APOE4 impairs the microglial response in Alzheimer’s disease by inducing TGFβ-mediated checkpoints

In the paper

“Thus, APOE4 converges to impair the MGnD response to neurodegeneration, which plays a protective role in glaucoma 14 and is detrimental in AD.”

What the sources say

• Disputed

  The source supports the claim that APOE4 dampens the MGnD response, but says the opposite about that response’s role in glaucoma. Its Results section (“MGnD microglia directly induce RGC degeneration in vivo”; page not available) reports that MGnD microglia caused retinal ganglion cell loss. The Abstract says impaired activation of APOE4 microglia—not the MGnD response—is protective in glaucoma. (LLM, conf=0.90)

  Checked by a reasoning model — may be wrong.

  cites [14] Margeta, M. A. et al. Apolipoprotein E4 impairs the response of neurodegenerative retinal microglia and prevents neuronal loss in glaucoma. Immunity 55, 1627–1644 (2022). sourceExperimental — accuracy not yet measured

In the paper

“The APOE4 allele is a major genetic risk factor for late-onset AD and was previously shown to accelerate AD progression in humans and in mouse models 6-11 .”

What the sources say

• ?Not checked — no full text of the sourcecites [6] Farrer, L. A. et al. Effects of age, sex, and ethnicity on the association between apolipoprotein E genotype and Alzheimer disease. A meta-analysis. APOE and Alzheimer Disease Meta Analysis Consortium. JAMA 278, 1349–1356 (1997). source
• ?Not checked — no full text of the sourcecites [7] Corder, E. H. et al. Gene dose of apolipoprotein E type 4 allele and the risk of Alzheimer’s disease in late onset families. Science 261, 921–923 (1993). source
• Partly supported

  The allele-association passage reports a significantly higher APOE-e4 frequency in people with familial Alzheimer disease than in controls, supporting the genetic-risk portion of the citing sentence. It does not show that APOE4 accelerates disease progression in humans or mouse models; searches for progression and mouse models found no such result. (LLM, conf=0.86)

  cites [8] Strittmatter, W. J. et al. Apolipoprotein E: high-avidity binding to β-amyloid and increased frequency of type 4 allele in late-onset familial Alzheimer disease. Proc. Natl Acad. Sci. USA 90, 1977–1981 (1993). sourceExperimental — accuracy not yet measured
• ?Not checked — no full text of the sourcecites [9] Raber, J. et al. Isoform-specific effects of human apolipoprotein E on brain function revealed in ApoE knockout mice: increased susceptibility of females. Proc. Natl Acad. Sci. USA 95, 10914–10919 (1998). source
• Partly supported

  The Discussion reports accelerated Aβ accumulation in E4FAD mice, supporting the mouse-model portion of the claim. The Abstract reports greater plaque deposition with APOE4 in humans and transgenic mice and identifies APOE4 as a major AD risk factor, but it does not establish accelerated clinical AD progression in humans. The paper's evidence is chiefly about amyloid pathology, not the full course of AD. (LLM, conf=0.84)

  cites [10] Youmans, K. L. et al. APOE4-specific changes in Aβ accumulation in a new transgenic mouse model of Alzheimer disease. J. Biol. Chem. 287, 41774–41786 (2012). sourceExperimental — accuracy not yet measured
• Partly supported

  The Introduction reports earlier onset of cognitive deficits in human APOE4 carriers, but says evidence for a faster rate of cognitive decline is conflicting. The Discussion reports a more rapid early decline in spatial recognition memory in E4FAD mice. Thus, the source supports the mouse finding and earlier human onset, but not an unqualified claim that APOE4 accelerates AD progression in humans. (LLM, conf=0.86)

  cites [11] Liu, D. S. et al. APOE4 enhances age-dependent decline in cognitive function by down-regulating an NMDA receptor pathway in EFAD-Tg mice. Mol. Neurodegener. 10, 7 (2015). sourceExperimental — accuracy not yet measured

In the paper

“Of note, using Cx3cr1 CreERT2 mice to delete microglial genes may also affect border-associated macrophages (BAMs) 16 , albeit to a lesser extent as BAMs were shown to be continuously replenished from skull bone marrow, unlike microglia 17 .”

