similar, human microglia exhibit clear differences to their mouse counterparts, underlining the need to develop a better understanding of the human microglial profile. On examining published microglia gene signatures, limited consistency was observed between studies. Hence, we sought to derive a core microglia signature of the human central nervous system (CNS), through a comprehensive analysis of existing transcriptomic datasets. Nine datasets derived from cells and tissues, isolated from various regions of the CNS across numerous donors, were subjected independently to an unbiased correlation network analysis. From each dataset, a list of coexpressing genes corresponding to microglia was identified, with 249 genes highly conserved between them. This core signature included known microglial markers, and compared with other signatures provides a gene set specific to microglia in the context of the CNS. The utility of this signature was demonstrated by its use in detecting qualitative and quantitative region‐specific alterations in aging and Alzheimer's disease. These analyses highlighted the reactive response of microglia in vulnerable brain regions such as the entorhinal cortex and hippocampus, additionally implicating pathways associated with disease progression. We believe this resource and the analyses described here, will support further investigations to the contribution of human microglia in CNS health and disease.
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Analyzing the genes related to Alzheimer’s disease via a network and pathway-based approach
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Defining the Microglia Response during the Time Course of Chronic Neurodegeneration
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Self-citationMatrix Metalloproteinases in Alzheimer’s Disease and Concurrent Cerebral Microbleeds
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Genetic variation in APOE cluster region and Alzheimer's disease risk
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Apolipoprotein C-III is an Amyloid-β-Binding Protein and an Early Marker for Alzheimer's Disease
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Apolipoprotein C-I expression in the brain in Alzheimer's disease.
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Microglia recapitulate a hematopoietic master regulator network in the aging human frontal cortex
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Widespread Disruption of Functional Brain Organization in Early-Onset Alzheimer’s Disease
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APP Regulates Microglial Phenotype in a Mouse Model of Alzheimer's Disease
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Overexpression of the chromosome 21 transcription factor Ets2 induces neuronal apoptosis
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Neonatal rat microglia derived from different brain regions have distinct activation responses
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Self-citationLocation, Location, Location: Microglia Are Where They Live
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Machine learning identifies candidates for drug repurposing in Alzheimer’s disease
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Beyond Activation: Characterizing Microglial Functional Phenotypes
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Single-nucleus RNA-seq identifies Huntington disease astrocyte states
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Diverse human astrocyte and microglial transcriptional responses to Alzheimer’s pathology
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Diversity of transcriptomic microglial phenotypes in aging and Alzheimer's disease
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Engineering an inhibitor-resistant human CSF1R variant for microglia replacement
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“Similarly, MAFB was involved in 24% of the AD-specific trios (Figure 4F) where it was linked to the microglial marker gene CX3CR1 and genes involved in microglial activation (TLR3, CD84, HAVCR2).(50) In healthy microglia, MAFB inhibits inflammatory responses(51) consistent with our finding that target genes in AD-spec…”
ResultA loss of mature microglial markers without immune activation in schizophrenia
Snijders, G. J. L., van Zuiden, W., Sneeboer, M. A. M., van Berlekom, A. B., van der Geest, A. T., Schnieder, T. P., MacIntyre, D. J., Hol, E. M., Kahn, R. S., & de Witte, L. D. (2021) · Glia · doi:10.1002/glia.23962 · Cited by 66 · see citing works
Characterization of HIV-1 Infection in Microglia-Containing Human Cerebral Organoids
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The transcriptional signature associated with human motile cilia
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Tsatsanis, A., McCorkindale, A. N., Wong, B. X. W., Patrick, E., Ryan, T. M., Evans, R. W., Bush, A. I., Sutherland, G. T., Sivaprasadarao, A., Guennewig, B., et al. (2021) · Molecular Psychiatry · doi:10.1038/s41380-021-01248-1 · Cited by 55 · see citing works
Revealing cell vulnerability in Alzheimer’s disease by single-cell transcriptomics
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Transcriptional Networks of Microglia in Alzheimer’s Disease and Insights into Pathogenesis
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Species differences in immune‐mediated CNS tissue injury and repair: A (neuro)inflammatory topic
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Investigating Microglia in Health and Disease: Challenges and Opportunities
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A microglia-containing cerebral organoid model to study early life immune challenges
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Microglial transcription profiles in mouse and human are driven by APOE4 and sex
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Advanced patient-specific microglia cell models for pre-clinical studies in Alzheimer’s disease
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Mapping the Plasticity of Morphology, Molecular Properties and Function in Mouse Primary Microglia
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Applying causal discovery to single-cell analyses using CausalCell
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Deletion of Abi3/Gngt2 influences age-progressive amyloid β and tau pathologies in distinctive ways
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Gene expression profiling of monocytes in recent-onset schizophrenia
Kübler, R., Ormel, P. R., Sommer, I. E., Kahn, R. S., & de Witte, L. D. (2023) · Brain Behavior and Immunity · doi:10.1016/j.bbi.2023.04.019 · Cited by 13 · see citing works
Antiretroviral therapy restores the homeostatic state of microglia in SIV-infected rhesus macaques
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Self-citationHuman VCP mutant ALS/FTD microglia display immune and lysosomal phenotypes independently of GPNMB
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Molecular mapping of a core transcriptional signature of microglia-specific genes in schizophrenia
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Emerging Models to Study Human Microglia In vitro
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Zebrafish brain RNA sequencing reveals that cell adhesion molecules are critical in brain aging
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Applications of single‐cell multi‐omics sequencing in deep understanding of brain diseases
Zhang, X., Lü, P., & Shen, X. (2022) · Clinical and Translational Discovery · doi:10.1002/ctd2.95 · Cited by 5 · see citing works
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Abi3 regulates microglial ramification and dynamic tissue surveillance <i>in vivo</i>
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Functional genomic profiling of schizophrenia-associated genes reveals key microglial regulators
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Self-citationZhao, Y., Conghui, L., Yv, K., Wang, N., & Li, Z. (2026) · Journal of Alzheimer s Disease · doi:10.1177/13872877261452242
- Authors
- Patir, A., Shih, B., McColl, B. W., & Freeman, T. C.
- Affiliations
- Roslin Institute (GB)
- Corresponding author
- Freeman, Tom C.
- Venue
- Glia
- Publisher
- Wiley
- Published
- 2019-02-13
- Volume
- 67
- Issue
- 7
- Pages
- 1240-1253
- ISSN
- 0894-1491 (ISSN-L)
- 1098-1136
- OpenAlex
- W2949799705
- Cited by
- 90
- References
- 115
- Citations by year
- 2026: 10 · 2025: 4 · 2024: 11 · 2023: 9 · 2022: 27 · 2021: 14 · 2020: 13 · 2019: 2
- FWCI
- 1.46
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- Locations
- Glia (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Edinburgh Research Explorer (University of Edinburgh) (publishedVersion, other-oa)
- Lancaster EPrints (Lancaster University) (submittedVersion)
- Funders
- Medical Research Council Canada (MR/M003833, MR/L003384/1)
- Biotechnology and Biological Sciences Research Council (BB/J004227/1)
- Topics
- Life Sciences › Neuroscience › Neurology › Neuroinflammation and Neurodegeneration Mechanisms
- Health Sciences › Medicine › Physiology › Alzheimer's disease research and treatments
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Keywords
- human microglia, Alzheimer's disease, aging, microglial activation, entorhinal cortex, hippocampus, microglial markers, transcriptomic data
- MeSH terms
- Alzheimer Disease, Animals, Central Nervous System, Humans, Microglia, Gene Expression Profiling, Mice, Transcriptome
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