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Cited by 1Lipid metabolism and biosynthesisAlzheimer's disease research and treatmentsAutophagy in Disease and Therapy

APOE genotypes differentially remodel the astrocytic lipid droplet proteome to shape lipid droplet dynamics

Open access
Cuní-López, Carla, Root, Jessica T., Hao, Ying, Blomberg, Niek, Koppes-den Hertog, Sascha J., Sacks, Dylan, Trujillo, Amber E., Ghirlando, Rodolfo +9 more·2026·Nature Communications
DOI 10.1038/s41467-026-76565-6PMC PMC13582944
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Abstract

Lipid droplets are dynamic cellular organelles that store neutral lipids and coordinate metabolic and stress-response pathways. In the brain, lipid droplets in glial cells, including astrocytes, have been implicated in Alzheimer’s disease, but how genetic risk factors influence their composition and turnover remains poorly understood. APOE is the strongest genetic modulator of late-onset Alzheimer’s disease and exists in common variants that confer decreased, neutral, or increased risk. Here we show that APOE genotype shapes the lipid droplet proteome, lipidome, and degradation dynamics in human induced pluripotent stem cell-derived astrocytes. By comparing oleic acid-treated astrocytes carrying APOE2 , APOE3 , or APOE4 , we find that each variant is associated with distinct lipid droplet proteins and lipids. These molecular differences correspond to genotype-dependent changes in lipophagy, an autophagy-mediated pathway for lipid droplet clearance. Lipid droplets in APOE2 astrocytes undergo efficient autophagic turnover, whereas those in APOE4 astrocytes resist degradation. These findings identify impaired lipid droplet clearance as a potential mechanism linking APOE4 to Alzheimer’s disease risk.

AI snapshot

Written from the paper’s full text.

TL;DR

APOE genotype shapes the lipid droplet proteome, lipidome, and degradation dynamics in human iPSC-derived astrocytes. APOE2 lipid droplets undergo efficient autophagic turnover, whereas APOE4 lipid droplets resist degradation, implicating impaired lipid droplet clearance in APOE4-associated Alzheimer’s disease risk.

Key findings

  • From 3,256 buoyant-fraction proteins, the study defined a 265-protein human iPSC-derived astrocyte lipid droplet-associated proteome: 222 proteins unique to the buoyant fraction plus 43 strongly enriched over cytosol; 28% were newly identified, including RUFY2.
  • APOE genotype-specific lipid droplet proteomes differed: APOE2 had the highest number of genotype-specific proteins, with APOE2-exclusive proteins enriched in immune/cellular response pathways; APOE4-exclusive proteins were enriched in protein secretion and autophagosome assembly. HSD17B8 was higher in APOE2 lipid droplets, while DHRSX was higher in APOE4 lipid droplets.
  • APOE2 and APOE4 lipid droplets had similar cholesterol ester and triacylglycerol levels, whereas APOE3 lipid droplets showed high cholesterol esters, diacylglycerols, and fatty acids but reduced triacylglycerols. APOE2 lipid droplets contained more unsaturated lipids than APOE3 and APOE4, driven by PUFA-enriched triacylglycerol species.
  • APOE4 lipid droplets resisted degradation: after 42 h chase with ATGL inhibition, ~20% of the initial lipid droplet pool remained in APOE2 versus ~40% in APOE4; SQSTM1/p62 and LC3B co-localization with lipid droplets was higher in APOE4 under ATGL inhibition and starvation, and LipiDye-M ratiometric analysis suggested impaired lipophagy in APOE4 astrocytes.

Methods

  • Isogenic human iPSC-derived astrocytes from KOLF2.1J and BIONi037 lines homozygous for APOE2, APOE3, or APOE4 were treated with 80 μM oleic acid or 0.7% BSA vehicle for 48 h; lipid droplets were isolated by sucrose gradient ultracentrifugation.
  • Mass spectrometry-based proteomics and targeted lipidomics were performed on buoyant and cytosolic fractions, with validation by immunofluorescence and 3D co-localization; lipid droplet dynamics were assayed by BODIPY-C12 pulse-chase, ATGL inhibition with atglistatin, autophagy inhibitors, HBSS starvation, and LipiDye-M imaging.
  • Human post-mortem single-nuclei transcriptomic datasets were analyzed across APOE genotype groups: APOE2 carriers n = 39, APOE3-homozygous n = 172, and APOE4 carriers n = 87.

Limitations

  • The paper states that oleic acid treatment is an artificial lipid-loading condition, not a defined physiological or pathological stimulus, and that it reduced intracellular and secreted APOE levels; findings are therefore limited to lipid-loaded astrocytes, with future work needed under inflammatory, oxidative, and amyloid-associated conditions.
  • The paper states that the study could not capture heterogeneity within lipid droplets in a single cell type or genotype and focused on cell-autonomous regulation, leaving cell non-autonomous consequences for future work.
  • Evident from the text: differential abundance used an adjusted p-value threshold of <0.1 to avoid false negatives, which may increase false positives; some key dynamic findings are trends rather than significant effects, and parental iPSC genetic background partially drove variability, so analyses focused on proteins consistently observed across both isogenic sets.

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

Integrity signals

Registry

Crossref · 10.1038/s41467-026-76565-6

Cites

93 of 95 references verified0 citation errors · 2 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

86 of 99 cited sources checked · 60 supported · 0 flagged · accuracy not yet measured

  • Findingown data

    DHRSX was more abundantly associated with APOE4 lipid droplets than in the other two APOE genotypes.

