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

The APOE4 allele is a major genetic risk factor for late-onset Alzheimer's disease.

“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 .”

• cites [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). sourceNot checked — no full text of the source
• cites [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). sourceNot checked — no full text of the source
• 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). sourcePartly 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)

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• cites [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). sourceNot checked — no full text of the source
• 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). sourceSupported
• 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). sourceSupported

Neurodegenerative microglia (MGnD), also referred to as disease-associated microglia, are regulated by reciprocal suppression of TGFβ and induction of APOE signaling in different neurodegenerative models, including AD.

“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 .”

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

Microglia gene expression patterns are strongly correlated with late-onset Alzheimer's disease.

“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).”

• 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). sourcePartly 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)

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• 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). sourceSupported
• cites [3] Nott, A. et al. Brain cell type-specific enhancer–promoter interactome maps and disease-risk association. Science 366, 1134–1139 (2019). sourcePartly 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)

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In the central nervous system, APOE is upregulated in MGnD.

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

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

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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.

“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 .”

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

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In previous studies, the MGnD phenotype was similar between P301S: APOE4-KI and P301S: APOE3-KI mice.

“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 .”

• 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). sourcePartly 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)

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

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Neurodegeneration is exacerbated in a mouse model of tauopathy expressing APOE4.

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

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

SPI1 (PU.1) binds SMAD3 to establish a homeostatic gene regulatory landscape in microglia.

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

• cites [18] Gosselin, D. et al. Environment drives selection and function of enhancers controlling tissue-specific macrophage identities. Cell 159, 1327–1340 (2014). sourcePartly 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)

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The induction of MGnD genes in microglia with deletions in Itgb8, Tgfbr2, Nrros or Smad2/Smad3 is associated with the suppression of AD risk factor genes, including Bin1, Havcr2 and Inpp5d.

“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).”

• 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). sourceCould 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)

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• 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). sourcePartly 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)

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Analysis of public single-nucleus RNA-seq data of astrocytes from AD brains confirms that the percentage of GFAPhi and SERPINA3+ astrocytes is increased in donors homozygous for APOE3 compared to heterozygous APOE3/APOE4.

“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”

• 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). sourceSupported

• AssumptionRests on an assumption: Mouse models (APP/PS1, P301S) and APOE4-KI/cKO manipulations recapitulate key aspects of human AD and APOE4 biology.
• AssumptionRests on an assumption: Publicly available human scRNA-seq and snRNA-seq datasets are representative and comparable for APOE genotype analyses.

Additional characterization of microglia by analyzing the acute response to neurodegeneration via intracranial injection of apoptotic neurons showed upregulation of antigen presentation- and IFNγ signaling-related genes in Itgb8-cKO mice compared to control mice.

“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).”

• 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). sourceSupported

In an independent cohort described by Zhou et al., microglia from AD individuals heterozygous for APOE3/APOE4 show increased expression of SPI1, TGFB1, GRN.

“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).”

• 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). sourceSupported

• AssumptionRests on an assumption: Mouse models (APP/PS1, P301S) and APOE4-KI/cKO manipulations recapitulate key aspects of human AD and APOE4 biology.
• AssumptionRests on an assumption: Publicly available human scRNA-seq and snRNA-seq datasets are representative and comparable for APOE genotype analyses.

Recent studies showed that microglial deletion of Inpp5d protects against plaque-induced neuronal dystrophy in transgenic AD mice.

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

• 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). sourceSupported
• cites [42] Iguchi, A. et al. INPP5D modulates TREM2 loss-of-function phenotypes in a β-amyloidosis mouse model. iScience 26, 106375 (2023). sourceNot checked — no full text of the source

Analysis of publicly available human brain scRNA-seq data shows increased expression of TGFβ-signaling genes and downstream AD risk factor genes, including INPP5D, in females heterozygous for APOE3/APOE4.

“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.”

• 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). sourceSupported

• AssumptionRests on an assumption: Mouse models (APP/PS1, P301S) and APOE4-KI/cKO manipulations recapitulate key aspects of human AD and APOE4 biology.
• AssumptionRests on an assumption: Publicly available human scRNA-seq and snRNA-seq datasets are representative and comparable for APOE genotype analyses.

ITGB8 plays a critical role in the activation of latent TGFβ1.

“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.”

• 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). sourceSupported

In APOE4-KI glaucoma mice, MGnD responses are impaired, similar to Apoe-/- mice.

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

• 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). sourceSupported

APOE4 predisposes to AD pathology in part via the induction of TGFβ-dependent microglia homeostatic regulators that impair microglia-astrocyte cross-talk in response to neurodegeneration.

“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.”

• 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). sourceSupported

• AssumptionRests on an assumption: Mouse models of AD (APP/PS1, tau, P301S) faithfully represent key aspects of human AD pathology and microglial responses.
• AssumptionRests on an assumption: The MGnD signature observed in mouse microglia corresponds to the human MGnD signature.

Reactive astrocytes play a beneficial role in limiting AD pathology.

“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 .”

• 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). sourceSupported

Microglial APOE4 shows increased nuclear localization in AD brains.

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

• 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). sourcePartly 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)

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IFNγ response plays a critical role in the acquisition of beneficial pre-MGnD in AD mice.

“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 .”

