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Cited by 423Alzheimer's disease research and treatmentsDementia and Cognitive Impairment ResearchGenetic Associations and Epidemiology

A common haplotype lowers PU.1 expression in myeloid cells and delays onset of Alzheimer's disease

Open access
The International Genomics of Alzheimer's Project, Huang, Kuan-lin, The Alzheimer's Disease Neuroimaging Initiative, Marcora, Edoardo, Pimenova, Anna A, Di Narzo, Antonio F, Kapoor, Manav, Jin, Sheng Chih +41 more·2017·Nature Neuroscience
DOI 10.1038/nn.4587PMC PMC5759334

Published version of a preprint

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Abstract

A genome-wide survival analysis of 14,406 Alzheimer's disease (AD) cases and 25,849 controls identified eight previously reported AD risk loci and 14 novel loci associated with age at onset. Linkage disequilibrium score regression of 220 cell types implicated the regulation of myeloid gene expression in AD risk. The minor allele of rs1057233 (G), within the previously reported CELF1 AD risk locus, showed association with delayed AD onset and lower expression of SPI1 in monocytes and macrophages. SPI1 encodes PU.1, a transcription factor critical for myeloid cell development and function. AD heritability was enriched within the PU.1 cistrome, implicating a myeloid PU.1 target gene network in AD. Finally, experimentally altered PU.1 levels affected the expression of mouse orthologs of many AD risk genes and the phagocytic activity of mouse microglial cells. Our results suggest that lower SPI1 expression reduces AD risk by regulating myeloid gene expression and cell function.

Integrity signals

Registry

Crossref · 10.1038/nn.4587

Cites

85 of 85 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

49 of 62 cited sources checked · 13 supported · 0 flagged · accuracy not yet measured

  • Findingown data

    In HL60 cells, AD heritability showed significant enrichment for SPI1 (PU.1) that was much stronger than for POLR2AphosphoS5.

    “We observed a significant enrichment for SPI1 (PU.1) (34.58 fold enrichment, P=1.31×10−3 in first replicate; 58.12 fold enrichment, P=4.95×10−3 in second replicate) much stronger than that for POLR2AphosphoS5 (15.78 fold enrichment, P=1.71×10−2 in first replicate; 16.34 fold enrichment, P=1.25×10−1 in second replicate)”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [37] Sakai, K. et al. A neuronal VLDLR variant lacking the third complement-type repeat exhibits high capacity binding of apoE containing lipoproteins. Brain Res. 1276, 11–21 (2009). source

      The Results (§2.5) concern VLDLR splicing in mouse neurons and astrocytes, not AD heritability enrichment in HL60 cells. Searches for SPI1/PU.1, POLR2AphosphoS5, and the reported fold-enrichment values found no passage addressing the claim; no page numbers were available in our copy. (LLM, conf=0.78)

      Experimental — accuracy not yet measured
  • Premisecitation

    PU.1 binds to active enhancers of Trem2 and Tyrobp in ChIP-Seq experiments using mouse BV2 cells or bone marrow-derived mouse macrophages.

    “Further, PU.1 binds to active enhancers of Trem2 and Tyrobp in ChIP-Seq experiments using mouse BV2 cells42 or bone marrow-derived mouse macrophages43.”
    Quote in the paperNot a substantial claim1 of 2 sources checked
    • cites [42] Daniel, B. et al. The active enhancer network operated by liganded RXR supports angiogenic activity in macrophages. Genes Dev. 28, 1562–1577 (2014). source

      The Results section on mapping cistromes in BMDMs reports PU.1 ChIP-seq peaks and active histone marks in bone marrow-derived macrophages. Our copy does not identify PU.1 binding at enhancers of Trem2 or Tyrobp, so it does not support the gene-specific part of the claim. The BV2-cell experiment is attributed to a different citation in the citing sentence. (LLM, conf=0.83)

      Experimental — accuracy not yet measured
    • cites [43] McKercher, S.R. et al. Targeted disruption of the PU.1 gene results in multiple hematopoietic abnormalities. EMBO J. 15, 5647–5658 (1996). source
  • Findingcitation

    SPI1, MS4A4A, MS4A6A, and SELL are specifically expressed in microglia based on RNA-Seq data.

    “Further, SPI1, MS4A4A, MS4A6A, and SELL are specifically expressed in microglia based on RNA-Seq data29–31”
    Quote in the paperSubstantial claim3 of 3 sources checked
    • cites [29] Zhang, Y. et al. An RNA-sequencing transcriptome and splicing database of glia, neurons, and vascular cells of the cerebral cortex. J. Neurosci. 34, 11929–11947 (2014). source

      The section ‘RNA-Seq analysis revealed cell type-specific gene expression profiles’ reports microglia-enriched genes, but the passages in our copy do not identify SPI1, MS4A4A, MS4A6A, or SELL as among them. Searches for the four gene names and their mouse-style capitalization found no passage establishing their microglia-specific expression; page numbers were unavailable. (LLM, conf=0.76)

      Experimental — accuracy not yet measured
    • cites [30] Bennett, M.L. et al. New tools for studying microglia in the mouse and human CNS. Proc. Natl. Acad. Sci. USA 113, E1738–E1746 (2016). source

      The sections on Tmem119-purified transcriptomes and microglial maturation describe RNA-seq profiling and identify other microglia-enriched genes, but do not identify SPI1, MS4A4A, MS4A6A, or SELL as specifically expressed in microglia. Searches for the four genes, including mouse-style capitalization, found no passage establishing the claim. Page numbers were not available in our copy. (LLM, conf=0.72)

      Experimental — accuracy not yet measured
    • cites [31] Giambartolomei, C. et al. Bayesian test for colocalisation between pairs of genetic association studies using summary statistics. PLoS Genet. 10, e1004383 (2014). source

      The Materials and Methods section (Expression dataset; page unavailable) describes gene-expression arrays from human liver samples, not microglial RNA-Seq. Searches for SPI1, MS4A4A, MS4A6A, SELL, and microglial RNA-Seq found no passage in our copy addressing the claimed cell-specific expression. (LLM, conf=0.76)

      Experimental — accuracy not yet measured
  • Premisecitation

    Genes expressed in myeloid cells display abnormal patterns of chromatin modification in AD mouse models and human samples.

    “At the epigenetic level, genes expressed in myeloid cells display abnormal patterns of chromatin modification in AD mouse models and human samples18–20.”
    Quote in the paperSubstantial claim3 of 3 sources checked
    • cites [18] Zhang, B. et al. Integrated systems approach identifies genetic nodes and networks in late-onset Alzheimer's disease. Cell 153, 707–720 (2013). source

      The Results section reports altered gene expression in human Alzheimer’s brain tissue and in mouse microglia after TYROBP perturbation, including down-regulation of genes involved in histone assembly. It does not report abnormal chromatin modifications in myeloid-cell genes in AD mouse models or human samples. Searches for chromatin modification, histone methylation, and acetylation found no passage establishing that claim; page numbers were unavailable in our copy. (LLM, conf=0.75)

      Experimental — accuracy not yet measured
    • cites [19] Gjoneska, E. et al. Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer's disease. Nature 518, 365–369 (2015). source

      The paper’s epigenome analysis and Extended Data Figures 4–5 report altered histone marks at regulatory regions in the AD mouse model, alongside increased immune-gene expression. Its human analyses compare gene expression in AD patients and identify immune-cell enhancer activity at regions corresponding to the altered mouse enhancers; they do not show abnormal chromatin modifications measured in human AD samples. No page numbers are provided in our copy. (LLM, conf=0.87)

      Experimental — accuracy not yet measured
    • cites [20] Chan, G. et al. CD33 modulates TREM2: convergence of Alzheimer loci. Nat. Neurosci. 18, 1556–1558 (2015). source

      The Abstract reports protein-expression and genetic-association findings in human monocytes, not abnormal chromatin modification in myeloid-cell genes. Searches for chromatin modification and histone changes in AD mouse models and human samples found no passage addressing the claim in our copy. (LLM, conf=0.76)

      Experimental — accuracy not yet measured
  • Premisecitation

    AD-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.”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [21] Raj, T. et al. Polarization of the effects of autoimmune and neurodegenerative risk alleles in leukocytes. Science 344, 519–523 (2014). source
  • Classified as probably not a substantial claim. 44
  • May combine two claims. 45
  • The quote only partly states this claim. 1

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Transcriptomic and proteomic analyses of microglial cells suggested a microglial homeostatic signature that is perturbed during aging and under pathological conditions.

