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Genetics of the human microglia regulome refines Alzheimer’s disease risk loci
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Abstract
Microglia are brain myeloid cells that play a critical role in neuroimmunity and the etiology of Alzheimer's disease (AD), yet our understanding of how the genetic regulatory landscape controls microglial function and contributes to AD is limited. Here, we performed transcriptome and chromatin accessibility profiling in primary human microglia from 150 donors to identify genetically driven variation and cell-specific enhancer-promoter (E-P) interactions. Integrative fine-mapping analysis identified putative regulatory mechanisms for 21 AD risk loci, of which 18 were refined to a single gene, including 3 new candidate risk genes (KCNN4, FIBP and LRRC25). Transcription factor regulatory networks captured AD risk variation and identified SPI1 as a key putative regulator of microglia expression and AD risk. This comprehensive resource capturing variation in the human microglia regulome provides insights into the etiology of neurodegenerative disease.
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“Our iMG and iAst cells were epigenetically similar to hMGs6 and other reported iMGs22 and Ast (hAst)6 cells (Extended Data Fig. 1i).”
From PICALM Alzheimer’s risk allele causes aberrant lipid droplets in microglia (2025) · cites this paper as [6]
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“Recent human genetic studies revealed that Alzheimer's disease risk loci are enriched in genes expressed in myeloid cells, including microglia, the brain's resident immune cells.”
From Targeting Microglial Transcriptional Reprogramming as a Therapy Strategy for Alzheimer's Disease (2026) · cites this paper as [5]
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“Interestingly, some Alzheimer's disease risk loci are highly enriched within or near genes encoding microglia‐specific transcription factors, highlighting their crucial roles in the pathogenesis of Alzheimer's disease (Table 1) [5, 7, 20, 21].”
From Targeting Microglial Transcriptional Reprogramming as a Therapy Strategy for Alzheimer's Disease (2026) · cites this paper as [5]
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“In human microglial regulome studies, transcription factor network analyses nominated SPI1 as a key regulator of microglial gene expression and Alzheimer’s disease risk, helping connect noncoding genetic risk loci to cell-type-specific gene regulation [30].”
From Lymphoid-like Suppressive Microglia in Alzheimer’s Disease: A New Neuroimmune Regulatory Axis? (2026) · cites this paper as [30]
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Metadata
- Authors
- Kosoy, R., Fullard, J. F., Zeng, B., Bendl, J., Dong, P., Rahman, S., Kleopoulos, S. P., Shao, Z., Girdhar, K., Humphrey, J., de Paiva Lopes, K., Charney, A. W., Kopell, B. H., Raj, T., Bennett, D., Kellner, C. P., Haroutunian, V., Hoffman, G. E., & Roussos, P.
- Affiliations
- Icahn School of Medicine at Mount Sinai (US)
- Rush University Medical Center (US)
- James J. Peters VA Medical Center (US)
- Nathan Kline Institute for Psychiatric Research (US)
- Corresponding author
- Kosoy, Roman
- Hoffman, Gabriel E.
- Roussos, Panos
- ORCID
- Venue
- Nature Genetics
- Published
- 2022-08
- Volume
- 54
- Issue
- 8
- Pages
- 1145-1154
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- PMC
- PMC9388367
- OpenAlex
- W4295079251
- Cited by
- 168
- References
- 70
- Citations by year
- 2026: 40 · 2025: 49 · 2024: 44 · 2023: 25 · 2022: 10
- FWCI
- 11.23
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Locations
- Nature Genetics (publishedVersion)
- medRxiv (acceptedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- U.S. Department of Health & Human Services | NIH | National Institute on Aging (R01-AG067025, R01-AG065582)
- Alzheimer’s Association (AARF-21-722200)
- Topics
- Life Sciences › Neuroscience › Neurology › Neuroinflammation and Neurodegeneration Mechanisms
- Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Alzheimer's disease research and treatments
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Keywords
- Alzheimer's disease, microglia, enhancer-promoter interactions, chromatin accessibility, gene expression profiling, fine mapping, transcriptional regulatory networks, KCNN4, neuroimmunity, gene regulatory mechanisms
- MeSH terms
- Alzheimer Disease, Brain, Carrier Proteins, Humans, Membrane Proteins, Microglia, Neurodegenerative Diseases, Transcriptome
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
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