CoChat
Sign Up
Cited by 18Alzheimer's disease research and treatmentsNeurogenesis and neuroplasticity mechanismsNeuroinflammation and Neurodegeneration Mechanisms

The DOI matches its Crossref record; 80 of the 81 references it cites were found in a registry or an index; 17 of the 43 sources its claims cite were checked for support.

Inhibiting USP16 rescues stem cell aging and memory in an Alzheimer’s model

Open access
Reinitz, Felicia, Chen, Elizabeth Y, Nicolis di Robilant, Benedetta, Chuluun, Bayarsaikhan, Antony, Jane, Jones, Robert C, Gubbi, Neha, Lee, Karen, Ho, William Hai Dang, Kolluru, Sai Saroja, Qian, Dalong, Adorno, Maddalena, Piltti, Katja, Anderson, Aileen, Monje, Michelle, Heller, H Craig, Quake, Stephen R, Clarke, Michael F·2022·eLife
DOI 10.7554/elife.66037PMC PMC9122497

Published version of a preprint

Open this paper in CoChat — free account

Abstract

Alzheimer’s disease (AD) is a progressive neurodegenerative disease observed with aging that represents the most common form of dementia. To date, therapies targeting end-stage disease plaques, tangles, or inflammation have limited efficacy. Therefore, we set out to identify a potential earlier targetable phenotype. Utilizing a mouse model of AD and human fetal cells harboring mutant amyloid precursor protein, we show cell intrinsic neural precursor cell (NPC) dysfunction precedes widespread inflammation and amyloid plaque pathology, making it the earliest defect in the evolution of the disease. We demonstrate that reversing impaired NPC self-renewal via genetic reduction of USP16, a histone modifier and critical physiological antagonist of the Polycomb Repressor Complex 1, can prevent downstream cognitive defects and decrease astrogliosis in vivo. Reduction of USP16 led to decreased expression of senescence gene Cdkn2a and mitigated aberrant regulation of the Bone Morphogenetic Signaling (BMP) pathway, a previously unknown function of USP16. Thus, we reveal USP16 as a novel target in an AD model that can both ameliorate the NPC defect and rescue memory and learning through its regulation of both Cdkn2a and BMP signaling.

Overview

AI snapshot

Written from the paper’s full text.

TL;DR

In Tg-SwDI Alzheimer’s model mice and human fetal neural precursor cells with mutant APP, cell-intrinsic neural precursor cell self-renewal defects precede inflammation, amyloid plaques, and cognitive decline. Reducing Usp16 rescues NPC self-renewal through Cdkn2a and BMP signaling, decreases astrogliosis, and restores memory without changing plaque burden.

Key findings

  • NPC dysfunction is the earliest detectable defect in Tg-SwDI mice: at 3–4 months, SVZ proliferation was increased threefold (p=0.0153), while neurosphere-initiating cell frequency was reduced to 1 in 14.5 versus 1 in 7.5 in controls (p=0.00166), before inflammation, plaques, or cognitive impairment.
  • Human fetal neurospheres expressing APP SwI showed reduced NIC frequency versus empty vector and WT APP (1 in 10.44 versus 1 in 3.31 and 1 in 5.26; p=3.7e–06 and p=0.00507), supporting a cell-intrinsic APP effect.
  • Usp16 haploinsufficiency rescued self-renewal in Tg-SwDI mice: SVZ NIC p=0.0492 and DG NIC p=0.00233 versus Tg-SwDI; cortical Cdkn2a was reduced (p=0.0365 WT vs Tg-SwDI; p=0.0318 Tg-SwDI vs Tg-SwDI/Usp16+/-). Cdkn2a knockout fully restored NIC frequency in SVZ (p=7.7e–05) and DG (p=2.09e–9).
  • BMP signaling was enriched in Tg-SwDI and rescued by Usp16 haploinsufficiency; BMPR inhibitor LDN-193189 reduced pSMAD1/5/8 (p<0.0001) and restored colony formation. Usp16 haploinsufficiency also reduced GFAP+ astrogliosis (p=0.0012 WT vs Tg-SwDI; p=0.0188 Tg-SwDI vs Tg-SwDI/Usp16+/-) and rescued memory at 6 months (NOR preference index 49% in Tg-SwDI versus >65% in WT and Tg-SwDI/Usp16+/-; p=0.001 and p=0.0099), without altering plaque burden.

Methods

  • Used Tg-SwDI mice carrying Swedish, Dutch, and Iowa APP mutations, crossed with Cdkn2a-/- or Usp16+/- mice, plus human fetal NPCs infected with pHIV-Zsgreen, APP WT, or APP SwI lentivirus.
  • Assays included EdU/SOX2/GFAP immunofluorescence, neurosphere limiting dilution with ELDA, RT-qPCR, Luminex cytokine arrays, microarray, single-cell RNA-seq of FACS-sorted lineage-CD24- SVZ cells, GSEA, Thioflavin S plaque staining, and NOR/Barnes maze behavior.
  • Statistics used ANOVA with Tukey correction, two-tailed t-tests, and ELDA for limiting dilution; significance thresholds reported as *p<0.05, p<0.01, *p<0.001.