    “DHRSX, a protein involved in multiple steps of dolichol biosynthesis50, was more abundantly associated with APOE4 lipid droplets than in the other two APOE genotypes (Fig. 3F), and we were able to confirm this with immunofluorescence (Fig. 3G, H).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [50] Wilson, M. P. et al. A pseudoautosomal glycosylation disorder prompts the revision of dolichol biosynthesis. Cell 187, 3585–3601 (2024). source
  • Premisecitation

    Studies in various model systems have linked APOE4 with increased astrocytic lipid droplets.

    “studies in various model systems have linked APOE4 with increased astrocytic lipid droplets15,16,20,24.”
    Quote in the paperSubstantial claim4 of 4 sources checked
    • cites [15] Farmer, B.C., Kluemper, J. & Johnson, L.A. Apolipoprotein E4 alters astrocyte fatty acid metabolism and lipid droplet formation. Cells 8, https://doi.org/10.3390/cells8020182 (2019). source
    • cites [16] Windham, I.A. et al. APOE traffics to astrocyte lipid droplets and modulates triglyceride saturation and droplet size. J. Cell Biol. 223, https://doi.org/10.1083/jcb.202305003 (2024). source
    • cites [20] Qi, G. et al. ApoE4 Impairs Neuron-Astrocyte Coupling of Fatty Acid Metabolism. Cell Rep. 34, 108572 (2021). source
    • cites [24] Sienski, G. et al. APOE4 disrupts intracellular lipid homeostasis in human iPSC-derived glia. Sci. Transl. Med. 1–12 (2021). source
  • Findingown data

    A side-by-side comparison between our protocol and that used in Feringa et al. revealed changes in the abundance of lipid classes, particularly neutral lipids, in an APOE genotype-specific manner.

    “A side-by-side comparison between our protocol (48 h treatment with 0.7% BSA in FBS-free media) and that used in Feringa et al. (FBS-free media for 24 h) revealed changes in the abundance of lipid classes, particularly neutral lipids, in an APOE genotype-specific manner (Supplementary Fig. S3C and Supplementary Data 22).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [30] Feringa, F. M. et al. The Neurolipid Atlas: a lipidomics resource for neurodegenerative diseases. Nat. Metab. 7, 2142–2164 (2025). source

      The Limitations section says Feringa et al. removed serum during terminal iAstrocyte experiments, supporting the description of an FBS-free protocol. The Methods passage specifies 24 hours for a cholesterol-treatment experiment, but the retrieved passages do not establish that duration for the APOE-genotype lipidomics protocol. The side-by-side comparison and its findings are presented as the citing authors’ own results, not Feringa et al.’s. (LLM, conf=0.78)

      Experimental — accuracy not yet measured
  • Findingown data

    The 265-protein proteome is primarily associated with lipid droplets and lipid metabolism.

    “We used overrepresentation analysis45 to determine the functional enrichment of these proteins and reassuringly found that they primarily were associated with lipid droplets and lipid metabolism (Fig. 2F and Supplementary Data 8).”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [45] Zhou, Y. et al. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat. Commun. 10, 1523 (2019). source
  • Premisecitation

    APOE4 astrocytes accumulate unsaturated triglycerides in lipid droplets in both mouse and human iPSC-derived astrocytes.

    “APOE4 astrocytes accumulate unsaturated triglycerides in lipid droplets in both mouse15,16 and human iPSC-derived astrocytes24,30.”
    Quote in the paperSubstantial claim4 of 4 sources checked
    • cites [15] Farmer, B.C., Kluemper, J. & Johnson, L.A. Apolipoprotein E4 alters astrocyte fatty acid metabolism and lipid droplet formation. Cells 8, https://doi.org/10.3390/cells8020182 (2019). source

      The Methods (§2.1) identify the studied astrocytes as mouse-derived, and the Results (§3.1) show that APOE4 cells had more lipid droplets than APOE3 cells. The paper does not establish that the accumulated droplets specifically contain unsaturated triglycerides. Its own experiments also do not use human iPSC-derived astrocytes, though the citing sentence attaches other citations to that portion. (LLM, conf=0.87)

      Experimental — accuracy not yet measured
    • cites [16] Windham, I.A. et al. APOE traffics to astrocyte lipid droplets and modulates triglyceride saturation and droplet size. J. Cell Biol. 223, https://doi.org/10.1083/jcb.202305003 (2024). source
    • cites [24] Sienski, G. et al. APOE4 disrupts intracellular lipid homeostasis in human iPSC-derived glia. Sci. Transl. Med. 1–12 (2021). source
    • cites [30] Feringa, F. M. et al. The Neurolipid Atlas: a lipidomics resource for neurodegenerative diseases. Nat. Metab. 7, 2142–2164 (2025). source
  • Classified as probably not a substantial claim. 64
  • May combine two claims. 35
  • The quote only partly states this claim. 1

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

    Findingown data

    The cellular lipid composition of iPSC-derived astrocytes is impacted by culturing conditions, as our whole cell lipidomics findings differed from a previous study.

    “It is important to note that the cellular lipid composition of iPSC-derived astrocytes is impacted by culturing conditions, as our whole cell lipidomics findings differed from a previous study30 (Supplementary Fig. S3B).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [30] Feringa, F. M. et al. The Neurolipid Atlas: a lipidomics resource for neurodegenerative diseases. Nat. Metab. 7, 2142–2164 (2025). source

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

    Premisecitation

    Previous work has identified that the APOE genotype correlates with changes in fatty acid saturation in whole cell lipidomics measurements.

