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Cited by 120Neuroinflammation and Neurodegeneration MechanismsAlzheimer's disease research and treatmentsNeurological Disease Mechanisms and Treatments

Identification of a protective microglial state mediated by miR-155 and interferon-γ signaling in a mouse model of Alzheimer’s disease

Open access
Yin, Zhuoran, Herron, Shawn, Silveira, Sebastian, Kleemann, Kilian, Gauthier, Christian, Mallah, Dania, Cheng, Yiran, Margeta, Milica A. +15 more·2023·Nature Neuroscience
DOI 10.1038/s41593-023-01355-yPMC PMC10619638
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Abstract

Microglia play a critical role in brain homeostasis and disease progression. In neurodegenerative conditions, microglia acquire the neurodegenerative phenotype (MGnD), whose function is poorly understood. MicroRNA-155 (miR-155), enriched in immune cells, critically regulates MGnD. However, its role in Alzheimer's disease (AD) pathogenesis remains unclear. Here, we report that microglial deletion of miR-155 induces a pre-MGnD activation state via interferon-γ (IFN-γ) signaling, and blocking IFN-γ signaling attenuates MGnD induction and microglial phagocytosis. Single-cell RNA-sequencing analysis of microglia from an AD mouse model identifies Stat1 and Clec2d as pre-MGnD markers. This phenotypic transition enhances amyloid plaque compaction, reduces dystrophic neurites, attenuates plaque-associated synaptic degradation and improves cognition. Our study demonstrates a miR-155-mediated regulatory mechanism of MGnD and the beneficial role of IFN-γ-responsive pre-MGnD in restricting neurodegenerative pathology and preserving cognitive function in an AD mouse model, highlighting miR-155 and IFN-γ as potential therapeutic targets for AD.

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Crossref · 10.1038/s41593-023-01355-y

Cites

71 of 71 references verified0 citation errors · 0 not checkable

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Claims the paper makes

7 of 16 cited sources checked · 3 supported · 0 flagged · accuracy not yet measured

  • Findingown data

    Shared DEGs between Clec7a+ plaque-associated microglia from APP/PS1 vs WT and APP/PS1:miR-155 cKO vs APP/PS1 microglia were associated with enhanced IFN signaling.

    “Shared DEGs from both datasets were associated with enhanced IFN signaling, indicating the IFN pathway as an early response in microglia reacting to remote pathological changes 7,34 (Fig 1h,i).”
    Quote in the paperSubstantial claim2 of 2 sources checked
    • cites [7] Krasemann, S. et al. The TREM2–APOE pathway drives the transcriptional phenotype of dysfunctional microglia in neurodegenerative diseases. Immunity 47, 566–581 (2017). source

      The Results section on the MGnD subset identifies Clec7a+ microglia associated with plaques in APP-PS1 mice, and the Discussion notes some overlap between the MGnD phenotype and an IFNγ-induced phenotype (page numbers unavailable). But our copy does not report shared DEGs between the specified APP-PS1 and APP-PS1:miR-155 cKO comparisons or show that those DEGs are associated with enhanced IFN signaling. (LLM, conf=0.78)

      Experimental — accuracy not yet measured
    • cites [34] Roy, E. R. et al. Type I interferon response drives neuroinflammation and synapse loss in Alzheimer disease. J. Clin. Invest. 130, 1912–1930 (2020). source

      In “Prevalent IFN pathway activation in Aβ models and amyloid-induced IFN response” (Figure 4B; page unavailable), the paper reports upregulated IFN-pathway genes in Clec7a+ microglia from APP-PS1 mice. It does not report the APP/PS1:miR-155 cKO comparison or identify DEGs shared between the two datasets, so it cannot establish the claimed shared-gene result. Its principal finding concerns plaque-associated microglia, not an early response to remote pathology. (LLM, conf=0.86)

      Experimental — accuracy not yet measured
  • Findingown data

    The pre-MGnD cluster size was expanded in APP/PS1:miR-155 cKO compared to APP/PS1 mice.

    “Interestingly, the pre-MGnD cluster size was expanded in APP/PS1:miR-155 cKO compared to APP/PS1 mice (Extended Data Figs.6f,o)”
    Quote in the paperSubstantial claim
  • Findingown data

    The IFN signaling pathway was enhanced in APP/PS1:miR-155 cKO microglia.

    “Gene set enrichment analysis (GSEA), gene ontology (GO) enrichment analysis, and IPA canonical pathway analysis showed that IFN signaling pathway was enhanced in APP/PS1:miR-155 cKO microglia (Fig. 1j and Extended Data Fig. 5a,b).”
    Quote in the paperSubstantial claim
  • Findingown data

    There were significantly more synapses preserved in cortical peri-plaque regions in 8-month-old APP/PS1:miR-155 cKO mice as compared to APP/PS1 mice.

    “We validated these findings by immunohistochemistry of synaptic molecules and found significantly more synapses preserved in cortical peri-plaque regions in 8-month-old APP/PS1:miR-155 cKO mice as compared to APP/PS1 mice (Fig. 5e,f).”
    Quote in the paperSubstantial claim
  • Findingown data

    Pseudotime analysis showed that homeostatic microglia progressed towards mature MGnD via the early and late pre-MGnD clusters, in both sexes.

