APOE4 impairs myelination via cholesterol dysregulation in oligodendrocytes

In the paper

“All these effects are consistent with reported roles of APOE4 in inflammation, synaptic impairment, MAPK1 signaling and downstream APP transcription, and early endosomes7,18.”

What the sources say

• Partly supported

  The Neuroinflammation and Synaptic function sections report APOE4-associated inflammatory activation and synaptic impairment. The Aβ production section reports greater APP transcription in human stem-cell-derived neurons exposed to APOE4, while noting conflicting mouse findings. The paper discusses intracellular endosomal compartments but does not identify early endosomes specifically, and the searched passages do not establish MAPK1 signaling as the pathway to APP transcription (pages unavailable in our copy). (LLM, conf=0.86)

  cites [7] Yamazaki, Y., Zhao, N., Caulfield, T. R., Liu, C.-C. & Bu, G. Apolipoprotein E and Alzheimer disease: pathobiology and targeting strategies. Nat. Rev. Neurol. 15, 501–518 (2019). sourceExperimental — accuracy not yet measured
• Partly supported

  The Discussion (page unavailable) reports that ApoE4 is more potent than other ApoE isoforms in activating an ERK1/2 MAP-kinase pathway that stimulates APP transcription. The passages do not establish the other attributed roles—inflammation, synaptic impairment, or early endosomes—and the paper describes ERK1/2 rather than naming MAPK1 specifically. (LLM, conf=0.86)

  cites [18] Huang, Y.-W. A., Zhou, B., Wernig, M. & Südhof, T. C. ApoE2, ApoE3, and ApoE4 differentially stimulate APP transcription and Aβ secretion. Cell 168, 427–441 (2017). sourceExperimental — accuracy not yet measured

In the paper

“Insight into APOE4-mediated pathogenesis is complicated by the fact that APOE is a soluble factor expressed by many cell types12,13.”

What the sources say

• Partly supported

  The section on cell-type-specific alterations reports APOE expression changes in both microglia and astrocytes, supporting expression in multiple cell types. Our copy does not say that APOE is a soluble factor, so that part of the claim is unsupported. (LLM, conf=0.82)

  cites [12] Mathys, H. et al. Single-cell transcriptomic analysis of Alzheimer’s disease. Nature 570, 332–337 (2019). sourceExperimental — accuracy not yet measured
• ?Not checked — no full text of the sourcecites [13] Xu, Q. et al. Profile and regulation of apolipoprotein E (ApoE) expression in the CNS in mice with targeting of green fluorescent protein gene to the ApoE locus. J. Neurosci. 26, 4985–4994 (2006). source

In the paper

“Annotations were supported by expression patterns of curated marker genes16,17 (Extended Data Fig. 1e; Supplementary Table S2).”

What the sources say

• Partly supported

  In “Transcriptome analysis: Bulk and single cell” (page not provided), the paper describes brain cell-type profiles and expression signatures comprising marker genes, and reports that biomarker-gene expression for the same cell type correlated across two data formats. Our copy does not say the marker genes were curated or that their expression patterns were used to support the cell-type annotations. (LLM, conf=0.78)

  cites [16] Wang, D. et al. Comprehensive functional genomic resource and integrative model for the human brain. Science 362, eaat8464 (2018). sourceExperimental — accuracy not yet measured
• Supported

  In “Clustering and cell-type inference” (page not provided), the paper describes a manually curated cell-type marker database and a cell-type activity score based on normalized marker-gene expression. This supports using expression patterns of curated marker genes to inform cell-type annotations. (LLM, conf=0.90)

  cites [17] Franzén, O., Gan, L.-M. & Björkegren, J. L. M. PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data. Database 2019, baz046 (2019). source

In the paper

“APOE4 is the strongest genetic risk factor for Alzheimer’s disease (AD)1–3.”