• 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). sourceSupported

APOE4-expressing microglia exhibit reduced phagocytic IBA1+ cell numbers in the injection site compared to APOE3-expressing microglia.

“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).”

APOE4-expressing microglia demonstrate an impaired response to acute neurodegeneration compared to APOE3-expressing microglia.

“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).”

IPA comparing phagocytic to non-phagocytic APOE3- and APOE4-expressing microglia reveals a dysfunctional response of APOE4-expressing microglia to phagocytosis of dead neurons and antigen presentation.

“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).”

Immunostaining of microglia in the injection site shows accumulation of LAMP1+ lysosomes in IBA1+ APOE4-expressing microglia compared to APOE3-expressing microglia.

“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).”

APOE4-expressing microglia display reduced chromatin acetylation compared to APOE3-expressing microglia.

“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).”

APOE4-expressing phagocytic microglia fail to induce an MGnD response of key genes, including Clec7a, Itgax, Lilr4b, Lpl, Lgals3 and Spp1.

“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).”

APOE4-expressing microglia fail to upregulate expression of genes associated with phagocytosis, antigen presentation, IFNγ signaling and autophagosome maturation in response to phagocytosis of apoptotic neurons.

“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).”

APOE4 mice show reduced LGALS3 immunoreactivity compared to APOE3 mice in response to apoptotic neuron injection.

“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).”

Deletion of microglial APOE4 restores the MGnD phenotype associated with neuroprotection in P301S tau transgenic mice.

“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 brains of AD donors carrying the APOE4 allele, there is 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 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.”

Deletion of Inpp5d in microglia restores MGnD-astrocyte cross-talk in APP/PS1 mice.

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

Phagocytosis of dead neurons by FCRLS+ CD11b+ APOE4-expressing microglia is impaired compared to APOE3-expressing microglia.

“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).”

APOE3-expressing phagocytic microglia show induction of an MGnD profile compared to non-phagocytic microglia isolated from the same mice.

“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).”

Deletion of microglial APOE4 decreases pathology in APP/PS1 mice.

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

Genomic regions associated with a homeostatic microglia signature, such as Inpp5d, Havcr2 and Smad3, show enrichment for H3K9ac in APOE4-expressing microglia compared to APOE3-expressing microglia.

“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).”

Deletion of Inpp5d in microglia facilitates plaque clearance in APP/PS1 mice.

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

Cluster 3 was enriched for reactive astrocyte genes, including Gfap, Vim, Cd9 and Serpina3n, compared to cluster 5.

“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).”

• cites ref. 29Not matched

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

Microglial APOE4 deletion further induced the expression of Apoe, Ttr, Cd9, Vim, Gfap and Serpina3n in cluster 3.

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

Microglia from P301S: APOE3-KI mice at 9 months show downregulation of TGFβ-signaling molecules, including Smad3 and Tgfb1, compared to WT: APOE3-KI mice.

“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).”

Reduced expression of Serpina3n and Gfap in mice injected with APOE4-MGnD compared to those injected with APOE3-MGnD.

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

Neuronal loss is significantly reduced in P301S mice with a deletion in microglial APOE4 compared to age-matched P301S: APOE4-KI mice.

“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).”

Microglial Spi1 deletion in APP/PS1 mice results in a reduction in plaque load.

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

Comparing Spi1 deletion and APOE4 deletion in phagocytic microglia identified common homeostatic genes downregulated in both conditions.

“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).”

scRNA-seq of brain cells from APP/PS1: APOE4-KI and APP/PS1: APOE4-cKO mice identified six clusters showing microglia-like expression profiles.

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

GFAP immunoreactivity around Aβ plaques is decreased in APP/PS1: APOE4-KI mice compared to APP/PS1: APOE3-KI mice.

“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).”

Conditional deletion of APOE4 in microglia reduces Plin2+ lipid droplet accumulation in APP/PS1 mice.

“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).”

Restoration of an MGnD phenotype in APP/PS1: APOE4-cKO mice was accompanied by a significant reduction in LAMP1+ dystrophic neurites.

“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).”

Cross-talk analysis identified LGALS3 as the top microglial ligand interacting with astrocyte receptors after deletion of APOE4 in microglia.

“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).”

Deletion of microglial APOE4 restores downregulation of homeostatic genes in response to phagocytosis of apoptotic neurons.

“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).”

Microglial APOE4 deletion in P301S mice is associated with reduced tau hyperphosphorylation.

“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).”

RNA-seq analysis of microglia from APP/PS1: APOE4-KI mice treated with PU.1 pharmacological inhibitors shows induction of the MGnD signature.

“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).”

Microglia from P301S: APOE4-KI mice show reduced MGnD compared to age-matched P301S: APOE3-KI mice.

“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).”

Microglial APOE4 deletion is sufficient to restore CLEC7A immunoreactivity in P301S mice.

“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).”

Clec7a hi Lgals3 hi microglia exhibited an enhanced MGnD signature compared to Clec7a hi Lgals3 lo microglia in APP/PS1: APOE4-cKO mice.

“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).”

Immunohistochemistry confirmed decreased CLEC7A immunoreactivity in cortical microglia of P301S: APOE4-KI mice compared to age-matched P301S: APOE3-KI mice.

“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).”

Deletion of microglial APOE4 restores expression of key MGnD genes in response to phagocytosis of apoptotic neurons.

“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).”

