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

In the paper

“The APOE4 allele is the strongest genetic risk factor for late-onset Alzheimer's disease (AD).”

• Also stated in: § A list of authors and their affiliations appears at the end of the paper · p. 2 · plain

  “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 (labeled Materials and Methods; page not provided) reports a significantly higher APOE-e4 frequency in familial Alzheimer disease patients than in controls, supporting its importance as a genetic risk factor. The paper does not compare APOE-e4 with other genetic risk factors to establish the citing sentence’s claim that it is the strongest, and its findings concern predominantly late-onset familial disease rather than all late-onset Alzheimer’s disease. (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
• Supported

  The Abstract states that APOE4 is the primary genetic risk factor for Alzheimer disease and gives increased risks for carriers of one or two alleles. The paper does not explicitly say “late-onset” in that passage, but its risk-factor statement supports the citing sentence’s characterization. (LLM, conf=0.89)

  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). source
• Supported

  The Introduction explicitly calls APOE4 “the greatest genetic risk factor for sporadic Alzheimer’s disease” and reports substantially increased risk compared with APOE3. This supports the citing sentence’s description of APOE4 as the strongest genetic risk factor for late-onset AD. (LLM, conf=0.94)

  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). source

In the paper

“We identified that neurodegenerative microglia (MGnD) 4 , also referred to as disease-associated microglia 5 , are regulated by the reciprocal suppression of transforming growth factor-β (TGFβ) and induction of apolipoprotein E (APOE) signaling in different neurodegenerative models, including AD 4 .”

What the sources say

• Supported

  The Results section titled “Reciprocal induction of APOE and suppression of TGFβ signaling in disease-associated microglia” identifies this pattern across EAE, SOD1 and APP-PS1 models, including the AD model. The Discussion calls MGnD disease-associated microglia and identifies APOE and TGFβ as major regulators. Page numbers are not provided in our copy. (LLM, conf=0.94)

  cites [4] Krasemann, S. et al. The TREM2–APOE pathway drives the transcriptional phenotype of dysfunctional microglia in neurodegenerative diseases. Immunity 47, 566–581 (2017). source
• Supported

  Citation 5 identifies the cells as disease-associated microglia (DAM); the Introduction and Results explicitly use that name for a microglial subtype found in an AD mouse model. The TGFβ–APOE regulatory claim is attached to citation 4, not this source. (LLM, conf=0.94)

  cites [5] Keren-Shaul, H. et al. A unique microglia type associated with restricting development of Alzheimer’s disease. Cell 169, 1276–1290 (2017). source

In the paper

“Genome -wide association meta -analysis studies (GWASs) 1,2 and interactome investigation 3 identified microglia gene expression patterns as strongly correlated with late-onset Alzheimer's disease (AD).”

What the sources say

• Partly supported

  The Results section (page unavailable) reports associations between Alzheimer’s disease risk genes and microglia-specific expression in both mouse and human datasets. But the associations did not survive the stringent Bonferroni correction, and the paper does not report a strong correlation between microglial expression patterns themselves and late-onset Alzheimer’s disease. (LLM, conf=0.87)

  cites [1] Jansen, I. E. et al. Genome-wide meta-analysis identifies new loci and functional pathways influencing Alzheimer’s disease risk. Nat. Genet. 51, 404–413 (2019). sourceExperimental — accuracy not yet measured
• Supported

  The Tissue type, cell type and gene-set enrichment section reports that expression of LOAD-associated genes was significantly associated in six single-cell RNA-sequencing datasets, with microglia the only significant cell type in all six. This supports the citing sentence’s broad characterization of a strong association, though the paper describes enrichment rather than reporting a correlation coefficient. (LLM, conf=0.88)

  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
• Partly supported

  The indexed passage on AD genetics and the microglia interactome (page unavailable) links AD-risk variants to microglia-specific enhancers and identifies 25 microglial genes linked to those variants. This supports an association between microglial gene regulation and AD risk, but it does not report that microglial gene-expression patterns are strongly correlated with late-onset AD. (LLM, conf=0.83)

  cites [3] Nott, A. et al. Brain cell type-specific enhancer–promoter interactome maps and disease-risk association. Science 366, 1134–1139 (2019). sourceExperimental — accuracy not yet measured

In the paper

“In the central nervous system, APOE is upregulated in MGnD 4,5 .”

What the sources say

• Supported

  The Results section on disease-associated microglia reports that Apoe was among the most upregulated genes in the MGnD-associated microglial subset. Another Results section reports Apoe upregulation during disease progression in CNS disease models. These passages support the citing sentence’s claim. (LLM, conf=0.93)

  cites [4] Krasemann, S. et al. The TREM2–APOE pathway drives the transcriptional phenotype of dysfunctional microglia in neurodegenerative diseases. Immunity 47, 566–581 (2017). source
• Partly supported

  The Results report that Apoe expression increases as microglia transition from a homeostatic state to disease-associated microglia (DAM) in an Alzheimer’s mouse model (page unavailable). The paper calls this population DAM, not MGnD, and does not establish in our copy that the two labels are interchangeable. (LLM, conf=0.85)

  cites [5] Keren-Shaul, H. et al. A unique microglia type associated with restricting development of Alzheimer’s disease. Cell 169, 1276–1290 (2017). sourceExperimental — accuracy not yet measured

In the paper

“In previous studies, brain regions of P301S: APOE4 -KI mice demonstrate marked neurodegeneration compared to P301S: APOE3 -KI mice at 9.5 months of age, although the MGnD phenotype was similar between the two groups 12,21 .”