What the sources say

• Partly supported

  The paper states that the APOE gene is a major genetic risk factor for Alzheimer’s disease (Abstract; page not available), and its references identify the APOE type 4 allele as associated with risk (References; page not available). Our copy does not establish that APOE4, specifically, is the strongest genetic risk factor. (LLM, conf=0.83)

  cites [1] Lambert, J. C. et al. Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer’s disease. Nat. Genet. 45, 1452–1458 (2013). sourceExperimental — accuracy not yet measured
• ?Not checked — no full text of the sourcecites [2] Corder, E. H. et al. Gene dose of apolipoprotein E type 4 allele and the risk of Alzheimer’s disease in late onset families. Science 261, 921–923 (1993). source
• Partly supported

  The paper reports a significant association between APOE-e4 and late-onset familial Alzheimer’s disease: its allele frequency was 0.50 in affected patients versus 0.16 in controls. It does not compare APOE4 with other genetic risk factors to establish that it is the strongest, or establish the claim for Alzheimer’s disease generally. (LLM, conf=0.87)

  cites [3] Strittmatter, W. J. et al. Apolipoprotein E: high-avidity binding to beta-amyloid and increased frequency of type 4 allele in late-onset familial Alzheimer disease. Proc. Natl Acad. Sci. USA 90, 1977–1981 (1993). sourceExperimental — accuracy not yet measured

In the paper

“and increases cholesterol sequestration in astrocytes leading to changes in the brain matrisome11.”

What the sources say

• Partly supported

  The Results section, “Matrisome exacerbates lipid dysregulation in APOE4 astrocytes” (page unavailable), states that APOE4 drives lysosomal cholesterol sequestration in astrocytes and that matrisome dysregulation occurs. It does not say sequestration leads to matrisome changes; instead, it links those changes partly to astrocyte–neuron communication and says they worsen lipid dysregulation. (LLM, conf=0.88)

  cites [11] Tcw, J. et al. Cholesterol and matrisome pathways dysregulated in astrocytes and microglia. Cell 185, 2213–2233 (2022). sourceExperimental — accuracy not yet measured

In the paper

“Recent in vitro studies discovered that APOE4 promotes the accumulation of unsaturated triglycerides and lipid droplets in iPSC-derived astrocytes10”

What the sources say

• Supported

  The Results section, “Human iPSC-derived APOE4-expressing astrocytes display intracellular lipid dysregulation,” reports higher triacylglyceride levels and greater fatty-acid unsaturation in APOE4 astrocytes than in APOE3 astrocytes. It also reports more lipid droplets in the APOE4 cells. Triacylglycerides are triglycerides, so this supports the citing sentence. (LLM, conf=0.94)

  cites [10] Sienski, G. et al. APOE4 disrupts intracellular lipid homeostasis in human iPSC-derived glia. Sci. Transl. Med. 13, eaaz4564 (2021). source

In the paper

“APOE4 is associated with increased amyloid-β deposition, hyperphosphorylation and aggregation of tau, and accelerated cognitive decline4–7.”

What the sources say

• Partly supported

  The Introduction states that Aβ plaques are more abundant in APOE4 carriers, and the Discussion describes apoE4’s role in early amyloid plaque formation (page numbers unavailable). The passages do not link APOE4 to tau hyperphosphorylation or aggregation, or to accelerated cognitive decline; the Discussion mentions cognitive decline only as a later clinical event relative to Aβ deposition. (LLM, conf=0.88)

  cites [4] Liu, C.-C. et al. ApoE4 accelerates early seeding of amyloid pathology. Neuron 96, 1024–1032 (2017). sourceExperimental — accuracy not yet measured
• Supported

  The paper’s introductory passage (labeled Abstract in our copy; page unavailable) describes greater Aβ deposition with ApoE4 and greater tau hyperphosphorylation with E4 than E3. Its mouse results report more accumulated, less-soluble tau in ApoE4 mice, while Extended Data Figure 8 reports faster progression on a dementia-rating scale in APOE4 carriers with symptomatic Alzheimer’s disease. (LLM, conf=0.86)

  cites [5] Shi, Y. et al. ApoE4 markedly exacerbates tau-mediated neurodegeneration in a mouse model of tauopathy. Nature 549, 523–527 (2017). source
• Partly supported

