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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The iMG and iAst cells were epigenetically similar to hMGs and other reported iMGs and Ast cells.
“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]
The Results section, “Chromatin accessibility and gene expression in microglia” (page unavailable), confirms that this paper generated chromatin-accessibility data from primary human microglia, supporting its use as an hMG comparator. The cited paper does not establish that the citing authors’ iMG or iAst cells were epigenetically similar to those cells, and our copy does not identify an hAst epigenetic dataset from this paper. The comparison with other reported iMGs is attached to citation 22, not this source. (LLM, conf=0.83)
Experimental — accuracy not yet measuredAlzheimer's disease risk loci are enriched in genes expressed in myeloid cells, including microglia.
“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]
The Results section (‘Chromatin accessibility and gene expression in microglia’; page unavailable) reports enrichment of Alzheimer’s disease risk variants in microglial open chromatin regions. That supports a role for microglia, which the paper identifies as brain myeloid cells, but it does not establish the claimed enrichment in genes expressed across myeloid cells. (LLM, conf=0.84)
Experimental — accuracy not yet measuredSome Alzheimer's disease risk loci are highly enriched within or near genes encoding microglia-specific transcription factors.
“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]
The Results section, “AD etiology through transcription factor regulatory networks” (page unavailable), identifies microglia-specific transcription factors and examines AD-risk enrichment among their targets. The Discussion (page unavailable) says that the regulatory neighborhoods of some transcription factors are enriched in AD risk genes. Neither passage establishes the claimed enrichment of AD risk loci within or near genes encoding those factors. (LLM, conf=0.86)
Experimental — accuracy not yet measuredIn human microglial regulome studies, transcription factor network analyses nominated SPI1 as a key regulator of microglial gene expression and Alzheimer's disease risk, connecting noncoding genetic risk loci to cell-type-specific gene regulation.
“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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- 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
- Health Sciences › Medicine › Physiology › 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
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