What the sources say

• Supported

  The Results section (“Maintenance of pvMΦ, mMΦ and cpMΦ in adulthood”) reports that Cx3cr1CreER-mediated recombination labeled macrophages at CNS borders as well as microglia. This supports the cited point that using this system to delete microglial genes may also affect border-associated macrophages. The sentence attributes the separate claim about skull-bone-marrow replenishment to citation 17, not this paper. (LLM, conf=0.90)

  cites [16] Goldmann, T. et al. Origin, fate and dynamics of macrophages at central nervous system interfaces. Nat. Immunol. 17, 797–805 (2016). source
• Partly supported

  The Discussion (page not available) says skull and vertebral marrow continuously replenish monocytes and neutrophils at CNS borders and that marrow-derived monocytes can become meningeal macrophages. The Introduction describes microglia as self-maintained. The paper does not establish that BAMs as a group are continuously replenished, or that Cx3cr1 CreERT2-mediated deletion affects them to a lesser extent; the latter part of the citing sentence is the portion attached to this citation. (LLM, conf=0.85)

  cites [17] Cugurra, A. et al. Skull and vertebral bone marrow are myeloid cell reservoirs for the meninges and CNS parenchyma. Science 373, eabf7844 (2021). sourceExperimental — accuracy not yet measured

In the paper

“A recent report showed that deletion of APOE4 in astrocytes markedly reduced neurodegeneration in a mouse model of tauopathy 12 .”

What the sources say

• Supported

  The Abstract states that removing astrocytic APOE4 markedly reduced tau-mediated neurodegeneration in P301S tau mice. The Discussion likewise reports that genetic deletion after the onset of tau pathology strongly attenuated neurodegeneration. (LLM, conf=0.95)

  cites [12] Wang, C. et al. Selective removal of astrocytic APOE4 strongly protects against tau-mediated neurodegeneration and decreases synaptic phagocytosis by microglia. Neuron 109, 1657–1674 (2021). source

In the paper

“Importantly, low expression of PU.1 was suggested by a recent GWAS to be protective against AD 19 .”

What the sources say

• Supported

  The Abstract reports that a protective allele identified in a genome-wide survival analysis is associated with lower SPI1 expression in myeloid cells; SPI1 encodes PU.1. It concludes that lower SPI1 expression may reduce AD risk, matching the citing sentence’s tentative wording. (LLM, conf=0.94)

  cites [19] Huang, K. L. et al. A common haplotype lowers PU.1 expression in myeloid cells and delays onset of Alzheimer’s disease. Nat. Neurosci. 20, 1052–1061 (2017). source

In the paper

“Neurodegeneration is a pathological hallmark of AD 20 , which is exacerbated in a mouse model of tauopathy expressing APOE4 (refs. 12,21).”

What the sources say

• Supported

  The paper’s Abstract identifies neuronal and synaptic loss as neuropathological hallmarks of AD. It also describes losses of neurons, neuropil, and synaptic elements as core features. Citation 20 supports the first clause; the separate claim about the APOE4 mouse model is attributed to other references. (LLM, conf=0.94)

  cites [20] Serrano-Pozo, A., Frosch, M. P., Masliah, E. & Hyman, B. T. Neuropathological alterations in Alzheimer disease. Cold Spring Harb. Perspect. Med. 1, a006189 (2011). source

In the paper

“the latter of which encodes the checkpoint molecule TIM3, one of the most promising new therapeutic approaches in cancer 32 that was recently described in a GWAS as an AD risk gene 2 .”

What the sources say

• Supported

  The cited review identifies TIM3 as an inhibitory receptor linked to HAVCR2 and, in ‘Role of TIM3 in cancer and chronic viral infections’ (page not provided), calls it an attractive target for checkpoint-targeted cancer immunotherapy. Its ‘Conclusion and perspective’ reports promising clinical results from targeting TIM3. The AD GWAS assertion is attached to a different citation and is not attributed to this source. (LLM, conf=0.91)

  cites [32] Wolf, Y., Anderson, A. C. & Kuchroo, V. K. TIM3 comes of age as an inhibitory receptor. Nat. Rev. Immunol. 20, 173–185 (2020). source
• Supported