Limitations

  • Stated: RNA-seq was performed on SVZ-enriched cells, so inflammation in other brain areas cannot be excluded; sorted cells may not be equivalent to EdU/SOX2/GFAP-stained cells; the mechanism by which mutant APP causes the NPC defect was outside the scope; Cdkn2a knockout is not feasible in 1-year-old mice due to tumor formation and is less ideal therapeutically.
  • Stated: Usp16 haploinsufficiency only partially rescued the self-renewal defect in some assays.
  • Evident from the text: in vivo rescue used genetic Usp16 reduction rather than a pharmacologic USP16 inhibitor, and human validation was in vitro; plaque burden remained unchanged despite cognitive rescue.

Model-written summary. Check it against the paper before relying on it.

Integrity signals

Registry

Crossref · 10.7554/elife.66037

Cites

80 of 80 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Verification

Claims the paper makes

17 of 43 cited sources checked · 6 supported · 0 flagged · accuracy not yet measured

  • Interpretationcitation

    The timeline of Tg-SwDI mice mimics that of humans with both dominantly inherited AD and late-onset sporadic AD.

    “a timeline which mimics that of humans with both dominantly inherited AD and late-onset sporadic AD (Bateman et al., 2012).”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites Bateman et al., 2012 source

      The Results (Combined Model; page unavailable) estimate a biomarker timeline for humans with dominantly inherited Alzheimer’s disease. The Discussion suggests possible common pathophysiology with sporadic Alzheimer’s disease but notes differences. The paper does not compare either human timeline with Tg-SwDI mice, so the claimed mimicry is not supported by this source. (LLM, conf=0.88)

      Experimental — accuracy not yet measured
  • Findingcitation

    The NPC defect discovered is partly regulated by Cdkn2a.

    “The NPC defect that we discovered is partly regulated by Cdkn2a, a central component of aging responsible for decreased neurogenesis and differentiation of NPCs (Abdouh et al., 2012; Molofsky et al., 2006).”
    Quote in the paperSubstantial claim1 of 2 sources checked
    • cites Abdouh et al., 2012 source

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

    • cites Molofsky et al., 2006 source

      The paper’s results report that p16INK4a deficiency partly rescues age-related declines in subventricular-zone progenitor activity and olfactory-bulb neurogenesis, supporting a role for Cdkn2a in those defects. It does not establish that Cdkn2a regulates the citing authors’ particular NPC defect or show that it decreases NPC differentiation; the discussion also notes that the effect varies by brain region. Page numbers are unavailable in our copy. (LLM, conf=0.82)

      Experimental — accuracy not yet measured
  • Premisecitation

    The timing of therapeutic treatment in AD is crucial as treating the disease too late has little efficacy.

    “The timing of therapeutic treatment in AD seems to be crucial as studies have shown that treating the disease too late has little efficacy (Sperling et al., 2011; Yiannopoulou et al., 2019).”
    Quote in the paperSubstantial claim2 of 2 sources checked
    • cites Sperling et al., 2011 source
    • cites Yiannopoulou et al., 2019 source

      Section 3.2 reports a lack of efficacy in previous phase 3 trials and raises the possibility that treatment after symptoms appear is too late. The Introduction also lists late treatment initiation as a proposed explanation for failed trials. The paper does not establish that studies have shown late timing itself to cause low efficacy; it presents that link as a question and a hypothesis. (LLM, conf=0.83)

      Experimental — accuracy not yet measured
  • Premisecitation

    Treatments to decrease formation of plaques have shown only minimal or no improvement in disease progression or outcomes.

    “however, thus far, treatments to decrease formation of plaques have shown only minimal or no improvement in disease progression or outcomes (Knopman et al., 2021; Selkoe, 2019).”
    Quote in the paperSubstantial claim1 of 2 sources checked
    • cites Knopman et al., 2021 source
    • cites Selkoe, 2019 source
  • Premisecitation

    There is no treatment to stop, prevent, or reverse Alzheimer's disease.

    “Currently, there is no treatment to stop, prevent, or reverse AD, and recent advances with monoclonal antibody therapy targeting plaques, although controversial, might at best only slow progression (Huang and Mucke, 2012; Selkoe, 2019; Sevigny et al., 2016).”
    Quote in the paperSubstantial claim1 of 3 sources checked
    • cites Huang and Mucke, 2012 source
    • cites Selkoe, 2019 source
    • cites Sevigny et al., 2016 source
  • It may state two separate claims as one. 44
  • Probably not a substantial claim. 24
  • The quote only partly states this claim. 3

  • It may state two separate claims as one.

    Interpretationcitation

    The increase in GFAP-expressing cells and impaired cognitive function seen in this AD model are purely attributable to mutant APP as Tg-SwDI mice do not develop neurofibrillary tangles that require mutations in tau.

    “The increase in GFAP-expressing cells and impaired cognitive function seen in this AD model are purely attributable to mutant APP as Tg-SwDI mice do not develop neurofibrillary tangles that require mutations in tau (Wilcock et al., 2008).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites Wilcock et al., 2008 source

      The Results report cognitive impairment in APPSwDI mice, and the Introduction says APP-transgenic mice show some cognitive decline without tau pathology. However, the paper does not report an increase in GFAP-expressing cells or establish that the impairment is purely due to mutant APP: the Results find further cognitive decline after NOS2 removal. The Discussion also contradicts the assertion that tangles require tau mutations, describing aggregation of native mouse tau in APPSwDI/NOS2-knockout mice (page numbers unavailable in our copy). (LLM, conf=0.86)

      Experimental — accuracy not yet measured

  • It may state two separate claims as one.

