Polarization of the Effects of Autoimmune and Neurodegenerative Risk Alleles in Leukocytes
Open accessAbstract
Immunogenetic Variation: Many genetic variants have been implicated in disease but their effects in function across tissues and cell-types remain to be resolved. Raj et al. (p. 519 ) present an analysis of expression quantative trait loci (eQTL) measuring messenger RNA levels and examined correlations between genotypes and gene expression in purified monocytes and T cells in healthy individuals of European, African, and Asian descent. Most, but not all, of the eQTLs and their effects on expression were shared between the populations, as well as a substantial proportion between the cell types. Links were found with disease-associated variants and loci that previous genome-wide analyses have implicated in neurodegenerative and autoimmune diseases.
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The findings strengthen the growing evidence linking AD to a network of genes expressed in microglia.
“These results reinforce the emerging genetic and epigenetic association between AD and a network of microglial expressed genes2,5,17–21”
From A common haplotype lowers PU.1 expression in myeloid cells and delays onset of Alzheimer's disease (2017) · cites this paper as [21]
The paper reports that AD susceptibility alleles are enriched for monocyte-specific effects and suggests that monocytes may be proxies for resident microglia (Abstract; page unavailable). This supports a genetic link to myeloid cells, but it does not establish an AD-associated network of microglial-expressed genes or an epigenetic association specific to that network. (LLM, conf=0.85)
Experimental — accuracy not yet measuredEnrichment for MS susceptibility loci is observed not only in T cells but also in B cells.
“An important finding is that the enrichment is observed not only in immune cells that have long been studied in MS, e.g. T cells, but also in B cells whose role has emerged more recently.(25)”
From Multiple sclerosis genomic map implicates peripheral immune cells and microglia in susceptibility (2019) · cites this paper as [25]
The passage discussing disease-associated cis-eQTLs (indexed as Abstract; page unavailable) reports a preponderance of T-cell-specific effects among multiple-sclerosis susceptibility alleles. The study profiled T cells and monocytes, not B cells, so it does not support the claimed enrichment in B cells. (LLM, conf=0.90)
Experimental — accuracy not yet measuredMultiple sclerosis genome-wide association study loci are enriched for expression quantitative trait loci in multiple tissues, supporting the idea that much risk is due to changes to gene regulation.
“MS GWAS loci are also enriched for expression quantitative trait loci (eQTL) in multiple tissues,46, 57 supporting the idea that much risk is due to changes to gene regulation.”
From Genome‐wide association studies of multiple sclerosis (2018) · cites this paper as [57]
The paper reports significant cis-eQTL enrichment among autoimmune-disease GWAS variants in monocytes and/or T cells, and identifies multiple sclerosis susceptibility alleles as having predominantly T-cell-specific regulatory effects (Abstract; page unavailable). It does not establish that MS GWAS loci specifically are enriched for eQTLs in multiple tissues, or quantify how much MS risk is due to regulatory changes. (LLM, conf=0.84)
Experimental — accuracy not yet measuredAD-risk alleles are polarized for cis-eQTL effects in monocytes.
“Further, AD-risk alleles are polarized for cis-expression quantitative trait locus (cis-eQTL) effects in monocytes21.”
From A common haplotype lowers PU.1 expression in myeloid cells and delays onset of Alzheimer's disease (2017) · cites this paper as [21]
Many elements of innate immunity, such as natural killer cells and dendritic cells, display strong enrichment for MS susceptibility genes.
“Furthermore, while the adaptive immune system has been proposed to play a predominant role in MS onset,(26) we now demonstrate that many elements of innate immunity, such as natural killer (NK) cells and dendritic cells also display strong enrichment for MS susceptibility genes.”
From Multiple sclerosis genomic map implicates peripheral immune cells and microglia in susceptibility (2019) · cites this paper as [26]
Human genome-wide association studies support a causal role for immune mechanisms in AD.
“human genome-wide association studies (GWASs) support a causal role for immune mechanisms (Jansen et al., 2019; Kunkle et al., 2019; Raj et al., 2014).”
From Meta-Analysis of the Alzheimer’s Disease Human Brain Transcriptome and Functional Dissection in Mouse Models (2020) · cites this paper as Raj et al., 2014
Our sample size is still small in comparison to monocyte and brain datasets.
“First, our sample size is still small in comparison to monocyte and brain datasets22,41–43.”
From Genetic analysis of the human microglial transcriptome across brain regions, aging and disease pathologies (2022) · cites this paper as [22]
CLECL1 has previously been linked to altered CLECL1 RNA expression in monocytes.
“On the other hand, CLECL1 represents a simpler case of a known susceptibility effect that has previously been linked to altered CLECL1 RNA expression in monocytes (26, 32); its enrichment in microglial cells, which share many molecular pathways with other myeloid cells, is more straightforward to understand.”