Microglial Spi1 deletion in APP/PS1 mice results in enhanced CLEC7A+ MGnD around plaques.

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

RNA-seq analysis of sorted microglia shows restoration of MGnD signature in APP/PS1: APOE4-cKO mice compared to APP/PS1: APOE4-KI mice.

“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).”

Comparing Spi1 deletion and APOE4 deletion in phagocytic microglia identified common MGnD genes induced in both conditions.

“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).”

An increased proportion of Clec7a hi Lgals3 hi MGnD was detected following microglial deletion of APOE4 in APP/PS1 mice.

“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).”

Microglia from P301S: APOE3-KI mice at 9 months show upregulation of key MGnD genes, including Clec7a, Lgals3 and Itgax, compared to WT: APOE3-KI mice.

“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).”

Deletion of Spi1 in microglia downregulates homeostatic genes, including Tgfb1, Cd33 and Inpp5d.

“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).”

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).

“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).”

RNA-seq analysis of microglia from APP/PS1: APOE4-KI mice treated with PU.1 pharmacological inhibitors shows suppression of homeostatic genes.

“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).”

Restoration of an MGnD phenotype in APP/PS1: APOE4-cKO mice was accompanied by a significant reduction in HJ3.4B+ Aβ plaque pathology.

“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).”

APOE4-KI microglia display increased levels of certain lipid species compared to APOE3-KI microglia, more pronounced on the APP/PS1 background.

“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).”

Plin2+ lipid droplets accumulate more in microglia in APP/PS1: APOE4-KI mice.

“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).”

scRNA-seq identified three major microglial subtypes: M0 (homeostatic microglia), MGnD, and IFN microglia.

“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”

APOE4-cKO mice show increased recruitment of FCRLS+ CD11b+ microglia compared to APOE4-KI mice.

“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).”

APOE immunoreactivity in GFAP+ astrocytes was restored in APP/PS1: APOE4-cKO mice.

“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).”

LGALS3 immunoreactivity is increased in the injection site of APOE4-cKO mice compared to APOE4-KI mice.

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

Deletion of Spi1 in microglia enhances expression of MGnD genes, including Clec7a and Lgals3.

“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).”

NicheNetR analysis identified LGALS3 as one of the top ligands highly affected by APOE4 deletion in phagocytic microglia.

“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).”

Microglial APOE4 deletion is sufficient to restore the MGnD signature in P301S mice.

“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).”

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.

“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).”

P301S: APOE4-KI mice show increased neuronal loss in cortical layer 5 compared to P301S: APOE3-KI mice.

“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).”

P301S: APOE4-KI mice exhibit increased tau hyperphosphorylation compared to age-matched P301S: APOE3-KI mice.

“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).”

LAMP1+ dystrophic neurite immunoreactivity was enhanced in microglia with an APOE3 deletion.

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

Microglia from P301S: APOE4-KI mice show increased TGFβ-signaling signature compared to age-matched P301S: APOE3-KI mice.

“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).”

APP/PS1: APOE4-cKO mice show restored GFAP immunoreactivity around Aβ plaques.

“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).”

APP/PS1 mice expressing APOE4 have increased plaque pathology compared to APOE3.

“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).”

The proportion of CLEC7A+ and LGALS3+ microglia associated with Aβ plaques was significantly reduced in APP/PS1: APOE4-KI mice.

“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).”

Deletion of microglial APOE4 in APP/PS1 mice resulted in increased recruitment of CLEC7A+ and LGALS3+ MGnD to Aβ plaques.

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

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.

“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 APP/PS1:APOE4-KI mice, anti-ITGB8 treatment restored CLEC7A and GFAP expression.

“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).”

Lgals3 expression was absent in astrocytes.

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

Microglial deletion of Inpp5d induced the MGnD response in APP/PS1 mice associated with reduced Aβ plaque load, as determined by Thioflavin-S and HJ3.4B staining.

“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).”

APOE4-expressing microglia showed enriched Inpp5d locus histone acetylation.

“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).”

APOE4-expressing microglia showed increased Inpp5d expression levels.

“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 APP/PS1 mice, 14 days after anti-ITGB8 injection, Aβ plaque size was significantly decreased compared to control-treated mice.

“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.”

NichNetR receptor-ligand analysis of microglia-astrocyte cross-talk in response to apoptotic neurons identified LGALS3 as the top ligand.

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

Increased GFAP immunoreactivity colocalized with CLEC7A+ MGnD in the cortex of Itgb8-cKO mice.

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

LGALS3 colocalizes with IBA1+ microglia associated with Aβ plaques in female AD individuals heterozygous for APOE3/APOE4.

“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).”

• AssumptionRests on an assumption: Mouse models (APP/PS1, P301S) and APOE4-KI/cKO manipulations recapitulate key aspects of human AD and APOE4 biology.

Functional characterization showed induced phagosome formation, antigen presentation, chemokine signaling and IFNγ signaling in cortical microglia of Itgb8-cKO mice.

“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 brains of females with AD heterozygous for APOE3/APOE4, expression of SMAD3, a downstream adaptor of TGFβ signaling, is upregulated.

“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).”

• AssumptionRests on an assumption: Gene expression changes measured in whole human brain RNA-seq reflect changes in microglial/astrocyte gene expression rather than only changes in cell composition.
• AssumptionRests on an assumption: Mouse models (APP/PS1, P301S) and APOE4-KI/cKO manipulations recapitulate key aspects of human AD and APOE4 biology.