    Premisecitation

    USP16 counteracts self-renewal regulator BMI1 by deubiquitinating histone H2A on Lysine 119 at the Cdkn2a locus, resulting in increased expression of P16 (Ink4a) and P14 (Arf).

    “USP16 counteracts self-renewal regulator BMI1 by deubiquitinating histone H2A on Lysine 119 at the Cdkn2a locus, resulting in increased expression of protein products P16 (Ink4a) and P14 (Arf) (Adorno et al., 2013).”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites Adorno et al., 2013 source

      In Results, under “Modulation of Ink4a/Arf by Usp16 in Ts65Dn cells” (page unavailable), the paper reports reduced H2AK119 ubiquitination at the Ink4a/Arf locus and increased p16Ink4a and p19Arf expression in mouse cells. It describes USP16-mediated removal of ubiquitin at this locus as a strongly suggested model requiring further testing, not a confirmed causal mechanism. The claim also names p14Arf, whereas the paper’s reported expression result concerns p19Arf. (LLM, conf=0.88)

      Experimental — accuracy not yet measured

  • Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.

    Premisecitation

    Removal of p16Ink4a-positive senescent cells using a suicide gene under the Cdkn2a promoter attenuates progression of age-related decline and preserves cognitive function in an accelerated aging AD mouse model and a tauopathy mouse model.

    “Removal of the p16Ink4a-positive senescent cells, for instance, using a suicide gene under the regulation of the Cdkn2a promoter has been shown to attenuate progression of age-related decline and preserve cognitive function in both an accelerated aging AD mouse model and a tauopathy mouse model (Baker et al., 2011; Bussian et al., 2018).”
    Quote in the paperNot a substantial claim2 of 2 sources checked
    • cites Baker et al., 2011 source

      The Methods describe a p16Ink4a-promoter-driven INK-ATTAC construct that enables drug-induced cell clearance. The main text (Fig. 4) reports attenuated age-related decline in BubR1 hypomorphic progeroid mice, but this paper does not report an Alzheimer’s disease or tauopathy mouse model or preservation of cognitive function. (LLM, conf=0.89)

      Experimental — accuracy not yet measured
    • cites Bussian et al., 2018 source

  • Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.

    Premisecitation

    31% of healthy control subjects had high PiB retention indicating Aß deposition, and 25% of these developed mild cognitive impairment or AD by 3 years.

    “In a study characterizing sporadic AD, for instance, Villemagne et al. used Pittsburgh compound B (PiB) positron emission tomography (PET) to show that 31% of healthy control subjects had high PiB retention indicating Aß deposition and of these, 25% developed mild cognitive impairment or AD by 3 years (Villemagne et al., 2011).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites Villemagne et al., 2011 source

  • It may state two separate claims as one.

    Premisecitation

    USP16 is an antagonist of BMI1 and a de-repressor of Cdkn2a that acts through enzymatic removal of ubiquitin from histone H2A.

    “Upstream of Cdkn2a is USP16, an antagonist of BMI1 and a de-repressor of Cdkn2a that acts through the enzymatic removal of ubiquitin from histone H2A (Figure 4C; Adorno et al., 2013; Joo et al., 2007).”
    Quote in the paperSubstantial claim1 of 2 sources checked
    • cites Adorno et al., 2013 source

      The Results section reports that Usp16 opposes PRC1, can remove ubiquitin from histone H2A, and that reducing Usp16 lowers p16Ink4a and p19Arf expression at the Cdkn2a locus. It describes the proposed link between H2A deubiquitination and effects at that locus as strongly suggested, but says mutational analysis is needed to confirm the enzymatic mechanism. (LLM, conf=0.87)

      Experimental — accuracy not yet measured
    • cites Joo et al., 2007 source

  • Probably not a substantial claim. The paper’s conclusions may not depend on it.

    Premisecitation

    Levels of BMP2, 4, 6, and 7 expression increase in the hippocampus and SVZ with age.

    “Levels of BMP2, 4, 6, and 7 expression have been found to increase in the hippocampus and SVZ with age (Yousef et al., 2015; Apostolopoulou et al., 2017).”
    Quote in the paperNot a substantial claim2 of 2 sources checked
    • cites Yousef et al., 2015 source

      The Results section (‘BMP signaling increases in the aged murine hippocampus’; page unavailable) reports increased Bmp2, Bmp4, and Bmp6 expression in aged mouse hippocampi. It does not report an age-related increase in BMP7 or establish the claimed increases in the SVZ. (LLM, conf=0.90)

      Experimental — accuracy not yet measured
    • cites Apostolopoulou et al., 2017 source

      The Results section on global V-SVZ transcriptome analysis reports age-related gene-expression changes, but does not identify increases in BMP2, BMP4, BMP6, or BMP7. The Introduction mentions the hippocampus without reporting BMP expression there. Searches for those BMPs and bone morphogenetic proteins found no passage addressing the claimed increase. (LLM, conf=0.76)

      Experimental — accuracy not yet measured

  • It may state two separate claims as one.

    Findingown data

    Neurospheres from Tg-SwDI mice show a significant decrease in Bmi1 expression and a significant increase in Cdkn2a expression compared to WT.

    “Indeed, we measured a significant decrease in Bmi1 expression and a significant increase in its downstream target Cdkn2a expression in neurospheres from Tg-SwDI mice compared to wild type (WT) (Figure 2C).”
    Quote in the paperSubstantial claim

  • It may state two separate claims as one.