    “Previous work has identified that the APOE genotype correlates with changes in fatty acid saturation in whole cell lipidomics measurements16,24,30.”
    Quote in the paperNot a substantial claim3 of 3 sources checked
    • cites [16] Windham, I.A. et al. APOE traffics to astrocyte lipid droplets and modulates triglyceride saturation and droplet size. J. Cell Biol. 223, https://doi.org/10.1083/jcb.202305003 (2024). source
    • cites [24] Sienski, G. et al. APOE4 disrupts intracellular lipid homeostasis in human iPSC-derived glia. Sci. Transl. Med. 1–12 (2021). source
    • cites [30] Feringa, F. M. et al. The Neurolipid Atlas: a lipidomics resource for neurodegenerative diseases. Nat. Metab. 7, 2142–2164 (2025). source

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

    Premisecitation

    Sequestration of membrane PUFA lipids into lipid droplets could be protective by preventing peroxidation and subsequent lipotoxicity.

    “Moreover, the sequestration of membrane PUFA lipids into lipid droplets could be protective, as it prevents peroxidation and subsequent lipotoxicity57.”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [57] Danielli, M., Perne, L., Jarc Jovičić, E. & Petan, T. Lipid droplets and polyunsaturated fatty acid trafficking: Balancing life and death. Front. Cell Dev. Biol. 11, 1104725 (2023). source

  • Classified as probably not a substantial claim.

    Premisecitation

    One route for lipid droplet turnover is via lipophagy, the selective autophagy of lipid droplets, which involves ubiquitination and binding to autophagy adapter proteins like SQSTM1/p62.

    “One route for lipid droplet turnover is via lipophagy–the selective autophagy of lipid droplets–which involves ubiquitination and binding to autophagy adapter proteins like SQSTM1/p621.”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [1] Olzmann, J. A. & Carvalho, P. Dynamics and functions of lipid droplets. Nat. Rev. Mol. Cell Biol. 20, 137–155 (2019). source

      The ‘Lipid droplet–lysosome contacts’ section describes clearance of lipid droplets by microlipophagy, supporting lipophagy as a route for turnover. It does not say that this route involves ubiquitination or binding to SQSTM1/p62; the ‘Lipid droplets protect against ER stress’ section mentions polyubiquitylated proteins but says their location relative to droplets is unclear. Page numbers are unavailable in our copy. (LLM, conf=0.86)

      Experimental — accuracy not yet measured

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

    Premisecitation

    Lipid droplets impact antigen presentation on astrocytes as well as cell non-autonomous effects on neuronal oxidative stress.

    “These lipid droplets impact antigen presentation on astrocytes30 as well as cell non-autonomous effects on neuronal oxidative stress20,21.”
    Quote in the paperNot a substantial claim2 of 3 sources checked
    • cites [20] Qi, G. et al. ApoE4 Impairs Neuron-Astrocyte Coupling of Fatty Acid Metabolism. Cell Rep. 34, 108572 (2021). source

      The Results section, “Bioenergetic Support of Astrocyte-to-Neuron Is Dependent on Neuronal LD Clearance” (page unavailable), links astrocyte-mediated neuronal lipid-droplet clearance to improved neuronal mitochondrial function, supporting a cell-non-autonomous effect. The Introduction and Discussion describe neuronal oxidative stress as a condition associated with glial lipid-droplet accumulation or fatty-acid transfer, but do not show that lipid droplets affect neuronal oxidative stress. The antigen-presentation clause carries a different citation and is not assessed here. (LLM, conf=0.83)

      Experimental — accuracy not yet measured
    • cites [21] Moulton, M.J. et al. Neuronal ROS-induced glial lipid droplet formation is altered by loss of Alzheimer’s disease-associated genes. Proc. Natl Acad Sci USA 118, https://doi.org/10.1073/pnas.2112095118 (2021). source
    • cites [30] Feringa, F. M. et al. The Neurolipid Atlas: a lipidomics resource for neurodegenerative diseases. Nat. Metab. 7, 2142–2164 (2025). source

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

    Premisecitation

    Several lipid metabolism genes have been identified as modifiers of AD risk and progression (such as APOE, PICALM, ABCA7, INPP5D, CLU, TREM2, ABCA1, MS4A4A and PLCG2).

    “Several lipid metabolism genes have been identified as modifiers of AD risk and progression (such as APOE, PICALM, ABCA7, INPP5D, CLU, TREM2, ABCA1, MS4A4A and PLCG2)33,34.”
    Quote in the paperNot a substantial claim1 of 2 sources checked
    • cites [33] Bellenguez, C. et al. New insights into the genetic etiology of Alzheimer’s disease and related dementias. in Nat. Gene. 54, 412–436 (2022).

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

    • cites [34] Sims, R. et al. Rare coding variants in PLCG2, ABI3, and TREM2 implicate microglial-mediated innate immunity in Alzheimer’s disease. Nat. Genet. 49, 1373–1384 (2017). source

      The Abstract (page unavailable) reports AD-risk associations for PLCG2 and TREM2, identifies INPP5D in an AD-related network, and finds enrichment in cholesterol-transport and lipoprotein pathways. It does not establish that every gene listed is a lipid-metabolism gene or that the listed genes modify AD progression; the paper’s principal genetic findings concern disease risk. (LLM, conf=0.86)

      Experimental — accuracy not yet measured

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

    Premisecitation

    Both cell type and cellular environment modulate the lipid droplet proteome and lipidome.