  The Results section on Aβ and amyloid deposition reports greater deposition in apoE4 mice than in apoE3 or apoE2 mice; the human biomarker Results section also links APOE ε4 to greater amyloid burden. The paper does not establish the attributed association with tau hyperphosphorylation or aggregation, or accelerated cognitive decline. Its Introduction describes an earlier age of Alzheimer’s onset, which is not the same as a faster rate of cognitive decline. Page numbers were not available in our copy. (LLM, conf=0.88)

  cites [6] Castellano, J. M. et al. Human apoE isoforms differentially regulate brain amyloid-β peptide clearance. Sci. Transl. Med. 3, 89ra57 (2011). sourceExperimental — accuracy not yet measured
• Partly supported

  The ‘APOE4 and Aβ pathology’ section (page unavailable) reports greater Aβ deposition in APOE4 carriers. The ‘Tau, α-synuclein and TDP43 proteinopathies’ section (page unavailable) reports increased tau phosphorylation in experimental models and more tau aggregates in people with two APOE4 alleles when Aβ pathology is present. The copy links APOE4 to earlier symptom onset, but the passages found do not establish accelerated cognitive decline; the claim also omits the condition on the human tau-aggregation finding. (LLM, conf=0.84)

  cites [7] Yamazaki, Y., Zhao, N., Caulfield, T. R., Liu, C.-C. & Bu, G. Apolipoprotein E and Alzheimer disease: pathobiology and targeting strategies. Nat. Rev. Neurol. 15, 501–518 (2019). sourceExperimental — accuracy not yet measured

In the paper

“The APOE genotype has a widespread impact on cell-autonomous and non-autonomous biological processes14.”

What the sources say

• Supported

  The Results section on the APOE3-to-APOE4 switch reports widespread genotype-dependent gene-expression changes across iPSC-derived neurons and glia, supporting cell-autonomous effects. The Results section on microglia-like cells also reports that changing the APOE genotype of cells co-cultured with organoids changed extracellular Aβ accumulation, supporting effects beyond the genotype-bearing cells. These findings are in human iPSC-derived brain-cell models. (LLM, conf=0.90)

  cites [14] Lin, Y.-T. et al. APOE4 causes widespread molecular and cellular alterations associated with Alzheimer’s disease phenotypes in human iPSC-derived brain cell types. Neuron 98, 1141–1154 (2018). source

In the paper

“Altered amyloid-β processing and DNA damage have been associated with APOE4 and AD19–21.”

What the sources say

• Partly supported

  The Abstract and Results report correlations between neuronal apoE expression and DNA-damage-and-repair pathways in an Alzheimer’s disease context, but do not establish that association specifically for APOE4. The passages do not support the other part of the claim, altered amyloid-β processing; the paper’s reported findings instead focus on MHC-I and Tau pathology. (LLM, conf=0.82)

  cites [19] Zalocusky, K. A. et al. Neuronal ApoE upregulates MHC-I expression to drive selective neurodegeneration in Alzheimer’s disease. Nat. Neurosci. 24, 786–798 (2021). sourceExperimental — accuracy not yet measured
• ?Could not verify

  The supplied passages and the retrieved passages are labeled as a Parkinson’s disease paper, not the cited Alzheimer’s disease paper. Searches for APOE4 and altered amyloid-β processing did not yield passages from our copy of the cited paper, so the attributed association cannot be assessed. (LLM, conf=0.72)

  cites [20] Thadathil, N. et al. DNA double-strand break accumulation in Alzheimer’s disease: evidence from experimental models and postmortem human brains. Mol. Neurobiol. 58, 118–131 (2021). sourceExperimental — accuracy not yet measured
• Partly supported

  The Discussion (p. 18703) reports that apoE4 enhances amyloid-β production more than apoE3 and relates this finding to amyloid deposition in Alzheimer’s disease. The paper does not address DNA damage, so it supports only the amyloid-β part of the claim. (LLM, conf=0.88)

  cites [21] Ye, S. et al. Apolipoprotein (apo) E4 enhances amyloid beta peptide production in cultured neuronal cells: apoE structure as a potential therapeutic target. Proc. Natl Acad. Sci. USA 102, 18700–18705 (2005). sourceExperimental — accuracy not yet measured

In the paper

“two lipid classes known to promote brain inflammation and demyelination (Extended Data Fig. 6; Supplementary Table S11)26.”