  Table 1 (Functional enrichment of significantly associated regions) lists HAVCR2 at a genomic risk locus for Alzheimer’s disease, and Gene prioritization reports that the locus’s lead variant lies in a HAVCR2 intron. Citation 2 supports the GWAS risk-gene attribution; the separate citation 32 is attached to the statement about cancer therapy. (LLM, conf=0.92)

  cites [2] Wightman, D. P. et al. A genome-wide association study with 1,126,563 individuals identifies new risk loci for Alzheimer’s disease. Nat. Genet. 53, 1276–1282 (2021). source

In the paper

“subunits of integrin α v β8 (ref. 30; Fig. 6b,c and Supplementary Table 5), which plays a critical role in TGFβ activation and microglia homeostatic maturation 31”

What the sources say

• Partly supported

  The section “TGF-b Activation by RGD-Binding Integrins” (page unavailable) says that αvβ8 activates TGF-β1 and TGF-β3. Our copy does not address microglial homeostatic maturation, so it supports the activation claim but not that additional role. (LLM, conf=0.88)

  cites [30] Munger, J. S. & Sheppard, D. Cross talk among TGF-β signaling pathways, integrins, and the extracellular matrix. Cold Spring Harb. Perspect. Biol. 3, a005017 (2011). sourceExperimental — accuracy not yet measured
• Supported

  The Discussion describes integrin αvβ8 and TGFβ signaling as essential to coordinating microglial maturation with early brain development. It also identifies latent TGFβ activation as αvβ8’s principal biological function. The paper cautions that it did not directly prove the proposed mechanism by which activated TGFβ signals to microglia, but the citing sentence does not specify that mechanism. (LLM, conf=0.91)

  cites [31] Arnold, T. D. et al. Impaired αVβ8 and TGFβ signaling lead to microglial dysmaturation and neuromotor dysfunction. J. Exp. Med. 216, 900–915 (2019). source

In the paper

“These results support previous reports demonstrating that higher PU.1 expression in humans is likely to result in earlier AD onset 19,48 .”

What the sources say

• Supported

  The Abstract reports that an allele associated with lower SPI1 expression in human monocytes and macrophages is also associated with delayed AD onset; SPI1 encodes PU.1. The Conditional and SMR analysis section says the shared genetic association supports a possible causal link. Together, these support the citing sentence’s hedged inference about higher expression and earlier onset, though they do not establish it experimentally in humans. (LLM, conf=0.88)

  cites [19] Huang, K. L. et al. A common haplotype lowers PU.1 expression in myeloid cells and delays onset of Alzheimer’s disease. Nat. Neurosci. 20, 1052–1061 (2017). source
• Partly supported

  The Results section reports a human-associated SPI1 haplotype linked to lower PU.1 expression and delayed AD onset, which supports the claimed direction of association. It does not report that higher PU.1 expression was shown to cause earlier onset in humans; this paper’s own experiments used mouse microglial cells. No page number is available in our copy. (LLM, conf=0.82)

  cites [48] Pimenova, A. A. et al. Alzheimer’s-associated PU.1 expression levels regulate microglial inflammatory response. Neurobiol. Dis. 148, 105217 (2021). sourceExperimental — accuracy not yet measured

In the paper

“We recently demonstrated that APOE4 impairs the response of neurodegenerative retinal microglia via LGALS3 signaling associated with neuroprotection in glaucoma 14 .”

What the sources say

• Supported

  The Abstract reports that APOE4-expressing retinal microglia did not upregulate Lgals3 after intraocular-pressure elevation and that APOE4 mice were protected from retinal ganglion cell loss. The Discussion identifies APOE–Galectin-3 signaling as a pathway relevant to neuroprotective treatment in glaucoma. (LLM, conf=0.91)

  cites [14] Margeta, M. A. et al. Apolipoprotein E4 impairs the response of neurodegenerative retinal microglia and prevents neuronal loss in glaucoma. Immunity 55, 1627–1644 (2022). source

In the paper

“Moreover, reactive astrocytes play a beneficial role in limiting AD pathology, and their depletion in AD mice results in increased plaque load, synaptic dysfunction and memory loss 51 .”

