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Cited by 1,150Neuroinflammation and Neurodegeneration MechanismsAlzheimer's disease research and treatmentsSingle-cell and spatial transcriptomics

Human and mouse single-nucleus transcriptomics reveal TREM2-dependent and TREM2-independent cellular responses in Alzheimer’s disease

Open access
Zhou, Yingyue, Song, Wilbur M., Andhey, Prabhakar S., Swain, Amanda, Levy, Tyler, Miller, Kelly R., Poliani, Pietro L., Cominelli, Manuela +17 more·2020·Nature Medicine
DOI 10.1038/s41591-019-0695-9PMC PMC6980793
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Abstract

Glia have been implicated in Alzheimer’s disease (AD) pathogenesis. Variants of the microglia receptor triggering receptor expressed on myeloid cells 2 (TREM2) increase AD risk, and activation of disease-associated microglia (DAM) is dependent on TREM2 in mouse models of AD. We surveyed gene-expression changes associated with AD pathology and TREM2 in 5XFAD mice and in human AD by single-nucleus RNA sequencing. We confirmed the presence of Trem2-dependent DAM and identified a previously undiscovered Serpina3n+C4b+ reactive oligodendrocyte population in mice. Interestingly, remarkably different glial phenotypes were evident in human AD. Microglia signature was reminiscent of IRF8-driven reactive microglia in peripheral-nerve injury. Oligodendrocyte signatures suggested impaired axonal myelination and metabolic adaptation to neuronal degeneration. Astrocyte profiles indicated weakened metabolic coordination with neurons. Notably, the reactive phenotype of microglia was less evident in TREM2-R47H and TREM2-R62H carriers than in non-carriers, demonstrating a TREM2 requirement in both mouse and human AD, despite the marked species-specific differences. Single-nucleus RNA sequencing in a mouse model of Aβ accumulation and postmortem brain tissue from people with Alzheimer’s disease reveals substantial species-specific differences in transcriptional signatures, but both point to the contribution of glia and the importance of TREM2.

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Crossref · 10.1038/s41591-019-0695-9

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Claims the paper makes

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  • Findingown data

    The microglial cluster was larger in 5XFAD cortex than in Trem2-deficient 5XFAD and non-5XFAD cortices.

    “Notably, the microglia cluster was much larger in the 5XFAD cortex than in the Trem2−/− 5XFAD and non-5XFAD cortices”
    Quote in the paperSubstantial claim
  • Findingown data

    The study confirmed that Trem2-dependent disease-associated microglia are present in 5XFAD mice.

    “We confirmed the presence of Trem2-dependent DAM”
    Quote in the paperSubstantial claim
  • Findingown data

    The reactive microglial phenotype is less evident in TREM2 R47H and R62H carriers than in non-carriers.

    “the reactive phenotype of microglia was less palpable in TREM2 R47H and R62H carriers than in non-carriers”
    Quote in the paperSubstantial claim
  • Findingown data

    The Trem2-deficient 5XFAD cortex contained a neuronal cluster with fewer UMIs but relatively high Pam expression.

    “the Trem2−/− 5XFAD cortex contained a neuronal cluster with significantly fewer UMIs but relatively high expression of peptidylglycine alpha-amidating monooxygenase (Pam)”
    Quote in the paperNot a substantial claim
  • Findingown data

    At 15 months, the difference between microglial clusters in 5XFAD and Trem2-deficient 5XFAD cortices was minimal.

    “the difference between microglial clusters in 5XFAD and Trem2−/− 5XFAD cortices was minimal at this stage”
    Quote in the paperSubstantial claim
  • May combine two claims. 53
  • Classified as probably not a substantial claim. 55
  • The quote only partly states this claim. 1

  • May combine two claims.

    Findingown data

    The human Alzheimer's disease-associated microglial signature was present in aged controls and highly upregulated during disease.

    “this human AD-associated signature was present in aged controls, and highly upregulated during disease.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The proportion of astrocytes was increased in Alzheimer's disease compared with controls, indicating reactive astrocytosis.

    “the proportion of astrocytes was increased in AD compared to control samples, indicating reactive astrocytosis”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Other disease-associated microglia homologues were similarly expressed, not detected, or downregulated in human Alzheimer's disease microglia.

    “Other DAM gene homologues were either similarly expressed in AD and control samples (TYROBP), not detected (CST7, GPNMB, LPL), or even downregulated (SPP1) in human AD microglia”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Microglial sub-cluster 1 was highly represented in 5XFAD mice, less so in Trem2-deficient 5XFAD mice, and barely detectable in wild-type and Trem2-deficient mice.

    “sub-cluster 1 was highly represented in 5XFAD mice, less so in Trem2−/− 5XFAD mice and barely detectable in WT and Trem2−/− mice”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Adding C4b to amyloid beta 42 strongly accelerated aggregation; Serpina3n alone modestly promoted aggregation at high amyloid beta 42 concentrations and did not synergize with C4b.

    “We found that addition of C4b to Aβ42 peptides strongly accelerated aggregation of Aβ; Serpina3n alone modestly promoted aggregation at high Aβ42 concentrations and did not synergize with C4b”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Little colocalization of Serpina3n with astrocytes or amyloid beta plaques was detected.

    “We also detected little colocalization of Serpina3n with astrocytes (Extended Data Fig. 4j) and Aβ plaques”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    In human Alzheimer's disease microglia, homeostatic genes TMEM119, P2RY12, and CX3CR1 were notably upregulated compared with controls, along with higher IRF8.

    “In the microglia cluster, genes normally considered as ‘homeostatic” in mouse (TMEM119, P2RY12, CX3CR1) were, in fact, notably upregulated in AD compared to controls (Fig. 4c), along with higher expression of the transcription factor IRF8.”
    Quote in the paperSubstantial claim

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    Findingown data

    Oligodendrocyte precursor cells strongly upregulated C4b, with fold change and p-value similar to oligodendrocyte activation genes.

    “OPCs strongly upregulated C4b, with a fold change and p-value similar to oligodendrocyte activation genes”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Increased C4b and Serpina3n expression was partially dependent on Trem2 at 7 months but not at 15 months.

    “Increased expression of C4b and Serpina3n was partially dependent on Trem2 in 7-month-old (Extended Data Fig. 4a) but not in 15-month-old mice”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    In 5XFAD compared with wild-type microglia, disease-associated microglia genes were upregulated and homeostatic genes were downregulated.