What the sources say

• Partly supported

  Section 1.3 reports that LPC induces demyelination in the central nervous system and inflammation in the brain microvasculature. Section 5.2 discusses LPA in inflammatory disorders and the central nervous system, but does not say that LPA promotes brain inflammation or demyelination. The claim is therefore supported for LPC, not for both lipid classes. (LLM, conf=0.88)

  cites [26] Law, S.-H. et al. An updated review of lysophosphatidylcholine metabolism in human diseases. Int. J. Mol. Sci. 20, 1149 (2019). sourceExperimental — accuracy not yet measured

In the paper

“Accumulation of lipid droplets is a common hallmark of ER stress27,28.”

What the sources say

• ?Not checked — no full text of the sourcecites [27] Ye, J. et al. ER stress induces cleavage of membrane-bound ATF6 by the same proteases that process SREBPs. Mol. Cell 6, 1355–1364 (2000). source
• Supported

  The “LDs and ER stress” section states that lipid-droplet accumulation is often observed in mammals when ER stress is induced. This supports the claim’s description of it as a common hallmark. (LLM, conf=0.92)

  cites [28] Hapala, I., Marza, E. & Ferreira, T. Is fat so bad? Modulation of endoplasmic reticulum stress by lipid droplet formation. Biol. Cell 103, 271–285 (2011). source

In the paper

“Cyclodextrin is a molecule known to reduce intracellular cholesterol accumulation in Niemann-Pick disease type C30.”

What the sources say

• Supported

  The HISTORY OF 2-HYROXYPROPYL-β-CYCLODEXTRIN AND NPC1 DISEASE section states that HP-β-CD reverses intracellular accumulation of unesterified cholesterol in vitro and reduces stored cholesterol in primary neurons and astrocytes. This supports the claim, although the passage describes cell-based evidence rather than a demonstrated effect in patients. (LLM, conf=0.92)

  cites [30] Ottinger, E. A. et al. Collaborative development of 2-hydroxypropyl-β-cyclodextrin for the treatment of Niemann-Pick type C1 disease. Curr. Top. Med. Chem. 14, 330–339 (2014). source

In the paper

“Reduced myelin volume and integrity often occur prior to the onset of dementia and are predictive of future cognitive impairment23,24,33,36.”

What the sources say

• ?Not checked — no full text of the sourcecites [23] Brun, A. & Englund, E. A white matter disorder in dementia of the Alzheimer type: a pathoanatomical study. Ann. Neurol. 19, 253–262 (1986). source
• ?Not checked — no full text of the sourcecites [24] Bartzokis, G. Age-related myelin breakdown: a developmental model of cognitive decline and Alzheimer’s disease. Neurobiol. Aging 25, 5–18 (2004). source
• Partly supported

  The Conclusions (page not provided) suggest that myelin alterations may be among the earliest features of Alzheimer disease, and the study examined asymptomatic adults. But the Discussion’s Limitations describe the analyses as cross-sectional and call for longitudinal studies; this paper does not show that reduced myelin predicts future cognitive impairment. It also does not establish how often the alterations occur before dementia. (LLM, conf=0.88)

  cites [33] Dean, D. C. 3rd et al. Association of amyloid pathology with myelin alteration in preclinical Alzheimer disease. JAMA Neurol. 74, 41–49 (2017). sourceExperimental — accuracy not yet measured
• Partly supported