    “We found that homeostatic microglia progressed towards mature MGnD via the early and late pre-MGnD clusters, in both sexes (Fig. 2g and Extended Data Fig. 6m).”
    Quote in the paperSubstantial claim
  • May combine two claims. 38
  • Classified as probably not a substantial claim. 46

  • May combine two claims.

    Premisecitation

    Increased miR-155 expression has been observed in mouse models of AD and in hippocampal tissue from AD donors.

    “Additionally, increased miR-155 expression has been observed in mouse models of AD and in hippocampal tissue from AD donors 28,47 .”
    Quote in the paperNot a substantial claim2 of 2 sources checked
    • cites [28] Readhead, B. et al. miR-155 regulation of behavior, neuropathology, and cortical transcriptomics in Alzheimer’s disease. Acta Neuropathol. 140, 295–315 (2020). source
    • cites [47] Sierksma, A. et al. Deregulation of neuronal miRNAs induced by amyloid-β or TAU pathology. Mol. Neurodegener. 13, 54 (2018). source

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

    Premisecitation

    Other previous studies have shown no differential expression of miR-155 in AD brains.

    “Other previous studies have shown no differential expression of miR-155 in AD brains [48][49][50] .”
    Quote in the paperNot a substantial claim3 of 3 sources checked
    • cites [48] Culpan, D., Kehoe, P. G. & Love, S. Tumour necrosis factor-α (TNF-α) and miRNA expression in frontal and temporal neocortex in Alzheimer’s disease and the effect of TNF-α on miRNA expression in vitro. Int. J. Mol. Epidemiol. Genet. 2, 156–162 (2011).
    • cites [49] Patrick, E. et al. Dissecting the role of non-coding RNAs in the accumulation of amyloid and tau neuropathologies in Alzheimer’s disease. Mol. Neurodegener. 12, 51 (2017). source

      The Results section on miRNAs associated with pathologic AD identifies two significant miRNAs, but does not report a result for miR-155. Searches for miR-155 and variant wording found no passage establishing whether it was tested or differentially expressed in AD brains. (LLM, conf=0.76)

      Experimental — accuracy not yet measured
    • cites [50] Lau, P. et al. Alteration of the microRNA network during the progression of Alzheimer’s disease. EMBO Mol. Med. 5, 1613–1634 (2013). source

      The Results sections report differentially expressed miRNAs in AD brain samples, but the passages found do not report a result for miR-155 or establish whether it was tested. Searches for “miR-155” and its differential expression found no passage that settles the claim. (LLM, conf=0.68)

      Experimental — accuracy not yet measured

  • May combine two claims.

    Findingown data

    The MGnD cluster was strongly enriched in MGnD genes including Clec7a, Apoe, Trem2 compared to M0, early and late IFN-responsive pre-MGnD clusters, but significantly reduced expression of Clec2d and IFN-responsive genes.

    “The MGnD cluster was strongly enriched in MGnD genes including Clec7a, Apoe, Trem2 as compared to the M0, early and late IFN-responsive pre-MGnD clusters, but significantly reduced the expression of Clec2d and IFN-responsive genes (Fig. 2f, Extended Data Fig. 6l, and Supplementary Table 2).”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim.

    Findingown data

    The pre-MGnD cluster was defined by intermediate expression of both Tmem119 and Clec7a.

    “The pre-MGnD cluster was defined by the intermediate expression of both Tmem119 and Clec7a.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The overlap of DEGs between APP/PS1 and APP/PS1:miR-155 cKO microglia at 8 months was minimal, involving only 9 genes, none of which were canonical MGnD genes.

    “the overlap of DEGs was minimal involving only 9 genes, none of which were canonical MGnD genes (Extended Data Fig. 2d).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    APP/PS1:miR-155 cKO mice exhibited a preference for the novel arm over the familiar arms, confirming restoration of functional recognition memory.

    “In contrast, APP/PS1:miR-155 cKO mice exhibited a preference for the novel arm over the familiar arms, confirming restoration of functional recognition memory.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    There was enhanced phagocytosis of Aβ by Clec7a+ microglia in 4-month-old APP/PS1:miR-155 cKO mice compared to controls, which was not detected in 8-month-old mice.

    “We found enhanced phagocytosis of Aβ by Clec7a + microglia in 4-month-old APP/PS1:miR-155 cKO mice compared to controls (Fig. 4a,f), which was not detected in 8-month-old mice (Fig. 4f).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The early pre-MGnD cluster retained high expression of M0 genes and low expression of MGnD genes, whereas the late pre-MGnD cluster preferentially expressed several MGnD genes including Clec7a, Apoe, and Axl, and had reduced expression of homeostatic microglial genes.

    “Interestingly, the early pre-MGnD cluster retained a high expression of M0 genes and low expression of MGnD genes (Fig. 2f and Extended Data Fig. 6l), whereas the late pre-MGnD cluster preferentially expressed several MGnD genes including Clec7a, Apoe, and Axl, and had reduced expression of homeostatic microglial genes.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    There was a significant reduction in 6E10+ Aβ plaque number and area in APP/PS1:miR-155 cKO brains at 4 months, but not at 8 months.