    “Importantly, both cell type and cellular environment modulate the lipid droplet proteome and lipidome3–9.”
    Quote in the paperNot a substantial claim6 of 7 sources checked
    • cites [3] Bersuker, K. et al. A proximity labeling strategy provides insights into the composition and dynamics of lipid droplet proteomes. in Developmental Cell (2018). source

      The Results section (‘An Integrated U2OS and Huh7 High-Confidence LD Proteome’; page unavailable) says lipid droplets differ in both lipid composition and associated proteins across cell types. The Introduction says proteins are recruited to droplets in response to changes in cellular metabolism. Our copy does not establish that cellular environment also modulates the lipid droplet lipidome. (LLM, conf=0.86)

      Experimental — accuracy not yet measured
    • cites [4] Bosch, M. et al. Mammalian lipid droplets are innate immune hubs integrating cell metabolism and host defense. Science 370, eaay8085 (2020). source
    • cites [5] Casey, C. A. et al. Lipid droplet membrane proteome remodeling parallels ethanol-induced hepatic steatosis and its resolution. J. Lipid Res. 62, 100049 (2021). source

      The Discussion reports that ethanol feeding altered 338 lipid-droplet membrane-associated proteins, supporting an effect of cellular environment on the proteome. The study examines liver lipid droplets; our copy does not establish that cell type modulates their composition or that either factor modulates the lipid-droplet lipidome. (LLM, conf=0.85)

      Experimental — accuracy not yet measured
    • cites [6] Friday, C. M. et al. APOE4 reshapes the lipid droplet proteome and modulates microglial inflammatory responses. Neurobiol. Dis. 212, 106983 (2025). source
    • cites [7] Khan, S. A., Wollaston-Hayden, E. E., Markowski, T. W., Higgins, L. & Mashek, D. G. Quantitative analysis of the murine lipid droplet-associated proteome during diet-induced hepatic steatosis. J. Lipid Res. 56, 2260–2272 (2015). source

      The paper’s opening summary (p. 2260) reports changes in the hepatic lipid-droplet proteome after high-fat feeding, supporting an effect of cellular environment. Its Discussion also describes diet-dependent regulation of droplet-associated proteins. The cited paper does not establish that cell type modulates the proteome or that either factor modulates the lipidome. (LLM, conf=0.86)

      Experimental — accuracy not yet measured
    • cites [8] Krahmer, N. et al. Organellar proteomics and phospho-proteomics reveal subcellular reorganization in diet-induced hepatic steatosis. Dev. Cell 47, 205–221.e207 (2018). source

      The Results report that lipid-droplet proteins change their localization under a high-fat diet, and the Discussion suggests that some may be tissue- or cell-type-specific. This supports modulation of the lipid-droplet proteome, but the cited passages do not establish that cell type and environment both modulate the lipid-droplet lipidome. (LLM, conf=0.86)

      Experimental — accuracy not yet measured
    • cites [9] Mejhert, N. et al. Partitioning of MLX-family transcription factors to lipid droplets regulates metabolic gene expression. Mol. Cell 77, 1251–1264 (2020). source

      The Results (Systematic Classification of Regulators of Lipid Storage in Human Macrophages; page unavailable) report lipid droplets containing triglycerides and cholesterol esters after lipoprotein loading, and the Methods distinguish loading conditions that induce different lipid storage. The Results (Transcription Factor MLX Binds to LDs; page unavailable) show that oleate-induced droplet formation affects MLX localization. The paper does not establish the broader claim that both cell type and cellular environment modulate both the droplet proteome and lipidome. (LLM, conf=0.82)

      Experimental — accuracy not yet measured

  • Classified as probably not a substantial claim.

    Premisecitation

    In hepatocytes, lipid droplet catabolism occurs as a sequential, two-step process.

    “In hepatocytes, lipid droplet catabolism has been reported to occur as a sequential, two-step process63.”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [63] Schott, M. B. et al. Lipid droplet size directs lipolysis and lipophagy catabolism in hepatocytes. J. Cell Biol. 218, 3320–3335 (2019). source

  • The quote only partly states this claim.

    Findingown data

    Stratifying human astrocyte transcriptomes from four published single-nuclei datasets by APOE genotype revealed differential expression patterns consistent with our proteomics data.

    “We analyzed human astrocyte transcriptomes taken from four published single-nuclei transcriptomic datasets to determine whether genotype-specific lipid droplet proteome changes are reflected in post-mortem brain samples51–54.”
    Quote in the paperSubstantial claim3 of 4 sources checked
    • cites [51] Hawrylycz, M. et al. SEA-AD is a multimodal cellular atlas and resource for Alzheimer’s disease. Nat. Aging 4, 1331–1334 (2024). source
    • cites [52] Wang, C. et al. A single-cell and spatial RNA-seq database for Alzheimer’s disease (ssREAD). Nat. Commun. 15, 4710 (2024). source
    • cites [53] Morabito, S. et al. Single-nucleus chromatin accessibility and transcriptomic characterization of Alzheimer’s disease. Nat. Genet. 53, 1143–1155 (2021). source
    • cites [54] Mathys, H. et al. Single-cell atlas reveals correlates of high cognitive function, dementia, and resilience to Alzheimer’s disease pathology. Cell 186, 4365–4385 (2023). source

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

    Premisecitation

    Lipid droplets have been associated with AD risk genes beyond APOE (PICALM and INPP5D in microglia and ABCA7 in neurons), suggesting convergent biology across risk genes.