In APP/PS1 mice, 100 ng rLGALS3 treatment reduces plaque load 14 days after injection compared to PBS.

“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).”

• AssumptionRests on an assumption: Recombinant LGALS3 injected into hippocampus and cortex mimics endogenous LGALS3 signaling in APP/PS1 mice.

In APP/PS1:APOE4-KI mice, injection of rLGALS3 reduces plaque load.

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

• AssumptionRests on an assumption: Recombinant LGALS3 injected into hippocampus and cortex mimics endogenous LGALS3 signaling in APP/PS1 mice.

In APP/PS1 mice, anti-ITGB8 treatment increased MHC class II+ immunoreactivity around the injection site.

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

Astrocytes from APOE4-cKO mice show reciprocal upregulation of Gfap, Serpina3n, Ttr, Vim and downregulation of Itgav, Tgfb1.

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

In individuals heterozygous for APOE3/APOE4, expression of TGFβ1-signaling-related genes including TGFBR3, TGFB2, ITGB8 is significantly increased.

“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).”

• AssumptionRests on an assumption: Mouse models (APP/PS1, P301S) and APOE4-KI/cKO manipulations recapitulate key aspects of human AD and APOE4 biology.

In female AD individuals heterozygous for APOE3/APOE4, brain expression of S100A, GFAP, VIM, LGALS3 is reduced.

“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).”

• AssumptionRests on an assumption: Gene expression changes measured in whole human brain RNA-seq reflect changes in microglial/astrocyte gene expression rather than only changes in cell composition.
• AssumptionRests on an assumption: Mouse models (APP/PS1, P301S) and APOE4-KI/cKO manipulations recapitulate key aspects of human AD and APOE4 biology.

GFAP immunoreactivity associated with Aβ plaques is reduced in brains of females with AD heterozygous for APOE3/APOE4 compared to homozygous APOE3.

“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).”

• AssumptionRests on an assumption: Mouse models (APP/PS1, P301S) and APOE4-KI/cKO manipulations recapitulate key aspects of human AD and APOE4 biology.

In 4-month-old APP/PS1 mice, three days after injection of anti-ITGB8 antibody, microglia showed increased antigen presentation and IFNγ signaling compared to controls.

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

LGALS3-mediated interactions with astrocytes are reduced in APOE4-expressing microglia phagocytosing apoptotic neurons compared to APOE3-expressing microglia.

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

In cortical tissue from female AD individuals heterozygous for APOE3/APOE4, LGALS3 immunoreactivity is reduced.

“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).”

• AssumptionRests on an assumption: Mouse models (APP/PS1, P301S) and APOE4-KI/cKO manipulations recapitulate key aspects of human AD and APOE4 biology.

Microglial APOE4 cell-autonomously negatively regulates the acquisition of the MGnD phenotype in response to neurodegeneration.

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

The increased MGnD response in association with Aβ plaques was accompanied by increased GFAP+ immunoreactivity following the deletion of microglial Inpp5d.

“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).”

RNAscope shows reduced Itgb8 expression in astrocytes from APP/PS1:APOE4-cKO mice compared to APP/PS1:APOE4-KI mice.

“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).”

Microglial Smad2/Smad3 deletion results in the suppression of Tmem119 and enhanced expression of MGnD molecules, including Cd68 and Apoe, associated with astrocyte activation.

“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 APP/PS1 mice, rLGALS3 suppresses astrocytic expression of Itgb8 and Itgav.

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

• AssumptionRests on an assumption: Recombinant LGALS3 injected into hippocampus and cortex mimics endogenous LGALS3 signaling in APP/PS1 mice.

In APP/PS1:APOE4-KI mice, anti-ITGB8 treatment reduced plaque pathology.

“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 APP/PS1 mice, injection of recombinant LGALS3 (rLGALS3) into hippocampus and cortex upregulates astrocytic Serpina3n and Vim in a dose-dependent manner 3 days after injection.

“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).”

• AssumptionRests on an assumption: Recombinant LGALS3 injected into hippocampus and cortex mimics endogenous LGALS3 signaling in APP/PS1 mice.

Inpp5d deletion in microglia was sufficient to reduce LAMP1+ dystrophic neurites in APP/PS1 mice.

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

Deletion of Itgb8 promoted microglial Aβ phagocytosis in response to acute cranial injection of Aβ.

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

In APP/PS1 mice, 100 ng rLGALS3 treatment increases astrocyte association with Aβ plaques 14 days after injection compared to PBS.

“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).”

• AssumptionRests on an assumption: Recombinant LGALS3 injected into hippocampus and cortex mimics endogenous LGALS3 signaling in APP/PS1 mice.

In male AD individuals heterozygous for APOE3/APOE4, whole brain RNA-seq shows significant reduction in expression of MGnD genes including CLEC7A, AXL, LYZ, CD300LG, HLA-DQB2.

“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).”

• AssumptionRests on an assumption: Gene expression changes measured in whole human brain RNA-seq reflect changes in microglial/astrocyte gene expression rather than only changes in cell composition.
• AssumptionRests on an assumption: Mouse models (APP/PS1, P301S) and APOE4-KI/cKO manipulations recapitulate key aspects of human AD and APOE4 biology.