    “We observed a significant reduction in 6E10 + Aβ plaque number and area in APP/PS1:miR-155 cKO brains at 4 months (Extended Data Fig. 9a,b), but not at 8 months (Extended Data Fig. 9c).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    APP/PS1 mice at 8 months of age showed reduced spontaneous alternation compared to non-transgenic mice in the Y-maze task, indicating an impairment in visuospatial working memory.

    “APP/PS1 mice at 8 months of age showed reduced spontaneous alternation (SA) compared to non-transgenic mice in the Y-maze task (Fig. 6a,c), indicating an impairment in visuospatial working memory.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    APP/PS1 mice at 8 months of age did not demonstrate a significant preference to enter the novel arm in the forced alternation task, indicating an impairment in recognition memory.

    “APP/PS1 mice at 8 months of age did not demonstrate a significant preference to enter the novel arm, indicating an impairment in recognition memory (Fig. 6b,d).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    qPCR analysis showed significant upregulation of Clec2d and downregulation of P2ry12 in the early- and late-pre-MGnD clusters.

    “Furthermore, qPCR analysis showed a significant upregulation of Clec2d and downregulation of P2ry12 in the early-and late-pre-MGnD clusters (Extended Data Fig. 7f).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Deletion of microglial miR-155 upregulated expression of MGnD genes such as Clec7a, Tyrobp and Lpl, and suppressed the homeostatic gene Tmem119 in proliferating microglia clusters.

    “However, deletion of microglial miR-155 upregulated the expression of MGnD genes, such as Clec7a, Tyrobp and Lpl, and suppressed the level of homeostatic genes, such as Tmem119, in the proliferating microglia clusters (Clusters 8 and 9, Extended Data Fig. 6e).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    APP/PS1:miR-155 cKO mice showed rescued performance in the spontaneous alternation task, and miR-155 cKO had no effect in non-transgenic mice.

    “Notably, APP/PS1:miR-155 cKO mice showed rescued performance in the SA task, and miR-155 cKO had no effect in nontransgenic mice.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    miR-155 was highly expressed in microglia from APP/PS1 mice at 4 and 8 months of age, but significantly reduced in APP/PS1:miR-155 cKO mice.

    “miR-155 was highly expressed in microglia from APP/PS1 mice at 4 and 8 months of age, but significantly reduced in APP/PS1:miR-155 cKO (Fig. 1b and Extended Data Fig. 2a).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Quantification of % correct spontaneous alternations in Y-maze SA for 8-month-old WT and APP/PS1 mice with and without microglia specific miR-155 ablation. Two-way ANOVA with Tukey's post hoc test, APP/PS1 vs. APP/PS1:miR-155 cKO, P = 0.004.

    “Quantification of % correct spontaneous alternations in the Y-maze SA for 8-month-old WT and APP/PS1 mice with and without microglia specific miR-155 ablation.Two-way ANOVA with Tukey's post hoc test, APP/PS1 vs. APP/PS1:miR-155 cKO, P = 0.004 (n = 34 WT, n = 36 miR-155 cKO, n = 35 APP/PS1 and n = 30 APP/ PS1:miR-155 cKO mice).”
    Quote in the paperSubstantial claim

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

    Findingown data

    Quantification of % 6E10/Clec7a volume at 4 months (P = 0.0007) and 8 months (P = 0.6876) by two-tailed Student's unpaired t-test, n=6 mice per group.

    “Quantification of % 6E10/Celc7a volume at 4 (P = 0.0007 by two-tailed Students unpaired t-test test) and 8 months of age (P = 0.6876 by two-tailed Student's unpaired t-test), n = 6 mice per group.”
    Quote in the paperSubstantial claim

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

    Findingown data

    Center zone time did not differ significantly between any groups.

    “Center zone time for WT and APP/PS1 mice.There were no statistically significant differences between any groups by two-way ANOVA with Bonferoni's post hoc test (n = 34 WT, n = 37 miR-155 cKO, n = 35 APP/PS1 and n = 29 APP/PS1:miR-155 cKO mice).”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Findingown data

    qPCR of miR-155 expression of 4-month-old mice showing efficiency of tamoxifen treatment using one-way ANOVA, P < 0.0001 by one-way ANOVA with Tukey's post hoc test.

    “qPCR of miR-155 expression of 4-month-old mice showing the efficiency of tamoxifen treatment using one-way ANOVA, P < 0.0001 by one-way ANOVA with Tukey's post hoc test (n = 6 mice for miR-155 cKO group; n = 3 mice for the other three groups).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    In the forced alternation task, the number of entries into the novel arm versus the average number of entries into familiar arms differed in WT (P = 0.0002), miR-155 cKO (P = 0.0064), and APP/PS1:miR-155 cKO (P = 0.0212) mice but not APP/PS1 (P = 0.2361) mice.

    “entries into the familiar arms was compared for each mouse by repeated measure three-way ANOVA with Bonferoni's post hoc test, WT P = 0.0002, miR-155 cKO P= 0.0064, APP/PS1 P = 0.2361, APP/PS1:miR-155 cKO P = 0.0212 (n = 34 WT, n = 36 miR-155 cKO, n = 35 APP/PS1 and n = 30 APP/PS1:miR-155 cKO mice).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    6E10 plaque counts normalized to area and percent area 6E10 positivity in 4-month-old mice differed (P = 0.0084 and P = 0.0104, respectively, two-tailed Student's unpaired t-test).