    “DAM genes, including Cst7, Csf1, Apoe, Trem2, Lpl, Lilrb4a, MHC-I (H2-d1), MHC-II (Cd74), and various cathepsin genes were notably upregulated in 5XFAD compared to WT mice. Homeostatic genes, such as P2ry12, Selplg, Tmem119, and Cx3cr1 were downregulated.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Astrocytes upregulated Gfap and C4b, but to a lesser extent than oligodendrocytes.

    “Astrocytes upregulated Gfap and C4b, but to a lesser extent than did oligodendrocytes”
    Quote in the paperNot a substantial claim

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

    Findingown data

    Human snRNA-seq analyzed 66,311 nuclei with a median of 1,312 genes per nucleus.

    “We analyzed a total of 66,311 individual nuclei with a median of 1,312 genes per nucleus”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Overexpression of Irf8 in mouse microglia-like cultures upregulated P2RY12, which was reduced in Irf8-deficient cells.

    “overexpression of Irf8 in mouse microglia-like cell cultures upregulated the expression of P2RY12, which was conversely reduced in Irf8−/− cells”
    Quote in the paperSubstantial claim

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    Findingown data

    Re-clustering astrocytes demarcated six sub-clusters and confirmed contraction of Astro3 in Alzheimer's disease samples.

    “we demarcated 6 sub-clusters (Astro0-5) of astrocytes and confirmed the contraction of Astro3 in AD samples”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Expression of Alzheimer's disease-reactive oligodendrocyte genes was lower in AD R62H carriers than in AD CV carriers, yet significantly higher than in controls.

    “Expression of AD-reactive oligodendrocyte genes was lower in AD R62H carriers than in AD CV carriers, yet was significantly higher in AD R62H carriers than in controls”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Upregulated CA2 marked sub-cluster Oligo3, while downregulated MIR219A2 delineated clusters Oligo1 and Oligo2.

    “Upregulated genes, such as CA2, marked sub-cluster Oligo3, while downregulated genes such as MIR219A2, delineated clusters Oligo1 and Oligo2.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    R47H brains had elevated expression of genes involved in oxidative stress and lipid metabolism, along with decreased expression of genes involved in autophagy, growth factor signaling, and neural connectivity.

    “R47H brains also had elevated expression of genes involved in oxidative stress and lipid metabolism, along with decreased expression of genes involved in autophagy, growth factor signaling, and neural connectivity”
    Quote in the paperSubstantial claim

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    Findingown data

    NanoString data confirmed increased expression of microglial IRF8 and oligodendrocyte CA2 in Alzheimer's disease compared with controls.

    “NanoString data confirmed increased expression of microglia IRF8, and oligodendrocyte CA2 in AD compared to controls”
    Quote in the paperNot a substantial claim

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    Findingown data

    NanoString data confirmed increased astrocyte expression of EGFR, which has been proposed as a potential amyloid beta receptor and a regulator of astrocytes in multiple sclerosis.

    “as well as increased astrocyte expression of EGFR, which has been proposed as a potential receptor for Aβ37, and a regulator of astrocytes in multiple sclerosis38.”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [37] Wang, L. et al. Epidermal growth factor receptor is a preferred target for treating amyloid-β-induced memory loss. Proc. Natl Acad. Sci. USA 109, 16743–16748 (2012). source

      Not checked in the free run.

    • cites [38] Rothhammer, V. et al. Microglial control of astrocytes in response to microbial metabolites. Nature 557, 724–728 (2018). source

      Not checked in the free run.

  • May combine two claims.

    Findingown data

    Alzheimer's disease astrocytes had elevated expression of NCAN and COL5A3, enriched in Astro0 and Astro1.

    “AD astrocytes also had elevated expression of genes encoding the proteoglycan NCAN and collagen COL5A3, which were enriched in Astro0 and Astro1”
    Quote in the paperSubstantial claim

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    Findingown data

    Oligodendrocytes upregulated genes controlling pH and electrolytes, osmotic imbalance, lipid accumulation, and oxidative stress.

    “oligodendrocytes upregulated the expression of genes controlling pH and electrolytes (CA2), osmotic imbalance (SLC38A2), lipid accumulation (MID1IP1) and oxidative stress (SEPP1)”
    Quote in the paperSubstantial claim

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

    Findingown data

    snRNA-seq of 7-month-old mouse brain identified cell type-specific clusters using marker expression.

    “tSNE plots of snRNA-seq of 7-month-old mouse brain showing cell type specific markers identifying each cluster.”
    Quote in the paperNot a substantial claim

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

    Findingown data

    Cluster 12 was very rare and lacked a clear marker profile, so it was excluded from analysis.

    “Cluster 12 had very low frequency and did not have a clear marker profile and was thus omitted from analysis.”
    Quote in the paperNot a substantial claim

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

    Findingown data

    NanoString analysis showed slight variation in glial and neuronal gene signatures across the three cohorts.

    “Notably, NanoString analysis revealed that the precise glial and neuronal gene signatures varied slightly between the three distinct cohorts analyzed”
    Quote in the paperNot a substantial claim
    • Rests on an assumption: Post-mortem human brain tissue processed for snRNA-seq reflects the transcriptional state of the brain before death.

  • May combine two claims.

    Findingown data

    The 5XFAD mouse model did not show a clear decrease in memory-network gene expression, and its neuronal pathology is restricted to neurite dystrophy.

    “A clear reduction in the expression of genes controlling memory networks was not evident in the 5XFAD mouse model, in which neuronal pathology is limited to neurite dystrophy.”
    Quote in the paperSubstantial claim
    • Rests on an assumption: The 5XFAD mouse model recapitulates key aspects of human AD relevant to glial and neuronal transcriptional responses.

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

    Findingown data

    Some transcriptional changes matched protein changes that prior work detected in CSF as AD biomarkers.

    “Some of these transcriptional changes correspond to protein changes previously detected in the CSF as AD biomarkers (see Supplementary Table 3).”
    Quote in the paperNot a substantial claim
    • Rests on an assumption: Post-mortem human brain tissue processed for snRNA-seq reflects the transcriptional state of the brain before death.

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

    Findingown data

    The 15-month-old mouse snRNA-seq data resolved into 13 clusters (0-12), with cell type identities assigned by specific markers.

    “t-SNE plot showing 13 distinguished clusters, 0–12, with cell type identities determined by expression of specific markers.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Both C4b and Serpina3n transcripts were detected in human astrocytes.