    “Transcriptomic and proteomic analyses of microglial cells suggested a microglial homeostatic signature that is perturbed during aging and under pathological conditions48.”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [48] Wang, Y. et al. IL-34 is a tissue-restricted ligand of CSF1R required for the development of Langerhans cells and microglia. Nat. Immunol. 13, 753–760 (2012). source

      The Results section on IL-34 deficiency and the Discussion address microglial abundance, CNS protection and possible roles in neurodegenerative pathology (page unavailable). Searches for transcriptomic or proteomic analyses, a homeostatic signature and aging found no passage addressing the claimed signature or its perturbation. (LLM, conf=0.77)

      Experimental — accuracy not yet measured

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Previous data showed decreased uptake of Aβ42 in primary microglial cells isolated from adult human brain tissue and transfected with siRNA targeting SPI1.

    “This is in line with previous data showing decreased uptake of Aβ42 (also a TLR2 agonist) in primary microglial cells isolated from adult human brain tissue and transfected with siRNA targeting SPI147.”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [47] Butovsky, O. et al. Identification of a unique TGF-β-dependent molecular and functional signature in microglia. Nat. Neurosci. 17, 131–143 (2014). source

      The Methods section on human microglia isolation and cell culture describes isolating cells from adult human brain tissue. Searches for SPI1, siRNA, Aβ42 uptake, and related terms found no passage reporting the claimed transfection or decreased uptake; the available copy therefore does not verify the result. (LLM, conf=0.73)

      Experimental — accuracy not yet measured

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    VLDLR is a receptor for lipoproteins containing APOE and CLU/APOJ.

    “VLDLR is a receptor for lipoproteins containing APOE38 and CLU/APOJ39, another AD risk gene.”
    Quote in the paperNot a substantial claim1 of 2 sources checked
    • cites [38] Bajari, T.M., Strasser, V., Nimpf, J. & Schneider, W.J. A model for modulation of leptin activity by association with clusterin. FASEB J. 17, 1505–1507 (2003). source
    • cites [39] Speliotes, E.K. et al. Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index. Nat. Genet. 42, 937–948 (2010). source

      The Results sections on functional variants and pathways discuss BMI-associated genes and other receptors, but do not describe VLDLR as a receptor for APOE- or CLU/APOJ-containing lipoproteins. Searches for VLDLR, CLU/APOJ, and related receptor terms found no passage addressing that relationship; page numbers were unavailable in our copy. (LLM, conf=0.77)

      Experimental — accuracy not yet measured

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    PU.1 is required for the development and function of myeloid and B-lymphoid cells.

    “PU.1 is required for the development and function of myeloid and B-lymphoid cells44,45.”
    Quote in the paperNot a substantial claim1 of 2 sources checked
    • cites [44] Beers, D.R. et al. Wild-type microglia extend survival in PU.1 knockout mice with familial amyotrophic lateral sclerosis. Proc. Natl. Acad. Sci. USA 103, 16021–16026 (2006). source
    • cites [45] Mak, K.S., Funnell, A.P.W., Pearson, R.C.M. & Crossley, M. PU.1 and haematopoietic cell fate: dosage matters. Int. J. Cell Biol. 2011, 808524 (2011). source

      Section 4 says PU.1 is required for myeloid differentiation and enables committed cells to respond to myeloid growth factors. Section 5 supports a requirement for B-cell production, but says PU.1 is dispensable after lymphoid commitment: deletion after the pre-B-cell stage does not disrupt immunoglobulin expression or responses to mitogens. The claim therefore overstates its requirement for B-cell function. (LLM, conf=0.88)

      Experimental — accuracy not yet measured

  • Classified as probably not a substantial claim.

    Premisecitation

    GWAS and sequencing studies have found associations between AD and genes expressed in myeloid cells, including TREM2, ABCA7, and CD33.

    “At the genetic level, GWAS and sequencing studies have found associations between AD and genes expressed in myeloid cells, including TREM2, ABCA7, and CD331,2,5,15–17.”
    Quote in the paperSubstantial claim6 of 6 sources checked
    • cites [1] Lambert, J.-C. et al. Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer's disease. Nat. Genet. 45, 1452–1458 (2013). source

      The Abstract describes ABCA7 and CD33 as previously identified GWAS genes associated with Alzheimer’s disease and reports a rare TREM2 risk variant. It does not say that all three genes are expressed in myeloid cells. It also notes that this study did not replicate the CD33 association in stage 2 (P = 0.61). Page numbers are not available in our copy. (LLM, conf=0.87)

      Experimental — accuracy not yet measured
    • cites [2] Naj, A.C. et al. Common variants at MS4A4/MS4A6E, CD2AP, CD33 and EPHA1 are associated with late-onset Alzheimer's disease. Nat. Genet. 43, 436–441 (2011). source

      The section labelled Abstract (page unavailable) reports a genome-wide association between CD33 and late-onset AD. It also reports suggestive evidence for ABCA7 in this study and a stronger association reported by Hollingworth et al. Our copy does not establish the TREM2 association, sequencing findings, or expression of these genes in myeloid cells. (LLM, conf=0.85)

      Experimental — accuracy not yet measured
    • cites [5] Hollingworth, P. et al. Common variants at ABCA7, MS4A6A/MS4A4E, EPHA1, CD33 and CD2AP are associated with Alzheimer's disease. Nat. Genet. 43, 429–435 (2011). source

      The study reports GWAS associations with AD for ABCA7 and CD33, and states that ABCA7 is highly expressed in microglia (Abstract; page not supplied). It does not report a TREM2 association or a sequencing finding, and its discussion of CD33’s immune functions does not establish its expression in myeloid cells. (LLM, conf=0.86)

      Experimental — accuracy not yet measured
    • cites [15] Jonsson, T. et al. Variant of TREM2 associated with the risk of Alzheimer's disease. N. Engl. J. Med. 368, 107–116 (2013). source

      The Results report an association between a TREM2 variant and Alzheimer’s disease, and the Discussion identifies TREM2 in microglia and CD33 as a myeloid cell-surface receptor linked to Alzheimer’s disease by genomewide association studies. ABCA7 appears in a cited study’s title in the References, but the paper does not discuss its myeloid-cell expression; that part of the claim is not supported by this copy. (LLM, conf=0.84)

      Experimental — accuracy not yet measured
    • cites [16] Guerreiro, R. et al. TREM2 variants in Alzheimer's disease. N. Engl. J. Med. 368, 117–127 (2013). source
    • cites [17] Bradshaw, E.M. et al. CD33 Alzheimer's disease locus: altered monocyte function and amyloid biology. Nat. Neurosci. 16, 848–850 (2013). source

      The Abstract says genome-wide studies identified CD33 as an AD susceptibility locus and describes CD33 expression in myeloid cells. It does not address associations involving TREM2 or ABCA7, or sequencing findings for those genes, so it supports only the CD33 portion of the sentence. (LLM, conf=0.86)

      Experimental — accuracy not yet measured

  • May combine two claims.