    Findingown data

    Long-term memory impairment in Tg-SwDI mice and rescue in Tg-SwDI/Usp16+/- mice was supported by the Barnes maze, where Tg-SwDI mice spent more time exploring off-target quadrants and Tg-SwDI/Usp16+/- mice spent more time in the target quadrant (p=0.0128 and p=0.0251).

    “Long-term memory impairment in Tg-SwDI mice and rescue in Tg-SwDI/Usp16+/- mice was further supported by the Barnes maze (BM) where Tg-SwDI mice spent more time exploring off-target quadrants and Tg-SwDI/Usp16+/- mice spent more time in the target quadrant (p=0.0128 and p=0.0251, respectively; Figure 7—figure supplement 3).”
    Quote in the paperSubstantial claim

  • It may state two separate claims as one.

    Findingown data

    Tg-SwDI/Usp16+/- mice performed equally to age-matched WT controls, indicating memory of the familiar object with PIs in the 65-70% range (p=0.001 and p=0.0099).

    “The Tg-SwDI/Usp16+/- mice performed equally to their age-matched WT controls indicating memory of the familiar object with PIs in the 65–70% range (p=0.001 and p=0.0099, respectively; Figure 7C).”
    Quote in the paperSubstantial claim

  • It may state two separate claims as one.

    Findingown data

    Treatment of mutant APP neurospheres with LDN-193189 for one week resulted in colony numbers similar to control cells and significantly higher than untreated mutant APP neurospheres.

    “Furthermore, when we treated neurospheres expressing mutant APP with LDN-193189 for a week, the number of colonies originating from those cells were similar to control cells and significantly higher than untreated mutant APP neurospheres (Figure 6D E).”
    Quote in the paperSubstantial claim

  • It may state two separate claims as one.

    Findingown data

    TGF-ß signaling pathway is enriched in Tg-SwDI mice and rescued by Usp16 haploinsufficiency.

    “Enrichment plots show TGF-ß signaling pathway as enriched in Tg-SwDI mice and rescued by Usp16 haploinsufficiency.”
    Quote in the paperSubstantial claim

  • It may state two separate claims as one.

    Findingown data

    BMP signaling is enriched in Tg-SwDI mice and decreases with Usp16 haploinsufficiency.

    “BMP signaling is enriched in Tg-SwDI mice and decreases with Usp16 haploinsufficiency.”
    Quote in the paperSubstantial claim

  • It may state two separate claims as one.

    Findingown data

    USP16 has a new role in regulating the BMP pathway, a mechanism independent of Cdkn2a.

    “We also demonstrated a new role for USP16 in regulating the BMP pathway, a mechanism independent of Cdkn2a.”
    Quote in the paperSubstantial claim

  • The quote only partly states this claim.

    Findingown data

    Genetic reduction of USP16 prevents downstream cognitive defects in Tg-SwDI mice.

    “can prevent downstream cognitive defects and decrease astrogliosis in vivo.”
    Quote in the paperSubstantial claim

  • The quote only partly states this claim.

    Findingown data

    Genetic reduction of USP16 (Usp16 haploinsufficiency) partially rescues impaired NPC self-renewal in Tg-SwDI mice.

    “reversing impaired NPC self-renewal via genetic reduction of USP16, a histone modifier and critical physiological antagonist of the Polycomb Repressor Complex 1, can prevent downstream cognitive defects and decrease astrogliosis in vivo.”
    Quote in the paperSubstantial claim

  • It may state two separate claims as one.

    Findingown data

    Expression of mutant APP in human fetal NPCs induced phosphorylation of SMAD 1/5/8 and reduced neurosphere colony formation that was rescued by a BMP receptor inhibitor.

    “In line with this, our results reveal expression of mutant APP in human fetal NPCs induced phosphorylation of SMAD 1/5/8 and reduced neurosphere colony formation that was rescued by a BMP receptor inhibitor.”
    Quote in the paperSubstantial claim

  • It may state two separate claims as one.

    Findingown data

    BMP receptors were the most highly expressed TGF-ß receptors, with Bmpr2, Bmpr1a, Id2, and Id3 upregulated in Tg-SwDI mice and rescued in Tg-SwDI/Usp16+/- mice.

    “Heatmaps of average normalized single-cell gene expression showed BMP receptors as the most highly expressed TGF-ß receptors, with genes such as Bmpr2, Bmpr1a, Id2, and Id3 upregulated in Tg-SwDI mice and rescued in Tg-SwDI/Usp16+/- mice (Figure 5C).”
    Quote in the paperSubstantial claim

  • It may state two separate claims as one.

    Findingown data

    Cdkn2a expression is increased with aging and even more so in the Tg-SwDI cortex.

    “In line with our findings thus far, expression of the well-studied gene, Cdkn2a, known for its increased expression with aging and critical function of inhibiting stem cell self-renewal during development and throughout the lifespan, was increased with aging and even more so in the Tg-SwDI cortex (Figure 3E).”
    Quote in the paperSubstantial claim

  • It may state two separate claims as one.

    Findingown data

    In 2-year-old mice, microarray analyses of SVZ, DG, and cortex show an increase in Cd44, Vim, Serping1, and other markers related to pan- and A1-specific astrogliosis and a concomitant inflammatory signature in Tg-SwDI mice compared to WT.