    “although both transcripts were detected in human astrocytes.”
    Quote in the paperNot a substantial claim
    • Rests on an assumption: Post-mortem human brain tissue processed for snRNA-seq reflects the transcriptional state of the brain before death.
    • Rests on an assumption: The cell clusters identified by snRNA-seq correspond to bona fide astrocytes, oligodendrocytes, microglia, and neurons.

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

    Findingown data

    NEFL expression is especially in neuronal cluster Ex1.

    “t-SNE plot showing expression of NEFL in neuronal clusters, especially in cluster Ex1.”
    Quote in the paperNot a substantial claim

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

    Findingown data

    Pam is a representative gene enriched in cluster 4.

    “t-SNE plot showing expression of Pam, a representative gene enriched in cluster 4.”
    Quote in the paperNot a substantial claim

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

    Findingown data

    Serpina3n colocalizes with CA2+ oligodendrocytes in 7-month-old mice.

    “Representative immunofluorescence images of Serpina3n staining in 7-month-old mice of all genotypes showing colocalization of Serpina3n with oligodendrocyte marker CA2.”
    Quote in the paperNot a substantial claim

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

    Findingown data

    Serpina3n colocalizes with GFAP+ astrocytes in 15-month-old 5XFAD mice.

    “Representative confocal images showing colocalization of Serpina3n with GFAP+ astrocytes in 15-month-old 5XFAD mice.”
    Quote in the paperNot a substantial claim

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

    Findingown data

    Neuronal clusters 0 and 6 were exclusive to cortex.

    “clusters 0 and 6 (neuronal) were exclusive to cortex”
    Quote in the paperNot a substantial claim

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

    Findingown data

    Cluster 4 showed lower mean UMI counts than other neuronal clusters.

    “Cluster 4 has a lower average number of UMIs compared to other neurons.”
    Quote in the paperNot a substantial claim

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

    Findingown data

    Serpina3n colocalizes with X04+ plaques in 15-month-old 5XFAD mice.

    “Representative confocal images showing colocalization of Serpina3n with X04+ plaques in 15-month-old 5XFAD mice.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Findingown data

    Human snRNA-seq identified cell type-specific clusters using marker expression.

    “t-SNE plots of human snRNA-seq showing cell type specific markers identifying each cluster.”
    Quote in the paperSubstantial claim

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

    Findingown data

    IL10RA and HPGDS are expressed in human microglia.

    “t-SNE plots showing expression of IL10RA and HPGDS in human microglia.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationown data

    Trem2 deficiency delays microgliosis, but microgliosis can reach a plateau at late disease stages when aging becomes the main factor.

    “this suggests that, although delayed by Trem2-deficiency, microgliosis can reach a plateau at late stages of disease when aging becomes the major factor.”
    Quote in the paperSubstantial claim

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

    Premisecitation

    Disease-associated microglia have a transcriptional signature distinct from homeostatic microglia, which declines in mouse Alzheimer's disease models.

    “Such activated microglia, which have been referred to as disease-associated microglia (DAM), has a transcriptional signature quite distinct from that of homeostatic microglia that markedly declines in mouse models of AD10,11,12.”
    Quote in the paperSubstantial claim0 of 3 sources checked
    • cites [10] Keren-Shaul, H. et al. A unique microglia type associated with restricting development of Alzheimer’s disease. Cell 169, 1276–1290.e17 (2017). source

      Not checked in the free run.

    • cites [11] Krasemann, S. et al. The TREM2–APOE pathway drives the transcriptional phenotype of dysfunctional microglia in neurodegenerative diseases. Immunity 47, 566–581.e9 (2017). source

      Not checked in the free run.

    • cites [12] Mathys, H. et al. temporal tracking of microglia activation in neurodegeneration at single-cell resolution. Cell Rep. 21, 366–380 (2017). source

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    Single-nucleus analysis of human Alzheimer's disease brain has shown a microglial response that partly matches mouse disease-associated microglia, plus oligodendrocyte and myelination changes that depend on sex.

    “Single nuclei analysis of human AD brain specimens has revealed a microglial transcriptional response that partially recapitulates the mouse DAM signature along with perturbation of oligodendrocytes and myelination that is gender-dependent20.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [20] Mathys, H. et al. Single-cell transcriptomic analysis of Alzheimer’s disease. Nature 570, 332–337 (2019). source

      Not checked in the free run.

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

    Premisecitation

    Reactive astrocytosis and microgliosis are secondary cellular responses in diseased brain regions and may have both negative and positive effects.

    “Reactive astrocytosis and microgliosis are secondary cellular responses to pathology that occur in diseased brain regions2 and may have both negative and positive effects3,4.”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites [2] De Strooper, B. & Karran, E. The cellular phase of Alzheimer’s disease. Cell 164, 603–615 (2016). source

      Not checked in the free run.

    • cites [3] Heneka, M. T., Golenbock, D. T. & Latz, E. Innate immunity in Alzheimer’s disease. Nat. Immunol. 16, 229–236 (2015). source

      Not checked in the free run.

    • cites [4] Griciuc, A. et al. Alzheimer’s disease risk gene CD33 inhibits microglial uptake of amyloid beta. Neuron 78, 631–643 (2013). source

      Not checked in the free run.

  • May combine two claims.

    Interpretationreasoning

    Changes in the Alzheimer's disease brain reflect both direct amyloid beta pathology and secondary responses by TREM2-dependent activated microglia.

    “These findings suggest that changes in the AD brain are a combination of direct Aβ-mediated pathology and secondary responses by TREM2-dependent activated microglia.”
    Quote in the paperSubstantial claim

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

    Premisecitation

    Intraneuronal tau hyperphosphorylation and aggregation cause neuronal and synaptic dysfunction and cell death.

    “intraneuronal tau hyperphosphorylation and aggregation ensue, causing neuronal and synaptic dysfunction and cell death1.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [1] Long, J. M. & Holtzman, D. M. Alzheimer disease: an update on pathobiology and treatment strategies. Cell 179, 312–339 (2019). source

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    Loss of TREM2 function in Alzheimer's disease mouse models limits microglial plaque surrounding, proliferation, and conversion to disease-associated microglia, leading to more severe neuritic dystrophy.

    “loss of TREM2 function in AD mouse models restricts the ability of microglia to surround Aβ plaques15,16, proliferate, and convert to DAM10,15,17, which in turn leads to more profound neuritic dystrophy18,19.”
    Quote in the paperSubstantial claim0 of 6 sources checked
    • cites [15] Wang, Y. et al. TREM2 lipid sensing sustains the microglial response in an Alzheimer’s disease model. Cell 160, 1061–1071 (2015). source

      Not checked in the free run.