    “Interestingly, lipid droplets have now been associated with AD risk genes beyond APOE (PICALM and INPP5D in microglia and ABCA7 in neurons), suggesting convergent biology across risk genes11,31,32.”
    Quote in the paperNot a substantial claim3 of 3 sources checked
    • cites [11] Kozlova, A. et al. PICALM Alzheimer’s risk allele causes aberrant lipid droplets in microglia. Nature 646, 1178–1186 (2025). source
    • cites [31] Terzioglu, G. et al. INPP5D/SHIP1 is a dual regulator of endo-lysosome function and selective phagocytosis in human microglia. Preprint at https://doi.org/10.1101/2025.10.27.684632 (2025). source
    • cites [32] von Maydell, D. et al. ABCA7 variants impact phosphatidylcholine and mitochondria in neurons. Nature 647, 462–471 (2025). source

      The ‘ABCA7 LoF alters PC balance’ section reports accumulation of neutral lipids, including triglycerides, in ABCA7 loss-of-function neurons. The Discussion also links ABCA7-related lipid disruption with work on APOE4. Our copy does not show that the accumulated lipids form lipid droplets, so it supports the neuronal lipid-metabolism link but not the specific lipid-droplet association. (LLM, conf=0.82)

      Experimental — accuracy not yet measured

  • Classified as probably not a substantial claim.

    Premisecitation

    SQSTM1 (p62) is a selective autophagy receptor protein that encapsulates lipid droplets during autophagy.

    “We focused on SQSTM1 (p62), a selective autophagy receptor protein that has been shown to encapsulate lipid droplets during autophagy58.”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [58] Berkamp, S. et al. Structural organization of p62 filaments and the cellular ultrastructure of calcium-rich p62-enwrapped lipid droplet cargo. Nat. Commun. 16, 10810 (2025). source

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

    Premisecitation

    Lipid droplets with higher levels of unsaturation exhibit packing defects and increased protein binding.

    “Several biophysical studies have reported that lipid droplets with higher levels of unsaturation exhibit packing defects and increased protein binding55,56.”
    Quote in the paperSubstantial claim2 of 2 sources checked
    • cites [55] Sletten, A., Seline, A., Rudd, A., Logsdon, M. & Listenberger, L. L. Surface features of the lipid droplet mediate perilipin 2 localization. Biochem. Biophys. Res. Commun. 452, 422–427 (2014). source

      Results §3.4 shows that unsaturated phospholipid vesicles were less tightly packed and bound more perilipin 2 than the comparison vesicles. The Discussion §4 also reports perilipin 2 on unsaturated, fluid lipid droplets, but says the role of packing in protein binding to droplet surfaces in vivo remains obscure. The source therefore does not establish packing defects and increased protein binding as a general property of more-unsaturated lipid droplets. (LLM, conf=0.86)

      Experimental — accuracy not yet measured
    • cites [56] Dias Araújo, A.R. et al. Surface tension–driven sorting of human perilipins on lipid droplets. J. Cell Biol. 223, https://doi.org/10.1083/jcb.202403064 (2024). source

      The Results section on LD packing defects reports that greater PC unsaturation increased defects at high phospholipid coverage (low tension). The Results also report increased binding to more-unsaturated artificial lipid droplets for PLIN2 and a smaller increase for PLIN3. The claim omits these conditions: at higher tension, shallow defects increased regardless of PC unsaturation, so the paper does not support the relationship as a general property of lipid droplets. (LLM, conf=0.86)

      Experimental — accuracy not yet measured

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

    Premisecitation

    APOE is the strongest genetic modulator of late-onset Alzheimer's disease and exists in common variants that confer decreased, neutral, or increased risk.

    “Among these, coding variants of the APOE gene stand out as the strongest genetic risk and resilience factors for late-onset AD. The APOE3 allele is the most common and regarded as neutral with respect to AD risk, while single amino acid coding variants result in the APOE4 allele (C112R), which increases AD risk, and the APOE2 allele (R158C), which decreases AD risk12.”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [12] Yang, L.G., March, Z.M., Stephenson, R.A. & Narayan, P.S. Apolipoprotein E in lipid metabolism and neurodegenerative disease. in Trends in Endocrinology and Metabolism: TEM (2023). source

  • May combine two claims.

    Premisecitation

    Remaining lipid droplets are tagged with autophagic adapters, including SQSTM1/p62 and LC3B, and undergo lipophagic degradation in acidic vesicles.

    “Then the remaining lipid droplets are tagged with autophagic adapters, including SQSTM1/p62 and LC3B, and undergo lipophagic degradation in acidic vesicles.”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [63] Schott, M. B. et al. Lipid droplet size directs lipolysis and lipophagy catabolism in hepatocytes. J. Cell Biol. 218, 3320–3335 (2019). source

      The Results section (page unavailable) reports that small lipid droplets associate with GFP-LC3 autophagosomes and are terminally degraded by lipophagy in acidic organelles. The Discussion (page unavailable) says some may be remnants of larger droplets after lipolysis, supporting the sequence only as a possibility. The copy does not identify SQSTM1/p62 or specifically LC3B as adapters tagging those droplets. (LLM, conf=0.88)

      Experimental — accuracy not yet measured

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

    Premisecitation

    A few of these non-canonical functions have been associated with lipid droplets in other organisms like Drosophila melanogaster and in other cell systems.