From Multiple sclerosis genomic map implicates peripheral immune cells and microglia in susceptibility (2019) · cites this paper as [26]
The passages on monocyte-specific eQTLs and disease susceptibility variants (section labeled Abstract; page unavailable) discuss these effects generally but do not identify CLECL1. Searches for CLECL1 and altered CLECL1 RNA expression in monocytes found no passage addressing the specific link. (LLM, conf=0.72)
Experimental — accuracy not yet measuredMS4A6A 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 [22]
The paper’s Abstract describes gene-expression analyses in blood T cells and monocytes, including cell-type-specific effects of Alzheimer’s disease risk variants. It does not report a region-specific effect of age for MS4A6A; searches for MS4A6A and age-related brain-region effects found no passage addressing that claim. (LLM, conf=0.75)
Experimental — accuracy not yet measuredAlleles associated with AD show an effect on gene expression specifically in monocytes.
“This idea is supported by studies showing that alleles associated with AD show an effect on gene expression specifically in monocytes.”
From Genetic architecture of Alzheimer's disease (2020) · cites this paper as [193]
AD-associated variants were enriched for colocalization with eQTLs specifically regulating gene expression in monocytes, but not in T-cells.
“AD-associated variants were enriched for colocalization with eQTLs specifically regulating gene expression in monocytes, but not in T-cells, demonstrating AD variants have a cell-type specific effect on gene expression.”
From Genetic architecture of Alzheimer's disease (2020) · cites this paper as [193]
Genetic studies have highlighted a prominent role for microglia in susceptibility to different neurodegenerative diseases, particularly Alzheimer's disease.
“Genetic studies have highlighted a prominent role for microglia in susceptibility to different neurodegenerative diseases, particularly Alzheimer’s disease (AD)10–12.”
From Single cell RNA sequencing of human microglia uncovers a subset associated with Alzheimer’s disease (2020) · cites this paper as [12]
Recent evidence from GWAS and follow-up analyses suggests that a proportion of genetic risk for neurological and psychiatric diseases acts through myeloid cells.
“However, recent evidence from genome-wide association studies (GWAS) and other follow-up analyses has suggested that a proportion of the genetic risk of neurological and psychiatric diseases acts through myeloid cells22–25.”
From Genetic analysis of the human microglial transcriptome across brain regions, aging and disease pathologies (2022) · cites this paper as [22]
These results highlight shared genetic regulation between microglia and monocytes, which is only partly captured in whole-tissue brain data.
“Together, these results highlight shared genetic regulation between microglia and monocytes, which is only partly captured in whole-tissue brain data22.”
From Genetic analysis of the human microglial transcriptome across brain regions, aging and disease pathologies (2022) · cites this paper as [22]
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- Authors
- Raj, T., Rothamel, K., Mostafavi, S., Ye, C., Lee, M. N., Replogle, J. M., Feng, T., Lee, M., Asinovski, N., Frohlich, I., Imboywa, S., Von Korff, A., Okada, Y., Patsopoulos, N. A., Davis, S., McCabe, C., Paik, H.-I., Srivastava, G. P., Raychaudhuri, S., Hafler, D. A., Koller, D., Regev, A., Hacohen, N., Mathis, D., Benoist, C., Stranger, B. E., & De Jager, P. L.
- Affiliations
- Broad Institute (US)
- Harvard University (US)
- Stanford University (US)
- Brigham and Women's Hospital (US)
- Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Departments of Neurology and Psychiatry, Brigham and Women’s Hospital, Boston, MA 02115, USA.
- University of Chicago (US)
- Corresponding author
- Benoist, Christophe
- Stranger, Barbara E.
- ORCID
- Venue
- Science
- Published
- 2014-05-02
- Volume
- 344
- Issue
- 6183
- Pages
- 519-523
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC4910825
- OpenAlex
- W2101280135
- Cited by
- 506
- References
- 31
- Citations by year
- 2026: 11 · 2025: 18 · 2024: 17 · 2023: 34 · 2022: 43 · 2021: 38 · 2020: 58 · 2019: 46 · 2018: 56 · 2017: 54 · 2016: 53 · 2015: 53 · 2014: 24
- FWCI
- 40.18
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- Research Explorer (The University of Manchester) (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc-sa)
- eScholarship (California Digital Library) (submittedVersion)
- PMC
- Funders
- Howard Hughes Medical Institute
- National Institutes of Health (5r01ar063759-07)
- National Institute on Aging (F32AG043267)
- National Institute of General Medical Sciences (RC2GM093080)
- National Institute of Arthritis and Musculoskeletal and Skin Diseases (K08AR055688, R01-AR063759)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Health Sciences › Medicine › Pathology and Forensic Medicine › Multiple Sclerosis Research Studies
- Keywords
- expression quantitative trait loci, CD4+ T cells, monocytes, Alzheimer's disease, Parkinson's disease, cis-eQTL, trans-eQTL, cell-autonomous effects, multi-ethnic cohort
- MeSH terms
- Alleles, Alzheimer Disease, Autoimmune Diseases, Ethnicity, Humans, Immunity, Innate, Monocytes, Multiple Sclerosis, Parkinson Disease, Rheumatic Fever, CD4-Positive T-Lymphocytes, Autoimmunity, Neurodegenerative Diseases, Genetic Predisposition to Disease, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Genome-Wide Association Study, Adaptive Immunity, Transcriptome
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