What the sources say

• Supported

  The Results section (page unavailable) states that P301S mice with human APOE4 knocked in develop significantly more hippocampal and entorhinal/piriform cortex volume loss than APOE3-expressing mice at the age studied. The paper identifies that age as 9.5 months. This confirms the quoted neurodegeneration comparison. (LLM, conf=0.92)

  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
• Partly supported

  The paper reports significantly more brain atrophy in P301S/E4 than P301S/E3 mice, particularly in the hippocampus, piriform/entorhinal cortex, and amygdala. The reported comparison is at 9 months, not the claimed 9.5 months (main text, page unavailable). (LLM, conf=0.88)

  cites [21] Shi, Y. et al. ApoE4 markedly exacerbates tau-mediated neurodegeneration in a mouse model of tauopathy. Nature 549, 523–527 (2017). sourceExperimental — accuracy not yet measured

In the paper

“In previous studies, brain regions of P301S: APOE4 -KI mice demonstrate marked neurodegeneration compared to P301S: APOE3 -KI mice at 9.5 months of age, although the MGnD phenotype was similar between the two groups 12,21 .”

What the sources say

• Partly supported

  The Results section reports a DAM/MGnD microglial shift in both P301S/APOE3 and P301S/APOE4 mice and no major differences in microglial subcluster proportions. However, the Discussion says DAM/MGnD gene-expression elevations were greater with APOE4 than with APOE3, so describing the phenotype as simply similar omits that difference. Page numbers were not available in our copy. (LLM, conf=0.83)

  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). sourceExperimental — accuracy not yet measured
• ?Could not verify

  The paper reports greater brain atrophy and neuroinflammation in P301S/E4 than P301S/E3 mice (Abstract, page unavailable), but the claim at issue is that their MGnD phenotypes were similar. A search for “MGnD” found no passage in our copy assessing or comparing that phenotype; the reported microglial gene-expression differences do not settle this specific claim. (LLM, conf=0.75)

  cites [21] Shi, Y. et al. ApoE4 markedly exacerbates tau-mediated neurodegeneration in a mouse model of tauopathy. Nature 549, 523–527 (2017). sourceExperimental — accuracy not yet measured

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 Introduction reports that, in P301S tauopathy mice, APOE4 expression significantly increased neuronal loss and brain-volume loss compared with other APOE isoforms. The Discussion likewise concludes that astrocyte-derived APOE4 contributes to tau-mediated neurodegeneration in a mouse model of tauopathy. (LLM, conf=0.93)

  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
• Supported

  The paper states that ApoE4 aggravated neurodegeneration in the context of tau pathology. Its Extended Data Figure 9 summary also describes greater degeneration with ApoE4 than with other ApoE isoforms in the tauopathy model. (LLM, conf=0.94)

  cites [21] Shi, Y. et al. ApoE4 markedly exacerbates tau-mediated neurodegeneration in a mouse model of tauopathy. Nature 549, 523–527 (2017). source

In the paper

“SPI1, also known as PU.1, binds SMAD3 to establish a homeostatic gene regulatory landscape in microglia 18 .”

What the sources say

• Partly supported

  The Results sections on PU.1 co-localization and natural genetic variation (pages not provided) report that SMAD motifs, including a SMAD3 recognition motif, are associated with PU.1 binding at microglia-specific sites. They do not demonstrate that PU.1 directly binds SMAD3 or establish that this interaction creates a homeostatic gene regulatory landscape. (LLM, conf=0.87)

  cites [18] Gosselin, D. et al. Environment drives selection and function of enhancers controlling tissue-specific macrophage identities. Cell 159, 1327–1340 (2014). sourceExperimental — accuracy not yet measured

In the paper

“The induction of MGnD genes in microglia with deletions in Itgb8 , Tgfbr2 , Nrros or Smad2 / Smad3 (Extended Data Fig. 9e-h) is associated with the suppression of AD risk factor genes, including Bin1 , Havcr2 and Inpp5d 1,2 (Fig. 8j, Extended Data Fig. 9i-l and Supplementary Table 8).”

What the sources say

• ?Could not verify

  The Results sections on implicated genes and microglial gene sets discuss genetic associations with Alzheimer’s disease, but do not identify Bin1, Havcr2 or Inpp5d as risk-factor genes in the passages retrieved. Searches for those genes and for the specified deletions found no passage addressing their suppression or its association with MGnD induction. The cited paper’s copy therefore does not verify the claim. (LLM, conf=0.76)

  cites [1] Jansen, I. E. et al. Genome-wide meta-analysis identifies new loci and functional pathways influencing Alzheimer’s disease risk. Nat. Genet. 51, 404–413 (2019). sourceExperimental — accuracy not yet measured
• Partly supported

  Table 1 (Functional enrichment of significantly associated regions; page unavailable) lists BIN1 and HAVCR2 as Alzheimer’s disease risk loci, and Gene prioritization discusses HAVCR2. The table prints “INPPD5,” not INPP5D, so our copy does not clearly establish the third named gene. The microglial-deletion and gene-suppression findings are presented with the citing authors’ own figure and table references, not attributed to this GWAS. (LLM, conf=0.82)

  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). sourceExperimental — accuracy not yet measured