    Premisecitation

    rs1377416 is located in a predicted enhancer in the vicinity of SPI1 and altered enhancer activity when assayed in vitro using a reporter construct transfected in BV2 cells.

    “rs1377416, is located in a predicted enhancer in the vicinity of SPI1 and altered enhancer activity when assayed in vitro using a reporter construct transfected in BV2 cells19.”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [19] Gjoneska, E. et al. Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer's disease. Nature 518, 365–369 (2015). source

  • Probably not a substantial claim: may not pass S2 (checkable).

    Premisecitation

    Identifying causal genes and mechanisms underlying disease-associated loci requires integrative analyses of expression and epigenetic datasets in disease-relevant cell types.

    “Identifying causal genes and mechanisms underlying disease-associated loci requires integrative analyses of expression and epigenetic datasets in disease-relevant cell types14.”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [14] Gusev, A. et al. Integrative approaches for large-scale transcriptome-wide association studies. Nat. Genet. 48, 245–252 (2016). source

      The Discussion (page unavailable) describes integrating genetic and expression data to identify genes associated with complex traits, and the Results report tissue-specific findings. The paper does not say that identifying causal genes requires epigenetic datasets; its Discussion also cautions that some associations may be indistinguishable from confounding without further analysis. (LLM, conf=0.88)

      Experimental — accuracy not yet measured

  • Classified as probably not a substantial claim. May combine two claims.

    Premisecitation

    SPI1 encodes PU.1, a transcription factor critical for myeloid cell development and function.

    “SPI1 encodes PU.1, a transcription factor critical for myeloid cell development and function.”
    Quote in the paperSubstantial claim1 of 2 sources checked
    • cites [44] Beers, D.R. et al. Wild-type microglia extend survival in PU.1 knockout mice with familial amyotrophic lateral sclerosis. Proc. Natl. Acad. Sci. USA 103, 16021–16026 (2006). source
    • cites [45] Mak, K.S., Funnell, A.P.W., Pearson, R.C.M. & Crossley, M. PU.1 and haematopoietic cell fate: dosage matters. Int. J. Cell Biol. 2011, 808524 (2011). source

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    rs1057233 was previously found to be associated with systemic lupus erythematosus, body mass index, and proinsulin levels.

    “Interestingly, rs1057233 was previously found to be associated with systemic lupus erythematosus33, body mass index40 and proinsulin levels41”
    Quote in the paperNot a substantial claim3 of 3 sources checked
    • cites [33] Ward, L.D. & Kellis, M. HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants. Nucleic Acids Res. 40, D930–D934 (2012). source

      Citation 33 is attached to the lupus association, not the body-mass-index or proinsulin claims. The USAGE section discusses a lupus GWAS but names rs9271100 and rs9271055, not rs1057233; a search for rs1057233 found no passage linking it to lupus in our copy. (LLM, conf=0.75)

      Experimental — accuracy not yet measured
    • cites [40] Strawbridge, R.J. et al. Genome-wide association identifies nine common variants associated with fasting proinsulin levels and provides new insights into the pathophysiology of type 2 diabetes. Diabetes 60, 2624–2634 (2011). source

      Citation 41 is attached to the proinsulin-level association, not the lupus or BMI associations, which have separate citations. The Results tables report proinsulin associations for other SNPs, but a search for rs1057233 found no passage identifying it or linking it to proinsulin levels in our copy. (LLM, conf=0.76)

      Experimental — accuracy not yet measured
    • cites [41] Satoh, J., Asahina, N., Kitano, S. & Kino, Y. A comprehensive profile of ChIP-seq-based PU.1/Spi1 target genes in microglia. Gene Regul. Syst. Bio. 8, 127–139 (2014). source

      The Methods section describes a PU.1 ChIP-Seq dataset in mouse microglial cells, and the Results report Spi1 target genes and pathways (page numbers unavailable). Searches for rs1057233 and for systemic lupus erythematosus, body mass index, and proinsulin found no passage in our copy addressing the claimed associations. (LLM, conf=0.72)

      Experimental — accuracy not yet measured

  • Classified as probably not a substantial claim.

    Premisecitation

    Few studies have investigated the genetic basis of age at onset of AD.

    “For example, few studies6,7 have investigated the genetic basis of age at onset of AD (AAO).”
    Quote in the paperSubstantial claim2 of 2 sources checked
    • cites [6] Naj, A.C. et al. Effects of multiple genetic loci on age at onset in late-onset Alzheimer disease: a genome-wide association study. JAMA Neurol. 71, 1394–1404 (2014). source
    • cites [7] Kamboh, M.I. et al. Genome-wide association analysis of age-at-onset in Alzheimer's disease. Mol. Psychiatry 17, 1340–1346 (2012). source

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    APOE remains the only locus repeatedly associated with AAO, but PICALM and BIN1 have also been reported to affect AAO.

    “To date, APOE remains the only locus repeatedly associated with AAO8,9, but PICALM and BIN1 have also been reported to affect AAO6,10,11.”
    Quote in the paperNot a substantial claim4 of 5 sources checked
    • cites [8] Bennett, C. et al. Evidence that the APOE locus influences rate of disease progression in late onset familial Alzheimer's Disease but is not causative. Am. J. Med. Genet. 60, 1–6 (1995). source
    • cites [9] Slooter, A.J. et al. Risk estimates of dementia by apolipoprotein E genotypes from a population-based incidence study: the Rotterdam Study. Arch. Neurol. 55, 964–968 (1998). source

      The Comment section reports that APOE genotypes explained some variance in age at onset of dementia, supporting the APOE–AAO association. The paper does not establish that APOE was the only locus repeatedly associated with AAO; its introduction says APOE's role in age at onset was still controversial. PICALM and BIN1 are attached to other citations in the citing sentence, not this one. Page numbers are unavailable in our copy. (LLM, conf=0.85)

      Experimental — accuracy not yet measured
    • cites [6] Naj, A.C. et al. Effects of multiple genetic loci on age at onset in late-onset Alzheimer disease: a genome-wide association study. JAMA Neurol. 71, 1394–1404 (2014). source
    • cites [10] Thambisetty, M., An, Y. & Tanaka, T. Alzheimer's disease risk genes and the age-at-onset phenotype. Neurobiol. Aging 34, 2696 e1–2696.e5 (2013). source

      The Discussion (page unavailable) discusses APOE ε4 in relation to cerebral blood flow and Alzheimer’s disease risk, not age at onset (AAO). Searches for PICALM, BIN1, and APOE associations with age at onset found no passage in our copy addressing the attributed claim. (LLM, conf=0.76)

      Experimental — accuracy not yet measured
    • cites [11] Jones, E.L. et al. Evidence that PICALM affects age at onset of Alzheimer's dementia in Down syndrome. Neurobiol. Aging 34, 2441 e1–2441.e5 (2013). source

      The Results (page unavailable) report an association between PICALM variants and age at onset of Alzheimer’s dementia in people with Down syndrome. The Introduction lists BIN1 as an Alzheimer’s disease risk gene, but the paper does not report a BIN1 association with age at onset. The APOE clause has separate citations and is not attributed to this source. (LLM, conf=0.88)

      Experimental — accuracy not yet measured

  • May combine two claims.

    Premisecitation

    rs1057233 changes the target sequence and binding of miR-569.