    “When we looked at 2-year-old mice by microarray analyses of SVZ, DG, and cortex, we saw an increase in Cd44, Vim, Serping1, and other markers related to pan- and A1-specific astrogliosis and a concomitant inflammatory signature of Tg-SwDI mice compared to WT mice (Figure 3—figure supplement 4A, B, respectively, Reinitz et al., 2022).”
    Quote in the paperSubstantial claim

  • It may state two separate claims as one.

    Findingown data

    The Tg-SwDI cohort exhibited impaired performance in the NOR task as early as 6 months of age, with preference indexes not significantly different 24 hr after training, indicating no memory of the familiar object.

    “As expected, when studying the cognitive decline in the Tg-SwDI cohort, we found that the Tg-SwDI cohort exhibited impaired performance in the NOR task as early as 6 months of age, with preference indexes (PIs) that were not significantly different 24 hr after training, indicating no memory of the familiar object (Figure 7C).”
    Quote in the paperSubstantial claim

  • It may state two separate claims as one.

    Findingown data

    An NPC defect predates the development of measurable inflammation and amyloid plaque accumulation in a mutant APP model and is cell intrinsic.

    “One of the primary findings in this study is that an NPC defect predates the development of measurable inflammation and amyloid plaque accumulation in a mutant APP model and that this defect is cell intrinsic.”
    Quote in the paperSubstantial claim

  • It may state two separate claims as one.

    Findingown data

    TGFß pathway, Oxidative phosphorylation, and MYC Targets V2 were rescued in both 3 and 4 months and 1-year-old mice by Usp16 haploinsufficiency.

    “TGFß pathway, Oxidative phosphorylation, and MYC Targets V2 were selected as they were rescued in both 3 and 4 months and 1-year-old mice by Usp16 haploinsufficiency.”
    Quote in the paperNot a substantial claim

  • It may state two separate claims as one.

    Findingown data

    USP16 reduction reduced astrocyte proliferation and restored cognitive function as measured by the NOR and Barnes Maze tests, independently of plaques and widespread inflammation.

    “It is important to note that USP16 reduction also reduced astrocyte proliferation and restored cognitive function as measured by the NOR and Barnes Maze tests, independently of plaques and widespread inflammation.”
    Quote in the paperSubstantial claim

  • The quote only partly states this claim.

    Interpretationown data

    In Tg-SwDI mice and human fetal cells with mutant APP, the neural precursor cell self-renewal defect is initially cell-intrinsic.

    “we show cell intrinsic neural precursor cell (NPC) dysfunction precedes widespread inflammation and amyloid plaque pathology, making it the earliest defect in the evolution of the disease.”
    • Also stated in: § Introduction · plain
      “Here, we report that the NPC defects seen in an AD mouse model harboring Swedish, Dutch, and Iowa mutations in the amyloid precursor protein (Tg-SwDI) is initially cell-intrinsic and predates inflammation and widespread plaque deposition, which play a role later in the disease.”
    • Also stated in: § Neural precursor cell exhaustion is the earliest sign of disease in Tg-SwDI mice · hedged
      “This result suggests that the self-renewal defect is cell-intrinsic and can be observed in two different AD models with different mutations.”
    Quote in the paperSubstantial claim

  • It may state two separate claims as one.

    Interpretationown data

    Modulating Usp16 gene dosage does not affect amyloid plaque burden but ameliorates stem cell self-renewal defects and some cognitive defects in these mice.

    “These data indicate that although modulating Usp16 gene dosage does not affect amyloid plaque burden, it ameliorates stem cell self-renewal defects that may be the earliest indication of pathology, as well as some of the cognitive defects in these mice that occur later (Figure 7D).”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim. The paper’s conclusions may not depend on it.

    Study design and conductnone given

    The use of neural progenitor cells as non-hESC stem cells in this study was compliant with Stanford Stem Cell Research Oversight (SCRO) Protocol 194, pre-approved by the Internal Review Board (IRB)/SCRO of the Stanford Research Compliance Office (RCO).

    “The use of neural progenitor cells as non-hESC stem cells in this study is compliant to Stanford Stem Cell Research Oversight (SCRO) Protocol 194 pre-approved by the Internal Review Board (IRB)/SCRO of the Stanford Research Compliance Office (RCO).”
    Quote in the paperNot a substantial claim

  • It may state two separate claims as one.

    Interpretationown data

    Reactive astrogliosis is exacerbated by and strongly correlated with aging and later disease progression.

    “This suggests that reactive astrogliosis is exacerbated by and strongly correlated with aging and later disease progression.”
    Quote in the paperNot a substantial claim

  • It may state two separate claims as one.

    Interpretationown data

    In the Tg-SwDI model, there is a premature reduction of self-renewal capacity of NPCs, but not necessarily a decrease in the total number of neural progenitor cells.

    “Taken together with our data showing an increase in EdU+SOX2+GFAP+ cells in Tg-SwDI mice SVZ at an early age, our extreme limiting dilution assay in older mice, and expression changes of Cdkn2a and Bmi1, we infer a premature reduction of self-renewal capacity of NPCs, but not necessarily a decrease in the total number of neural progenitor cells in our Tg-SwDI model.”
    Quote in the paperSubstantial claim

  • It may state two separate claims as one.

    Premisecitation

    Adult neurogenesis is compromised in Alzheimer's disease, contributing to early dementia.

    “Adult neurogenesis is thought to be compromised in AD, contributing to early dementia (Alipour et al., 2019).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Alipour et al., 2019 source

  • Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.

    Study design and conductown data

    The human fetal neural stem cell line used was negative for mycoplasma and viral contaminants by qPCR and had a normal karyotype.