    “Interestingly, a few of these non-canonical functions have been associated with lipid droplets in other organisms like Drosophila melanogaster46,66 and in other cell systems3,9.”
    Quote in the paperNot a substantial claim4 of 4 sources checked
    • cites [46] Gingras, R. M., Warren, M. E., Nagengast, A. A. & Diangelo, J. R. The control of lipid metabolism by mRNA splicing in Drosophila. Biochem. Biophys. Res. Commun. 443, 672–676 (2014). source
    • cites [66] Stephenson, R.A. et al. Sequestration to lipid droplets promotes histone availability by preventing turnover of excess histones. Development 148, https://doi.org/10.1242/dev.199381 (2021). source
    • cites [3] Bersuker, K. et al. A proximity labeling strategy provides insights into the composition and dynamics of lipid droplet proteomes. in Developmental Cell (2018). source
    • cites [9] Mejhert, N. et al. Partitioning of MLX-family transcription factors to lipid droplets regulates metabolic gene expression. Mol. Cell 77, 1251–1264 (2020). source

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

    Premisecitation

    Astrocytes produce the most APOE in the brain.

    “Astrocytes produce the most APOE in the brain35”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [35] Blumenfeld, J., Yip, O., Kim, M. J. & Huang, Y. Cell type-specific roles of APOE4 in Alzheimer disease. Nat. Rev. Neurosci. 25, 91–110 (2024). source

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

    Premisecitation

    Microglia from APOE4 mouse models, as well as human microglia from post-mortem brain tissue in AD and APOE4 carriers, exhibit lipid dysregulation and upregulation of neutral lipid storage.

    “Microglia from APOE4 mouse models, as well as human microglia from post-mortem brain tissue in AD and APOE4 carriers, exhibit lipid dysregulation and upregulation of neutral lipid storage17,27–29.”
    Quote in the paperNot a substantial claim3 of 4 sources checked
    • cites [17] Haney, M.S. et al. APOE4/4 is linked to damaging lipid droplets in Alzheimer’s disease microglia. Nature 628, 154–161 (2024). source
    • cites [27] Green, G. S. et al. Cellular communities reveal trajectories of brain ageing and Alzheimer’s disease. Nature 633, 634–645 (2024). source

      In “Two disease-associated microglial states,” the paper reports that human Mic.12 and Mic.13 microglia have increased expression of genes involved in cholesterol storage and lipid metabolism. “Linking cell subpopulations to AD traits” associates these populations with AD pathology, and “Causal modelling of glia in the AD cascade” associates Mic.13 with APOE ε4. The paper does not report findings from APOE4 mouse models or directly demonstrate increased neutral lipid storage in microglia. (LLM, conf=0.86)

      Experimental — accuracy not yet measured
    • cites [28] Sun, N. et al. Human microglial state dynamics in Alzheimer’s disease progression. Cell 186, 4386–4403 (2023). source
    • cites [29] Lee, S. et al. APOE modulates microglial immunometabolism in response to age, amyloid pathology, and inflammatory challenge. Cell Rep. 42, https://doi.org/10.1016/j.celrep.2023.112196 (2023). source

      The Results section on MALDI MSI reports altered lipid metabolism in APOE4 mouse brains, with changes most pronounced in microglia at the single-cell level. The Discussion’s spatial-view section also reports lipid changes in post-mortem human AD brain and notes an association between APOE4 and lipid-droplet accumulation. It does not establish increased neutral-lipid storage specifically in microglia isolated from post-mortem human AD brains or APOE4 carriers. (LLM, conf=0.86)

      Experimental — accuracy not yet measured

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

    Premisecitation

    Altered lipid droplet biology has been linked to both brain aging and neurodegenerative diseases.

    “Altered lipid droplet biology has been linked to both brain aging and neurodegenerative diseases10–24.”
    Quote in the paperNot a substantial claim9 of 10 sources checked
    • cites [10] Stephenson, R. A. et al. Triglyceride metabolism controls inflammation and microglial phenotypes associated with APOE4. Cell Rep. 44, 115961 (2025). source
    • cites [11] Kozlova, A. et al. PICALM Alzheimer’s risk allele causes aberrant lipid droplets in microglia. Nature 646, 1178–1186 (2025). source
    • cites [12] Yang, L.G., March, Z.M., Stephenson, R.A. & Narayan, P.S. Apolipoprotein E in lipid metabolism and neurodegenerative disease. in Trends in Endocrinology and Metabolism: TEM (2023). source
    • cites [13] Victor, M.B. et al. Lipid accumulation induced by APOE4 impairs microglial surveillance of neuronal-network activity. in Cell Stem Cell (2022). source
    • cites [14] Farmer, B. C., Walsh, A. E., Kluemper, J. C. & Johnson, L. A. Lipid droplets in neurodegenerative disorders. Front. Neurosci. 14, 742 (2020). source
    • cites [15] Farmer, B.C., Kluemper, J. & Johnson, L.A. Apolipoprotein E4 alters astrocyte fatty acid metabolism and lipid droplet formation. Cells 8, https://doi.org/10.3390/cells8020182 (2019). source