    • cites [16] Jay, T. R. et al. TREM2 deficiency eliminates TREM2+ inflammatory macrophages and ameliorates pathology in Alzheimer’s disease mouse models. J. Exp. Med. 212, 287–295 (2015). source

      Not checked in the free run.

    • cites [10] Keren-Shaul, H. et al. A unique microglia type associated with restricting development of Alzheimer’s disease. Cell 169, 1276–1290.e17 (2017). source

      Not checked in the free run.

    • cites [17] Song, W. M. et al. Humanized TREM2 mice reveal microglia-intrinsic and -extrinsic effects of R47H polymorphism. J. Exp. Med. 215, 745 (2018). source

      Not checked in the free run.

    • cites [18] Yuan, P. et al. TREM2 haplodeficiency in mice and humans impairs the microglia barrier function leading to decreased amyloid compaction and severe axonal dystrophy. Neuron 90, 724–739 (2016). source

      Not checked in the free run.

    • cites [19] Wang, Y. et al. TREM2-mediated early microglial response limits diffusion and toxicity of amyloid plaques. J. Exp. Med. 213, 667–675 (2016). source

      Not checked in the free run.

  • May combine two claims.

    Interpretationown data

    Oligodendrocyte signatures in human Alzheimer's disease suggest impaired axonal myelination and metabolic adaptation to neuronal degeneration.

    “Oligodendrocyte signatures suggested impaired axonal myelination and metabolic adaptation to neuronal degeneration.”
    Quote in the paperSubstantial claim

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

    Premisecitation

    Amyloid beta peptides produced by neurons form extracellular aggregates that initiate Alzheimer's disease.

    “amyloid beta (Aβ) peptides produced by neurons form extracellular aggregates that initiate disease”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [1] Long, J. M. & Holtzman, D. M. Alzheimer disease: an update on pathobiology and treatment strategies. Cell 179, 312–339 (2019). source

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    Genetic risk studies suggest that microglia not only respond to Alzheimer's disease but also modulate its course.

    “Studies of genetic risk for sporadic AD have suggested that microglia not only respond to disease but modulate disease course13.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [13] Bohlen, C. J., Friedman, B. A., Dejanovic, B. & Sheng, M. Microglia in brain development, homeostasis, and neurodegeneration. Annu. Rev. Genet. https://doi.org/10.1146/annurev-genet-112618-043515 (2019). source

      Not checked in the free run.

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

    Premisecitation

    Previous omics studies concluded that microglia show the most prominent changes in Alzheimer's disease brains, due to increased numbers and strong per-cell transcriptional activation.

    “These studies have largely concluded that microglia undergo the most prominent changes in diseased brains, due to a combination of increased microglia numbers along with a robust transcriptional activation signature on a per-microglia basis.”
    Quote in the paperNot a substantial claim0 of 5 sources checked
    • cites [5] Gjoneska, E. et al. Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer’s disease. Nature 518, 365–369 (2015). source

      Not checked in the free run.

    • cites [6] Seyfried, N. T. et al. A multi-network approach identifies protein-specific co-expression in asymptomatic and symptomatic Alzheimer’s disease. Cell Syst. 4, 60–72.e4 (2017). source

      Not checked in the free run.

    • cites [7] Gosselin, D. et al. An environment-dependent transcriptional network specifies human microglia identity. Science 356, eaal3222 (2017). source

      Not checked in the free run.

    • cites [8] Olah, M. et al. A transcriptomic atlas of aged human microglia. Nat. Commun. 9, 539 (2018). source

      Not checked in the free run.

    • cites [9] Masuda, T. et al. Spatial and temporal heterogeneity of mouse and human microglia at single-cell resolution. Nature 566, 388–392 (2019). source

      Not checked in the free run.

  • May combine two claims.

    Interpretationown data

    Both amyloid beta and Trem2 are required for disease-associated microglia.

    “indicating that both Aβ and Trem2 are required for DAM.”
    Quote in the paperSubstantial claim

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

    Premisecitation

    Altered iron homeostasis has been associated with senescence.

    “altered iron homeostasis has been associated with senescence29.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [29] Angelova, D. M. & Brown, D. R. Microglia and the aging brain: are senescent microglia the key to neurodegeneration? J. Neurochem. https://doi.org/10.1111/jnc.14860 (2019). source

      Not checked in the free run.

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

    Premisecitation

    SORL1 polymorphisms have been linked to Alzheimer's disease susceptibility, and CHI3L1 is a prognostic fluid biomarker for preclinical Alzheimer's disease.

    “SORL1 polymorphisms have been linked to susceptibility to AD28 and CHI3L1 is a prognostic fluid biomarker for preclinical AD26”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [28] Vardarajan, B. N. et al. Coding mutations in SORL1 and Alzheimer’s disease. Ann. Neurol. 77, 215–227 (2015). source

      Not checked in the free run.

    • cites [26] Molinuevo, J. L. et al. Current state of Alzheimer’s fluid biomarkers. Acta Neuropathol. (Berl.) 136, 821–853 (2018). source

      Not checked in the free run.

  • May combine two claims.

    Interpretationown data

    Reactive oligodendrocytes secrete C4b and Serpina3n, which may facilitate amyloid beta aggregation.

    “Reactive oligodendrocytes secrete C4b and Serpina3n, which may facilitate Aβ aggregation.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    The human microglial signature in Alzheimer's disease is distinct from mouse disease-associated microglia, resembles the peripheral nerve injury phenotype, and may be partly instructed by IRF8.

    “Altogether, these data suggest that the signature of human microglia in AD is quite distinct from that of DAM in the 5XFAD model10,11: it is reminiscent of the reactive phenotype observed in PNI and may be in part instructed by IRF8.”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites [10] Keren-Shaul, H. et al. A unique microglia type associated with restricting development of Alzheimer’s disease. Cell 169, 1276–1290.e17 (2017). source

      Not checked in the free run.

    • cites [11] Krasemann, S. et al. The TREM2–APOE pathway drives the transcriptional phenotype of dysfunctional microglia in neurodegenerative diseases. Immunity 47, 566–581.e9 (2017). source

      Not checked in the free run.

  • May combine two claims.

    Study design and conductown data

    The microglial gene changes were highly concordant between the 7-month and 15-month datasets and with previously published single-cell RNA-seq of sorted microglia.