    “The cells were negative for mycoplasma and viral contaminants using qPCR (IDEXX BioResearch) and had normal karyotype.”
    Quote in the paperNot a substantial claim

  • It may state two separate claims as one.

    Premisecitation

    Treatment of human neural stem cells with secreted APPα or overexpression of APP promoted phosphorylation of SMAD 1/5/8 and induced massive glial differentiation through the BMP pathway.

    “Furthermore, Kwak, Lohuizen, and colleagues showed that treatment of human neural stem cells with secreted APPα or overexpression of APP promoted phosphorylation of SMAD 1/5/8 and induced massive glial differentiation (by expression of GFAP) through the BMP pathway (Kwak et al., 2014).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Kwak et al., 2014 source

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

  • It may state two separate claims as one.

    Interpretationreasoning

    Early therapeutic reduction of USP16 or BMP signaling in neural stem cells may reverse the neurogenic defect that may contribute to symptomatic AD later in life, especially if applied before cognitive deficits are present.

    “The translatability of our study therefore comes from observing that early therapeutic reduction of USP16 or BMP signaling in neural stem cells may reverse the neurogenic defect that may contribute to symptomatic AD later in life, especially if applied before cognitive deficits are present in the patient.”
    Quote in the paperSubstantial claim

  • It may state two separate claims as one.

    Interpretationown data

    The self-renewal defect is cell-intrinsic and can be observed in two different AD models with different mutations.

    “This result suggests that the self-renewal defect is cell-intrinsic and can be observed in two different AD models with different mutations.”
    Quote in the paperSubstantial claim

  • It may state two separate claims as one.

    Premisecitation

    Use of a suicide gene is not directly translatable into humans, and other senolytics such as BCL2-inhibitors or the combination of Dasatinib and quercetin have toxicities that can limit their use.

    “However, the use of a suicide gene is not directly translatable into humans, and other senolytics such as BCL2-inhibitors or the combination of Dasatinib and quercetin have toxicities which can limit their use (Amaya-Montoya et al., 2020; Zhu et al., 2015).”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites Amaya-Montoya et al., 2020 source
    • cites Zhu et al., 2015 source

  • It may state two separate claims as one.

    Interpretationown data

    Impairment of NPC regeneration, as measured by NIC frequencies, is a function of aging that is accelerated by APP mutations and is mitigated through loss of Cdkn2a.

    “These results demonstrate that impairment of NPC regeneration, as measured by NIC frequencies, is a function of aging that is accelerated by APP mutations and is mitigated through loss of Cdkn2a, a known regulator of NPC self-renewal (Molofsky et al., 2003).”
    Quote in the paperSubstantial claim

  • It may state two separate claims as one.

    Interpretationown data

    The data provide further evidence of cell-intrinsic impaired self-renewal in the Tg-SwDI model of familial AD, and reversal of this impairment is possible through targeting Cdkn2a upstream regulator, USP16.

    “Similar to the NIC rescue in the Tg-SwDI/Cdkn2a-/- mice, these data provide further evidence of cell-intrinsic impaired self-renewal in the Tg-SwDI model of familial AD, and that reversal of this impairment is possible through targeting Cdkn2a upstream regulator, USP16.”
    Quote in the paperSubstantial claim
    • Rests on an assumption: Usp16+/- mice do not show tumor formation.

  • Probably not a substantial claim. The paper’s conclusions may not depend on it.

    Study design and conductnone given

    All animal procedures and behavioral studies were compliant with Stanford Administrative Panel on Laboratory Animal Care Protocol 10,868 pre-approved by the Stanford Institutional Animal Care and Use Committee.

    “All animal procedures and behavioral studies involved in this manuscript are compliant to Stanford Administrative Panel on Laboratory Animal Care Protocol 10,868 pre-approved by the Stanford Institutional Animal Care and Use Committee.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim. The paper’s conclusions may not depend on it.

    Study design and conductnone given

    The experiment was repeated three times, with each infection and subsequent limiting dilution experiment being a biological replicate.

    “Experiment was repeated three times (each infection and subsequent limiting dilution experiment performed being a biological replicate).”
    Quote in the paperNot a substantial claim

  • It may state two separate claims as one.

    Interpretationreasoning

    USP16 is a potential therapeutic target acting on both BMP and Cdkn2a pathways independently.

    “Here, we present USP16 as a potential therapeutic target acting on both BMP and Cdkn2a pathways independently.”
    Quote in the paperSubstantial claim

  • It may state two separate claims as one.

    Interpretationown data

    Targeting USP16 in a mouse model of AD rescues two aberrant aging pathways, Cdkn2a and BMP, which can restore self-renewal of NPCs, decrease astrogliosis, and retard cognitive decline.

    “For the first time, we show that targeting USP16 in a mouse model of AD rescues two aberrant aging pathways, Cdkn2a and BMP, which can restore self-renewal of NPCs, decrease astrogliosis, and retard cognitive decline (Figure 1).”
    Quote in the paperSubstantial claim
    • Rests on an assumption: Usp16+/- mice do not show tumor formation.

  • Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.

    Study design and conductown data

    The immunofluorescence experiment on human neurospheres was performed three times (each round of infection with subsequent experiment being a biological replicate) in triplicate (each slide with at least 3 neurospheres, each neurosphere having at least 100 cells).