  The Discussion (page unavailable) reports reduced white-matter integrity in cognitively normal women at high risk for Alzheimer’s disease and says the imaging pattern is consistent with early myelin loss. It does not establish reduced myelin volume or show that these changes predict future cognitive impairment; the authors say longitudinal follow-up is needed to test prediction. (LLM, conf=0.87)

  cites [36] Gold, B. T., Powell, D. K., Andersen, A. H. & Smith, C. D. Alterations in multiple measures of white matter integrity in normal women at high risk for Alzheimer’s disease. Neuroimage 52, 1487–1494 (2010). sourceExperimental — accuracy not yet measured

In the paper

“Per-gene expression levels per cell type were modeled as a negative binomial model with random effects that model both within-individual and between-individual effects, as implemented in the R package NEBULA (version 1.2.1)40”

What the sources say

• Supported

  The Methods section (‘The model specification in NEBULA’; page unavailable) describes a per-gene negative binomial mixed model with fixed-effect predictors, cell-level dispersion, and subject-level random effects. This supports the citation-bearing sentence’s identification of NEBULA as the modeling method. The APOE4 and adjustment variables in the supplied paraphrase are not part of that sentence’s attribution to the source. (LLM, conf=0.90)

  cites [40] He, L. et al. NEBULA is a fast negative binomial mixed model for differential or co-expression analysis of large-scale multi-subject single-cell data. Commun. Biol. 4, 629 (2021). source

In the paper

“Pharmacologically facilitating cholesterol transport increases axonal myelination and improves learning and memory in APOE4 mice.”

In the paper

“We establish that pharmacologically facilitating cholesterol transport improves myelination and learning and memory in aged APOE4/4 mice, thus providing new insight into the mechanistic connection between APOE4, myelination, and AD pathogenesis.”

In the paper

“As expected, associated pathways included amyloid-β and protein processing, lipid metabolism, and synaptic-related processes.”

In the paper

“We also identified decreased glycosyltransferase activity (e.g., ALG6, ALG3) in APOE4 neurons and widespread alterations to amyloid-β metabolism genes in excitatory neurons, oligodendrocytes, and OPCs (amyloid-β formation, e.g., BIN1, ROCK1; Fig. 1a).”

In the paper

“Cell type expression profiles were strongly correlated between individual donors (average Pearson r=0.94 and r=0.65 for high and low-abundant cell types, respectively; Extended Data Fig. 1h, i; Supplementary Table S3).”

In the paper

“Chaperone-mediated protein folding was increased in most cell types (e.g., DNAJB14, HSPA1A), and ATF-mediated unfolded protein response was increased in neurons and oligodendrocytes.”

In the paper

“In APOE4 excitatory neurons, we identified upregulation of ERK1/2 signaling (e.g., MAPK1, MAP2K1, and MAP2K2) and endosomal-related transport genes (e.g., RAB21 and SNX12) (Supplementary Table S4).”

In the paper

“and (2) is associated with endoplasmic reticulum stress and reduced myelination.”

In the paper

“Punctate, perinuclear PLIN1 stained lipid droplets appeared in both APOE3/3 and APOE3/4 tissue; staining was more prominent around distinct nuclei in APOE4-carriers (Extended Data Fig. 4a).”

In the paper

“We find that APOE4-carriers have decreased localization of cholesterol along neurofilaments and increased intracellular accumulation or storage of cholesterol as compared to brains from age-matched APOE3/3 individuals.”

In the paper

“APOE mRNA and protein were expressed at low to moderate levels in iPSC-derived oligodendroglia, with no significant (p = 0.2635) difference between isogenic APOE3/3 and APOE4/4 iPSC-derived oligodendroglia (Extended Data Fig. 5i, j).”

In the paper

“PLIN1 immunoreactivity around OLIG2-positive nuclei in APOE3/4 human PFC from AD individuals also exhibited a minimal but non-significant increase compared to APOE3/3 (p = 0.1521, n = 3 per genotype) (Extended Data Fig. 4d, e).”

In the paper

“Genes associated with cholesterol biosynthesis and droplet formation (DHCR24, LPIN2, IRS2, NR1H2, LBR, LPIN1, and MBTPS1) were upregulated, while cholesterol transport genes were downregulated (PCYT1B, SEC23A, PRKN, SCP2, and LPCAT3; Fig. 2c).”