    “These results were highly concordant between the 7-month- and 15-month-old datasets (Fig. 2d) and with previously published single cell RNA-seq data of sorted microglia10,11,12.”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites [10] Keren-Shaul, H. et al. A unique microglia type associated with restricting development of Alzheimer’s disease. Cell 169, 1276–1290.e17 (2017). source

      Not checked in the free run.

    • cites [11] Krasemann, S. et al. The TREM2–APOE pathway drives the transcriptional phenotype of dysfunctional microglia in neurodegenerative diseases. Immunity 47, 566–581.e9 (2017). source

      Not checked in the free run.

    • cites [12] Mathys, H. et al. temporal tracking of microglia activation in neurodegeneration at single-cell resolution. Cell Rep. 21, 366–380 (2017). source

      Not checked in the free run.

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

    Study design and conductown data

    Most human samples had a median of over 2,000 UMIs per nucleus.

    “Most samples had a median of over 2,000 UMIs per nucleus”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationown data

    This underrepresentation likely reflects neuronal loss in Alzheimer's disease and is consistent with NEFL as a cerebrospinal fluid biomarker.

    “likely reflecting neuronal loss associated with AD and consistent with NEFL being identified as an AD biomarker in the cerebrospinal fluid (CSF)26”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [26] Molinuevo, J. L. et al. Current state of Alzheimer’s fluid biomarkers. Acta Neuropathol. (Berl.) 136, 821–853 (2018). source

      Not checked in the free run.

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

    Interpretationreasoning

    Gene signatures differed somewhat between the two sample sets, likely reflecting differences in transcriptional and functional profiles of glia and neurons in prefrontal and occipital cortices.

    “gene signatures indicative of glial responses and neuronal depletion detected by NanoString in the Rush and the BRI cohorts differed somewhat between the two sets of specimens, likely reflecting differences in the transcriptional and functional profiles of glia and neurons in prefrontal and occipital cortices, respectively.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationown data

    IRF8 expression in human Alzheimer's disease microglia was validated by NanoString and immunofluorescence, and IRF8 drives expression of microglial markers linked to Alzheimer's disease, suggesting IRF8 is likely a major driver of this signature.

    “We validated IRF8 expression in human AD microglia by NanoString and IF and showed that IRF8 drives the expression of microglial markers linked to AD, suggesting that IRF8 is likely a major driver of this signature.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    This suggests fewer microglia in R47H than in CV TREM2 brain specimens and/or reduced expression of these microglial genes per cell.

    “suggesting fewer microglia in the R47H than in the CV TREM2 brain specimens and/or reduced expression of these microglial genes on a per cell basis.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationcitation

    These extracellular matrix molecules may contribute to glial scarring and probably prevent axonal regeneration.

    “These extracellular matrix molecules may contribute to glial scarring, probably preventing axonal regeneration31.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [31] McKeon, R. J., Jurynec, M. J. & Buck, C. R. The chondroitin sulfate proteoglycans neurocan and phosphacan are expressed by reactive astrocytes in the chronic CNS glial scar. J. Neurosci. 19, 10778–10788 (1999). source

      Not checked in the free run.

  • May combine two claims.

    Interpretationcitation

    The Alzheimer's disease astrocyte profile is quite different from A1 astrocytes induced by microglial inflammatory mediators, reiterating a lack of bona fide inflammation in the Alzheimer's disease brain.

    “Overall, the AD astrocyte profile was quite different from that of A1 astrocytes induced by inflammatory mediators released by microglia33, reiterating a lack of bona fide inflammation in the AD brain.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [33] Liddelow, S. A. et al. Neurotoxic reactive astrocytes are induced by activated microglia. Nature 541, 481–487 (2017). source

      Not checked in the free run.

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

    Interpretationreasoning

    The contraction of this astrocyte subset likely reflects loss of metabolic coordination between neurons and astrocytes.

    “likely reflecting loss of metabolic coordination between neurons and astrocytes.”
    Quote in the paperNot a substantial claim
    • Rests on an assumption: Post-mortem human brain tissue processed for snRNA-seq reflects the transcriptional state of the brain before death.
    • Rests on an assumption: The cell clusters identified by snRNA-seq correspond to bona fide astrocytes, oligodendrocytes, microglia, and neurons.

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

    Premisecitation

    Reduced ADCYAP1 in human cerebrospinal fluid and brain specimens has been associated with cognitive decline in mild cognitive impairment due to Alzheimer's disease.

    “reduced ADCYAP1 in human CSF and brain specimens has been associated with cognitive decline in mild cognitive impairment due to AD40”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [40] Han, P. et al. Association of pituitary adenylate cyclase-activating polypeptide with cognitive decline in mild cognitive impairment due to Alzheimer disease. JAMA Neurol. 72, 333–339 (2015). source

      Not checked in the free run.

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

    Interpretationreasoning

    Neuronal loss in AD may reduce the need for astrocytic scavenger functions that clear neuronal toxic waste.

    “Neuronal loss in AD may dampen the need for astrocytic scavenger functions devoted to disposal of neuronal toxic waste.”
    Quote in the paperNot a substantial claim
    • Rests on an assumption: Post-mortem human brain tissue processed for snRNA-seq reflects the transcriptional state of the brain before death.

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

    Premisecitation

    NCAN polymorphisms have been associated with bipolar disorder, schizophrenia, and major depression.

    “NCAN polymorphisms have been associated with bipolar disorder, schizophrenia and major depression32.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [32] Schultz, C. C. et al. Common variation in NCAN, a risk factor for bipolar disorder and schizophrenia, influences local cortical folding in schizophrenia. Psychol. Med. 44, 811–820 (2014). source

      Not checked in the free run.

  • May combine two claims.

    Interpretationown data

    The R47H variant appears to have a greater impact than R62H on the microglial response to Alzheimer's disease pathology, consistent with its higher penetrance.

    “Overall, the R47H variant seems to have a greater impact than the R62H variant on microglial response to AD pathology, consistent with the relatively higher penetrance of the R47H variant for AD.”
    Quote in the paperSubstantial claim

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

    Study design and conductnone given

    NanoString nCounter analysis used multivariate linear regression with Benjamini-Yekutieli adjustment.

    “NanoString nCounter analysis was based on multivariate linear regression with Bejamani-Yekutieli adjustment.”
    Quote in the paperNot a substantial claim

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

    Study design and conductnone given

    All samples and data were processed in a high-throughput or automated fashion.