    “Experiment was performed three times (1 biological replicate = 1 round of infection with subsequent experiment) in triplicate (1 technical replicate = 1 slide with at least 3 neurospheres with 1 neurosphere having at least 100 cells).”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim. The paper’s conclusions may not depend on it.

    Study design and conductown data

    The differentiation experiment was performed with three biological replicates in triplicate (three technical replicates and three images per technical replicate/well).

    “Experiment was performed with three biological replicates in triplicate (three technical replicates and three images were taken of differing regions of each technical replicate/well).”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim.

    Study design and conductnone given

    All cell counting was performed by experimenters blinded to the experimental conditions.

    “All cell counting was performed by experimenters blinded to the experimental conditions using a Zeiss LSM700 scanning confocal microscope (Carl Zeiss).”
    Quote in the paperSubstantial claim

  • It may state two separate claims as one.

    Interpretationown data

    The findings are translatable to other APP mutations and to human cells.

    “suggesting that our findings are translatable to other APP mutations and to human cells.”
    Quote in the paperSubstantial claim

  • It may state two separate claims as one.

    Interpretationreasoning

    A neural stem cell defect and early cognitive decline predate detectable inflammation and reactive astrogliosis in Tg-SwDI mice.

    “These results suggest that a neural stem cell defect and early cognitive decline predate detectable inflammation and reactive astrogliosis in Tg-SwDI mice.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim. The paper’s conclusions may not depend on it.

    Premisecitation

    NPCs from Bmi1 knockout mice treated with BMP4 experience further growth arrest than untreated NPCs.

    “NPCs from Bmi1 knockout mice treated with BMP4 experience even further growth arrest than those untreated (Gargiulo et al., 2013).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Gargiulo et al., 2013 source

  • It may state two separate claims as one.

    Premisecitation

    Increased expression of P16 and P14 results in increased senescence with a concomitant decrease in self-renewal.

    “This results in increased senescence with a concomitant decrease in self-renewal.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Adorno et al., 2013 source

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

  • Probably not a substantial claim. The paper’s conclusions may not depend on it.

    Study design and conductnone given

    Total plaque area from images taken of 6 sections was analyzed from each mouse with n = 3 mice in each group.

    “Total plaque area from images taken of 6 sections (1 technical replicate = 1 section) were analyzed from each mouse with n = 3 mice (1 biological replicate = 1 mouse) in each group.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.

    Study design and conductown data

    Brain homogenates were run in technical duplicates with three biological replicates.

    “Brain homogenates were run in technical duplicates (2 wells with 200 μg each from each biology replicate) with three biological replicates (1 biological replicate = 1 brain from 1 mouse).”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim.

    Premisecitation

    Bmi1 represses BMP signaling.

    “Previously, Gargiulo et al. found that self-renewal gene Bmi1, whose PRC1 activity is counterbalanced by USP16, represses BMP signaling (Gargiulo et al., 2013).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Gargiulo et al., 2013 source

  • Probably not a substantial claim. The paper’s conclusions may not depend on it.

    Premisecitation

    Monoclonal antibody therapy targeting plaques might at best only slow Alzheimer's disease progression.

    “Currently, there is no treatment to stop, prevent, or reverse AD, and recent advances with monoclonal antibody therapy targeting plaques, although controversial, might at best only slow progression (Huang and Mucke, 2012; Selkoe, 2019; Sevigny et al., 2016).”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Huang and Mucke, 2012 source
    • cites Selkoe, 2019 source
    • cites Sevigny et al., 2016 source

  • Probably not a substantial claim. It may state two separate claims as one.

    Premisecitation

    Overexpression of Bmi1 leads to increased self-renewal and maintenance of multipotency.

    “This is supported by previous data that showed overexpression of USP16 in human-derived neurospheres led to a marked decrease in the formation of secondary neurospheres (Adorno et al., 2013), and overexpression of Bmi1 led to increased self-renewal and maintenance of multipotency (Fasano et al., 2009).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Fasano et al., 2009 source

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

  • Probably not a substantial claim. The paper’s conclusions may not depend on it.

    Study design and conductnone given

    The limiting dilution experiment was repeated three times, with each infection and subsequent limiting dilution experiment being a biological replicate.

    “Experiment was repeated three times (each infection and subsequent limiting dilution experiment performed being a biological replicate).”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.

    Study design and conductnone given

    Biological replicates of a minimum of 3 mice and N = 2 technical replicates for each mouse were used.

    “Biological replicates of a minimum of 3 mice and N = 2 technical replicates for each mouse were used.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.

    Study design and conductnone given

    Informed consent was obtained and a standard material transfer agreement was signed for the human fetal neural stem cell line.

    “Informed consent was obtained, and standard material transfer agreement signed.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim.

    Study design and conductnone given

    For EdU stereology, all EdU-labeled cells in every 6th coronal section of the SVZ were counted by blinded experimenters at ×40 magnification.

    “For EdU stereology, all EdU-labeled cells in every 6th coronal section of the SVZ were counted by blinded experimenters at ×40 magnification.”
    Quote in the paperSubstantial claim

  • It may state two separate claims as one.

    Interpretationown data

    USP16 is a novel target in an AD model that can ameliorate the NPC defect and rescue memory and learning through its regulation of both Cdkn2a and BMP signaling.

    “Thus, we reveal USP16 as a novel target in an AD model that can both ameliorate the NPC defect and rescue memory and learning through its regulation of both Cdkn2a and BMP signaling.”
    Quote in the paperSubstantial claim
    • Rests on an assumption: Usp16+/- mice do not show tumor formation.