    “rs1057233 changes the target sequence and binding of miR-56933”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [33] Ward, L.D. & Kellis, M. HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants. Nucleic Acids Res. 40, D930–D934 (2012). source

      The Methods section describes predictions of regulatory motif changes, and the Usage section discusses a different SNP, rs9271055, affecting an Ets-family binding site. Searches for rs1057233 and miR-569 found no passage in our copy addressing their target sequence or binding. (LLM, conf=0.76)

      Experimental — accuracy not yet measured

  • Classified as probably not a substantial claim.

    Study design and conductcitation

    Cases received a diagnosis of dementia of the Alzheimer's type based on NINCDS-ADRDA criteria.

    “Cases were diagnosed with dementia of the Alzheimer’s type (DAT) according to the NINCDS-ADRDA20.”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [20] Chan, G. et al. CD33 modulates TREM2: convergence of Alzheimer loci. Nat. Neurosci. 18, 1556–1558 (2015). source

      The Online Methods describe ROS/MAP participants as cognitively normal at enrollment and receiving annual clinical evaluations, but do not state how Alzheimer’s dementia cases were diagnosed. Searches for NINCDS-ADRDA and dementia diagnosis found no passage specifying those criteria; the passages provide no page numbers. (LLM, conf=0.72)

      Experimental — accuracy not yet measured

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    Il34 and Csf1 are soluble factors that bind Csf1r and are necessary for microglial development and maintenance in vivo.

    “expression of Il34 and Csf1, soluble factors that bind to Csf1r and required for microglial development and maintenance in vivo49”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [49] Dagher, N.N. et al. Colony-stimulating factor 1 receptor inhibition prevents microglial plaque association and improves cognition in 3xTg-AD mice. J. Neuroinflammation 12, 139 (2015). source

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductcitation

    Monocyte eQTL findings in the Cardiogenics dataset were validated by querying statistics from Fairfax et al.

    “For additional monocyte eQTL analysis, we queried statistics from Fairfax et al.28 to validate findings in the Cardiogenics dataset.”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [28] Zhang, Y. et al. Purification and characterization of progenitor and mature human astrocytes reveals transcriptional and functional differences with mouse. Neuron 89, 37–53 (2016). source

      The Results section, “Validation of genes differentially expressed by human and mouse” (page unavailable), describes PCR and qPCR validation of astrocyte gene-expression findings, not monocyte eQTLs. Searches for Fairfax, Cardiogenics, and monocyte eQTL validation found no passage addressing the attributed claim. (LLM, conf=0.77)

      Experimental — accuracy not yet measured

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductcitation

    CSF collection followed a standardized protocol across all studies.

    “CSF in all studies was collected in a standardized manner12,64–67.”
    Quote in the paperNot a substantial claim4 of 5 sources checked
    • cites [12] Cruchaga, C. et al. GWAS of cerebrospinal fluid tau levels identifies risk variants for Alzheimer's disease. Neuron 78, 256–268 (2013). source
    • cites [64] Peskind, E., Nordberg, A., Darreh-Shori, T. & Soininen, H. Safety of lumbar puncture procedures in patients with Alzheimer's disease. Curr. Alzheimer Res. 6, 290–292 (2009). source
    • cites [65] Grimmer, T. et al. Beta amyloid in Alzheimer's disease: increased deposition in brain is reflected in reduced concentration in cerebrospinal fluid. Biol. Psychiatry 65, 927–934 (2009). source
    • cites [66] Blennow, K., Hampel, H., Weiner, M. & Zetterberg, H. Cerebrospinal fluid and plasma biomarkers in Alzheimer disease. Nat. Rev. Neurol. 6, 131–144 (2010). source
    • cites [67] Willer, C.J., Li, Y. & Abecasis, G.R. METAL: fast and efficient meta-analysis of genomewide association scans. Bioinformatics 26, 2190–2191 (2010). source

      The Methods and Results sections describe METAL’s genome-wide association meta-analysis software, not CSF collection. Searches for standardized CSF collection and cerebrospinal fluid collection protocols found no relevant passage in our copy. (LLM, conf=0.76)

      Experimental — accuracy not yet measured

  • May combine two claims.

    Findingown data

    rs7867518 near VLDLR showed the most significant association with CSF total tau but did not pass Bonferroni threshold.

    “a SNP adjacent to VLDLR, rs7867518, showed the most significant association with CSF total tau (P=3.02×10−3), but failed to pass the Bonferroni-corrected threshold.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    The protective rs1057233G allele is associated with higher CSF Aβ42 levels, and the risk rs1057233A allele with lower CSF Aβ42 levels.

    “the protective rs1057233G allele was associated with higher CSF Aβ42 levels and the risk rs1057233A allele was associated with lower CSF Aβ42 levels.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    At all suggestive loci, AD risk-increasing alleles were associated with hazard ratio above 1 and earlier AAO, while risk-decreasing alleles were associated with hazard ratio below 1 and later AAO.

    “The direction of effects were concordant with the previous IGAP GWAS logistic regression analysis for AD risk1 at all suggestive loci: AD risk-increasing alleles were all associated with a hazard ratio above 1 and earlier AAO, whereas AD risk-decreasing alleles were all associated with a hazard ratio below 1 and later AAO”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingown data

    The rs1057233G allele is associated with lower MYBPC3 expression in monocytes and macrophages.

    “This allele was also associated with lower expression of MYBPC3 (monocytes: P=5.58×10−23; macrophages: P=4.99×10−51)”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    GTEx analysis identified 50 unique associated SNP-gene pairs across 44 tissues, including 11 in brain regions.

    “Further analysis using the GTEx dataset24 identified 50 unique, associated snp-gene pairs across 44 tissues, including 11 snp-gene pairs in various brain regions”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Schizophrenia heritability is not enriched in hematopoietic cells but is significantly enriched in brain.

    “In contrast schizophrenia (SCZ) heritability was not enriched in hematopoietic cells (1.24 fold enrichment, P=0.53, as measured by summary statistics from the Psychiatric Genomics Consortium [PGC] GWAS26) but was significantly enriched in brain (18.61 fold enrichment, P=1.38×10−4 in fetal brain promoters/H3K4me3”
    Quote in the paperSubstantial claim

  • The quote only partly states this claim.

    Findingown data

    The genome-wide survival analysis of 14,406 AD cases and 25,849 controls identified eight previously reported AD risk loci associated with age at onset.

    “A genome-wide survival analysis of 14,406 Alzheimer’s disease (AD) cases and 25,849 controls identified eight previously reported AD risk loci and fourteen novel loci associated with age at onset.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    rs1057233 and tagging SNPs are associated with AD risk and survival, and CSF Aβ42.

    “Overall, rs1057233 and tagging SNPs are associated with AD risk and survival, and CSF Aβ42.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    MS4A4A and MS4A6E showed evidence of colocalization only in monocytes, while SELL did not show evidence of colocalization.

    “MS4A4A and MS4A6E in the MS4A locus showed evidence of co-localization only in monocytes, while SELL did not show evidence of colocalization.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    PU.1 is bound to cis-regulatory elements of many AD-associated genes, including ABCA7, CD33, MS4A4A, MS4A6A, PILRA, PILRB, TREM2, TREML2, and TYROBP, as well as SPI1 itself, but notably not APOE.

    “Further examination of PU.1 binding peaks and chromatin marks/states in human monocytes confirmed that PU.1 is bound to cis-regulatory elements of many AD-associated genes, including ABCA7, CD33, MS4A4A, MS4A6A, PILRA, PILRB, TREM2, TREML2, and TYROBP (as well as SPI1 itself, but notably not APOE)”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Findingnone given

    MYBPC3/Mybpc3 is either not expressed or expressed at low levels in human and mouse microglia.