    “but all samples and data were processed in a high-throughput or automated fashion.”
    Quote in the paperNot a substantial claim

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

    Study design and conductown data

    For phosphorylation data, a false discovery rate of less than 2.5% was set using linear discriminant analysis.

    “A regular expression for phosphorylation was used to perform using linear discriminant analysis (LDA) and set a false discovery rate (FDR) of < 2.5%”
    Quote in the paperNot a substantial claim

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

    Study design and conductnone given

    Peptide-spectrum matches with TMT reporter ion summed signal-to-noise ratios below 55 were excluded from quantitation.

    “PSMs with TMT reporter ion summed signal-to-noise ratios less than 55 were excluded from quantitation.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). The quote only partly states this claim.

    Study design and conductown data

    After filtering, 38,230 nuclei remained for the 15-month-old mouse brain snRNA-seq analysis.

    “After filtering, 38,230 nuclei were remained.”
    Quote in the paperNot a substantial claim

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

    Study design and conductnone given

    Experiments were repeated at least twice.

    “Experiments were repeated two or more times.”
    Quote in the paperNot a substantial claim

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

    Study design and conductnone given

    No animals were excluded from analysis.

    “No animals were excluded from analysis.”
    Quote in the paperNot a substantial claim

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

    Study design and conductnone given

    In snRNA-seq analyses, P values were adjusted using Bonferroni correction.

    “P values were adjusted based on Bonferroni correction.”
    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 conductown data

    After filtering, 73,419 individual nuclei across all genotypes remained for the 7-month-old mouse brain snRNA-seq analysis, with a median of 3,941 UMIs and 2,378 genes per nucleus.

    “After filtering, a total of 73,419 individual nuclei across all genotypes were remained, with a median of 3,941 UMIs and 2,378 genes per nucleus for downstream analysis.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Study design and conductown data

    Controls were age-matched to AD patients.

    “11 age-matched controls”
    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

    Sex distribution was balanced between AD (CV) and control groups (7 females, 4 males each), and the AD (R62H) group had 5 females and 5 males.

    “Sex was balanced between AD (CV) and control individuals, with 7 females and 4 males in each group; the AD (R62H) group has 5 females and 5 males.”
    Quote in the paperNot a substantial claim

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

    Interpretationown data

    This variation reflects disparate demographics and/or differing brain regions from which samples were obtained.

    “reflecting disparate demographics and/or differing regions of the brain from which the samples were obtained.”
    Quote in the paperNot a substantial claim
    • Rests on an assumption: Post-mortem human brain tissue processed for snRNA-seq reflects the transcriptional state of the brain before death.

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

    Study design and conductown data

    Validation assays used Tukey's multiple comparisons test to adjust for multiple comparisons.

    “All statistical analyses for validation assays were performed using GraphPad Prism (v.8) with unpaired Student’s t test or one- or two-way ANOVA with Tukey’s multiple comparisons test.”
    Quote in the paperNot a substantial claim

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

    Study design and conductcitation

    Peptide-spectrum matches were adjusted to a 1% false discovery rate.

    “Peptide-spectrum matches (PSMs) were adjusted to a 1% false discovery rate (FDR)52”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [52] Elias, J. E. & Gygi, S. P. Target-decoy search strategy for mass spectrometry-based proteomics. Methods Mol. Biol. Clifton NJ 604, 55–71 (2010). source

      Not checked in the free run.

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

    Study design and conductown data

    After filtering, 66,311 nuclei remained across 11 AD (CV), 10 AD (R62H) and 11 control samples for human brain snRNA-seq, with a median of 1,951 UMIs and 1,312 genes per nucleus.

    “After filtering, 66,311 nuclei were remained across 11 AD (CV), 10 AD (R62H) and 11 control samples, with a median of 1,951 UMIs and 1,312 genes per nucleus for downstream analysis.”
    Quote in the paperNot a substantial claim

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

    Study design and conductown data

    UMI and gene-number cutoffs were chosen from histograms of cell density against UMI/gene counts.

    “Cutoffs for UMI and gene number were determined based on histograms showing cell density as a function of UMI/gene counts.”
    Quote in the paperNot a substantial claim

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

    Study design and conductnone given

    Nuclei whose mitochondrial content exceeded 5 percent were discarded.

    “nuclei with mitochondrial content greater than 5 percent were removed.”
    Quote in the paperNot a substantial claim

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

    Study design and conductown data

    Confocal images for Fig. 3 and Extended Data Fig. 4 were quantified by averaging at least three images from each mouse brain.

    “For confocal images in Fig. 3 and Extended Data Fig. 4, at least three images per mouse brain were acquired and averaged for quantification.”
    Quote in the paperNot a substantial claim

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

    Premisecitation

    Some of these molecules have been linked in prior work to memory impairment and to mild cognitive impairment in AD.

    “Defects in some of these molecules have been implicated in impaired memory39 and associated with mild cognitive impairment in AD40.”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [39] Dickey, C. A. et al. Selectively reduced expression of synaptic plasticity-related genes in amyloid precursor protein + presenilin-1 transgenic mice. J. Neurosci. 23, 5219–5226 (2003). source

      Not checked in the free run.

    • cites [40] Han, P. et al. Association of pituitary adenylate cyclase-activating polypeptide with cognitive decline in mild cognitive impairment due to Alzheimer disease. JAMA Neurol. 72, 333–339 (2015). source

      Not checked in the free run.

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

    Study design and conductcitation

    Confidently localized phosphorylation sites with an AScore greater than 13 were selected for analysis.

    “confidently localized sites with a AScore > 13 were selected for analysis (p-value < 0.05)54.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [54] Beausoleil, S. A., Villén, J., Gerber, S. A., Rush, J. & Gygi, S. P. A probability-based approach for high-throughput protein phosphorylation analysis and site localization. Nat. Biotechnol. 24, 1285–1292 (2006). source

      Not checked in the free run.

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

    Study design and conductnone given

    Investigators were not blinded to experimental groups.

    “Investigators were not blinded to experimental groups”
    Quote in the paperNot a substantial claim

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

    Study design and conductnone given

    Bonferroni correction was used to calculate adjusted p-values.

    “Adjusted p-value was calculated based on Bonferroni correction.”
    Quote in the paperNot a substantial claim

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

    Interpretationnone given

    IRF8 may play a role in microglial reactivity.