  • Probably not a substantial claim. The paper’s conclusions may not depend on it.

    Study design and conductnone given

    For single-cell RNA-seq, four biological replicates from each genotype and at each age were combined (16 samples per age group).

    “As mentioned above, four biological replicates from each genotype and at each age were combined for the single-cell RNA-seq experiment (16 samples per age group).”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.

    Study design and conductnone given

    The colony counts experiment was performed in triplicate (1 technical replicate = 1 well), with 1 biological replicate defined as 1 round of infection with subsequent experiment.

    “Experiment was performed times times (1 biological replicate = 1 round of infection with subsequent experiment) in triplicate (1 technical replicate = 1 well).”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim. The paper’s conclusions may not depend on it.

    Premisecitation

    The BMP pathway plays a role in NPC function.

    “The BMP pathway has been known to play a role in NPC function.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Chang et al., 2018 source

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

  • Probably not a substantial claim. The paper’s conclusions may not depend on it.

    Study design and conductnone given

    Secondary-only stains were performed as negative controls.

    “Secondary-only stains were performed as negative controls.”
    Quote in the paperNot a substantial claim

  • It may state two separate claims as one.

    Premisecitation

    Tg-SwDI mice develop early plaque deposition and cognitive deficits, and express physiologic levels of transgenic human AβPP at approximately 50% the level of endogenous mouse APP.

    “We chose the Tg-SwDI model with mutations confined to APP because mice develop early plaque deposition and cognitive deficits, and express physiologic levels of transgenic human AβPP at approximately 50% the level of endogenous mouse APP (Davis et al., 2004).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Davis et al., 2004 source
62 of 62

  • The paper relies on this without support.

    Usp16+/- mice do not show tumor formation.

    “To test this, we crossed Tg-SwDI mice with Usp16+/- mice to generate Tg-SwDI/Usp16+/- mice, which do not show tumor formation.”

  • The paper relies on this without support.

    pSMAD 1/5/8 are downstream regulators of BMP activity.

    “First, we measured levels of phosphorylated-SMAD (pSMAD) 1, 5, and 8, known downstream regulators of BMP activity, and found they were significantly increased in the mutant neurospheres compared to control (p=0.0001, Figure 6A).”

  • The paper relies on this without support.

    BMP receptors and Id genes are involved in BMP signaling, a sub-pathway of TGF-ß.

    “In looking specifically at the leading-edge genes contributing to the enrichment plots of the TGF-ß pathway, we found upregulation of BMP receptors and Id genes, which are known to be involved in BMP signaling, a sub-pathway of TGF-ß (Figure 5B).”
3 of 3

Citations

Cites

Flagged first, then by citations

1 of the 81 references couldn’t be matched to a known paper.

Cited by

Sorted by citations

Related

Metadata

Authors
Reinitz, F., Chen, E. Y., Nicolis di Robilant, B., Chuluun, B., Antony, J., Jones, R. C., Gubbi, N., Lee, K., Ho, W. H. D., Kolluru, S. S., Qian, D., Adorno, M., Piltti, K., Anderson, A., Monje, M., Heller, H. C., Quake, S. R., & Clarke, M. F.
Affiliations
  • Institute for Stem Cell Biology and Regenerative Medicine (US)
  • Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine
  • Stanford University (US)
  • University of California, Irvine (US)
Corresponding author
Clarke, Michael F
ORCID
Venue
eLife
Publisher
eLife Sciences Publications, Ltd
Published
2022-03-21
Volume
11
ISSN
2050-084X (ISSN-L)
DOI
10.7554/elife.66037
PMC
PMC9122497
OpenAlex
W4221134166
Cited by
18
References
81
Citations by year
2026: 7 · 2025: 4 · 2024: 2 · 2023: 5
FWCI
0.95
Type
journal article
Language
en
Open access
Licence
Locations
  • eLife (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • eScholarship (California Digital Library) (submittedVersion, cc-by)
Funders
  • California Institute of Regenerative Medicine (Graduate Student Fellowship)
  • Chan Zucherberg Foundationg Biohub Initiative
  • National Institutes of Health (1R01AG059712-01, AG059712)
  • Tung Foundation
  • AIRC and Marie Curie Action
Topics
  • Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Alzheimer's disease research and treatments
  • Life Sciences › Neuroscience › Developmental Neuroscience › Neurogenesis and neuroplasticity mechanisms
  • Life Sciences › Neuroscience › Neurology › Neuroinflammation and Neurodegeneration Mechanisms
Keywords
Alzheimer's disease, USP16, neural progenitor cells, stem cell aging, cognitive memory, CDKN2A, BMP signaling, polycomb repressor complex 1, astrocyte activation, amyloid precursor protein, neural stem cell self-renewal, senescence
MeSH terms
Aging, Alzheimer Disease, Animals, Disease Models, Animal, Inflammation, Mice, Transgenic, Amyloid beta-Peptides, Amyloid beta-Protein Precursor, Cellular Senescence, Neurodegenerative Diseases, Ubiquitin Thiolesterase, 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.

A language model drew the claims from the paper on 2026-11-09, under version 3 of the claim definition (model deepseek-v4.1-flash, prompt extract-v3).

A second model labelled each claim on 2026-11-09 (model jev-1.13-20260917, definition revision gold-guideline-v0.2).

Cited sources are checked with a language model’s help (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.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review