In the paper

“Analysis of public single-nucleus RNA-seq data 35 of astrocytes from the brains of individuals with AD that are homozygous for the APOE3 allele and those that are heterozygous for the APOE3 and APOE4 alleles confirmed that the percentage of GFAP hi and SERPINA3 + astrocytes is increased in donors that are homozygous for the APOE3 allele compared to in those that are heterozygous for the APOE3 and”

What the sources say

• Supported

  The citation is attached to the public single-nucleus RNA-seq data, not to the citing authors’ subsequent APOE-genotype comparison. The Results section on astrocytes describes the source paper’s analysis of astrocyte nuclei from human AD samples, supporting its identification as the dataset used. That section does not itself report the claimed GFAP-high and SERPINA3-positive genotype comparison. (LLM, conf=0.87)

  cites [35] Zhou, Y. et al. Human and mouse single-nucleus transcriptomics reveal TREM2-dependent and TREM2-independent cellular responses in Alzheimer’s disease. Nat. Med. 26, 131–142 (2020). source

In the paper

“Additional characterization of microglia by analyzing the acute response to neurodegeneration via intracranial injection of apoptotic neurons 4 showed upregulation of antigen presentation- and IFNγ signaling-related genes in Itgb8 -cKO mice compared to in control mice (Extended Data Fig. 8e-g and Supplementary Table 8).”

What the sources say

• Supported

  Split into 2 atoms — 2 confirmed, 0 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.

  cites [4] Krasemann, S. et al. The TREM2–APOE pathway drives the transcriptional phenotype of dysfunctional microglia in neurodegenerative diseases. Immunity 47, 566–581 (2017). source

In the paper

“we found a similar observation in an independent cohort described by Zhou et al. 35 showing increased expression of SPI1 , TGFB1 and GRN in microglia isolated from the brains of individuals with AD that are heterozygous for the APOE3 and APOE4 alleles (Fig. 7h and Extended Data Fig. 6b,c).”

What the sources say

• Supported

  The citation identifies the independent cohort, while the SPI1, TGFB1 and GRN finding is presented as the citing authors’ own observation in their Fig. 7h. Zhou et al.’s Results section (‘Human brain AD gene signatures are distinct from those of the 5XFAD model’; page unavailable) describes the human AD brain cohort and its microglial transcriptomic analysis, supporting that identification. It does not itself report the three-gene, APOE3/APOE4-specific finding. (LLM, conf=0.88)

  cites [35] Zhou, Y. et al. Human and mouse single-nucleus transcriptomics reveal TREM2-dependent and TREM2-independent cellular responses in Alzheimer’s disease. Nat. Med. 26, 131–142 (2020). source

In the paper

“Similarly, recent studies showed that microglial deletion of Inpp5d protects against plaque-induced neuronal dystrophy in transgenic AD mice 41,42 .”

What the sources say

• Supported

  Section 3.4 reports significantly fewer APP-positive dystrophic neurites near Aβ plaques in 5xFAD mice with microglial Inpp5d deletion than in 5xFAD littermate controls. This supports the claim of protection against plaque-associated neuronal dystrophy in a transgenic AD mouse model. (LLM, conf=0.94)

  cites [41] Samuels, J. D. et al. The Alzheimer’s disease risk factor INPP5D restricts neuroprotective microglial responses in amyloid β-mediated pathology. Alzheimer’s Dement. https://doi.org/10.1002/alz.13089 (2023). source
• ?Not checked — no full text of the sourcecites [42] Iguchi, A. et al. INPP5D modulates TREM2 loss-of-function phenotypes in a β-amyloidosis mouse model. iScience 26, 106375 (2023). source

In the paper

“Analysis of publicly available human brain scRNA-seq data 34 showed increased expression of TGFβ-signaling genes and downstream AD risk factor genes, including INPP5D , in females that are heterozygous for the APOE3 and APOE4 alleles.”

What the sources say

• Supported

  The citation appears immediately after “publicly available human brain scRNA-seq data,” identifying the dataset used rather than attributing the subsequent analysis result to Olah et al. In Results > Nature and distribution of the single-cell RNA sequencing data (page unavailable), the paper says it generated human cortical single-cell RNA-seq data and made them publicly available. The claimed TGFβ- and INPP5D-expression finding is not reported in the cited passages, but is presented as the citing authors’ analysis. (LLM, conf=0.91)

  cites [34] Olah, M. et al. Single cell RNA sequencing of human microglia uncovers a subset associated with Alzheimer’s disease. Nat. Commun. 11, 6129 (2020). source

In the paper

“We detected upregulation of ITGB8, which plays a critical role in the activation of latent TGFβ1 (ref. 36) in males with AD that carry the APOE4 allele.”

What the sources say

• Supported

  The paper’s Abstract identifies αvβ8, which contains the ITGB8-encoded β8 subunit, as a TGF-β-activating integrin and identifies TGF-β1 as an isoform activated by integrins. It also reports reduced TGF-β activity in β8-deficient dendritic cells. This supports the attributed role in latent TGF-β1 activation; the citation does not support the separate observation about APOE4 carriers, which is presented as the citing authors’ own finding. (LLM, conf=0.91)

  cites [36] Travis, M. A. et al. Loss of integrin αvβ8 on dendritic cells causes autoimmunity and colitis in mice. Nature 449, 361–365 (2007). source

In the paper

“We recently showed impaired MGnD responses in APOE4 -KI glaucoma mice, similar to Apoe -/-mice 14 .”