AD risk factor genes, including Bin1, Inpp5d and Havcr2, were reduced in expression in all datasets.

“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).”

Microglial APOE4 deletion restores LGALS3-mediated interactions with astrocytes.

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

Among top genes upregulated in brains of females with AD heterozygous for APOE3/APOE4 are several AD risk factor genes, including ABCA7, IFNAR1, APP, BIN1, CD33, HAVCR2.

“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)”

• AssumptionRests on an assumption: Gene expression changes measured in whole human brain RNA-seq reflect changes in microglial/astrocyte gene expression rather than only changes in cell composition.
• AssumptionRests on an assumption: Mouse models (APP/PS1, P301S) and APOE4-KI/cKO manipulations recapitulate key aspects of human AD and APOE4 biology.

In mice with tau and amyloid pathology, deletion of microglial APOE4 restored induction of an MGnD response.

“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.”

Immunohistochemistry confirms SMAD3 activation and pSMAD3 immunoreactivity in IBA1+ microglia in females with AD heterozygous for APOE3/APOE4.

“Immunohistochemistry confirmed SMAD3 activation and phosphorylated SMAD3 (pSMAD3) immunoreactivity in IBA1 + microglia in females with AD that are heterozygous for the APOE3 and APOE4 alleles (Fig. 7i,j and Supplementary Table 7).”

• AssumptionRests on an assumption: Mouse models (APP/PS1, P301S) and APOE4-KI/cKO manipulations recapitulate key aspects of human AD and APOE4 biology.

In APP/PS1:APOE4-KI mice, injection of rLGALS3 restores CLEC7A and GFAP induction.

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

• AssumptionRests on an assumption: Recombinant LGALS3 injected into hippocampus and cortex mimics endogenous LGALS3 signaling in APP/PS1 mice.

In male AD individuals heterozygous for APOE3/APOE4, whole brain RNA-seq shows induction of ITGB8 expression.

“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).”

• AssumptionRests on an assumption: Gene expression changes measured in whole human brain RNA-seq reflect changes in microglial/astrocyte gene expression rather than only changes in cell composition.
• AssumptionRests on an assumption: Mouse models (APP/PS1, P301S) and APOE4-KI/cKO manipulations recapitulate key aspects of human AD and APOE4 biology.

KEGG analysis shows enrichment of pathways associated with neurodegenerative diseases, reactive oxygen species, phagosome formation and proteolysis in females with AD homozygous for APOE3.

“KEGG analysis showed enrichment of pathways associated with neurodegenerative diseases, reactive oxygen species, phagosome formation and proteolysis in females with AD that are homozygous for the APOE3 allele (Fig. 7e).”

• AssumptionRests on an assumption: Gene expression changes measured in whole human brain RNA-seq reflect changes in microglial/astrocyte gene expression rather than only changes in cell composition.
• AssumptionRests on an assumption: Mouse models (APP/PS1, P301S) and APOE4-KI/cKO manipulations recapitulate key aspects of human AD and APOE4 biology.

In individuals heterozygous for APOE3/APOE4, expression of astrocyte activation genes including CST3, HSP90AB1, ALDOC is reduced.

“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).”

• AssumptionRests on an assumption: Mouse models (APP/PS1, P301S) and APOE4-KI/cKO manipulations recapitulate key aspects of human AD and APOE4 biology.

Expression of MGnD genes, such as APOE, SPP1, HLA-DQB1, LGALS3, is reduced in females heterozygous for APOE3/APOE4.

“Notably, the expression of MGnD genes, such as APOE , SPP1 , HLA-DQB1 and LGALS3 , was reduced in females that are heterozygous for the APOE3 and APOE4 alleles (Extended Data Fig. 6a).”

• AssumptionRests on an assumption: Mouse models (APP/PS1, P301S) and APOE4-KI/cKO manipulations recapitulate key aspects of human AD and APOE4 biology.
• AssumptionRests on an assumption: Publicly available human scRNA-seq and snRNA-seq datasets are representative and comparable for APOE genotype analyses.

Astrocytes from APOE4-cKO mice in acute and chronic neurodegeneration models show marked overlap with cluster 3 astrocytes from APP/PS1:APOE4-cKO mice.

“These astrocytes showed a marked overlap with cluster 3 astrocytes from APP/PS1: APOE4 -cKO mice”

Gene expression profiles of cortical microglia from Emx1Cre:Itgb8fl/fl mice were correlated with Tgfbr2-cKO microglia and previously published microglia transcriptomes from Nrros-KO and Smad2/Smad3-cKO mice.

“Gene expression profiles of cortical microglia from Emx1 Cre : Itgb8 fl/fl mice were correlated with Tgfbr2 -cKO microglia (Fig. 8j) and previously published microglia transcriptomes from Nrros -KO 40 and Smad2 / Smad3 -cKO mice (Extended Data Fig. 9e-h).”

• cites [40] Wong, K. et al. Mice deficient in NRROS show abnormal microglial development and neurological disorders. Nat. Immunol. 18, 633–641 (2017). sourceNot checked — no full text of the source

RNAscope analysis confirms induction of ITGB8 in GFAP+ astrocytes in males with AD heterozygous for APOE3/APOE4 compared to homozygous APOE3.