    “However, MYBPC3/Mybpc3 (a myosin binding protein expressed at high levels in cardiac muscle cells) is either not expressed or expressed at low levels in human and mouse microglia, respectively.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    SPI1 is the strongest and most consistent colocalization target at the SPI1/CELF1 locus, and the only gene where AD survival and gene expression association signals are likely driven by the same causal genetic variant in both monocytes and macrophages.

    “These analyses (Supplementary Table 8) highlighted SPI1 at the SPI1/CELF1 locus as the strongest and most consistent colocalization target, and the only gene where the AD survival and gene expression association signals are likely (posterior probability ≥ 0.8) driven by the same causal genetic variant, in both monocytes and macrophages (PP.H4.abf of 0.85 and 0.83, respectively).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    In the survival analysis, rs10838725 showed weak association whereas rs1057233 showed the strongest association at the SPI1/CELF1 locus.

    “In our survival analysis, however, rs10838725 showed weak association (P=0.12, HR=1.02, 95% CI=0.99–1.05) whereas rs1057233, located in the 3′UTR of a neighboring gene, SPI1, showed the strongest association (Table 1, P=5.4×10−6).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    rs1057233 remained significantly associated with AD after adjusting for rs10838725, whereas rs10838725 showed no evidence of association after adjusting for rs1057233.

    “we found that rs1057233 remained significantly associated with AD after adjusting for rs10838725 (P=3.2×10−4), whereas rs10838725 showed no evidence of association after adjusting for rs1057233 (P=0.66).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The most significantly AAOS-associated SNP at the MS4A locus, rs7930318, shows a protective effect (HR = 0.93, 95% CI = 0.90-.95), consistent with the previous IGAP GWAS logistic regression analysis for AD risk (OR = 0.90, 95% CI = 0.87-.93).

    “The most significantly AAOS-associated SNP at this locus, rs7930318, shows a protective effect (HR = 0.93, 95% CI = 0.90–.95) in the survival analysis, consistent with the previous IGAP GWAS logistic regression analysis for AD risk (OR = 0.90, 95% CI = 0.87–.93).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    rs7867518 at the VLDLR locus shows suggestive associations with both AAOS and CSF tau.

    “In particular, rs7867518 at the VLDLR locus shows suggestive associations with both AAOS (P=9.1×10−6) and CSF tau (P=3.03×10−3).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    MYBPC3 and MS4A6A also showed evidence of colocalization in both myeloid cell types, albeit not surviving posterior probability cutoff in one.

    “MYBPC3 in the SPI1/CELF1 locus and MS4A6A in the MS4A locus also showed evidence of colocalization in both myeloid cell types albeit not surviving posterior probability cutoff in one of them.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Knock-down of PU.1 expression reduced engulfment of zymosan, whereas overexpression increased engulfment.

    “Knock-down of PU.1 expression reduced engulfment of zymosan, whereas overexpression of PU.1 increased engulfment of zymosan, a Toll-like receptor 2 (TLR2) agonist that mimics fungal pathogens.”
    Quote in the paperSubstantial claim
    • Rests on an assumption: Mouse BV2 microglial cells are a valid model for human microglial function relevant to AD.
    • Rests on an assumption: Zymosan phagocytosis is a valid proxy for microglial phagocytic activity relevant to AD pathogenesis.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingown data

    rs1057233 is associated with MYBPC3 expression in the replication dataset.

    “We found strong evidence for the association between rs1057233 and SPI1 expression (P=6.39×10−102) as well as MYBPC3 expression (P=5.95×10−33”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    AD heritability is significantly enriched in the PU.1 cistrome in both monocytes and macrophages, but not SCZ heritability.

    “We found a significant enrichment of AD heritability in both monocytes (47.58 fold enrichment, P=6.94×10−3) and macrophages (53.88 fold enrichment, P=1.65×10−3), but not SCZ heritability”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The minor allele of all these SNPs showed protective effects in AD risk and survival analyses and lower expression of associated genes.

    “Interestingly, the minor allele of all of these SNPs showed protective effects in both AD risk and survival analyses, as well as lower expression of the associated genes.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingcitation

    Among 112 AD-associated genes, 75 had evidence of expression in human brain microglial cells, and 60 of those also had evidence of association with PU.1 binding sites in human blood myeloid cells.

    “Among these genes, 75 had evidence of gene expression in human brain microglial cells, 60 of which also had evidence of association with PU.1 binding sites in human blood myeloid cells35”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [35] Steinberg, S. et al. Loss-of-function variants in ABCA7 confer risk of Alzheimer's disease. Nat. Genet. 47, 445–447 (2015). source

  • May combine two claims.

    Findingown data

    The protective allele at the MS4A locus is associated with lower expression of MS4A4A and MS4A6A in human myeloid cells, and lower Spi1 expression in BV2 cells led to lower expression of Ms4a4a and Ms4a6d.

    “Our genetic analyses show that the protective allele at the MS4A locus is associated with lower expression of MS4A4A and MS4A6A in human myeloid cells, and the BV2 experiment demonstrated that lower expression of Spi1 (which is protective in humans) led to lower expression of Ms4a4a and Ms4a6d (mouse ortholog of MS4A6A), which are also associated with reduced AD risk in humans.”
    Quote in the paperSubstantial claim
    • Rests on an assumption: Mouse BV2 microglial cells are a valid model for human microglial function relevant to AD.
    • Rests on an assumption: Mouse orthologs of human AD risk genes have conserved regulation by Spi1.

  • May combine two claims.

    Findingown data

    Phagocytic activity is augmented in BV2 cells overexpressing PU.1, while knock-down of PU.1 results in decreased phagocytic activity.

    “Analysis of zymosan uptake by flow cytometry revealed that phagocytic activity is augmented in BV2 cells overexpressing PU.1 (Fig. 3a), while knock-down of PU.1 resulted in decreased phagocytic activity (Fig. 3a).”
    Quote in the paperSubstantial claim
    • Rests on an assumption: Mouse BV2 microglial cells are a valid model for human microglial function relevant to AD.
    • Rests on an assumption: Zymosan phagocytosis is a valid proxy for microglial phagocytic activity relevant to AD pathogenesis.

  • May combine two claims.

    Findingown data

    After knock-down of Spi1 in BV2 cells, expression of Cd33, Tyrobp, Ms4a4a, and Ms4a6d decreased, and expression of Apoe and Clu/ApoJ increased.

    “After knock-down of Spi1 in BV2 cells, expression of Cd33, Tyrobp, Ms4a4a and Ms4a6d decreased and expression of Apoe and Clu/ApoJ increased (Fig. 4a, 4c).”
    Quote in the paperSubstantial claim
    • Rests on an assumption: Mouse BV2 microglial cells are a valid model for human microglial function relevant to AD.
    • Rests on an assumption: Mouse orthologs of human AD risk genes have conserved regulation by Spi1.

  • May combine two claims.

    Findingcitation

    The minor allele of rs1057233 (G) is suggestively associated with lower AD risk, later AAO, and significantly associated with higher CSF Aβ42.

    “Notably, the minor allele of rs1057233 (G) is suggestively associated with lower AD risk (P=5.4×10−6, 5.9×10−7 in IGAP stage I, stage I and II combined, respectively)1, later AAO (P=8.4×10−6) and significantly associated with higher CSF Aβ42 (P=4.11×10−4)”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingown data

    Joint analyses and meta-analyses yielded no major differences.

    “No major differences were found between the joint-analyses and the meta-analyses.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Knockdown of Spi1 increased Il34 and Csf1 expression and decreased Csf1r expression.

    “expression of Il34 and Csf1, soluble factors that bind to Csf1r and required for microglial development and maintenance in vivo49, were elevated after knock-down of Spi1, while expression of Csf1r was reduced (Fig. 4a, 4c).”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim.

