Functional characterization of Alzheimer’s disease genetic variants in microglia
Open accessAbstract
Candidate cis-regulatory elements (cCREs) in microglia demonstrate the most substantial enrichment for Alzheimer's disease (AD) heritability compared to other brain cell types. However, whether and how these genome-wide association studies (GWAS) variants contribute to AD remain elusive. Here we prioritize 308 previously unreported AD risk variants at 181 cCREs by integrating genetic information with microglia-specific 3D epigenome annotation. We further establish the link between functional variants and target genes by single-cell CRISPRi screening in microglia. In addition, we show that AD variants exhibit allelic imbalance on target gene expression. In particular, rs7922621 is the effective variant in controlling TSPAN14 expression among other nominated variants in the same cCRE and exerts multiple physiological effects including reduced cell surface ADAM10 and altered soluble TREM2 (sTREM2) shedding. Our work represents a systematic approach to prioritize and characterize AD-associated variants and provides a roadmap for advancing genetic association to experimentally validated cell-type-specific phenotypes and mechanisms.
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The functional linkage between rs6733839 and BIN1 has been well established.
“including the two loci with the strongest associations with LOAD: the BIN1 locus for which the functional linkage between rs6733839 and BIN1 has been well established7,23”
From PICALM Alzheimer’s risk allele causes aberrant lipid droplets in microglia (2025) · cites this paper as [7]
The Results section ('AD variants affect multiple target genes in microglia'; page unavailable) reports that perturbing a candidate regulatory element at the BIN1 locus significantly affects nearby gene expression. That supports a functional link at the locus, but the copy does not identify rs6733839 as the responsible variant or establish its specific functional linkage to BIN1. (LLM, conf=0.84)
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 [7]
The Introduction reports that microglial regulatory elements have high enrichment for AD-associated variants, and the Results section on AD fine-mapping reports enrichment of AD SNP heritability in microglial regulatory elements. This supports the microglia connection, but these passages do not establish enrichment in genes expressed across myeloid cells generally. (LLM, conf=0.84)
Experimental — accuracy not yet measuredTwo studies using proximity-ligation assays in human primary or iPSC-derived microglia have reported 3D genomic interactions between GWAS-associated variants and gene promoters in LOAD.
“Recently, two studies using proximity-ligation assays in either human primary or iPSC-derived microglia have reported 3D genomic interactions between GWAS-associated variants and gene promoters in LOAD22,65.”
Some 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 [7]
The Results section on AD fine-mapping reports enrichment of AD SNP heritability in microglial cis-regulatory elements, not within or near genes encoding microglia-specific transcription factors. The Results section on dynamic transcription reports enrichment of transcription-factor binding sites in regions that gain accessibility after stimulation, but does not link those sites to AD risk loci. Our copy does not establish the claimed enrichment near transcription-factor genes; page numbers are unavailable. (LLM, conf=0.72)
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- Authors
- Yang, X., Wen, J., Yang, H., Jones, I. R., Zhu, X., Liu, W., Li, B., Clelland, C. D., Luo, W., Wong, M. Y., Ren, X., Cui, X., Song, M., Liu, H., Chen, C., Eng, N., Ravichandran, M., Sun, Y., Lee, D., Van Buren, E., Jiang, M.-Z., Chan, C. S. Y., Ye, C. J., Perera, R. M., Gan, L., Li, Y., & Shen, Y.
- Affiliations
- University of California, San Francisco (US)
- University of North Carolina at Chapel Hill (US)
- Weill Cornell Medicine (US)
- Corresponding author
- Li, Yun
- Shen, Yin
- ORCID
- Venue
- Nature Genetics
- Published
- 2023-09-21
- Volume
- 55
- Issue
- 10
- Pages
- 1735-1744
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- PMC
- PMC10939305
- OpenAlex
- W4386923851
- Cited by
- 71
- References
- 73
- Citations by year
- 2026: 20 · 2025: 33 · 2024: 15 · 2023: 3
- FWCI
- 11.77
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- Locations
- Nature Genetics (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Carolina Digital Repository (University of North Carolina at Chapel Hill) (submittedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- UNC Libraries
- Funders
- U.S. Department of Health and Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging (R01AG057497, RF1AG079557, R56AG079271, R01AG079271, R01AG072758, R01AG054214)
- U.S. Department of Health and Human Services | NIH | National Eye Institute (R01EY027789)
- U.S. Department of Health and Human Services | NIH | National Human Genome Research Institute (UM1HG009402, U01HG011720)
- Hillblom Foundation American Federation for Aging Research
- U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (P50HD103573)
- U.S. Department of Health and Human Services | NIH | National Institute of Mental Health (R01MH125236, R01MH123724)
- Topics
- Health Sciences › Medicine › Physiology › Alzheimer's disease research and treatments
- Life Sciences › Neuroscience › Neurology › Neuroinflammation and Neurodegeneration Mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Keywords
- Alzheimer's disease, microglia, cis-regulatory elements, genetic risk variants, ADAM10, soluble TREM2, allelic imbalance, genetic fine-mapping, cell type-specific gene regulation
- MeSH terms
- Alzheimer Disease, Cell Membrane, Humans, Phenotype, Microglia, Genome-Wide Association Study
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