What the sources say

• Partly supported

  The Results sections on synaptic density and memory report synaptic loss and worsened spatial-memory performance after ablation of proliferating reactive astrocytes in APP23 mice. But the Results section on amyloid-β (page unavailable) explicitly reports no significant change in amyloid plaque burden measured by Thio-S staining; increased amyloid-β staining is not the same as increased plaque load. (LLM, conf=0.91)

  cites [51] Katsouri, L. et al. Ablation of reactive astrocytes exacerbates disease pathology in a model of Alzheimer’s disease. Glia 68, 1017–1030 (2020). sourceExperimental — accuracy not yet measured

In the paper

“Interestingly, APOE4 was shown to be associated with a decreased risk of glaucoma 54-56 .”

What the sources say

• ?Not checked — no full text of the sourcecites [54] Mabuchi, F. et al. The apolipoprotein E gene polymorphism is associated with open angle glaucoma in the Japanese population. Mol. Vis. 11, 609–612 (2005).
• ?Not checked — no full text of the sourcecites [55] Lam, C. Y. et al. Association of apolipoprotein E polymorphisms with normal tension glaucoma in a Chinese population. J. Glaucoma 15, 218–222 (2006). source
• Supported

  The Discussion states that APOE ε4 is inversely associated with primary open-angle glaucoma, most strongly with normal-tension glaucoma. This supports the citing sentence’s general description of a decreased risk of glaucoma. (LLM, conf=0.93)

  cites [56] Margeta, M. A. et al. Association of APOE with primary open-angle glaucoma suggests a protective effect for APOE ε4. Invest. Ophthalmol. Vis. Sci. 61, 3 (2020). source

In the paper

“Although TGFβ signaling was suggested to play both beneficial and detrimental roles in AD 57 , its overproduction in astrocytes promotes cerebrovascular fibrosis and amyloidosis 58 .”

What the sources say

• Supported

  The Introduction explicitly says that previous findings suggest TGF-βs are likely to have both beneficial and detrimental effects in AD. The separate claim about astrocytic overproduction is attached to citation 58, not the citation being audited. (LLM, conf=0.95)

  cites [57] Tesseur, I. et al. Deficiency in neuronal TGF-β signaling promotes neurodegeneration and Alzheimer’s pathology. J. Clin. Invest. 116, 3060–3069 (2006). source

In the paper

“Moreover, TGFβ1 is implicated in vascular dementia to promote abnormal vascular remodeling and was proposed as a therapeutic target for AD 59 .”

What the sources say

• Partly supported

  The sections on VaD pathogenesis and vascular remodeling link TGF-β1 to vascular degeneration, fibrosis, and abnormal remodeling in vascular dementia. The paper proposes targeting TGF-β signaling to treat vascular dementia, but does not specifically propose it as a therapeutic target for Alzheimer’s disease (pages unavailable in our copy). (LLM, conf=0.87)

  cites [59] Kandasamy, M. et al. TGF-β signaling: a therapeutic target to reinstate regenerative plasticity in vascular dementia? Aging Dis. 11, 828–850 (2020). sourceExperimental — accuracy not yet measured

In the paper

“A TGFβ-enriched milieu in the brains of individuals with AD that carry the APOE4 allele suppressed astrocyte activation, consistent with previous reports showing astrocyte suppression in response to the TGFβ ligand 50 , and deletion of Tgfbr2 (ref. 31) or Smad2 / Smad3 activates astrocytes.”

What the sources say

• Supported

  The citation is attached specifically to Tgfbr2 deletion, not Smad2/Smad3 deletion. The Results section (page unavailable) reports that loss of TGFβ signaling in microglia following Tgfbr2 deletion leads to early postnatal astrocyte activation; it does not establish that Tgfbr2 was deleted in astrocytes themselves. (LLM, conf=0.91)

  cites [31] Arnold, T. D. et al. Impaired αVβ8 and TGFβ signaling lead to microglial dysmaturation and neuromotor dysfunction. J. Exp. Med. 216, 900–915 (2019). source

In the paper

“Although LGALS3 was reported to promote Aβ oligomerization and toxicity, these studies were performed using either global Lgals3 -KO mice or Aβ monomers precultured with LGALS3 before injection into the brain 52,53 .”