    Findingown data

    Among the 751 suggestive SNPs (P < 1×10−5), standard errors and confidence intervals were lower as the number of cohorts showing consistent directionality of effect increased.

    “Of the 751 suggestive SNPs (P < 1×10−5), we found these SNPs to show lower standard errors and confidence intervals with the increasing number of cohorts showing consistent directionalities of effect.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingown data

    The average standard error for SNPs showing 1 to 7 consistent directionalities ranged from 0.171 to 0.01795.

    “the average standard error for SNPs showing 1 to 7 consistent directionalities ranges from 0.171, 0.109, 0.0744, 0.0346, 0.0234, 0.0173 to 0.01795 (Supplementary Fig. 1b).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationcitation

    Several AD-associated genes are involved in phagocytic clearance of pathogens or host-derived cellular material, suggesting a strong link between perturbation of microglial phagocytosis and AD pathogenesis.

    “Interestingly, several AD-associated genes (e.g., CD33, TYROBP, TREM2, TREML2, CR1, ABCA7, APOE, CLU/APOJ) have been shown to be involved in the phagocytic clearance of pathogens or host-derived cellular material (e.g., β-amyloid, apoptotic cells, myelin debris, lipoproteins, etc.), suggesting a strong link between perturbation of microglial phagocytosis and AD pathogenesis.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationown data

    Low MYBPC3 expression in human myeloid cells is possibly due to leaky transcription driven by the adjacent highly expressed SPI1 gene.

    “suggesting that low levels of MYBPC3 expression in human myeloid cells are possibly due to leaky transcription driven by the adjacent highly expressed SPI1 gene.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    PU.1 expression is dynamically and tightly controlled during haematopoiesis to direct specification of CD34+ hematopoietic stem and progenitor cells toward myeloid and B-lymphoid lineage.

    “In particular, PU.1 expression is dynamically and tightly controlled during haematopoiesis to direct the specification of CD34+ hematopoietic stem and progenitor cells toward the myeloid and B-lymphoid lineage by progressively partitioning into CD14+ monocytes/macrophages, CD15+ neutrophils, and CD19+ B cells46”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [46] Smith, A.M. et al. The transcription factor PU.1 is critical for viability and function of human brain microglia. Glia 61, 929–942 (2013). source

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    The VLDLR-5-repeat allele was found to be associated with dementia.

    “Additionally, the VLDLR-5-repeat allele was found to be associated with dementia38.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [38] Bajari, T.M., Strasser, V., Nimpf, J. & Schneider, W.J. A model for modulation of leptin activity by association with clusterin. FASEB J. 17, 1505–1507 (2003). source

  • May combine two claims.

    Interpretationown data

    rs1057233 and its tagging SNPs likely represent the underlying disease locus and may modulate AD risk through variation in SPI1 expression.

    “Thus, rs1057233 and its tagging SNPs likely represent the underlying disease locus and may modulate AD risk through variation in SPI1 expression.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Study design and conductown data

    The western blotting used two independent experiments, without randomization of sample processing, and the researcher was not blinded to sample identity.

    “Two independent experiments were performed without randomization of sample processing, n = 2. Researcher was not blinded to the samples identification.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Study design and conductown data

    Every AD case satisfied criteria for probable AD by NINCDS-ADRDA or DSM-IV, or definite AD by CERAD.

    “All AD cases met criteria for either probable (NINCDS-ADRDA, DSM-IV) or definite (CERAD) AD.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Study design and conductnone given

    Controls were assessed with the same criteria and had no cognitive impairment symptoms.

    “Control individuals were evaluated using the same criteria and showed no symptoms of cognitive impairment.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Study design and conductnone given

    All studies obtained written consent from participants or their proxies, and their protocols received approval from the relevant institutional review boards.

    “For all studies, written informed consent was obtained from study participants or, for those with substantial cognitive impairment, from a caregiver, legal guardian, or other proxy, and the study protocols for all populations were reviewed and approved by the appropriate Institutional review boards.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductown data

    Genomic inflation was low (λ = 1.026).

    “which showed little evidence of genomic inflation (λ = 1.026).”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Study design and conductnone given

    Sex, site and the first three principal components were included in all regression models to control for their effects.

    “We incorporated sex, site and the first three principal components from EIGENSTRAT30 in all our regression models to control for their effects.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Study design and conductown data

    At a minor allele frequency of 0.15, power was about 80% for odds ratios above 1.23 or below 0.81; at 0.3, about 80% for odds ratios above 1.18 or below 0.85.

    “For variants with a MAF of 0.15, we would have approximately 80% power to detect effects for OR > 1.23 or < 0.81; for variants with a MAF of 0.3, we would have approximately 80% power to detect effects for OR > 1.18 (or < 0.85).”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    Alpha was adjusted to 5×10−8.

    “Alpha was adjusted to 5×10−8.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductown data

    Routine testing showed that the BV2 cell line was negative for mycoplasma contamination.

    “Routine testing of cell lines using MycoAlert PLUS mycoplasma detection kit (Lonza) showed that BV2 cells were negative for mycoplasma contamination.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim. May combine two claims.

    Study design and conductnone given

    Elderly controls underwent dementia screening with MMSE or ADAS-cog and were either free of dementia on neuropathology or had a Braak score no higher than 2.5.

    “All elderly controls were screened for dementia using the MMSE or ADAS-cog, were determined to be free from dementia at neuropathological examination or had a Braak score of 2.5 or lower.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductown data

    The imputed GERAD data were analyzed by logistic regression with covariates for country, sex, age, and three principal components.

    “The imputed data was then analysed using logistic regression including covariates for country of origin, gender, age and 3 principal components obtained with EIGENSTRAT software based on individual genotypes for the GERAD study participants.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    Prior studies have shown that the relationship between CSF Aβ42 levels and age differs between individuals under 45 years and those over 45 years, which is why individuals under 45 were removed from the CSF analysis.

    “individuals under age 45 years were removed because prior studies have demonstrated that the relationship between CSF Aβ42 levels and age appears to differ in individuals below 45 years vs. those above 45 years69.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [69] Purcell, S. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559–575 (2007). source

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Study design and conductnone given

    Every participant gave written informed consent, and the ethics committee approved the consent procedure.

    “All participants provided written informed consent and the ethics committee approved the informed consent procedure (IRB ID #: 201105364).”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductown data

    The null distribution of the Wald test P values for the eQTL analysis was estimated by rerunning the analysis on a permuted dataset in which expression sample identifiers were permuted.

    “The distribution of the Wald test P values under the null hypothesis of no correlation between genotype and gene expression was estimated by rerunning the same analysis on a null dataset obtained by permuting the expression samples identifiers.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Study design and conductown data

    The proportional hazards assumption of the Cox model was validated by the Schoenfeld test in the 22 prioritized SNPs, and none of the SNPs had a Schoenfeld P value below 0.035 in any of the 7 cohorts.

    “We validated the assumption of proportional hazards assumed by the Cox model by conducting the Schoenfeld test in the 22 prioritized SNPs. None of the SNPs has a Schoenfeld P value, which is the P value for Pearson product-moment correlation between the scaled Schoenfeld residuals and time, lower than 0.035 (multiple test correction threshold = 0.00227) in any of the 7 cohorts.”
    Quote in the paperSubstantial claim
    • The authors state this as an assumption: The Cox model's proportional hazards assumption holds.

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Study design and conductnone given

    The quantitative PCR used four independent experiments, without randomization of sample processing, and the researcher was not blinded to sample identity.