    “a potential role for IRF8 in microglia reactivity”
    Quote in the paperNot a substantial claim
    • Rests on an assumption: Post-mortem human brain tissue processed for snRNA-seq reflects the transcriptional state of the brain before death.
    • Rests on an assumption: The cell clusters identified by snRNA-seq correspond to bona fide astrocytes, oligodendrocytes, microglia, and neurons.

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

    Study design and conductnone given

    Filtered peptide-spectrum matches were collapsed to a final protein-level false discovery rate of less than 2%.

    “Filtered PSMs were collapsed to a final protein-level FDR of < 2%.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Study design and conductown data

    Nuclei that were duplets or multiplets were filtered out.

    “Nuclei that are duplets or multiplets were filtered out by two steps.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    The findings extend earlier work in mouse Aβ aggregation models that pointed to a pathogenic role for C4b and Serpina3n, and genetic evidence connecting human SERPINA3 with AD risk.

    “Together these data expand previous studies in mouse models of Aβ aggregation suggesting a pathogenic role for C4b and Serpina3n23,24,44,45, as well as genetic studies linking the human homologue SERPINA3 to AD risk46”
    Quote in the paperSubstantial claim0 of 5 sources checked
    • cites [23] Mucke, L. et al. Astroglial expression of human α1-antichymotrypsin enhances alzheimer-like pathology in amyloid protein precursor transgenic mice. Am. J. Pathol. 157, 2003–2010 (2000). source

      Not checked in the free run.

    • cites [24] Nilsson, L. N. et al. α-1-antichymotrypsin promotes β-sheet amyloid plaque deposition in a transgenic mouse model of Alzheimer’s disease. J. Neurosci. 21, 1444–1451 (2001). source

      Not checked in the free run.

    • cites [44] Hong, S. et al. Complement and microglia mediate early synapse loss in Alzheimer mouse models. Science 352, 712–716 (2016). source

      Not checked in the free run.

    • cites [45] Ma, J., Yee, A., Brewer, H. B., Das, S. & Potter, H. Amyloid-associated proteins α1-antichymotrypsin and apolipoprotein E promote assembly of Alzheimer β-protein into filaments. Nature 372, 92–94 (1994). source

      Not checked in the free run.

    • cites [46] Kamboh, M. I., Sanghera, D. K., Ferrell, R. E. & DeKosky, S. T. APOE*4-associated Alzheimer’s disease risk is modified by α1-antichymotrypsin polymorphism. Nat. Genet. 10, 486–488 (1995). source

      Not checked in the free run.

    • Rests on an assumption: In vitro Aβ aggregation induced by C4b is relevant to AD pathogenesis in vivo.

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

    Study design and conductcitation

    PSMs with poor quality or MS3 spectra with TMT reporter ion summed signal-to-noise ratios less than 110 were excluded from quantitation.

    “PSMs with poor quality, MS3 spectra with TMT reporter ion summed signal-to-noise ratios less than 110 were excluded from quantitation53.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [53] McAlister, G. C. et al. Increasing the multiplexing capacity of TMTs using reporter ion isotopologues with isobaric masses. Anal. Chem. 84, 7469–7478 (2012). source

      Not checked in the free run.

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

    Interpretationown data

    Reads from Trem2-deficient mice map to Trem2 exon1, which the authors attribute to early termination caused by removing exons 3 and 4 in the knockout design.

    “Alignment of reads from Trem2-deficient mice to Trem2 exon1 reflects early transcriptional termination due to deletion of exons 3 and 4 in the design of Trem2 knockout constructs.”
    Quote in the paperNot a substantial claim
94 of 94

  • The paper relies on this without support.

    Little is known about how TREM2-dependent microglial functions affect the Alzheimer's disease brain as a whole.

    “Nonetheless, little is known about how TREM2-dependent microglial functions impact the AD brain as a whole.”

  • The paper relies on this without support.

    Post-mortem human brain tissue processed for snRNA-seq reflects the transcriptional state of the brain before death.

    “Post-mortem prefrontal cortical tissues from 11 AD patients with TREM2 common variant (CV), 10 AD patients carrying TREM2 R62H variant, and 11 age-matched controls from the Rush cohort were analyzed by snRNA-seq.”

  • The paper relies on this without support.

    The 5XFAD mouse model recapitulates key aspects of human AD relevant to glial and neuronal transcriptional responses.

    “In the 5XFAD model, astrocytes assumed a very modest Aβ-dependent signature marked by expression of Gfap.”

  • The paper relies on this without support.

    The cell clusters identified by snRNA-seq correspond to bona fide astrocytes, oligodendrocytes, microglia, and neurons.

    “Nuclei from broad cell types (astrocytes, microglia and oligodendrocytes clusters) were taken and re-clustered to further analyze the sub-clusters in each cell type.”

  • The paper relies on this without support.

    In vitro Aβ aggregation induced by C4b is relevant to AD pathogenesis in vivo.

    “Moreover, C4b was particularly effective in inducing Aβ aggregation in vitro.”
5 of 5

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?

  • The snRNA-seq dataset contains over 100,000 astrocyte nuclei in each brain region with ≈6,000 average total reads and ≈2,500 average total genes detected, which is orders of magnitude higher than previous studies.

    “resulting in over 100,000 astrocyte nuclei in each brain region with ≈6,000 average total number of reads and ≈2,500 average total number of genes detected, which is orders of magnitude higher than previous studies9–15”

    From Astrocyte transcriptomic changes along the spatiotemporal progression of Alzheimer’s disease (2024) · cites this paper as [11]

    Extended Data Fig. 7 reports 9,019 astrocyte nuclei out of 66,311 total human nuclei, contrary to over 100,000 astrocyte nuclei in each brain region. The Online Methods report median UMIs and genes per nucleus, not the claimed average reads and genes. (LLM, conf=0.90)

    Checked by a reasoning model — may be wrong.

    Experimental — accuracy not yet measured

  • The disease-associated microglia signaling pathway appears conserved in human microglia.

    “This signaling pathway seems to be conserved in human microglia (Zhou et al., 2020)”

    From Alzheimer's-associated PU.1 expression levels regulate microglial inflammatory response (2021) · cites this paper as Zhou et al., 2020

    The Results section on TREM2 variants reports a reduced microglial response in human AD, supporting a shared role for TREM2 in mouse and human disease. But the Results section on human AD gene signatures and the Discussion say the human microglial signature is quite distinct from mouse disease-associated microglia (DAM); they do not establish that the DAM signaling pathway is conserved. The indexed passages provide no page numbers. (LLM, conf=0.85)

    Experimental — accuracy not yet measured

  • Stage 2 DAMs are activated microglia that are closely associated with amyloid plaques.