    “6E10 plaque counts normalized to area and percent area 6E10 positivity in 4-month-old mice.P Values were determined using two-tailed Student's unpaired t-test, P = 0.0084 and P = 0.0104, respectively (n = 10 APP/PS1, n = 9 APP/PS1:miR-155 cKO).”
    Quote in the paperSubstantial claim

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

    Findingown data

    Volcano plots of DEPs between APP/PS1:miR-155 cKO and APP/PS1 whole brain tissue, P < 0.05 using two-sided Wald test.

    “Volcano plots of DEPs between APP/PS1:miR-155 cKO and APP/PS1 whole brain tissue, P < 0.05 using two-sided Wald test.”
    Quote in the paperNot a substantial claim

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

    Findingown data

    59 and 160 pre-MGnD markers were identified in females and males, respectively.

    “59 and 160 pre-MGnD markers were identified in females and males, respectively.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Findingown data

    Violin plots showing mean Z-score of pre-MGnD markers in APP/PS1 and APP/PS1:miR-155 cKO male mice; P = 3.54507e-91 by Kruska-Wallis test, FDR corrected using Benjamini Hochberg.

    “Violin plots showing the mean Z-score of pre-MGnD markers in APP/PS1 and APP/PS1:miR-155 cKO male mice.P = 3.54507e-91 by Kruska-Wallis test, FDR corrected using Benjamini Hochberg.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Total distance traveled over time in the open field locomotor activity task showed a main effect of APP transgene (WT vs. APP/PS1, P < 0.0001), and APP/PS1 and APP/PS1:miR-155 cKO were not statistically different.

    “Total distance traveled over time in the open field locomotor activity task.Main effect of APP transgene by two-way ANOVA, WT vs. APP/PS1, P < 0.0001; APP/PS1 and APP/PS1:miR-155 cKO are not statistically different by two-way ANOVA with Bonferoni's post hoc test (n = 34 WT, n = 37 miR-155 cKO, n = 35 APP/PS1 and n = 29 APP/PS1:miR-155 cKO mice).”
    Quote in the paperNot a substantial claim

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

    Findingown data

    The method returned 16 cell clusters for females and 20 clusters for males.

    “The method returned 16 cell clusters for females and 20 clusters for males which were then visualized using UMAP for dimensionality reduction.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Findingown data

    Heatmap of DEGs identified in APP/PS1:miR-155 cKO microglia compared to APP/PS1 microglia using DESeq2 analysis, FDR-corrected P < 0.05, sex-specific DEGs removed.

    “Heatmap of DEGs identified in APP/PS1:miR-155 cKO microglia, compared to APP/PS1 microglia using DESeq2 analysis.FDR-corrected P < 0.05, sex-specific DEGs removed (n = 4-6 mice per sex/group).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Quantification of percentage of colocalized area of Vglut2/Psd95 in plaque and peri-plaque regions of 8-month-old mice compared using two-tailed Mann-Whitney test, P = 0.0275, 36 plaques from APP/PS1 (n=6) mice and 29 plaques from APP/PS1:miR-155 cKO (n=5) mice.

    “Quantification of the percentage of colocalized area of Vglut2/Psd95 in the plaque and peri-plaque regions of 8-month-old mice compared using two-tailed Mann-Whitney test, P = 0.0275, 36 plaques from APP/PS1 (n = 6) mice and 29 plaques from APP/PS1:miR-155 cKO (n = 5) mice.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Quantification of percentage of four clusters from WT, 2- and 8-month-old APP/PS1 mice showed differences: P < 0.0001 for M0 and late pre-MGnD, P = 0.0011 (WT vs. 8-month-old APP/PS1) and P = 0.0084 (2-month-old APP/PS1 vs. 8-month-old APP/PS1) for early pre-MGnD, P = 0.0017 (WT vs. 8-month-old APP/PS1) and P = 0.0014 (2-month-old APP/PS1 vs. 8-month-old APP/PS1) for MGnD as determined by one-way.

    “Quantification of percentage of four clusters mentioned in d from WT, 2-and 8-month-old APP/PS1 mice, P < 0.0001 for M0 and late pre-MGnD, P = 0.0011 (WT vs. 8-month-old APP/PS1) and P = 0.0084 (2-month-old APP/PS1 vs. 8-month-old APP/PS1) for early pre-MGnD, P = 0.0017 (WT vs. 8-month-old APP/PS1) and P = 0.0014 (2-month-old APP/PS1 vs. 8-month-old APP/PS1) for MGnD as determined by one-way ANOVA”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim.

    Findingown data

    Heatmap of DEGs identified in miR-155 cKO microglia compared to WT microglia for male and female groups using DESeq2 (two-sided Wald test, FDR-corrected P < 0.05).

    “Heatmap of DEGs identified in miR-155 cKO microglia, compared to WT microglia for male (c) and female (d) groups using DESeq2 analysis, two-sided Wald test, FDR-corrected P < 0.05 (n = 5-6 mice per sex group).”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim.