“RNAscope analysis confirmed the induction of ITGB8 in GFAP + astrocytes in males with AD that are heterozygous for the APOE3 and APOE4 alleles compared to those that are homozygous for the APOE3 allele (Extended Data Fig. 6g-i).”

• AssumptionRests on an assumption: Mouse models (APP/PS1, P301S) and APOE4-KI/cKO manipulations recapitulate key aspects of human AD and APOE4 biology.

Cortical microglia in Itgb8-cKO mice did not express the peripheral monocyte lineage gene Ms4a3.

“Of note, cortical microglia in Itgb8 -cKO mice did not express the peripheral monocyte lineage gene Ms4a3 (ref. 39; Supplementary Table 8).”

• cites ref. 39Not matched

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

In mice with tau and amyloid pathology, deletion of microglial APOE4 increased microglial and astrocytic association with Aβ plaques.

“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.”

In P301S mice, deletion of microglial APOE3 reduced CLEC7A expression to levels comparable to APOE4 KI.

“Deletion of microglial APOE3 reduced CLEC7A expression to levels comparable to APOE4 KI in P301S mice.”

In mice with tau and amyloid pathology, deletion of microglial APOE4 improved neuronal survival.

“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.”

Targeting microglial APOE4 restores neurodegenerative microglia in APP/PS1 mice.

“Targeting microglial APOE4 restores neuro­ degenerative microglia in APP/PS1 mice.”

Deletion of PU.1 in microglia resulted in robust induction of MGnD genes, including Lgals3.

“Consistent with these findings, we found that expression of the transcription factor PU.1 was upregulated in APOE4 -KI microglia, and its deletion in microglia resulted in a robust induction of MGnD genes, including Lgals3 .”

In brains of female AD donors with the APOE4 allele, LGALS3 is reduced among the top 100 differentially regulated genes.

“Importantly, we found reduced LGALS3 among the top 100 differentially regulated genes in the brains of female AD donors with the APOE4 allele.”

• AssumptionRests on an assumption: The MGnD signature observed in mouse microglia corresponds to the human MGnD signature.

Lipids are significantly altered by genotype in microglia isolated from APOE3-KI, APOE4-KI, APP/PS1:APOE3-KI, and APP/PS1:APOE4-KI mice.

“Heat map of lipids significantly altered by genotype in microglia isolated from APOE3-KI, APOE4-KI, APP/PS1:APOE3-KI, and APP/PS1:APOE4-KI.”

In APOE ε4 AD brains, astrocyte activation is impaired.

“Extended Data Fig. 6 | Impaired induction of MGnD signature and astrocyte activation in APOE ε4 AD brains.”

• cites Olah et al. 34Not matched

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

• cites Zhou et al. 35Not matched

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

In brains from females with AD carrying the APOE4 allele, PU.1 expression was associated with increased SMAD3 expression levels.

“In brains from females with AD that carry the APOE4 allele, PU.1 expression was associated with increased SMAD3 expression levels, which would reinforce the microglial homeostatic signature as a downstream molecule of TGFβ signaling 13,18,49 .”

Deletion of microglial APOE4 promotes astrocyte activation in APP/PS1 mice.

“Deletion of microglial APOE4 promotes astrocyte activation in APP/PS1 mice.”

In mice with tau and amyloid pathology, deletion of microglial APOE4 reduced plaque pathology.

“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.”

Pharmacological blockade of ITGB8-TGFβ signaling enhanced the response of MGnD associated with increased plaque clearance in mice with AD.

“Furthermore, pharmacological blockade of ITGB8-TGFβ signaling enhanced the response of MGnD associated with increased plaque clearance in mice with AD.”

There are no differences in APOE expression between P301S:APOE3-KI and P301S:APOE4-KI mice.

“No differences of APOE expression between P301S:APOE3-KI and P301S:APOE4-KI mice.”

ITGB8 blockade resulted in an increased IFNγ response.

“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 .”

In APOE ε4 AD brains, induction of the MGnD signature is impaired.

“Extended Data Fig. 6 | Impaired induction of MGnD signature and astrocyte activation in APOE ε4 AD brains.”

• cites Olah et al. 34Not matched

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

• cites Zhou et al. 35Not matched

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

In males with AD carrying the APOE4 allele, ITGB8 is upregulated.

“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.”

• AssumptionRests on an assumption: The MGnD signature observed in mouse microglia corresponds to the human MGnD signature.

Deletion of microglial APOE4 alleviates lipid dysregulation in APP/PS1 mice.

“Deletion of microglial APOE4 alleviates lipid dysregulation in APP/PS1 mice.”

In APOE4-KI microglia, expression of transcription factor PU.1 was upregulated.

“Consistent with these findings, we found that expression of the transcription factor PU.1 was upregulated in APOE4 -KI microglia, and its deletion in microglia resulted in a robust induction of MGnD genes, including Lgals3 .”

Deletion of microglial APOE4 in APP/PS1 mice promotes astrocyte activation and encapsulation of Aβ plaques.

“We also found that deletion of microglial APOE4 in APP/PS1 mice promotes astrocyte activation and encapsulation of Aβ plaques.”

In brains of females with AD carrying the APOE4 allele, induction of SMAD3 and INPP5D signaling is associated with downregulation of MGnD genes.

“In the brains of females with AD that carry the APOE4 allele, we identified the induction of SMAD3 and INPP5D signaling associated with downregulation of MGnD genes.”

