Integration of Alzheimer’s disease genetics and myeloid genomics identifies disease risk regulatory elements and genes
Open accessAbstract
Genome-wide association studies (GWAS) have identified more than 40 loci associated with Alzheimer’s disease (AD), but the causal variants, regulatory elements, genes and pathways remain largely unknown, impeding a mechanistic understanding of AD pathogenesis. Previously, we showed that AD risk alleles are enriched in myeloid-specific epigenomic annotations. Here, we show that they are specifically enriched in active enhancers of monocytes, macrophages and microglia. We integrated AD GWAS with myeloid epigenomic and transcriptomic datasets using analytical approaches to link myeloid enhancer activity to target gene expression regulation and AD risk modification. We identify AD risk enhancers and nominate candidate causal genes among their likely targets (including AP4E1, AP4M1, APBB3, BIN1, MS4A4A, MS4A6A, PILRA, RABEP1, SPI1, TP53INP1 , and ZYX ) in twenty loci. Fine-mapping of these enhancers nominates candidate functional variants that likely modify AD risk by regulating gene expression in myeloid cells. In the MS4A locus we identified a single candidate functional variant and validated it in human induced pluripotent stem cell (hiPSC)-derived microglia and brain. Taken together, this study integrates AD GWAS with multiple myeloid genomic datasets to investigate the mechanisms of AD risk alleles and nominates candidate functional variants, regulatory elements and genes that likely modulate disease susceptibility.
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Alzheimer's disease risk alleles are enriched in PU.1-binding motifs.
“Notably, AD risk alleles were recently shown to be enriched in PU.1-binding motifs (Novikova et al., 2021).”
From A novel molecular class that recruits HDAC/MECP2 complexes to PU.1 motifs reduces neuroinflammation (2023) · cites this paper as Novikova et al., 2021
PU.1-binding motifs are enriched in AD risk alleles.
“PU.1-binding motifs are enriched in AD risk alleles (Novikova et al., 2021)”
From A novel molecular class that recruits HDAC/MECP2 complexes to PU.1 motifs reduces neuroinflammation (2023) · cites this paper as Novikova et al., 2021
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 [22]
MS4A6A showed a region-specific effect of age.
“MS4A6A, a gene related to AD risk22,68,69, was one of the genes that showed a region-specific effect of age68,70.”
From Genetic analysis of the human microglial transcriptome across brain regions, aging and disease pathologies (2022) · cites this paper as [70]
The Results section on the MS4A locus links MS4A6A expression to an Alzheimer’s disease risk allele, but does not report an effect of age that differs by brain region. Searches for “MS4A6A region-specific effect of age” and “age brain regions MS4A6A expression” found no passage addressing that claim. (LLM, conf=0.75)
Experimental — accuracy not yet measuredLinked peaks identified in microglia were significantly enriched for heritability of AD across five different studies.
“Consistent with previous studies,55,56 linked peaks identified in microglia were significantly enriched for heritability of AD across five different studies2,3,4,5,6”
From Single nucleus multiomics identifies ZEB1 and MAFB as candidate regulators of Alzheimer’s disease-specific cis-regulatory elements (2023) · cites this paper as [56]
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Sp1/Sp3 and PU.1 Differentially Regulate β5Integrin Gene Expression in Macrophages and Osteoblasts*
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Neuroinflammation in Alzheimer disease
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TREM2 dependent and independent functions of microglia in Alzheimer’s disease
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Genetics of the human microglia regulome refines Alzheimer’s disease risk loci
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Self-citationMicroglial amyloid beta clearance is driven by PIEZO1 channels
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Insights into Alzheimer’s disease from single-cell genomic approaches
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Inflammatory aspects of Alzheimer’s disease
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Microglial efferocytosis: Diving into the Alzheimer’s disease gene pool
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Self-citationNeuronal and glial 3D chromatin architecture informs the cellular etiology of brain disorders
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Self-citationHistone Modifications in Alzheimer’s Disease
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A neurodegenerative cellular stress response linked to dark microglia and toxic lipid secretion
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Microglia-mediated synaptic pruning as a key deficit in neurodevelopmental disorders: Hype or hope?
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Genomics of Alzheimer’s disease implicates the innate and adaptive immune systems
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Neuroinflammation as a Potential Therapeutic Target in Alzheimer’s Disease
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The role of Alzheimer's disease risk genes in endolysosomal pathways
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Current challenges in understanding the role of enhancers in disease
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APOE4 confers transcriptomic and functional alterations to primary mouse microglia
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Self-citationDissecting the human leptomeninges at single-cell resolution
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Genomics and Functional Genomics of Alzheimer's Disease
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Translational approaches to understanding resilience to Alzheimer’s disease
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GRaNIE and GRaNPA: inference and evaluation of enhancer‐mediated gene regulatory networks
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Omics-based biomarkers discovery for Alzheimer's disease
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PICALM Alzheimer’s risk allele causes aberrant lipid droplets in microglia
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“210,833 peaks from the previous studies 6,22 were used for PCA.”