    Findingown data

    Heatmap of DEG in phagocytic and non-phagocytic microglia isolated from WT and Ifngr1 cKO mice using DESeq2 analysis, two-sided LRT with FDR-corrected P < 0.05.

    “Heatmap of DEG in phagocytic and non-phagocytic microglia isolated from WT and Ifngr1 cKO mice using DESeq2 analysis.Two-sided LRT statistical test with an FDRcorrected P < 0.05, n = 3 mice per group.”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim.

    Findingown data

    Violin plots showing mean Z-score of pre-MGnD markers in all cells from APP/PS1 and APP/PS1:miR-155 cKO mice; P = 6.829469e-12 by Kruskal-Wallis test, FDR corrected using Benjamini Hochberg.

    “Violin plots showing the mean Z-score of pre-MGnD markers in all the cells from APP/PS1 and APP/PS1:miR-155 cKO mice; P = 6.829469e-12 by Kruskal-Wallis test, FDR corrected using Benjamini Hochberg.”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim.

    Findingown data

    Heatmaps of significantly changed proteins between male APP/PS1:miR-155 cKO and APP/PS1 whole brain tissue at 4 and 8 months of age (one-way ANOVA with Student's t-test, P < 0.05).

    “Heatmaps of significantly changed proteins between male APP/PS1:miR-155 cKO and APP/PS1 whole brain tissue at 4 and 8 months of age (one-way ANOVA with Student's t-test between APP/PS1 and APP/PS1:miR-155 cKO mice, P < 0.05, n = 3-4 male mice per group).”
    Quote in the paperSubstantial claim

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

    Findingown data

    Fold changes of luciferase activity after non-mutated Stat1 3'UTR co-transfected with non-relevant miRNA mimic (miR-18), P = 0.0072 by one-way ANOVA with post hoc Tukey's test.

    “Fold changes of luciferase activity after non-mutated Stat1 3'UTR co-transfected with the non-relevant miRNA mimic (miR-18), P = 0.0072 by one-way ANOVA with post hoc Tukey's test (n = 3).”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Findingown data

    Validation of Stat1 and Clec2d pre-MGnD markers.

    “Validation of Stat1 and Clec2d pre-MGnD markers.”
    Quote in the paperSubstantial claim

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

    Findingown data

    After filtering all databases for high-confidence targets, 1680 potential target genes were selected.

    “After filtering all databases for high-confidence targets, 1680 potential target genes were selected.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Decreased 6E10+ amyloid plaque burden and enhanced phagocytosis function in APP/PS1:miR-155 cKO mice.

    “Decreased 6E10 + amyloid plaque burden and enhanced phagocytosis function in APP/PS1:miR-155 cKO mice.”
    Quote in the paperSubstantial claim

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

    Findingown data

    Bar graphs depicting expression levels of select genes from (a) using two-way ANOVA with Holm-Sidak post hoc analysis, P = 0.042 for Lpl, P = 0.0331 for Spp1, P = 0.0031 for Egr1, P = 0.0018 for Cst3 and Mertk.

    “Bar graphs depicting expression levels of select genes from (a) using two-way ANOVA with Holm-Sidak post hoc analysis, P = 0.042 for Lpl, P = 0.0331 for Spp1, P = 0.0031 for Egr1, P = 0.0018 for Cst3 and Mertk (n = 3 mice).”
    Quote in the paperNot a substantial claim

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

    Findingown data

    Quantification of Tmem119 positive area/plaque in 4-month-old (P = 0.0063) and 8-month-old mice (P = 0.5687) by two-tailed Student's unpaired t-test, n=6 mice per group.

    “Quantification of Tmem119 positive area/plaque in 4-month-old (P = 0.0063 by two-tailed Student's unpaired t-test) and 8-month-old mice (P = 0.5687 by two-tailed Student's unpaired t-test), n = 6 mice per group.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    miR-155 ablation expands the number of microglia in the pre-MGnD cluster and augments immune pathway enrichment within this cluster.

    “These data demonstrate that miR-155 ablation expands the number of microglia in the pre-MGnD cluster and augments the immune pathway enrichment within this cluster.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    Microglial-specific deletion of miR-155 potentiates the transition from homeostatic to pre-MGnD microglia and enhances microglial immune functions within the pre-MGnD cluster.

    “Here we demonstrate that microglial-specific deletion of miR-155 potentiates the transition from homeostatic to pre-MGnD microglia and enhances microglial immune functions within the pre-MGnD cluster.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    Pre-MGnD microglia serve as restrictors of plaque associated pathology, highlighting a therapeutically relevant role for this cluster in rescuing cognitive function.

    “Furthermore, our study suggests that pre-MGnD microglia serve as restrictors of plaque associated pathology, highlighting a therapeutically relevant role for this cluster in rescuing cognitive function.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    miR-155 deletion enhanced the MGnD signature in APP/PS1:miR-155 cKO microglia and enriched IFN signaling and phagocytic pathways at 4 months of age.

    “Taken together, these data show that miR-155 deletion enhanced MGnD signature in APP/PS1:miR-155 cKO microglia and enriched IFN signaling and phagocytic pathways at 4 months of age.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    miR-155 regulates IFNγ signaling which governs the transition from homeostatic to pre-MGnD and MGnD.