      The Introduction reports increased lipid-droplet content in Parkinson’s disease and Alzheimer’s disease, supporting the neurodegenerative-disease link. The passages found do not establish a link between altered lipid-droplet biology and brain aging; the References list a study of lipid-laden cells in the aging brain, but the paper does not state that broader claim. (LLM, conf=0.82)

      Experimental — accuracy not yet measured
    • cites [16] Windham, I.A. et al. APOE traffics to astrocyte lipid droplets and modulates triglyceride saturation and droplet size. J. Cell Biol. 223, https://doi.org/10.1083/jcb.202305003 (2024). source
    • cites [17] Haney, M.S. et al. APOE4/4 is linked to damaging lipid droplets in Alzheimer’s disease microglia. Nature 628, 154–161 (2024). source
    • cites [18] Marschallinger, J. et al. Lipid-droplet-accumulating microglia represent a dysfunctional and proinflammatory state in the aging brain. Nat. Neurosci. 23, 194–208 (2020). source
    • cites [19] Hamilton, L.K. et al. Aberrant lipid metabolism in the forebrain niche suppresses adult neural stem cell proliferation in an animal model of alzheimer’s disease. Cell Stem Cell 17, 397–411 (2015). source

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

    Study design and conductcitation

    Protein values were normalized using variance stabilizing normalization.

    “then values were normalized using variance stabilizing normalization86.”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [86] Huber, W., von Heydebreck, A., Sültmann, H., Poustka, A. & Vingron, M. Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics 18, S96–S104 (2002). source

  • Classified as probably not a substantial claim.

    Study design and conductcitation

    Proteome lists were filtered for common mass spectrometry contaminants using a published database.

    “all proteome lists were filtered for common mass spectrometry contaminants using a published database42.”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [42] Mellacheruvu, D. et al. The CRAPome: a contaminant repository for affinity purification–mass spectrometry data. Nat. Methods 10, 730–736 (2013). source

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

    Premisecitation

    Previous work has linked disruptions to autophagy and lysosomal biology with AD.

    “Previous work has linked disruptions to autophagy and lysosomal biology with AD72–74.”
    Quote in the paperNot a substantial claim2 of 3 sources checked
    • cites [72] Guo, J. L. et al. Decreased lipidated ApoE-receptor interactions confer protection against pathogenicity of ApoE and its lipid cargoes in lysosomes. Cell 188, 187–206 (2025). source

      The Discussion links perturbed lysosomes and lipofuscin accumulation to vulnerability in AD, supporting the lysosomal-biology part of the claim. The Results also report lysosomal defects after lipofuscin induction. Our copy does not establish a link between autophagy disruption and AD (searched: autophagy, autophagic flux). (LLM, conf=0.84)

      Experimental — accuracy not yet measured
    • cites [73] Nixon, R. A. & Rubinsztein, D. C. Mechanisms of autophagy–lysosome dysfunction in neurodegenerative diseases. Nat. Rev. Mol. Cell Biol. 25, 926–946 (2024). source
    • cites [74] Roussel, B. D. et al. Endoplasmic reticulum dysfunction in neurological disease. Lancet Neurol. 12, 105–118 (2013). source

  • May combine two claims.

    Premisecitation

    PUFAs in membrane phospholipids can promote ferroptosis through lipid peroxidation, while their sequestration in triacylglycerol-rich lipid droplet cores mitigates ferroptosis and lipotoxicity.

    “While PUFAs in membrane phospholipids can promote ferroptosis through lipid peroxidation, their sequestration in the triacylglycerol-rich lipid droplet cores mitigates ferroptosis and lipotoxicity57.”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [57] Danielli, M., Perne, L., Jarc Jovičić, E. & Petan, T. Lipid droplets and polyunsaturated fatty acid trafficking: Balancing life and death. Front. Cell Dev. Biol. 11, 1104725 (2023). source

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

    Premisecitation

    Genetic knockdown studies show RUFY2 influences lipid droplet morphology and distribution.

    “Genetic knockdown studies show RUFY2 influences lipid droplet morphology and distribution9,41, hinting at a potential link between vesicle trafficking defects69 and altered lipid biology in astrocytes, particularly in neurodegenerative contexts.”
    Quote in the paperNot a substantial claim2 of 2 sources checked
    • cites [9] Mejhert, N. et al. Partitioning of MLX-family transcription factors to lipid droplets regulates metabolic gene expression. Mol. Cell 77, 1251–1264 (2020). source

      The Results section describes an RNAi screen measuring lipid-droplet size, shape, and dispersion, but the passages available from our copy do not identify RUFY2 as a hit or report its knockdown phenotype. Searches for RUFY2 and for RUFY2 knockdown effects on lipid droplets found no passage establishing the claimed effect. (LLM, conf=0.72)

      Experimental — accuracy not yet measured
    • cites [41] Mejhert, N. et al. The lipid droplet knowledge portal: A resource for systematic analyses of lipid droplet biology. Dev. Cell 57, 387–397 (2022). source

      The Results section describes lipid-droplet size, shape, and dispersion measurements after gene knockdown, but the specific knockdown result it reports concerns C16orf54, not RUFY2. Searches for “RUFY2” and “RUFY2 knockdown lipid droplet morphology distribution” found no passage in our copy linking RUFY2 to those phenotypes. (LLM, conf=0.72)

      Experimental — accuracy not yet measured

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

    Premisecitation

    Various studies have shown that lipid droplets influence intercellular communication.