In the paper

“APOE3/3 subjects with and without pathology exhibited the lowest cholesterol biosynthesis gene expression, and those with both APOE4 and AD pathology the largest (Extended Data Fig. 2k).”

In the paper

“Approximately ~2% of Bodipy-cholesterol particles localized to the endosome, ~18% to the lysosome, and ~80% to the ER”

In the paper

“In contrast, PFC from APOE3/4 had a significant (p = 0.0031) reduction in the area positive for Black Gold II staining, and axonal fasciculation was largely absent”

In the paper

“Mass-spectrometry-based lipidomic profiling of APOE3/3 and APOE4/4 isogenic iPSC-derived oligodendroglia detected 88 lipid species increased (adjusted p-value < 0.05) in APOE4/4 oligodendroglia compared to APOE3/3 controls, and only one species decreased (Fig. 3a; Extended Data Fig. 6; Supplementary table S11).”

In the paper

“In contrast, PFC white matter regions from APOE4-carriers exhibited significantly (p = 0.0027, p = 0.0294) decreased MBP immunoreactivity as compared to APOE3/3 non-carriers, with fewer MBP regions surrounding neurofilament-positive axons (Fig. 4c and Extended Data Fig. 8b).”

In the paper

“In contrast, the area within a 2 μm radius of OLIG2-positive nuclei exhibited significantly (p < 0.0001) more Bodipy-cholesterol staining, with 77% of OLIG2-positive nuclei surrounded by intense Bodipy-cholesterol signal, suggesting that cholesterol may aberrantly accumulate in APOE4 oligodendrocytes (Extended Data Fig. 4c).”

In the paper

“Cholesterol biosynthesis gene expression increased in individuals without AD pathology (Extended Data Fig. 2e, f; lipid storage pathways also increased) and a non-significant increase in individuals with AD (Extended Data Fig. 2g), indicating an APOE4 effect independent of AD pathology.”

In the paper

“The levels of MBP surrounding neurofilament in APOE4/4 oligodendroglia co-cultured with APOE3 iNeurons were similar (p > 0.9999) to all-APOE4/4 co-cultures, with only ~20% of neurofilament-positive axons surrounded by MBP staining (Fig. 5b).”

In the paper

“Total distance traveled and time spent in the center of the home cage (p = 0.1275 and p = 0.4478, respectively) was similar in control (n = 12) and cyclodextrin-treated (n = 14) APOE4/4-TR mice”

In the paper

“APOE4/4-TR mice had fewer myelinated axons (p = 0.0265, 140 myelinated axons in average per field of view, n=3 mice), and higher g-ratios compared to APOE3/3-TR mice (p < 0.0001; Fig. 4e).”

In the paper

“MBP immunoreactivity and axonal localization in the APOE−/− co-cultures were significantly (p = 0.0005) lower than APOE3/3 co-cultures and were similar to APOE4/4 co-cultures (Extended Data Fig. 9j).”

In the paper

“High-magnification imaging confirmed that the cells surrounding neurofilaments were positive for MBP (Extended Data Fig. 9e, Supplemental Video 1), and transmission electron microscopy (TEM) showed axonal segments surrounded by electron-dense membrane rings at a low frequency”

In the paper

“Lipid-related genesets with evidence of having an APOE4 effect (p-value < 0.05) are shown in Extended Fig. 2d.”

In the paper

“Cyclodextrin-treated APOE4/4-TR mice exhibited a decrease in latency to enter the goal box (p-value = 0.02), while saline-treated APOE4/4-TR mice (control) did not improve between the trial days (p-value > 0.6; Fig. 6f).”

In the paper

“In cyclodextrin-treated APOE4/4 oligodendroglia, we observed a significant (p = 0.0092) reduction in the number of intracellular droplets of Bodipy-cholesterol, as well as a significant (p < 0.0001) reduction of neutral lipid droplets stained with Bodipy.”

In the paper

“This procedure resulted in prioritized candidate pathways for all major cell types.”