    “Stage 2 DAMs (sometimes referred to as TREM2-dependent) are activated microglia that are closely associated with amyloid plaques.42,43”

    From TET2-mutant myeloid cells mitigate Alzheimer’s disease progression via CNS infiltration and enhanced phagocytosis in mice (2025) · cites this paper as [42]

    The Results section, “DAM signature is Trem2-dependent at early and late stages of Aβ accumulation” (page not provided), identifies an Aβ- and Trem2-dependent microglial cluster expressing DAM genes. It does not identify that cluster as stage 2 DAM or establish that those cells are closely associated with amyloid plaques. (LLM, conf=0.84)

    Experimental — accuracy not yet measured

  • TREM2 is one of the strongest risk factors for AD, and evidence suggests that TREM2 acts to recognize Aβ pathology and direct microglial responses toward the pathology.

    “For instance, TREM2 is one of the strongest risk factors for AD, and evidence suggests that TREM2 acts to recognize Aβ pathology and direct microglial responses toward the pathology (Guerreiro et al., 2013; Zhou et al., 2020).”

    From β-amyloid accumulation enhances microtubule associated protein tau pathology in an APPNL-G-F/MAPTP301S mouse model of Alzheimer’s disease (2024) · cites this paper as Zhou et al., 2020

    The introductory passage in the Abstract (page unavailable) says TREM2 variants raise AD risk several-fold and that loss of TREM2 function restricts microglia from surrounding Aβ plaques. The Results section on DAM signatures (page unavailable) also reports that both Aβ and TREM2 are required for the disease-associated microglial response. These passages support a role in directing microglial responses to Aβ pathology, but do not establish that TREM2 itself recognizes that pathology. (LLM, conf=0.83)

    Experimental — accuracy not yet measured

  • Only a subset, often a mix of A1 and A2 or pan-reactive transcripts, are upregulated in astrocytes from brains of study participants with HD or AD, or from several mouse models of acute injuries and chronic diseases of the CNS.

    “Importantly, only a subset, often a mix of A1 and A2 or pan-reactive transcripts, are upregulated in astrocytes from brains of study participants with HD74 or AD75,76, or from several mouse models of acute injuries and chronic diseases of the CNS42,69,76,77.”

    From Reactive astrocyte nomenclature, definitions, and future directions (2021) · cites this paper as [76]

    The Results report limited astrocyte transcriptional changes in the 5XFAD mouse model, while the Results and Discussion identify upregulated astrocyte genes in human AD. The paper does not characterize those upregulated genes as a mix of A1, A2, or pan-reactive transcripts; it says the human AD astrocyte profile was quite different from the A1 profile. The HD and other-model portions of the citing sentence carry separate citations and are not assessed against this source. (LLM, conf=0.84)

    Experimental — accuracy not yet measured

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Authors
Zhou, Y., Song, W. M., Andhey, P. S., Swain, A., Levy, T., Miller, K. R., Poliani, P. L., Cominelli, M., Grover, S., Gilfillan, S., Cella, M., Ulland, T. K., Zaitsev, K., Miyashita, A., Ikeuchi, T., Sainouchi, M., Kakita, A., Bennett, D. A., Schneider, J. A., Nichols, M. R., Beausoleil, S. A., Ulrich, J. D., Holtzman, D. M., Artyomov, M. N., & Colonna, M.
Affiliations
  • Washington University in St. Louis (US)
  • Bluefin Biomedicine (United States) (US)
  • Nanostring Technologies (United States) (US)
  • University of Brescia (IT)
  • University of Missouri–St. Louis (US)
  • University of Wisconsin–Madison (US)
  • ITMO University (RU)
  • Brain Research Institute, Niigata University (JP)
  • Rush University Medical Center (US)
Corresponding author
  • Artyomov, Maxim N.
  • Colonna, Marco
ORCID
Venue
Nature Medicine
Publisher
Springer Science and Business Media LLC
Published
2020-01-01
Volume
26
Issue
1
Pages
131-142
ISSN
  • 1078-8956 (ISSN-L)
  • 1546-170X
DOI
10.1038/s41591-019-0695-9
PMC
PMC6980793
OpenAlex
W2998795963
Semantic Scholar
99ea49ab0c1c1672b94039e5c61e1144b048cb80
Cited by
1,150
References
68
Citations by year
2026: 161 · 2025: 194 · 2024: 193 · 2023: 189 · 2022: 161 · 2021: 162 · 2020: 87 · 2019: 1 · 2013: 1 · 2012: 1
FWCI
58.45
Type
journal article
Language
en
Update notices
correction (2020-05-14)
Open access
Licence
Locations
  • Nature Medicine (publishedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
  • Archivio Istituzionale della Ricerca - Università Vita-Salute San Raffaele (submittedVersion, other-oa)
  • Institutional Research Information System (Università degli Studi di Brescia) (submittedVersion)
Funders
  • U.S. Department of Health & Human Services | NIH | National Institute on Aging (RF1 AG051485, R21 AG059176, RF1 AG059082, RF1 AG047644)
  • Cure Alzheimer’s Fund
  • U.S. Department of Health & Human Services | NIH | National Institute of Neurological Disorders and Stroke (R01 NS090934)
  • U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (R15 GM119070)
Topics
  • Life Sciences › Neuroscience › Neurology › Neuroinflammation and Neurodegeneration Mechanisms
  • Health Sciences › Medicine › Physiology › Alzheimer's disease research and treatments
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
Keywords
Alzheimer's disease, TREM2, disease-associated microglia, microglia, oligodendrocytes, astrocytes, glial response, Serpina3n, C4b, myelination, axonal degeneration, species differences, 5xFAD mice, amyloid-beta deposition, single-nucleus transcriptomics
MeSH terms
Aged, Alzheimer Disease, Animals, Astrocytes, Axons, Brain, Cell Nucleus, Female, Humans, Male, Membrane Glycoproteins, Mice, Inbred C57BL, Mice, Transgenic, Middle Aged, Nerve Degeneration, Oligodendroglia, Receptors, Immunologic, Transcription, Genetic, Amyloid beta-Peptides, Microglia, Transcriptome

About these checks

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 2026-10-04.

Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-10-04.

Statistics and arithmetic are recomputed, not judged.

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