    “Furthermore, we found an important role of miR-155 in regulating IFNγ signaling which governs the transition from homeostatic to pre-MGnD and MGnD.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    Microglia transition from homeostatic to MGnD via an IFN-responsive intermediate state, and miR-155 ablation enhances the size and immune response features of this pre-MGnD state.

    “Taken together, these data demonstrate that microglia transition from homeostatic to MGnD via an IFN-responsive intermediate state, and that miR-155 ablation enhances the size and immune response features of this pre-MGnD state.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    IFNγ blockade suppresses microglial phagocytosis and microglial response to MGnD induction in miR-155 cKO mice.

    “Taken together, these data demonstrate that there is a significant overlap in genes affected by miR-155 cKO and IFNγ manipulation, and that IFNγ blockade suppresses microglial phagocytosis and microglial response to MGnD induction in miR-155 cKO mice.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    miR-155 targets Stat1 and regulates interferon signaling pathway.

    “miR-155 targets Stat1 and regulates interferon signaling pathway.”
    Quote in the paperSubstantial claim

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

    Study design and conductown data

    Sample viability and counts were determined using hemocytometer and trypan blue and ranged from [510,000-1,300,000 counts/ml] and [72-89% viability].

    “Sample viability and counts were determined using hemocytometer and trypan blue and ranged from [510,000-1,300,000 counts/ml] and [72-89% viability].”
    Quote in the paperNot a substantial claim

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

    Study design and conductnone given

    Data for each experiment were collected and processed randomly and animals were assigned to various experimental groups randomly as well.

    “Data for each experiment were collected and processed randomly and animals were assigned to various experimental groups randomly as well.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    miR-155 is conserved between mice and humans, suggesting its conserved gene regulatory function.

    “miR-155 is conserved between mice and humans, suggesting its conserved gene regulatory function 24 .”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [24] Faraoni, I., Antonetti, F. R., Cardone, J. & Bonmassar, E. miR-155 gene: a typical multifunctional microRNA. Biochim. Biophys. Acta 1792, 497–505 (2009). source

      Checked before — its earlier verdict is held back until a new check runs.

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

    Study design and conductnone given

    For all comparisons groups were assessed for normal distribution.

    “For all comparisons groups were assessed for normal distribution.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Interpretationreasoning

    Enhancing the pre-MGnD cluster represents a potential immunomodulatory approach to treat AD.

    “Enhancing the pre-MGnD cluster represents a potential immunomodulatory approach to treat AD.”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim.

    Study design and conductown data

    Differentially expressed genes (DEGs) were identified by running comparisons using LRT where the cutoff for significant genes was a Benjamini-Hochberg FDR corrected P < 0.05.

    “differentially expressed genes (DEGs) were identified by running comparisons using LRT where the cutoff for significant genes was a Benjamini-Hochberg FDR corrected P < 0.05.”
    Quote in the paperSubstantial claim

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

    Study design and conductnone given

    Analysis of all images was done while blinded to mouse genotype.

    “Analysis of all images was done while blinded to mouse genotype.”
    Quote in the paperNot a substantial claim

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

    Study design and conductnone given

    No data points were excluded from analysis.

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

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

    Study design and conductnone given

    Data collection and analysis were blindly performed.

    “Data collection and analysis were blindly performed.”
    Quote in the paperNot a substantial claim

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

    Study design and conductown data

    A protein identification FDR of less than 1% was obtained.

    “to obtain a protein identification FDR of less than 1%.”
    Quote in the paperNot a substantial claim

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

    Study design and conductnone given

    Total signal-to-noise values for all peptides were summed for each TMT channel and all values were adjusted to account for variance and a total minimum signal-to-noise value of 200 was implemented.

    “Total signal-to-noise values for all peptides were summed for each TMT channel and all values were adjusted to account for variance and a total minimum signal-to-noise value of 200 was implemented.”
    Quote in the paperNot a substantial claim

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

    Premisecitation

    Previous studies using both the spontaneous and forced alternation tasks have shown no risk of confound from using the same maze with sufficient time between trials.

    “Previous studies using both the spontaneous and forced alternation tasks have shown no risk of confound from using the same maze with sufficient time between trials 71 .”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [71]

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

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

    Premisecitation

    miR-155 expression was highly specific to cells of hematopoietic origin.

    “a previous study showed that miR-155 expression was highly specific to cells of hematopoietic origin 51 .”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [51] Landgraf, P. et al. A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 129, 1401–1414 (2007). source

  • Classified as probably not a substantial claim.

    Study design and conductown data

    DEGs were identified using DESeq2 analysis with FDR-corrected P < 0.05 (n = 4-6 mice per group).

    “DEGs were identified using DESeq2 analysis with FDR-corrected P < 0.05 (n = 4-6 mice per group).”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim.

    Study design and conductown data

    DEGs between APP/PS1:miR-155 cKO and APP/PS1 were identified by running comparisons using LRT where the cutoff for significant genes was a Benjamini-Hochberg FDR corrected P < 0.05.