What the sources say

• Partly supported

  The Results section reports that galectin-3 accompanied the formation of insoluble Aβ aggregates after Aβ monomers were injected into mouse hippocampi; Aβ alone produced no such deposits. The Discussion also links galectin-3 to harmful Aβ-associated inflammatory responses and reduced cognitive performance in 5xFAD mice. But the paper does not establish that galectin-3 promotes Aβ oligomerization specifically, or directly demonstrate increased toxicity of Aβ oligomers. (LLM, conf=0.87)

  cites [52] Boza-Serrano, A. et al. Galectin-3, a novel endogenous TREM2 ligand, detrimentally regulates inflammatory response in Alzheimer’s disease. Acta Neuropathol. 138, 251–273 (2019). sourceExperimental — accuracy not yet measured
• Supported

  The Discussion (page unavailable) states that Gal-3 facilitates Aβ oligomerization, and the Results report significantly less oligomerization in Gal-3-knockout mice than in wild-type mice after Aβ injection. The paper also describes Gal-3 as promoting Aβ toxicity, consistent with the attributed claim. (LLM, conf=0.92)

  cites [53] Tao, C. C. et al. Galectin-3 promotes Aβ oligomerization and Aβ toxicity in a mouse model of Alzheimer’s disease. Cell Death Differ. 27, 192–209 (2020). source

In the paper

“In addition to the classical role of APOE in cholesterol transport, APOE4 acquires a novel function in the nucleus, where it translocates and directly binds DNA to affect the transcription of genes associated with AD 45,46 .”

What the sources say

• Supported

  The “Other Studies Supporting Nuclear Localization of ApoE” section reports ApoE4 nuclear localization, direct binding to DNA, and activation of genes involved in programmed cell death and inflammation. The Concluding Remarks describe this transcriptional role as a potential novel function beyond cholesterol transport. Page numbers are not provided in our copy. (LLM, conf=0.90)

  cites [45] Rohn, T. T. & Moore, Z. D. Nuclear localization of apolipoprotein E4: a new trick for an old protein. Int. J. Neurol. Neurother. 4, 067 (2017). source
• Supported

  The Abstract reports that ApoE4 translocates to the nucleus, binds double-stranded DNA, and functions as a transcription factor. The Discussion reports ApoE4-specific promoter-binding sites, including sites associated with genes implicated in AD. The supplied passages do not specify page numbers. (LLM, conf=0.93)

  cites [46] Theendakara, V. et al. Direct transcriptional effects of apolipoprotein E. J. Neurosci. 36, 685–700 (2016). source

In the paper

“Validation data for non-commercial antibodies: anti-Fcrls mab was published by Butovsky et al. 2014 (PMID: 24316888). Validation data for anti-Apoe mab was published by Kim et al. 2012 (PMID: 23129750), anti-Abeta mab was published by Bero et al. 2012 (PMID: 22457485), and anti-Itgb8 mAb was published by Dodagatta-Marri et al., 2021 (PMID: 34233193).”

What the sources say

• Supported

  The citation to Butovsky et al. applies specifically to the anti-FCRLS monoclonal antibody, not the other antibodies in the sentence. The Methods identify the newly generated antibody as clone 4G11, and the Results report its staining of adult microglia and lack of staining in the tested peripheral myeloid cells. Page numbers are not provided in our copy. (LLM, conf=0.93)

  cites Butovsky et al. 2014 source
• ?Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  cites Kim et al. 2012
• Partly supported

  The Materials and methods section (Aβ plaque deposition; page unavailable) identifies HJ3.4 as an in-house anti-Aβ monoclonal antibody, and the Results report its use to stain and quantify Aβ plaques. These passages support the antibody’s identification and use, but do not present antibody-specific validation data, such as specificity controls. The other antibodies in the citing sentence are attributed to other works, not to Bero et al. (LLM, conf=0.82)

  cites Bero et al. 2012 sourceExperimental — accuracy not yet measured

In the paper

“Validation data for all commercial antibodies are available on the manufacturer's website including previously published papers as below:”

What the sources say

• ?Could not verify

  The STAR*METHODS Key Resources Table lists antibody manufacturers and catalog numbers, but does not say that validation data for all commercial antibodies are available on manufacturers’ websites or in previously published papers. Searches for the quoted statement and for antibody validation and manufacturer websites found no passage addressing that availability claim; the indexed passages provide no page number. (LLM, conf=0.72)

  cites Krasemann et al., 2017 sourceExperimental — accuracy not yet measured
• ?Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  cites Lin et al., 2019
• ?Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  cites Staszewski et al., 2019

In the paper

“Sample sizes were chosen based on prior publications using the APP/PS1 and P301S mouse models, which provided estimations of expected effect sizes and variance.”