In the paper

“After two weeks in these 3D co-cultures, MBP-positive oligodendroglia spread and engaged neurofilament-positive axons (Extended Data Fig. 9b).”

In the paper

“We compared APOE3/4 and APOE4/4 vs APOE3/3 scores using a multivariate linear model controlling for sex, postmortem interval (PMI), amyloid, neurofibrillary tangles, and age at death.”

In the paper

“A total of 11 cell types supported by gene marker expression and significant enrichment (FDR < 0.01, permutation test) of marker sets (Extended Data Fig. 1g) were annotated.”

In the paper

“High-abundant cell types were well-represented across all donors, independent of AD diagnosis or genotypic background, with reproducible proportions in most cases (Extended Data Fig. 1l, m).”

In the paper

“One copy of the APOE4 allele, which differs from the major allele (APOE3) by a single amino acid change from Cys112 to Arg112, increases the risk of developing AD 3 to 4 fold, while two copies increase it by 8 to 12 fold2.”

What the sources say

• ?Not checked — no full text of the sourcecites [2] Corder, E. H. et al. Gene dose of apolipoprotein E type 4 allele and the risk of Alzheimer’s disease in late onset families. Science 261, 921–923 (1993). source

In the paper

“The APOE3/3 and APOE3/4 subgroups were balanced by AD pathological diagnosis (n=6 each for positive and negative diagnoses of AD) and gender (3 male and 3 female each; Extended Data Fig. 1a; Supplementary Table S1).”

In the paper

“All AD subjects presented high levels of both amyloid and neurofibrillary tangle (Tau) pathology, and there were no differences in age or post-mortem intervals between APOE3/3 and APOE3/4 groups and AD status (Extended Data Fig. 1b).”

In the paper

“DNA damage response was also altered in APOE4 microglia and OPCs, suggesting APOE4 may promote DNA damage in specific cell types.”

In the paper

“consistent with reports of hypomyelination and white matter changes in AD23,24.”

What the sources say

• ?Not checked — no full text of the sourcecites [23] Brun, A. & Englund, E. A white matter disorder in dementia of the Alzheimer type: a pathoanatomical study. Ann. Neurol. 19, 253–262 (1986). source
• ?Not checked — no full text of the sourcecites [24] Bartzokis, G. Age-related myelin breakdown: a developmental model of cognitive decline and Alzheimer’s disease. Neurobiol. Aging 25, 5–18 (2004). source

In the paper

“these further support an association between APOE4 and brain cholesterol potentially indicating increased cholesterol storage in lipid droplets (Supplementary Tables S7 and S8).”

In the paper

“This demonstrates that iPSC-derived oligodendroglia are transcriptionally similar to ex vivo human oligodendrocytes and OPCs, providing a reliable proxy for investigating the effect of APOE4 on human oligodendrocytes.”

In the paper

“Together, these results demonstrate that APOE4 is associated with reduced localization of cholesterol in the plasma membrane of oligodendrocytes, increased cholesteryl esters and lipid droplets, and upregulation of ATF6-mediated ER stress response.”

In the paper

“Following completion of the differentiation protocol, 65–81% of cells were immunoreactive for MBP and 69–82% were immunoreactive for PLP1 across cultures (Extended Data Fig. 5c).”

In the paper

“However, the increased bodipy-cholesterol in APOE4 oligodendroglia was not entirely localized to lysosome, suggesting cholesterol may be accumulating in other organelles.”

In the paper

“Oligodendrocytes myelinate the central nervous system and the bioavailability of cholesterol is rate-limiting for the formation and maintenance of myelin29.”

What the sources say

• ?Not checked — no full text of the sourcecites [29] Saher, G., Quintes, S. & Nave, K.-A. Cholesterol: a novel regulatory role in myelin formation. Neuroscientist 17, 79–93 (2011). source

In the paper

“suggesting ER stress and impaired cholesterol transport could have a central role in the observed intracellular cholesterol accumulation.”

In the paper

“suggesting that repeated cyclodextrin treatment did not affect general locomotion or induce anxiety-like behavior (Extended Data Fig. 10c).”