    “DEGs between APP/PS1:miR-155 cKO and APP/PS1 were identified by running comparisons using LRT where the cutoff for significant genes was a Benjamini-Hochberg FDR corrected P < 0.05.”
    Quote in the paperSubstantial claim

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

    Study design and conductnone given

    Cells with more than 1000 sequencing reads and less than 20 percent mitochondrial transcripts were selected.

    “Cells with more than 1000 sequencing reads and less than 20 percent mitochondrial transcripts were selected.”
    Quote in the paperNot a substantial claim

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

    Study design and conductcitation

    Our sample sizes for experiments were chosen based on our prior publication using APP/PS1 mice, which defined the expectations for the effect size and variance.

    “Our sample sizes for experiments were chosen based on our prior publication using APP/PS1 mice 58 , which defined the expectations for the effect size and variance 55 .”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [58] Zappia, L. & Oshlack, A. Clustering trees: a visualization for evaluating clusterings at multiple resolutions. Gigascience 7, giy083 (2018). source

      Queued — the background check reaches it, usually within a day.

    • cites [55] Garcia-Alonso, L., Holland, C. H., Ibrahim, M. M., Turei, D. & Saez-Rodriguez, J. Benchmark and integration of resources for the estimation of human transcription factor activities. Genome Res. 29, 1363–1375 (2019). source

      Queued — the background check reaches it, usually within a day.

  • Classified as probably not a substantial claim.

    Study design and conductnone given

    Clusters containing low-quality cells (high ribosome to mitochondria ratio), non-microglia cells and proliferating cells were removed for downstream analysis.

    “Clusters containing low-quality cells (high ribosome to mitochondria ratio), non-microglia cells and proliferating cells were removed for downstream analysis.”
    Quote in the paperSubstantial claim

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

    Study design and conductnone given

    All behavioral testing was performed in a blinded manner.

    “All behavioral testing was performed in a blinded manner.”
    Quote in the paperNot a substantial claim

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

    Study design and conductcitation

    Potential doublets were detected using scDblFinder (v1.12.0) and filtered out.

    “Potential dublets were detected using scDblFinder (v1.12.0) 62 and filtered out.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [62] Mantri, M. et al. Spatiotemporal single-cell RNA sequencing of developing chicken hearts identifies interplay between cellular differentiation and morphogenesis. Nat. Commun. 12, 1771 (2021). source

      Checked before — its earlier verdict is held back until a new check runs.

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

    Study design and conductnone given

    Only genes present in more than 3 cells were included.

    “Only genes present in more than 3 cells were included.”
    Quote in the paperNot a substantial claim

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

    Study design and conductnone given

    Images were captured using identical exposure times across samples for each fluorophore.

    “using identical exposure times across samples for each fluorophore”
    Quote in the paperNot a substantial claim

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

    Study design and conductnone given

    Data were obtained from one independent experiment.

    “Data were obtained from one independent experiment.”
    Quote in the paperNot a substantial claim

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

    Study design and conductown data

    The authors could not fully rule out the possibility that miR-155 genetic disruption in CAM/BAM might contribute to the transcriptomic changes observed in microglia.

    “While we could not detect miR-155 expression in CD206 + CAM using miRNAscope in aged APP/PS1 mice, we cannot fully rule out the possibility that miR-155 genetic disruption in CAM/BAM might contribute to the transcriptomic changes observed in microglia.”
    Quote in the paperNot a substantial claim
    • Rests on an assumption: Cx3cr1 CreERT2-mediated deletion of miR-155 in non-microglial Cx3cr1+ cells (CAM/BAM) does not contribute to the transcriptomic changes observed in microglia.

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

    Study design and conductnone given

    Low abundance genes below a mean count of 5 reads/sample were filtered out.

    “Low abundance genes below a mean count of 5 reads/sample were filtered out”
    Quote in the paperNot a substantial claim

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

    Study design and conductnone given

    All qRT-PCRs were performed in duplicate.

    “All qRT-PCRs were performed in duplicate”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationown data

    In summary, miR-155 ablation enhances microglia transition from homeostatic to pre-MGnD and the pre-MGnD phenotype is therapeutically relevant for restricting Aβ pathology.

    “In summary, we show that miR-155 ablation enhances microglia transition from homeostatic to pre-MGnD and that the pre-MGnD phenotype is therapeutically relevant for restricting Aβ pathology.”
    Quote in the paperSubstantial claim

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

    Study design and conductown data

    An MS2 spectra assignment false discovery rate (FDR) of less than 1% was implemented by applying the target-decoy database search strategy.

    “An MS2 spectra assignment false discovery rate (FDR) of less than 1% was implemented by applying the target-decoy database search strategy.”
    Quote in the paperNot a substantial claim

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

    Study design and conductnone given

    The study was limited in the number of timepoints for the scRNAseq of isolated myeloid cells.

    “First, we were limited in the number of timepoints for the scRNAseq of isolated myeloid cells.”
    Quote in the paperNot a substantial claim
76 of 76

  • The paper relies on this without support.

    Cx3cr1 CreERT2-mediated deletion of miR-155 in non-microglial Cx3cr1+ cells (CAM/BAM) does not contribute to the transcriptomic changes observed in microglia.