What the sources say

• Supported

  The Results section, “APOE4 retinal microglia remain homeostatic in glaucoma,” reports that APOE4 microglia had an attenuated MGnD molecular signature after IOP elevation and explicitly says this was similar to the response in Apoe−/− mice. The Methods section identifies the mice as carrying a human APOE4 allele in place of endogenous murine Apoe. (LLM, conf=0.95)

  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

“These findings in mice and in humans suggest that APOE4 predisposes to AD pathology in part via the induction of TGFβ-dependent microglia homeostatic regulators 13 that impair microglia-astrocyte cross-talk in response to neurodegeneration.”

What the sources say

• Supported

  The Results report that TGF-β is important for microglial development and maintenance, and the Discussion identifies a TGF-β1-dependent microglial molecular signature relevant to homeostatic function (page numbers unavailable). The citation is attached to the TGF-β-dependent microglial regulators, not to the citing authors’ broader APOE4 and microglia–astrocyte cross-talk hypothesis. (LLM, conf=0.90)

  cites [13] Butovsky, O. et al. Identification of a unique TGF-β-dependent molecular and functional signature in microglia. Nat. Neurosci. 17, 131–143 (2014). 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

• Supported

  The Discussion states that reactive proliferating astrocytes can exert a neuroprotective effect in AD and links their reduction to increased amyloid pathology in APP23 mice. The finding is bounded to this mouse model and this astrocyte population. (LLM, conf=0.93)

  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). source

In the paper

“Furthermore, microglial APOE4 shows increased nuclear localization in AD brains 45 .”

What the sources say

• Partly supported

  The “Nuclear Localization of ApoE4” section reports strong labeling of an ApoE4 fragment within microglia in AD brain tissue and nuclear trafficking of that fragment in cultured microglial cells. The “Mechanism of Nuclear Trafficking of ApoE” section also reports nuclear labeling in AD brain tissue. Neither passage establishes that nuclear localization is increased in microglia of AD brains relative to a comparator. (LLM, conf=0.86)

  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). sourceExperimental — accuracy not yet measured

In the paper

“Importantly, ITGB8 blockade resulted in an increased IFNγ response, which we recently showed to play a critical role in the acquisition of beneficial pre-MGnD in AD mice 60 .”

What the sources say

• Supported

  The Discussion states that experiments modulating IFNγ showed the pathway directly regulates the transition to pre-MGnD microglia. It also describes pre-MGnD microglia as protective against plaque-associated pathology in the AD mouse model. Page numbers are not provided in our copy. (LLM, conf=0.93)

  cites [60] Yin, Z. et al. Identification of a protective microglial state mediated by miR-155 and interferon-λ signaling in a mouse model of Alzheimer’s disease. Nat. Neurosci. 26, 1196–1207 (2023). source

In the paper

“Furthermore, APOE4-expressing microglia demonstrated an impaired response to acute neurodegeneration and exhibited reduced phagocytic IBA1 + cell numbers in the injection site compared to APOE3-expressing microglia (Fig. 1i and Extended Data Fig. 1g,h).”

In the paper

“Furthermore, APOE4-expressing microglia demonstrated an impaired response to acute neurodegeneration and exhibited reduced phagocytic IBA1 + cell numbers in the injection site compared to APOE3-expressing microglia (Fig. 1i and Extended Data Fig. 1g,h).”

In the paper

“Ingenuity pathway analysis (IPA) comparing phagocytic to non-phagocytic APOE3- and APOE4-expressing microglia revealed a dysfunctional response of APOE4-expressing microglia to phagocytosis of dead neurons and antigen presentation (Extended Data Fig. 1f and Supplementary Table 1).”

In the paper

“Immunostaining of microglia in the injection site showed accumulation of LAMP1 + lysosomes in IBA1 + APOE4-expressing microglia compared to in APOE3-expressing microglia (Fig. 1i,j).”

In the paper

“Epigenetic analysis of genomic DNA bound to lysine 9 acetylated histone 3 (H3K9ac) by anti-H3K9ac chromatin immunoprecipitation with sequencing (ChIP-seq) analysis of isolated microglia revealed that APOE4-expressing microglia displayed reduced chromatin acetylation compared to APOE3-expressing microglia (Extended Data Fig. 1a and Supplementary Table 1).”

In the paper

“APOE4-expressing phagocytic microglia, however, failed to induce an MGnD response of key genes, including Clec7a , Itgax , Lilr4b , Lpl , Lgals3 and Spp1 (Fig. 1g, Extended Data Fig. 1c-e and Supplementary Table 1).”

In the paper

“Moreover, APOE4-expressing microglia failed to upregulate the expression of genes associated with phagocytosis, antigen presentation, interferon-γ (IFNγ) signaling and autophagosome maturation in response to phagocytosis of apoptotic neurons (Fig. 1h and Supplementary Table 1).”

In the paper

“The reduction in LGALS3 immunoreactivity, a key MGnD marker 4,14 , was also observed in APOE4 mice compared to APOE3 mice in response to apoptotic neuron injection (Fig. 1k,l).”

In the paper

“Deletion of microglial APOE4 restores the MGnD phenotype associated with neuroprotection in P301S tau transgenic mice and decreases pathology in APP/PS1 mice.”

In the paper

“In the brains of AD donors carrying the APOE4 allele, we found a sex-dependent reciprocal induction of AD risk factors associated with suppression of MGnD genes in females, including LGALS3 , compared to individuals homozygous for the APOE3 allele.”