What the sources say

• Partly supported

  The Cerebral amyloidosis results and Fig. 6 report APPPS1-21 outcomes, sample sizes, and measures of variability that could inform estimates for that model. The paper does not study P301S mice or state that its results were used to choose the citing study’s sample sizes. (LLM, conf=0.82)

  cites Radde et al., 2006 sourceExperimental — accuracy not yet measured
• Partly supported

  The Methods > Animals passage says sample sizes were chosen using estimates to provide 80% power to detect differences of 20% or greater. It does not say those estimates came from prior APP/PS1 or P301S publications, or specify estimates of variance. No page number is available in our copy. (LLM, conf=0.86)

  cites Shi et al., 2017 sourceExperimental — accuracy not yet measured

In the paper

“Immunohistochemistry showed an enhanced CLEC7A + MGnD response and increased astrocytic activation, as determined by Serpina3n expression around β-amyloid (Aβ) plaques (Fig. 2i-m and Supplementary Table 2).”

In the paper

“Immunohistochemistry showed an enhanced CLEC7A + MGnD response and increased astrocytic activation, as determined by Serpina3n expression around β-amyloid (Aβ) plaques (Fig. 2i-m and Supplementary Table 2).”

In the paper

“IPA identified IGF-1 as the most activated upstream regulator, whereas TGFβ1 was the top suppressed upstream regulator in astrocytes in response to APOE4 -cKO MGnD (Fig. 5m).”

In the paper

“RNA-seq analysis of cortical microglia revealed an induction of MGnD-related genes ( Apoe , Cd300ld , Cd74 and Axl ), while the expression of homeostatic genes ( Tmem119 , Siglech , Mertk and Havcr2 ) was suppressed (Fig. 8e and Supplementary Table 8).”

In the paper

“Fig. 7 | Impaired induction of the MGnD signature and astrocyte activation in individuals with AD that carry the APOE4 allele.”

In the paper

“Moreover, we found reduced SMAD3 phosphorylation and increased APOE immunoreactivity in Itgb8 -cKO mice (Fig. 8g-i).”

In the paper

“Genetic deletion of Itgb8 specifically in the cortex in Emx1 Cre : Itgb8 fl/fl ( Itgb8 -cKO) mice showed a complete absence of homeostatic TMEM119 + microglia, while LGALS3 and CLEC7A were highly expressed in cortical microglia (Fig. 8a and Extended Data Fig. 8a-c).”

In the paper

“We identified LGALS3 as a critical MGnD molecule that is restored in microglia following the deletion of APOE4 and is associated with increased astrocytic activation and reduced plaque pathology.”

In the paper

“Moreover, microglial pSMAD3 immunoreactivity as a marker of TGFβ signaling was increased in the brains of females with AD that carry the APOE4 allele, indicative of a homeostatic microglial signature.”

In the paper

“Mechanistically, the genetic deletion of Itgb8 or Inpp5d was sufficient to restore the MGnD response and astrocyte activation and reduce plaque load in AD mice.”

In the paper

“In the brains of individuals with AD that carry the APOE4 allele, we found a sex-dependent impairment of the MGnD signature, with a pronounced reduction in astrocyte activation observed in females.”

In the paper

“These findings indicate that APOE4 predisposes microglia toward a homeostatic signature that interferes with microglial responses to acute neurodegeneration, and targeting microglial APOE4 or PU.1 can restore MGnD induction.”

In the paper

“Fig. 8 | Blocking ITGB8-TGFβ signaling enhances the MGnD response and reduces AD pathology in APP/PS1 mice.”

In the paper

“The reproducibility in microglial gene expression profiles indicates that regional deletion of Itgb8 suppresses TGFβ signaling, leading to an induction of the MGnD phenotype.”