    “we cannot fully rule out the possibility that miR-155 genetic disruption in CAM/BAM might contribute to the transcriptomic changes observed in microglia.”
1 of 1

Claims other papers make about this one

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

  • 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 .”

    From APOE4 impairs the microglial response in Alzheimer’s disease by inducing TGFβ-mediated checkpoints (2023) · cites this paper as [60]

  • Conditional knockout of microRNA miR155 in microglia in APP/PS1 mice leads to activation of interferon-mediated signalling, which was associated with increased phagocytosis and plaque compaction.

    “Recently it was reported that conditional knockout of microRNA miR155 in microglia in APP/PS1 mice leads to activation of interferon-mediated signalling, which was associated with increased phagocytosis and plaque compaction (Yin et al, 2023a).”

    From APOE from astrocytes restores Alzheimer’s Aβ-pathology and DAM-like responses in APOE deficient microglia (2024) · cites this paper as Yin et al, 2023a

  • Stage-1 DAM represents a transitory and functional subtype with a higher capacity of phagocytosis initiated by a TREM2-independent mechanism, whereas stage-2 DAM represents a dysfunctional state that contributes to AD pathology initiated by a TREM2-dependent mechanism.

    “Stage-1 DAM represents a transitory and functional subtype with a higher capacity of phagocytosis initiated by a TREM2-independent mechanism, whereas stage-2 DAM represents a dysfunctional state that contributes to AD pathology initiated by a TREM2-dependent mechanism.99,111”

    From Microbiota–gut–brain axis and its therapeutic applications in neurodegenerative diseases (2024) · cites this paper as [111]

Self-check

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

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

  • Female single-cell clustering is reported as both 16 and 17 clusters

    Minor

    The Results and figure legend say the initial female analysis generated 17 clusters, whereas the Methods say the clustering method returned 16 female clusters.

  • Synapse-analysis plaque count does not match the stated sampling protocol

    Minor

    The Methods specify six plaques per animal, which would give 30 plaques from the five APP/PS1:miR-155 cKO mice reported in the figure legend. The legend instead reports 29 plaques, without explaining the difference.

2 of 2

Cites

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Related

Authors
Yin, Z., Herron, S., Silveira, S., Kleemann, K., Gauthier, C., Mallah, D., Cheng, Y., Margeta, M. A., Pitts, K. M., Barry, J.-L., Subramanian, A., Shorey, H., Brandao, W., Durao, A., Delpech, J.-C., Madore, C., Jedrychowski, M., Ajay, A. K., Murugaiyan, G., Hersh, S. W., Ikezu, S., Ikezu, T., & Butovsky, O.
Affiliations
  • Brigham and Women's Hospital (US)
  • Boston University (US)
  • Broad Institute (US)
  • Harvard University (US)
Corresponding author
  • Ikezu, Tsuneya
  • Butovsky, Oleg
ORCID
Venue
Nature Neuroscience
Publisher
Springer Science and Business Media LLC
Published
2023-06-08
Volume
26
Issue
7
Pages
1196-1207
ISSN
  • 1097-6256 (ISSN-L)
  • 1546-1726
DOI
10.1038/s41593-023-01355-y
PMC
PMC10619638
OpenAlex
W4379878477
Cited by
120
References
69
Citations by year
2026: 36 · 2025: 32 · 2024: 42 · 2023: 10
FWCI
13.33
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Neuroscience (publishedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
  • HAL (submittedVersion)
  • Oskar-Bordeaux (Universite de Bordeaux) (submittedVersion)
Funders
  • U.S. Department of Health & Human Services | NIH | National Institute on Aging (R01AG054672, R01AG051812, R01AG075509, R21AG076982, R41AG073059, RF1AG054199, R01AG066429, R01AG072719, R01AG067763)
  • U.S. Department of Health & Human Services | NIH | National Institute of Neurological Disorders and Stroke (R01NS088137)
  • U.S. Department of Health & Human Services | NIH | National Eye Institute (R01EY027921, K12 EY016335, K08 EY030160)
  • BrightFocus Foundation (2020A016806)
  • Cure Alzheimer’s Fund (APOE consortium)
  • U.S. Department of Health & Human Services | National Institutes of Health (F31AG071106, T32GM008541)
  • Research to Prevent Blindness Career Development Award.
Topics
  • Life Sciences › Neuroscience › Neurology › Neuroinflammation and Neurodegeneration Mechanisms
  • Health Sciences › Medicine › Physiology › Alzheimer's disease research and treatments
  • Life Sciences › Neuroscience › Neurology › Neurological Disease Mechanisms and Treatments
Keywords
microglia, Alzheimer's disease, miR-155, interferon-gamma signaling, STAT1, CLEC2D, dystrophic neurites, cognitive function, microglial phagocytosis, therapeutic target
MeSH terms
Alzheimer Disease, Animals, Disease Models, Animal, Interferon-gamma, Mice, Transgenic, Signal Transduction, Amyloid beta-Peptides, Microglia, MicroRNAs, Mice, Plaque, Amyloid

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Claims read by deepseek-v4.1-flash under definition version 3 (extract-v3) on 2026-11-06.

Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-11-06.

Cited sources are checked by gpt-6-sol.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

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