In the paper

“Deletion of Inpp5d in microglia restores MGnD-astrocyte cross-talk and facilitates plaque clearance in APP/PS1 mice.”

In the paper

“Fluorescence-activated cell sorting (FACS) analysis of the injection site using the microglia-specific marker FCRLS 4,13,14 demonstrated impaired phagocytosis of dead neurons by FCRLS + CD11b + APOE4-expressing microglia compared to APOE3-expressing microglia (Fig. 1d,e).”

In the paper

“APOE3-expressing phagocytic microglia showed induction of an MGnD profile compared to non-phagocytic microglia isolated from the same mice (Fig. 1f,g and Supplementary Table 1).”

In the paper

“Deletion of microglial APOE4 restores the MGnD phenotype associated with neuroprotection in P301S tau transgenic mice and decreases pathology in APP/PS1 mice.”

In the paper

“Furthermore, genomic regions associated with a homeostatic microglia signature, such as Inpp5d , Havcr2 and Smad3 , showed enrichment for H3K9ac in APOE4-expressing microglia compared to in APOE3-expressing microglia (Extended Data Fig. 1b and Supplementary Table 1).”

In the paper

“Deletion of Inpp5d in microglia restores MGnD-astrocyte cross-talk and facilitates plaque clearance in APP/PS1 mice.”

In the paper

“Cluster 3 was enriched for reactive astrocyte genes, including Gfap , Vim , Cd9 and Serpina3n , compared to cluster 5 (ref. 29; Fig. 5a, Extended Data Fig. 5a,b and Supplementary Table 5).”

What the sources say

• ?Not matched

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

  cites ref. 29

In the paper

“Microglial APOE4 deletion further induced the expression of Apoe , Ttr , Cd9 , Vim , Gfap and Serpina3n in cluster 3 (Fig. 5b).”

In the paper

“Microglia sorted from the brains of P301S: APOE3 -KI mice at 9 months of age demonstrated upregulation of key MGnD genes, including Clec7a , Lgals3 and Itgax , and downregulation of TGFβ-signaling molecules, including Smad3 and Tgfb1 , compared to microglia isolated from WT: APOE3 -KI mice (Fig. 3c and Supplementary Table 3).”

In the paper

“We found reduced expression of Serpina3n and Gfap in mice injected with APOE4 -MGnD compared to those injected with APOE3 -MGnD (Fig. 5k).”

In the paper

“P301S: APOE 4-KI mice showed increased neuronal loss in cortical layer 5 compared to P301S: APOE3 -KI mice, whereas neuronal loss was significantly reduced in P301S mice with a deletion in microglial APOE4 compared to age-matched P301S: APOE4 -KI mice (Fig. 3g,h).”

In the paper

“Microglial Spi1 deletion in APP/PS1 mice resulted in a reduction in plaque load and enhanced CLEC7A + MGnD around plaques (Fig. 2d-g).”

In the paper

“Moreover, by comparing Spi1 deletion and APOE4 deletion in phagocytic microglia (Fig. 1o), we identified common MGnD and homeostatic genes induced and downregulated, respectively, in both conditions (Fig. 2c).”

In the paper

“Unsupervised clustering identified six clusters showing microglia-like expression profiles (Extended Data Fig. 3a-c and Supplementary Table 4).”

In the paper

“Immunohistochemistry showed decreased GFAP immunoreactivity around Aβ plaques in APP/PS1: APOE4 -KI mice compared to that observed in APP/PS1: APOE3 -KI mice, whereas APP/PS1: APOE4 -cKO mice showed restored GFAP immunoreactivity (Fig. 5e,f).”

In the paper

“Immunohistochemistry confirmed the increased accumulation of Plin2 + lipid droplets in microglia in APP/PS1: APOE4 -KI mice, which was reduced following the conditional deletion of APOE4 in microglia (Extended Data Fig. 4b,c).”

In the paper

“The restoration of an MGnD phenotype in APP/PS1: APOE4 -cKO mice was accompanied by a significant reduction in HJ3.4B + Aβ plaque pathology (Fig. 4k,l) and LAMP1 + dystrophic neurites (Fig. 4m,n).”

In the paper

“Cross-talk analysis identified LGALS3 as the top microglial ligand interacting with astrocyte receptors after deletion of APOE4 in microglia (Fig. 6a and Supplementary Table 5).”

In the paper

“Deletion of microglial APOE4 restored the expression of key MGnD genes and downregulation of homeostatic genes in response to phagocytosis of apoptotic neurons (Fig. 1o, Extended Data Fig. 1i and Supplementary Table 1).”

In the paper

“We found that microglial APOE4 deletion was sufficient to restore CLEC7A immunoreactivity and the MGnD signature in P301S mice, which was associated with reduced tau hyperphosphorylation (Fig. 3d-f and Supplementary Table 3).”

In the paper

“RNA-seq analysis of microglia isolated from APP/PS1: APOE4 -KI mice treated with PU.1 pharmacological inhibitors showed an induction of the MGnD signature and suppression of homeostatic genes (Fig. 2h).”

In the paper

“By contrast, microglia from P301S: APOE4 -KI mice showed reduced MGnD and an increased TGFβ-signaling signature compared to microglia from age-matched P301S: APOE3 -KI mice (Fig. 3c and Supplementary Table 3).”