• AssumptionRests on an assumption: The MGnD signature observed in mouse microglia corresponds to the human MGnD signature.

There are increased DEGs in microglia from Itgb8-cKO mice compared to WT littermates.

“Gene ontology network of increased DEGs in microglia from Itgb8-cKO mice compared to WT littermates.”

Blocking Itgb8 signaling enhances MGnD response in APP/PS1 mice.

“Extended Data Fig. 8 | Blocking Itgb8 signaling enhances MGnD response and reduces AD pathology in APP/PS1 mice.”

Blocking Itgb8 signaling reduces AD pathology in APP/PS1 mice.

“Extended Data Fig. 8 | Blocking Itgb8 signaling enhances MGnD response and reduces AD pathology in APP/PS1 mice.”

MGnD-astrocyte cross-talk associated with Aβ plaque encapsulation and clearance is mediated via LGALS3 signaling following microglial APOE4 deletion.

“MGnD-astrocyte cross-talk associated with β-amyloid (Aβ) plaque encapsulation and clearance are mediated via LGALS3 signaling following microglial APOE4 deletion.”

APOE4-mediated induction of ITGB8-TGFβ signaling impairs the MGnD response via upregulation of microglial homeostatic checkpoints, including Inpp5d, in mice.

“Mechanistically, APOE4-mediated induction of ITGB8transforming growth factor-β (TGFβ) signaling impairs the MGnD response via upregulation of microglial homeostatic checkpoints, including Inpp5d , in mice.”

The microglial APOE4-ITGB8-TGFβ pathway is a negative regulator of microglial response to AD pathology.

“We identify the microglial APOE4-ITGB8-TGFβ pathway as a negative regulator of microglial response to AD pathology”

Microglial APOE4 has a negative role in the induction of the MGnD response to neurodegeneration in mice and humans.

“Here, we show in mice and humans a negative role of microglial APOE4 in the induction of the MGnD response to neurodegeneration.”

Deletion of APOE4 in microglia is sufficient to restore the MGnD response to phagocytic stress and neurodegeneration.

“These results suggest a beneficial role of MGnD in limiting AD pathology, which is disrupted by APOE4, and the deletion of APOE4 in microglia is sufficient to restore the MGnD response to phagocytic stress and neurodegeneration.”

APOE4 predisposes microglia toward a homeostatic signature that interferes with microglial responses to acute neurodegeneration.

“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.”

Quantitative RT-qPCR confirmed deletion of human APOE gene in microglia expressing Cx3cr1 CreERT2.

“Quantitative reverse transcription PCR (RT-qPCR) analysis confirmed deletion of the human APOE gene in microglia expressing Cx3cr1 CreERT2 (Fig. 3b), with no significant difference in APOE immunoreactivity comparing P301S: APOE3 -KI and P301S: APOE4 -KI mice (Extended Data Fig. 2a,b).”

Microglial APOE4 deletion restored cross-talk with astrocytes.

“Importantly, microglial APOE4 deletion restored cross-talk with astrocytes (Fig. 5l and Supplementary Table 5).”

MGnD has a beneficial role in limiting AD pathology.

“These results suggest a beneficial role of MGnD in limiting AD pathology, which is disrupted by APOE4, and the deletion of APOE4 in microglia is sufficient to restore the MGnD response to phagocytic stress and neurodegeneration.”

Deletion of microglial APOE4 delays neuron loss.

“These results suggest that microglial expression of APOE4 is important for the MGnD response to tau-mediated neurodegeneration in the cortex, and its deletion in microglia delays neuron loss.”

Deletion of microglial APOE4 restores protective MGnD.

“Deletion of microglial APOE4 restores protective MGnD”

Deletion of microglial APOE4 mitigates AD pathology in mice.

“Deletion of microglial APOE4 mitigates AD pathology in mice”

APOE4 disrupts the beneficial role of MGnD in limiting AD pathology.

“These results suggest a beneficial role of MGnD in limiting AD pathology, which is disrupted by APOE4, and the deletion of APOE4 in microglia is sufficient to restore the MGnD response to phagocytic stress and neurodegeneration.”

Immunostaining for human APOE protein and GFAP validated the deletion of APOE in IBA1+ microglia in APP/PS1: APOE3-cKO and APP/PS1: APOE4-cKO mice.

“Immunostaining for human APOE protein and GFAP validated the deletion of APOE in IBA1 + microglia in APP/PS1: APOE3 -cKO and APP/PS1: APOE4 -cKO mice, despite the detection of APOE immunoreactivity in plaques and astrocytes (Fig. 5e).”

There is no significant difference in APOE immunoreactivity comparing P301S: APOE3-KI and P301S: APOE4-KI mice.

“Quantitative reverse transcription PCR (RT-qPCR) analysis confirmed deletion of the human APOE gene in microglia expressing Cx3cr1 CreERT2 (Fig. 3b), with no significant difference in APOE immunoreactivity comparing P301S: APOE3 -KI and P301S: APOE4 -KI mice (Extended Data Fig. 2a,b).”

APOE4 impairs the microglial response via PU.1.

“APOE4 impairs the microglial response via PU.1”

Microglial expression of APOE4 is important for the MGnD response to tau-mediated neurodegeneration in the cortex.

“These results suggest that microglial expression of APOE4 is important for the MGnD response to tau-mediated neurodegeneration in the cortex, and its deletion in microglia delays neuron loss.”