In the paper

“These results support the role of INPP5D as a microglial homeostatic checkpoint, and its deletion is beneficial in mitigating AD pathology via the induction of the MGnD response.”

In the paper

“Tissues that were not adequately perfused were not further analyzed to eliminate autofluorescence associated with blood contamination.”

In the paper

“These results suggest that nuclear localization of APOE4 may directly repress the transcription of MGnD genes, a function absent in APOE3-expressing microglia, which is alleviated following the deletion of APOE4 .”

In the paper

“Biological outliers were determined by PCA plotting and heat map visualization and removed for final analysis.”

In the paper

“All comparison groups were assessed for normal distribution.”

In the paper

“All the experimental procedures using animals were approved by the Institutional Animal Care and Use Committee at Brigham and Women's Hospital, Harvard Medical School and University of California, San Francisco.”

In the paper

“Thus, APOE may have a dual role in controlling MGnD responses based on its subcellular localization, which may be altered in APOE4-expressing microglia, accounting for the different impact on neurodegeneration detected in tau mice following the deletion of microglial APOE3 compared to APOE4 .”

In the paper

“The postmortem interval was limited to 10 h to ensure tissue quality.”

In the paper

“Potential technical outliers were removed for further analysis.”

In the paper

“Donors gave informed consent to donate their brains to NBB.”

In the paper

“The study was approved by the Ethics Committees of the Brigham Women's Hospital and was compliant with the World Medical Association Declaration of Helsinki on ethical principles for medical research involving humans.”

In the paper

“All RT-qPCRs were performed in duplicate, and levels of mRNA are presented as relative expression normalized to the expression of Gapdh (mean ± s.e.m.).”

In the paper

“Although TGFβ signaling was suggested to play both beneficial and detrimental roles in AD 57 , its overproduction in astrocytes promotes cerebrovascular fibrosis and amyloidosis 58 .”

What the sources say

• ?Not checked — no full text of the sourcecites [58] Wyss-Coray, T. et al. Amyloidogenic role of cytokine TGF-β1 in transgenic mice and in Alzheimer’s disease. Nature 389, 603–606 (1997). source

In the paper

“The study was approved by the Ethics Committees of the Brigham Women's Hospital and was compliant with the World Medical Association Declaration of Helsinki on ethical principles for medical research involving humans.”

In the paper

“Sample sizes for experiments were chosen based on prior publications using APP/PS1 and P301S mice and human analysis, which defined the expectations for the effect size and variance.”

In the paper

“The following two negative controls were routinely used in immunostaining procedures: (1) staining with isotype control antibody followed by the secondary antibody or (2) staining with the secondary antibody alone.”

In the paper

“In line with these findings, Liu et al. demonstrated that APOE4 reduces the activated microglia signature in response to AD pathology in human brains and in human induced pluripotent stem cell-derived microglia with the APOE4 allele.”

In the paper

“Cells with more than 200 sequencing reads and less than 20% mitochondrial transcripts were selected, and genes with more than 2 reads across all samples entered downstream analyses.”

In the paper

“All data were replicated in at least three biological replicates and independent experiments.”

In the paper

“Extended Data Fig. 7 | Expression of Itgb8 in the adult mouse brain.”

What the sources say

• ?Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  cites Zhang et al. 38
• ?Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  cites Allen Brain Atlas

In the paper

“We discarded unmapped and duplicate fragments.”

In the paper

“Data are representative of 2 independent experiments.”

• Also stated in: § Extended Data Fig. 8 | Blocking Itgb8 signaling enhances MGnD response · p. 32 · plain

  “Data are representative of 2 independent experiments.”

In the paper

“Mice were allocated to control or experimental groups randomly.”

In the paper

“No samples were excluded from analysis.”

In the paper

“All experimental procedures using animals were approved by the Institutional Animal Care and Use Committee at Brigham and Women's Hospital, Harvard Medical School and University of California San Francisco.”

In the paper

“For all the experiments, investigators were blinded to genotype for data collection and analysis.”

In the paper

“Gating for Ly6c negative and CD11b positive yielded a cell population which was >95% positive for FCRLS, a microglia specific marker which gates were drawn for and positive cells taken for analysis.”

In the paper

“Raw fastq files were first checked for quality using Multiqc sequence analysis.”