In the paper

“We found that microglial APOE4 deletion was sufficient to restore CLEC7A immunoreactivity and the MGnD signature in P301S mice, which was associated with reduced tau hyperphosphorylation (Fig. 3d-f and Supplementary Table 3).”

In the paper

“Importantly, Clec7a hi Lgals3 hi microglia exhibited an enhanced MGnD signature compared to Clec7a hi Lgals3 lo microglia in APP/ PS1: APOE4 -cKO mice (Fig. 4f and Supplementary Table 4).”

In the paper

“Immunohistochemistry confirmed decreased CLEC7A immunoreactivity in cortical microglia of P301S: APOE4 -KI mice, which exhibited increased tau hyperphosphorylation compared to age-matched P301S: APOE3 -KI mice (Fig. 3d,e).”

In the paper

“Deletion of microglial APOE4 restored the expression of key MGnD genes and downregulation of homeostatic genes in response to phagocytosis of apoptotic neurons (Fig. 1o, Extended Data Fig. 1i and Supplementary Table 1).”

In the paper

“Microglial Spi1 deletion in APP/PS1 mice resulted in a reduction in plaque load and enhanced CLEC7A + MGnD around plaques (Fig. 2d-g).”

In the paper

“RNA-seq analysis of sorted microglia showed restoration of the MGnD signature in APP/PS1: APOE4 -cKO mice compared to APP/PS1: APOE4 -KI mice (Fig. 4c and Supplementary Table 4).”

In the paper

“Moreover, by comparing Spi1 deletion and APOE4 deletion in phagocytic microglia (Fig. 1o), we identified common MGnD and homeostatic genes induced and downregulated, respectively, in both conditions (Fig. 2c).”

In the paper

“An increased proportion of Clec7a hi Lgals3 hi MGnD was detected following microglial deletion of APOE4 in APP/PS1 mice (Fig. 4d,e, Extended Data Fig. 3g,h and Supplementary Table 4).”

In the paper

“Microglia sorted from the brains of P301S: APOE3 -KI mice at 9 months of age demonstrated upregulation of key MGnD genes, including Clec7a , Lgals3 and Itgax , and downregulation of TGFβ-signaling molecules, including Smad3 and Tgfb1 , compared to microglia isolated from WT: APOE3 -KI mice (Fig. 3c and Supplementary Table 3).”

In the paper

“Deletion of Spi1 in microglia enhanced the expression of MGnD genes, including Clec7a and Lgals3 , whereas homeostatic genes were downregulated, including Tgfb1 , Cd33 and Inpp5d (Fig. 2b and Supplementary Table 2).”

In the paper

“scRNA-seq analysis of brain cells isolated from APP/PS1: APOE4 -KI and APP/PS1: APOE4 -cKO mice identified two astrocyte clusters (3 and 5).”

In the paper

“RNA-seq analysis of microglia isolated from APP/PS1: APOE4 -KI mice treated with PU.1 pharmacological inhibitors showed an induction of the MGnD signature and suppression of homeostatic genes (Fig. 2h).”

In the paper

“The restoration of an MGnD phenotype in APP/PS1: APOE4 -cKO mice was accompanied by a significant reduction in HJ3.4B + Aβ plaque pathology (Fig. 4k,l) and LAMP1 + dystrophic neurites (Fig. 4m,n).”

In the paper

“We detected increased levels of certain lipid species in APOE4 -KI microglia compared to that observed in APOE3 -KI microglia, which were more pronounced on the APP/PS1 background (Extended Data Fig. 4a and Supplementary Table 4).”

In the paper

“Immunohistochemistry confirmed the increased accumulation of Plin2 + lipid droplets in microglia in APP/PS1: APOE4 -KI mice, which was reduced following the conditional deletion of APOE4 in microglia (Extended Data Fig. 4b,c).”

In the paper

“identified three major subtypes, which we labeled (1) M0 (homeostatic microglia), which express Tmem119 , P2ry12 and Gpr34 , (2) MGnD, which express Clec7a , Lgals3 and Spp1 , and (3) IFN microglia, which are enriched for Stat1 , Irf7 and Ilfit1”

In the paper

“FACS analysis of cells isolated from the injection site showed increased recruitment of FCRLS + CD11b + microglia in APOE4 -cKO mice compared to in APOE4 -KI mice (Fig. 1m,n).”

In the paper

“Moreover, APOE immunoreactivity in GFAP + astrocytes was also restored in APP/PS1: APOE4 -cKO mice (Fig. 5e,g), confirming results from the scRNA-seq analysis (Fig. 5b).”

In the paper

“Furthermore, LGALS3 immunoreactivity was increased in the injection site of APOE4 -cKO mice compared to in APOE4 -KI mice (Fig. 1p,q).”

In the paper

“Deletion of Spi1 in microglia enhanced the expression of MGnD genes, including Clec7a and Lgals3 , whereas homeostatic genes were downregulated, including Tgfb1 , Cd33 and Inpp5d (Fig. 2b and Supplementary Table 2).”

In the paper

“NicheNetR analysis of differentially regulated ligands in phagocytic microglia and their autocrine interactions with microglial receptors identified LGALS3 as one of the top ligands that is highly affected by APOE4 deletion (Extended Data Fig. 1i and Supplementary Table 1).”

In the paper

“We found that microglial APOE4 deletion was sufficient to restore CLEC7A immunoreactivity and the MGnD signature in P301S mice, which was associated with reduced tau hyperphosphorylation (Fig. 3d-f and Supplementary Table 3).”