    “Four independent experiments were performed without randomization of sample processing, n = 4. Researcher was not blinded to the sample identity.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    Potentially related individuals were excluded so that all remaining individuals had a kinship coefficient below 0.05.

    “We excluded potentially related individuals so that all remaining individuals have kinship coefficient below 0.05.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    In the ADGC, GERAD, CHARGE and CSF datasets, SNPs that failed Hardy-Weinberg equilibrium in controls at a P value threshold of 1×10−6 were removed.

    “In the ADGC, GERAD, CHARGE, and CSF datasets, we then removed SNPs that failed the Hardy-Weinberg equilibrium in controls calculated based on the imputed best-guess genotypes using a P value threshold of 1×10−6.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    Within each study, biomarker assays used internal standards and controls to ensure consistency and reliability.

    “Biomarker measurements within each study were conducted using internal standards and controls to achieve consistency and reliability.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    In a 3xTg-AD mouse model, blocking Csf1r lowered the count of microglia linked to β-amyloid plaques and enhanced cognition.

    “inhibition of Csf1r in a 3xTg-AD mouse model led to a reduction in the number of microglia associated with β-amyloid plaques and improved cognition50.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [50] Alpérovitch, A. et al.; 3C Study Group. Vascular factors and risk of dementia: design of the Three-City Study and baseline characteristics of the study population. Neuroepidemiology 22, 316–325 (2003). source

  • May combine two claims.

    Interpretationown data

    Lower Spi1 expression might reduce the pro-inflammatory reaction of microglial cells and thereby improve disease outcomes.

    “suggesting that decreased Spi1 expression may blunt the pro-inflammatory response of microglial cells to improve disease outcomes.”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim. May combine two claims.

    Study design and conductnone given

    Individuals with more than 5% missing genotype rates, a discrepancy between reported and genetically estimated sex, or evidence of non-European ancestry based on principal component analysis were excluded.

    “we excluded individuals who had > 5% missing genotype rates, who showed a discrepancy between reported sex and sex estimated on the basis of genetic data, or who showed evidence of non-European ancestry based on principal component analysis using PLINK1.970.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Study design and conductown data

    The phagocytosis assay used three independent experiments with two technical replicates, without randomization of sample processing, and the researcher was not blinded to sample identity.

    “Three independent experiments were performed with two technical replicates without randomization of sample processing, n = 3. Researcher was not blinded to the samples identification.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Study design and conductown data

    After quality control, the imputed ADGC sample included 8,617 AD cases and 9,765 controls.

    “The imputed ADGC sample that passed quality control procedures comprised of 8,617 AD cases and 9,765 control subjects”
    Quote in the paperSubstantial claim
75 of 75

  • The paper relies on this without support.

    Mouse BV2 microglial cells are a valid model for human microglial function relevant to AD.

    “We modulated levels of PU.1 by Spi1 cDNA overexpression or shRNA knock-down in BV2 mouse microglial cells”
    “To validate these bioinformatic analyses, we show that experimentally altered PU.1 levels are correlated with phagocytic activity of mouse microglial cells”

  • The paper relies on this without support.

    Cis-eQTL effects observed in monocytes and macrophages reflect regulation in brain microglia relevant to AD.

    “we analyzed cis-eQTL effects of the AAOS-associated SNPs and their tagging SNPs in human cis-eQTL datasets composed of 738 monocyte and 593 macrophage samples from the Cardiogenics consortium27”
    “SPI1, MS4A4A, MS4A6A, and SELL are specifically expressed in microglia based on RNA-Seq data29–31”

  • The paper relies on this without support.

    Zymosan phagocytosis is a valid proxy for microglial phagocytic activity relevant to AD pathogenesis.

    “used zymosan bioparticles labeled with pHrodo (a pH-sensitive dye that emits a fluorescent signal when internalized in acidic vesicles during phagocytosis) to measure pathogen engulfment”
    “zymosan, a Toll-like receptor 2 (TLR2) agonist that mimics fungal pathogens”

  • The paper relies on this without support.

    The IGAP GWAS summary statistics and Cardiogenics eQTL datasets are from comparable populations and suitable for integration.

    “we used 14,406 AD case and 25,849 control samples from the IGAP consortium”
    “human cis-eQTL datasets composed of 738 monocyte and 593 macrophage samples from the Cardiogenics consortium27”

  • The paper relies on this without support.

    Mouse orthologs of human AD risk genes have conserved regulation by Spi1.

    “expression of mouse orthologs of many AD risk genes”
    “Ms4a6d (mouse ortholog of MS4A6A)”

  • The paper relies on this without support.

    Ccl2 and Cxcl2 correspond to MCP1 and MIP2α, proteins that draw circulating monocytes and neutrophils into the brain and drive neuroinflammation.

    “which are MCP1 and MIP2α proteins that help recruitcirculating monocytes and neutrophils to the brain to promote neuroinflammation.”

  • The paper relies on this without support.

    SPI1 codes for PU.1, a transcription factor present in microglia and other myeloid cells that directly controls other AD-associated genes in those cells.

    “SPI1 encodes PU.1, a transcription factor expressed in microglia and other myeloid cells that directly regulates other AD-associated genes expressed in these cell types.”

  • The authors state this as an assumption.

    The Cox model's log-linearity assumption holds.

    “The model assumes log-linearity and proportional hazards.”

  • The authors state this as an assumption.

    The Cox model's proportional hazards assumption holds.

    “The model assumes log-linearity and proportional hazards.”

  • The authors state this as an assumption.

    The effect of SNP dosage on the hazard is additive.

    “We conducted a genome-wide Cox proportional hazards regression72 assuming an additive effect from SNP dosage.”
10 of 10

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • Mybpc3 upregulation serves as a positive indicator of Spi1 downregulation.

    “which serves as a positive indicator of Spi1 downregulation.”

    From Lymphoid gene expression supports neuroprotective microglia function (2025) · cites this paper as [24]

    The Results section on cis-eQTL associations reports a positive correlation between MYBPC3 and SPI1 expression in monocytes and macrophages. It also reports that the same allele is associated with lower expression of both genes. Thus, the paper does not support MYBPC3 upregulation as an indicator of SPI1 downregulation; its reported association runs in the opposite direction. Page numbers are unavailable in our copy. (LLM, conf=0.90)

    Checked by a reasoning model — may be wrong.

    Experimental — accuracy not yet measured

  • The rs1057233 SNP in SPI1 is a protective allele (OR=0.93, 95% CI=0.91-0.97) associated with lower SPI1 mRNA levels in peripheral immune cells.

    “This study identified a specific variant within the SPI1 gene (rs1057233 SNP) as a protective allele (odds ratio [OR] = 0.93, 95% confidence interval [CI] = 0.91–0.97) and found it is associated with lower SPI1 mRNA levels in peripheral immune cells (monocytes and macrophages)7.”

    From Deletion of SPI1 in microglia exacerbates amyloid pathology by impairing microglial response in Alzheimer’s disease models (2026) · cites this paper as [7]

    The Results section (Cis-eQTL associations and colocalization analysis; page unavailable) identifies the protective rs1057233G allele and reports its association with lower SPI1 expression in monocytes and macrophages. The passages retrieved for the stated odds ratio and confidence interval do not establish OR = 0.93 or 95% CI = 0.91–0.97, so those figures are not verified by our copy. (LLM, conf=0.84)

    Experimental — accuracy not yet measured

  • AD SNP heritability showed its strongest enrichment in microglial regulatory elements, especially microglial enhancers.

    “In contrast, AD SNP heritability was most highly enriched in microglia regulatory elements (Fig. 1D), specifically microglia enhancers (18-23).”