Targeting microglial APOE4 promotes astrocyte activation and recruitment to plaques in APP/PS1 mice.

“Fig. 5 | Targeting microglial APOE4 promotes astrocyte activation and recruitment to plaques in APP/PS1 mice.”

ITGB8 is critical for the activation of latent TGFβ1.

“which is critical for the activation of latent TGFβ1 (ref. 36)”

• cites ref. 36Not matched

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

Pharmacological targeting of ITGB8-TGFβ signaling provides an approach for therapeutic modulation of innate immunity in AD and dementia.

“Thus, pharmacological targeting of ITGB8-TGFβ signaling in AD can promote the MGnD response and astrocyte activation and provides an approach for therapeutic modulation of innate immunity in AD and dementia.”

Increased TGFβ signaling in APOE4 carriers may predispose to AD via inhibition of MGnD and astrocyte responses to neurodegeneration.

“Together, these findings show increased TGFβ signaling in APOE4 carriers, which may predispose the development of AD via the inhibition of MGnD and astrocyte responses to neurodegeneration.”

• AssumptionRests on an assumption: Mouse models (APP/PS1, P301S) and APOE4-KI/cKO manipulations recapitulate key aspects of human AD and APOE4 biology.

ITGB8-TGFβ signaling plays a critical role in regulating the MGnD response in AD pathology.

“Overall, these results strongly support a critical role of ITGB8-TGFβ signaling in the regulation of an MGnD response in AD pathology.”

Deletion of microglial APOE4 promotes astrocyte activation and recruitment to plaques via LGALS3 in APP/PS1 and P301S mice.

“Fig. 6 | Deletion of microglial APOE4 promotes astrocyte activation and recruitment to plaques via LGALS3 in APP/PS1 and P301S mice.”

MGnD expressing LGALS3 promotes astrocyte activation and recruitment to plaques.

“These findings support the critical role of MGnD expressing LGALS3 in promoting astrocyte activation and their recruitment to plaques.”

Pharmacological targeting of ITGB8-TGFβ signaling in AD can promote the MGnD response and astrocyte activation.

“Thus, pharmacological targeting of ITGB8-TGFβ signaling in AD can promote the MGnD response and astrocyte activation and provides an approach for therapeutic modulation of innate immunity in AD and dementia.”

The human findings are in line with previous results demonstrating enriched Spi1 expression in APOE4-KI mice and restoration of the MGnD signature following genetic deletion of Spi1.

“These findings in humans are in line with our previous results demonstrating enriched Spi1 expression in APOE4 -KI mice (Fig. 1a,b) and restoration of the MGnD signature following genetic deletion of Spi1 (Fig. 2a,b and Supplementary Table 2).”

• AssumptionRests on an assumption: Mouse models (APP/PS1, P301S) and APOE4-KI/cKO manipulations recapitulate key aspects of human AD and APOE4 biology.

APOE4 carriers show increased TGFβ signaling.

“Together, these findings show increased TGFβ signaling in APOE4 carriers, which may predispose the development of AD via the inhibition of MGnD and astrocyte responses to neurodegeneration.”

• AssumptionRests on an assumption: Mouse models (APP/PS1, P301S) and APOE4-KI/cKO manipulations recapitulate key aspects of human AD and APOE4 biology.

The ITGB8-TGFβ axis is a therapeutic intervention for AD.

“These data support the beneficial role of MGnD in restricting AD pathology and identify the ITGB8-TGFβ axis as a therapeutic intervention for AD.”

• AssumptionRests on an assumption: Mouse models of AD (APP/PS1, tau, P301S) faithfully represent key aspects of human AD pathology and microglial responses.
• AssumptionRests on an assumption: The MGnD signature observed in mouse microglia corresponds to the human MGnD signature.

Increased SMAD3 expression would reinforce the microglial homeostatic signature as a downstream molecule of TGFβ signaling.

“In brains from females with AD that carry the APOE4 allele, PU.1 expression was associated with increased SMAD3 expression levels, which would reinforce the microglial homeostatic signature as a downstream molecule of TGFβ signaling 13,18,49 .”

APOE4 impairs the microglial response to acute neurodegeneration.

“APOE4 impairs microglial response to acute neurodegeneration.”

MGnD plays a beneficial role in restricting AD pathology.

“These data support the beneficial role of MGnD in restricting AD pathology and identify the ITGB8-TGFβ axis as a therapeutic intervention for AD.”

• AssumptionRests on an assumption: Mouse models of AD (APP/PS1, tau, P301S) faithfully represent key aspects of human AD pathology and microglial responses.
• AssumptionRests on an assumption: The MGnD signature observed in mouse microglia corresponds to the human MGnD signature.

A TGFβ-enriched milieu in the brains of individuals with AD carrying the APOE4 allele suppressed astrocyte activation.

“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.”

Microglial deletion of Smad2/3 induces an MGnD phenotype.

“Extended Data Fig. 9 | Microglial deletion of Smad2/3 induces MGnD phenotype.”

Microglial deletion of the homeostatic checkpoint Inpp5d facilitates plaque clearance via the induction of an MGnD response.

“Extended Data Fig. 10 | Microglial deletion of the homeostatic checkpoint Inpp5d facilitates plaque clearance via the induction of MGnD response.”