InfluentialPrimary Hypothyroidism and Alzheimer’s Disease: A Tale of Two
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Role of adaptin protein complexes in intracellular trafficking and their impact on diseases
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SARS-CoV-2 infection increases the gene expression profile for Alzheimer’s disease risk
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Pyroptosis as a candidate therapeutic target for Alzheimer’s disease
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CUT&Tag recovers up to half of ENCODE ChIP-seq histone acetylation peaks
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Infection and inflammation: New perspectives on Alzheimer's disease
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Self-citationRedefining the hypotheses driving Parkinson’s diseases research
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A novel molecular class that recruits HDAC/MECP2 complexes to PU.1 motifs reduces neuroinflammation
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“…AD (Cao et al., 2022; Huang et al., 2017), PU.1 activity is increased in mouse models of neurodegeneration (Crotti et al., 2014; Gjoneska et al., 2015), and PU.1-binding motifs are enriched in AD risk alleles (Novikova et al., 2021), PU.1 has emerged as a promising target for drug development.”
Self-citationThe Microbiota and Evolution of Obesity
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Genetic insights into immune mechanisms of Alzheimer’s and Parkinson’s disease
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Whole exome sequencing analyses identified novel genes for Alzheimer's disease and related dementia
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Self-citationImmune dysfunction in Alzheimer disease
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Whole genome deconvolution unveils Alzheimer’s resilient epigenetic signature
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Neuronal MAPT expression is mediated by long-range interactions with cis-regulatory elements
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Deep joint learning diagnosis of Alzheimer’s disease based on multimodal feature fusion
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Targeting Progranulin as an Immuno-Neurology Therapeutic Approach
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Advances in Genetic and Molecular Understanding of Alzheimer’s Disease
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Paradigm Shift: Multiple Potential Pathways to Neurodegenerative Dementia
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Alzheimer’s disease rewires gene coexpression networks coupling different brain regions
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Leveraging the Genetic Diversity of Human Stem Cells in Therapeutic Approaches
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- Authors
- Novikova, G., Kapoor, M., TCW, J., Abud, E. M., Efthymiou, A. G., Chen, S. X., Cheng, H., Fullard, J. F., Bendl, J., Liu, Y., Roussos, P., Björkegren, J. L., Liu, Y., Poon, W. W., Hao, K., Marcora, E., & Goate, A. M.
- Affiliations
- Icahn School of Medicine at Mount Sinai (US)
- University of California, Irvine (US)
- Indiana University Indianapolis (US)
- Karolinska University Hospital (SE)
- Corresponding author
- Marcora, Edoardo
- Goate, Alison M.
- ORCID
- Venue
- Nature Communications
- Published
- 2021-03-12
- Volume
- 12
- Issue
- 1
- Pages
- 1610-1610
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC7955030
- OpenAlex
- W3134303686
- Cited by
- 214
- References
- 80
- Citations by year
- 2026: 17 · 2025: 55 · 2024: 38 · 2023: 41 · 2022: 41 · 2021: 21 · 2020: 1
- FWCI
- 22.05
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Nature Communications (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- IUScholarWorks (Indiana University) (submittedVersion, cc-by)
- Funders
- U.S. Department of Health & Human Services | NIH | National Institute on Aging (K01AG062683, F31 AG059337-01, R01AG050986)
- Topics
- Health Sciences › Medicine › Physiology › Alzheimer's disease research and treatments
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Health Sciences › Medicine › Psychiatry and Mental health › Dementia and Cognitive Impairment Research
- Keywords
- Alzheimer's disease, genetic susceptibility loci, myeloid cells, regulatory elements, enhancers, microglia, macrophages, monocytes, epigenomics, transcriptomics, causal variants, fine mapping, BIN1, MS4A4A, MS4A6A, PU.1, TP53INP1, disease susceptibility, gene expression regulation
- MeSH terms
- Alleles, Alzheimer Disease, Gene Expression Regulation, Humans, Macrophages, Regulatory Sequences, Nucleic Acid, Microglia, Genetic Predisposition to Disease, Myeloid Cells, Genomics, Genome-Wide Association Study, Induced Pluripotent Stem Cells, Transcriptome
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