    From Brain cell type–specific enhancer–promoter interactome maps and disease <b>-</b> risk association (2019) · cites this paper as [20]

    The Results section (page not available) reports enrichment of AD heritability in myeloid and B-lymphoid cells, including monocyte enhancers. It does not report that microglial regulatory elements were tested or that microglial enhancers showed the strongest enrichment; the Discussion instead calls myeloid cells the top candidate cell types. (LLM, conf=0.84)

    Experimental — accuracy not yet measured

  • SPI1/PU.1 is a master regulator of microglial development and homeostasis and of several Alzheimer's disease genetic risk genes, and small changes in PU.1 expression can significantly affect cell function.

    “SPI1/PU.1 is a master regulator of microglial development and homeostasis and the expression of several AD genetic risk genes, e.g. ABCA7, CD33, MS4A4A, MS4A6A, TREM2, APOE and CLU, and small changes in PU.1 expression can significantly affect cell function (Huang et al., 2017; Satoh et al., 2014).”

    From Alzheimer's-associated PU.1 expression levels regulate microglial inflammatory response (2021) · cites this paper as Huang et al., 2017

    The Results section on the PU.1 cistrome reports binding at several AD-associated genes, and its functional experiments show that altering PU.1 changes gene expression and phagocytosis in mouse microglial cells. The Discussion describes PU.1 as required for myeloid-cell development and function, but the paper does not establish that *small* expression changes significantly affect cell function or specifically characterize PU.1 as a master regulator of microglial homeostasis. (LLM, conf=0.85)

    Experimental — accuracy not yet measured

  • The SPI1 locus is one of the few AD risk loci for which a mechanism of action based on modulation of gene expression by common disease risk alleles has been delineated.

    “The SPI1 locus is one of the few AD risk loci for which a mechanism of action based on the modulation of gene expression by common disease risk alleles has been delineated (Huang et al., 2017).”

    From Alzheimer's-associated PU.1 expression levels regulate microglial inflammatory response (2021) · cites this paper as Huang et al., 2017

    The Results (Cis-eQTL associations and colocalization analysis; page unavailable) link a protective allele to lower SPI1 expression in myeloid cells, and the Discussion proposes expression changes as a route by which the locus may affect AD risk. But the Discussion calls this a hypothesis, and the Results (Conditional and SMR analysis; page unavailable) say the functional variant has not been definitively identified. Saying the mechanism has been delineated is therefore stronger than the paper's conclusion. (LLM, conf=0.84)

    Experimental — accuracy not yet measured

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

Each contradiction between two passages listed here was confirmed by an independent check.

  • Two P values are given for the rs1057233 CSF Aβ42 association

    Minor

    The results report P=8.24×10−4, but the discussion reports P=4.11×10−4 for the same SNP-biomarker association. The text does not distinguish these as different analyses.

  • Two P values are given for the rs1057233 survival association

    Minor

    The survival results give P=5.4×10−6 for rs1057233, while the discussion gives P=8.4×10−6 for its association with later onset.

  • CHS exclusion categories fall short of the reported total

    Minor

    The listed reasons account for 1,616 people, not the reported 1,908. The stated rule of listing only one reason per person does not explain the 292-person gap.

    Reported 1908 · recomputed 1616

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Authors
The International Genomics of Alzheimer's Project, Huang, K.-L., Initiative, T. A. D. N., Marcora, E., Pimenova, A. A., Di Narzo, A. F., Kapoor, M., Jin, S. C., Harari, O., Bertelsen, S., Fairfax, B. P., Czajkowski, J., Chouraki, V., Grenier-Boley, B., Bellenguez, C., Deming, Y., McKenzie, A., Raj, T., Renton, A. E., Budde, J., Smith, A., Fitzpatrick, A., Bis, J. C., DeStefano, A., Adams, H. H. H., Ikram, M. A., van der Lee, S., Del-Aguila, J. L., Fernandez, M. V., Ibañez, L., Sims, R., Escott-Price, V., Mayeux, R., Haines, J. L., Farrer, L. A., Pericak-Vance, M. A., Lambert, J. C., van Duijn, C., Launer, L., Seshadri, S., Williams, J., Amouyel, P., Schellenberg, G. D., Zhang, B., Borecki, I., Kauwe, J. S. K., Cruchaga, C., Hao, K., & Goate, A. M.
Affiliations
  • Washington University in St. Louis (US)
  • Icahn School of Medicine at Mount Sinai (US)
  • Yale University (US)
  • Centre for Human Genetics (GB)
  • Boston University (US)
  • Inserm (FR)
  • University of Iceland (IS)
  • University of Washington (US)
  • Erasmus MC (NL)
  • Columbia University Irving Medical Center (US)
  • University of Miami (US)
  • National Institutes of Health (US)
  • Cardiff University (GB)
  • Brigham Young University (US)
Corresponding author
Goate, Alison M
ORCID
Venue
Nature Neuroscience
Publisher
Springer Science and Business Media LLC
Published
2017-06-19
Volume
20
Issue
8
Pages
1052-1061
ISSN
  • 1097-6256 (ISSN-L)
  • 1546-1726
DOI
10.1038/nn.4587
PMC
PMC5759334
OpenAlex
W2634812549
Cited by
423
References
85
Citations by year
2026: 30 · 2025: 45 · 2024: 33 · 2023: 37 · 2022: 56 · 2021: 58 · 2020: 55 · 2019: 47 · 2018: 48 · 2017: 14
FWCI
33.15
Type
journal article
Language
en
Open access
Licence
www.springer.com/tdm (tdm)
Locations
  • Nature Neuroscience (publishedVersion)
  • PubMed (publishedVersion)
  • EUR Research Repository (Erasmus University Rotterdam) (publishedVersion)
  • ORCA Online Research @Cardiff (Cardiff University) (acceptedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
  • EUR Research Repository (Erasmus University Rotterdam) (submittedVersion)
  • RePub (Erasmus University Rotterdam) (submittedVersion, other-oa)
Funders
  • Wellcome Trust (201488/Z/16/Z)
  • National Institute for Health and Care Research (CL-2012-13-004)
  • Agence Nationale de la Recherche (ANR-11-LABX-0009)
  • National Institutes of Health (5u01ag024904-10, Z99 AG999999)
  • Medical Research Council (MR/L023784/2, MR/P005748/1, MR/L010305/1, MC_PC_17112, MR/L023784/1)
  • National Institute on Aging (U01-AG-024904, RF1AG044546, U01AG049505, RF1AG053303, P50AG005138, R01AG035083, U01AG032984, R01AG044546, P50AG005681, P01AG003991, U01AG049508, R01AG033193, U01AG052411, RF1AG054011, U19AG024904, P01AG026276, U24AG021886)
  • National Institute on Drug Abuse (R25DA027995)
Topics
  • Health Sciences › Medicine › Physiology › Alzheimer's disease research and treatments
  • Health Sciences › Medicine › Psychiatry and Mental health › Dementia and Cognitive Impairment Research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
Keywords
Alzheimer's disease, PU.1, myeloid cells, monocytes, macrophages, microglia, age of onset, genetic susceptibility loci, CELF1, transcription factor binding, CD33, MS4A4A, MS4A6A, TYROBP, phagocytosis, heritability, haplotypes
MeSH terms
Proto-Oncogene Protein Spi-1, Alleles, Alzheimer Disease, Animals, Female, Haplotypes, Humans, Male, Proto-Oncogene Proteins, Risk Factors, Transcription Factors, Trans-Activators, Linkage Disequilibrium, Genetic Predisposition to Disease, Polymorphism, Single Nucleotide, Mice, Genome-Wide Association Study

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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.

Claims read by deepseek-v4.1-flash under definition version 3 (extract-v3) on 2026-10-01.

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