In the paper

“For each pathway-cell type combination, pathway activity scores were modeled using a multivariate linear model as follows: pathway activity ~ β0 * APOE4 + β1 * amyloid + β2 * nft + β3 * age_death + β4 * msex + β5 * pmi.”

In the paper

“After applying QC filtering steps, the dataset included 17,915 genes profiled in 164,741 nuclei.”

In the paper

“These effects are not observed when targeting biosynthesis, suggesting that APOE4 plays a role in cholesterol trafficking and that increased biosynthesis might be a compensatory mechanism.”

In the paper

“To avoid biased cell mixing due to independent sequencing batches or potential technical artifacts, a batch correction step considering sequencing batch as indicator vector was performed as part of the initial dimensionality reduction in all analyses.”

In the paper

“Cholesterol gene expression and localization are dysregulated in oligodendrocytes, leading to impaired myelination.”

In the paper

“This suggests that cyclodextrin reduced both intracellular cholesterol and accumulation of neutral lipids such as triacylglycerides (Fig. 6b and Extended Data Fig. 10a).”

In the paper

“Experimenters were not blinded to drug injections and when executing behavioral trials.”

In the paper

“Sample size was determined from previous publications from our lab.”

In the paper

“Individual-level normalized gene expression averages were fitted with the following linear model: gene expression ~ β0*APOE4 + β1*amyloid + β2*nft + β3*age_death + β4*msex + β5*pmi.”

In the paper

“Data analysis of the TEM images was done manually under blinded conditions.”

In the paper

“APOE4 expression in oligodendrocytes promotes both cholesterol accumulation and impaired myelination.”

In the paper

“suggesting that APOE4/4 neurons do not impair the ability of APOE3/3 oligodendroglia to produce MBP or engage neuronal axons (Fig. 5b).”

In the paper

“At least four images for each animal were analyzed.”

In the paper

“4 out of 17 peaks passed this quality control cutoff (Supplementary Table S8).”

In the paper

“Therefore, myelination defects are observed in APOE4/4 and APOE−/− oligodendrocytes and can be rescued with the addition of APOE3 protein.”

In the paper

“suggesting that APOE4/4 oligodendrocytes were producing less MBP and engaging less with neuronal processes than isogenic APOE3/3 co-cultures (Fig. 5a).”

In the paper

“Activity scores computed this way accurately recovered cell type signatures not recovered by equally-sized randomly sampled genesets (data not shown)”

In the paper

“We demonstrate facilitating cholesterol transport increases myelination and improves cognitive function in APOE4.”

In the paper

“For APOE3/3 and APOE3/4-carriers, subjects were balanced between sexes (12 each) and matched for age (median=84.6 for APOE3/3 and 85.2 for APOE3/4).”

In the paper

“Power analysis to determine sample size was not performed.”

In the paper

“The following parameters were used to evaluate the GSVA function: mx.diff=TRUE, kcdf=c(“Gaussian”), min.sz=5, max.sz=150.”

In the paper

“Treatment and genotype groups were matched on age as much as possible.”

In the paper

“We observed that pharmacologically promoting cholesterol efflux increases myelination in vitro and in vivo, and improves cognition in APOE4/4-TR mice.”

In the paper

“suggesting that corpus callosum from aged APOE4/4 individuals contains fewer myelinated axons and thinner overall myelin sheaths compared to APOE3/3 individuals (Fig. 4d).”

In the paper

“Both males and females were included in the experiments and sex was balanced across treatment and genotype conditions.”

In the paper

“These results establish a causal link between cholesterol dysregulation and myelination in APOE4-carriers, which may influence the onset and severity of cognitive decline in AD.”

In the paper

“Outlier cells with less than 500 or more than 10,000 genes detected were excluded, and only genes detected in at least 10 cells were considered.”

In the paper

“indicating an increased number of myelinated axons and thicker myelin sheaths (Fig 6d).”

In the paper

“Analysis was performed blinded.”

In the paper

“Each experiment consisted of at least 3 mice per a treatment group.”