In the paper

“IPA of astrocytes from APP/PS1: APOE4 -cKO mice showed upregulation of metabolic pathways, including cholesterol biosynthesis, response to oxidative stress, HIF1α and IGF-1 signaling (Fig. 5d).”

In the paper

“P301S: APOE 4-KI mice showed increased neuronal loss in cortical layer 5 compared to P301S: APOE3 -KI mice, whereas neuronal loss was significantly reduced in P301S mice with a deletion in microglial APOE4 compared to age-matched P301S: APOE4 -KI mice (Fig. 3g,h).”

In the paper

“Immunohistochemistry confirmed decreased CLEC7A immunoreactivity in cortical microglia of P301S: APOE4 -KI mice, which exhibited increased tau hyperphosphorylation compared to age-matched P301S: APOE3 -KI mice (Fig. 3d,e).”

In the paper

“neurites was enhanced in microglia with an APOE3 deletion (Fig. 4n).”

In the paper

“By contrast, microglia from P301S: APOE4 -KI mice showed reduced MGnD and an increased TGFβ-signaling signature compared to microglia from age-matched P301S: APOE3 -KI mice (Fig. 3c and Supplementary Table 3).”

In the paper

“Immunohistochemistry showed decreased GFAP immunoreactivity around Aβ plaques in APP/PS1: APOE4 -KI mice compared to that observed in APP/PS1: APOE3 -KI mice, whereas APP/PS1: APOE4 -cKO mice showed restored GFAP immunoreactivity (Fig. 5e,f).”

In the paper

“The proportion of CLEC7A + and LGALS3 + microglia associated with Aβ plaques was significantly reduced in APP/PS1: APOE4 -KI mice, despite the increased plaque pathology in APP/PS1 mice expressing APOE4 compared to APOE3 (Fig. 4g-j).”

In the paper

“The proportion of CLEC7A + and LGALS3 + microglia associated with Aβ plaques was significantly reduced in APP/PS1: APOE4 -KI mice, despite the increased plaque pathology in APP/PS1 mice expressing APOE4 compared to APOE3 (Fig. 4g-j).”

In the paper

“Deletion of microglial APOE4 in APP/PS1 mice resulted in increased recruitment of CLEC7A + and LGALS3 + MGnD to Aβ plaques (Fig. 4g-j).”

In the paper

“Furthermore, microglial APOE4 deletion increased the ratio of Gfap hi Apoe hi , Gfap hi Serpina3n hi , Gfap hi Vim hi and Gfap hi Cd9 hi astrocytes (Fig. 5c and Extended Data Fig. 5c).”

In the paper

“In APP/PS1: APOE4 -KI mice, treatment with monoclonal neutralizing antibody to ITGB8 restored the expression of CLEC7A and GFAP associated with reduced plaque pathology (Fig. 8o,p).”

In the paper

“Of note, Lgals3 expression was absent in astrocytes (Supplementary Table 4).”

In the paper

“Microglial deletion of Inpp5d induced the MGnD response in APP/PS1 mice (Extended Data Fig. 10a,b and Supplementary Table 8) associated with reduced Aβ plaque load, as determined by Thioflavin-S and HJ3.4B staining (Extended Data Fig. 10c,d,h,j).”

In the paper

“In addition, APOE4-expressing microglia showed increased Inpp5d expression levels (Fig. 1a and Extended Data Fig. 6d,e) and enriched Inpp5d locus histone acetylation (Extended Data Fig. 1b).”

In the paper

“In addition, APOE4-expressing microglia showed increased Inpp5d expression levels (Fig. 1a and Extended Data Fig. 6d,e) and enriched Inpp5d locus histone acetylation (Extended Data Fig. 1b).”

In the paper

“Moreover, 14 d after injection, we found a significant decrease in Aβ plaque size (Fig. 8m,n) in mice treated with anti-ITGB8 compared to control-treated mice.”

In the paper

“NichNetR receptor-ligand analysis of microglia-astrocyte cross-talk in response to apoptotic neurons (Fig. 1m) identified LGALS3 as the top ligand (Fig. 6h).”

In the paper

“We also observed increased GFAP immunoreactivity colocalized with CLEC7A + MGnD in the cortex of Itgb8 -cKO mice (Fig. 8b-d).”

In the paper

“Immunohistochemistry of cortical tissue from females with AD that are heterozygous for the APOE3 and APOE4 alleles confirmed the reduction in LGALS3 immunoreactivity and its colocalization with IBA1 + microglia associated with Aβ plaques (Fig. 7f,g and Supplementary Table 7).”

In the paper

“Functional characterization showed induced phagosome formation, antigen presentation, chemokine signaling and IFNγ signaling in cortical microglia of Itgb8 -cKO mice (Extended Data Fig. 8d).”

In the paper

“In addition, the expression of SMAD3 , a downstream adaptor of TGFβ signaling 33 , was upregulated in the brains of females with AD heterozygous for the APOE3 and APOE4 alleles (Fig. 7b,d and Supplementary Tables 6 and 7).”

In the paper

“Immunohistochemistry of APP/PS1 mice 14 d after treatment with 100 ng of rLGALS3 demonstrated increased astrocyte association with Aβ plaques and reduced plaque load compared to APP/PS1 mice treated with PBS (Fig. 6d,e).”

In the paper

“injection of rLGALS3 into APP/PS1: APOE4 -KI mice restored CLEC7A and GFAP induction and reduced plaque load (Fig. 6k,l).”

In the paper

“Immunohistochemistry confirmed increased major histocompatibility complex class II + (MHC class II + ) immunoreactivity around the injection site (Extended Data Fig. 8j,k).”

In the paper

“including reciprocal upregulation of Gfap , Serpina3n , Ttr and Vim (Fig. 6f) and downregulation of Itgav and Tgfb1 (Fig. 6g and Supplementary Table 5).”

In the paper

“Furthermore, the expression of astrocyte activation genes, including CST3 , HSP90AB1 and ALDOC , was reduced, while TGFβ1-signaling-related genes, including TGFBR3 , TGFB2 and ITGB8 , were significantly increased in expression in individuals that are heterozygous for the APOE3 and APOE4 alleles (Fig. 7n).”

In the paper

“we found reduced expression of S100A , GFAP , VIM and LGALS3 in the brains of female individuals heterozygous for the APOE3 and APOE4 alleles (Fig. 7b,c and Supplementary Tables 6 and 7).”

In the paper

“We also confirmed that GFAP immunoreactivity associated with Aβ plaques was reduced in the brains of females with AD that are heterozygous for the APOE3 and APOE4 alleles compared to those that are homozygous for the APOE3 allele (Fig. 7k,l and Supplementary Table 7).”

In the paper

“Three days after injection in 4-month-old APP/PS1 mice, microglia increased antigen presentation and IFNγ signaling (Fig. 8k,l).”

In the paper

“LGALS3-mediated interactions with astrocytes were reduced in APOE4-expressing microglia phagocytosing apoptotic neurons compared to APOE3-expressing microglia”

In the paper

“Immunohistochemistry of cortical tissue from females with AD that are heterozygous for the APOE3 and APOE4 alleles confirmed the reduction in LGALS3 immunoreactivity and its colocalization with IBA1 + microglia associated with Aβ plaques (Fig. 7f,g and Supplementary Table 7).”

In the paper

“Here, we show a cell-autonomous negative regulation of microglial APOE4 in the acquisition of the MGnD phenotype in response to neurodegeneration.”

In the paper

“Furthermore, the increased MGnD response in association with Aβ plaques was accompanied by increased GFAP + immunoreactivity following the deletion of microglial Inpp5d (Extended Data Fig. 10m,n).”

In the paper

“Furthermore, RNAscope showed reduced Itgb8 expression in astrocytes from APP/PS1: APOE4 -cKO mice compared to in those from APP/PS1: APOE4 -KI mice (Extended Data Fig. 6j,k).”

In the paper

“Using Cx3cr1 Cre : Smad2 / Smad3 fl/fl mice, we confirmed that microglial Smad2 / Smad3 deletion results in the suppression of Tmem119 and enhanced expression of MGnD molecules, including Cd68 and Apoe , associated with astrocyte activation (Extended Data Fig. 9a-d).”

In the paper

“rLGALS3 suppressed the astrocytic expression of Itgb8 and Itgav (subunits of integrin α v β8 (ref. 30; Fig. 6b,c and Supplementary Table 5)”

In the paper

“In APP/PS1: APOE4 -KI mice, treatment with monoclonal neutralizing antibody to ITGB8 restored the expression of CLEC7A and GFAP associated with reduced plaque pathology (Fig. 8o,p).”

In the paper

“RNA-seq analysis of astrocytes 3 d after rLGALS3 injection showed upregulation of Serpina3n and Vim 29 in a dose-dependent manner (Fig. 6b,c).”

In the paper

“Importantly, Inpp5d deletion in microglia was sufficient to reduce LAMP1 + dystrophic neurites in APP/PS1 mice (Extended Data Fig. 10k,l).”

In the paper

“Furthermore, deletion of Itgb8 promoted microglial Aβ phagocytosis in response to acute cranial injection of Aβ (Extended Data Fig. 8h,i).”

In the paper

“Immunohistochemistry of APP/PS1 mice 14 d after treatment with 100 ng of rLGALS3 demonstrated increased astrocyte association with Aβ plaques and reduced plaque load compared to APP/PS1 mice treated with PBS (Fig. 6d,e).”

In the paper

“We found a significant reduction in the expression levels of MGnD genes, including CLEC7A , AXL , LYZ , CD300LG and HLA -DQB2 , and an induction in expression of the upstream regulator of TGFβ signaling ITGB8 in the brains of male individuals with AD heterozygous for the APOE3 and APOE4 alleles (Fig. 7a and Supplementary Tables 6 and 7).”

In the paper

“Importantly, AD risk factor genes, including Bin1 , Inpp5d and Havcr2 , were reduced in expression in all datasets (Fig. 8j, Extended Data Fig. 9i-l and Supplementary Table 8).”

In the paper

“whereas microglial APOE4 deletion restored these interactions (Fig. 6h-j and Supplementary Table 5).”

In the paper

“among the top genes upregulated in the brains of females with AD heterozygous for the APOE3 and APOE4 alleles were several AD risk factor genes, including ABCA7 , IFNAR1 , APP , BIN1 , CD33 and HAVCR2 (Fig. 7b,d and Supplementary Table 6)”

In the paper

“Induction of an MGnD response was restored in mice with tau and amyloid pathology in which microglial APOE4 was deleted, resulting in improved neuronal survival, reduction in plaque pathology and increased microglial and astrocytic association with Aβ plaques.”