    “Various studies have shown that lipid droplets influence intercellular communication13,17,61.”
    Quote in the paperNot a substantial claim2 of 3 sources checked
    • cites [13] Victor, M.B. et al. Lipid accumulation induced by APOE4 impairs microglial surveillance of neuronal-network activity. in Cell Stem Cell (2022). source
    • cites [17] Haney, M.S. et al. APOE4/4 is linked to damaging lipid droplets in Alzheimer’s disease microglia. Nature 628, 154–161 (2024). source
    • cites [61] Ioannou, M. S. et al. Neuron-astrocyte metabolic coupling protects against activity-induced fatty acid toxicity. Cell 177, 1522–1535 (2019). source

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

    Premisecitation

    Reduced lipophagy has been shown to contribute to the progression of AD in disease mouse models.

    “Similarly, reduced lipophagy has been shown to contribute to the progression of AD in disease mouse models77.”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [77] Barnett, A. M. et al. Loss of lysosomal acid lipase contributes to Alzheimer’s disease pathology and cognitive decline. Alzheimers Dement 21, e70486 (2025). source

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

    Premisecitation

    This finding mirrors observations in other systems where lipid droplets regulate immune responses.

    “This finding mirrors observations in other systems where lipid droplets regulate immune responses4,70.”
    Quote in the paperNot a substantial claim1 of 2 sources checked
    • cites [4] Bosch, M. et al. Mammalian lipid droplets are innate immune hubs integrating cell metabolism and host defense. Science 370, eaay8085 (2020). source
    • cites [70] Zadoorian, A., Du, X. & Yang, H. Lipid droplet biogenesis and functions in health and disease. Nat. Rev. Endocrinol. 19, 443–459 (2023). source

  • Classified as probably not a substantial claim.

    Premisecitation

    Lipid droplets bud from the ER membrane.

    “Lipid droplets bud from the ER membrane1,16.”
    Quote in the paperSubstantial claim2 of 2 sources checked
    • cites [1] Olzmann, J. A. & Carvalho, P. Dynamics and functions of lipid droplets. Nat. Rev. Mol. Cell Biol. 20, 137–155 (2019). source
    • cites [16] Windham, I.A. et al. APOE traffics to astrocyte lipid droplets and modulates triglyceride saturation and droplet size. J. Cell Biol. 223, https://doi.org/10.1083/jcb.202305003 (2024). source

      The Results section describes APOE moving from the ER onto existing lipid droplets via membrane bridges, not the droplets budding from the ER membrane. The Introduction discusses droplet biogenesis without specifying budding; searches for ER budding and droplet formation found no passage stating the claim. Page numbers were not available in our copy. (LLM, conf=0.72)

      Experimental — accuracy not yet measured

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

    Premisecitation

    Our findings align with a recent study on human data that identified lipophagy genes as dysregulated in AD patients and AD risk.

    “Our findings align with a recent study on human data that identified lipophagy genes as dysregulated in AD patients and AD risk71.”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [71] Guo, H. et al. Identification of lipophagy-related gene signature for diagnosis and risk prediction of alzheimer’s disease. Biomedicines 13, https://doi.org/10.3390/biomedicines13020362 (2025). source

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

    Study design and conductcitation

    Samples were integrated based on SampleID using mnc correct (SnapATAC2) and astrocytes were identified and extracted from each dataset using astrocytic marker genes (SLC1A2, AQP4, ALDH1L1).

    “Samples were iIntegrated based on SampleID using mnc correct (SnapATAC2)90 and astrocytes were identified and extracted from each dataset using astrocytic marker genes (SLC1A2, AQP4, ALDH1L1) as described before91.”
    Quote in the paperSubstantial claim2 of 2 sources checked
    • cites [90] Zhang, K., Zemke, N. R., Armand, E. J. & Ren, B. A fast, scalable and versatile tool for analysis of single-cell omics data. Nat. Methods 21, 217–227 (2024). source
    • cites [91] Marsan, E. et al. Astroglial toxicity promotes synaptic degeneration in the thalamocortical circuit in frontotemporal dementia with GRN mutations. J. Clin. Invest. 133, https://doi.org/10.1172/jci164919 (2023). source

      The Methods section (“Clustering, differential gene expression, burden score, and nuclei count”; page unavailable) says cell types were annotated using known marker genes, and the Results identify astrocyte clusters. It does not say astrocytes were identified and extracted from each dataset using the specific three-gene set SLC1A2, AQP4, and ALDH1L1. The SnapATAC2 step is attached to citation 90, not this source’s citation 91. (LLM, conf=0.84)

      Experimental — accuracy not yet measured

  • Classified as probably not a substantial claim.

    Premisecitation

    PUFAs within lipid droplets can be metabolized into lipid signaling mediators in the inflammatory response.

    “In addition, PUFAs within lipid droplets can be metabolized into lipid signaling mediators in the inflammatory response57.”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [57] Danielli, M., Perne, L., Jarc Jovičić, E. & Petan, T. Lipid droplets and polyunsaturated fatty acid trafficking: Balancing life and death. Front. Cell Dev. Biol. 11, 1104725 (2023). source

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

    Study design and conductcitation

    Differential abundance analysis was conducted using the DEP2 package, which utilizes limma and fdrtools.

    “To determine differential abundance, statistical analysis was conducted using the DEP2 package85 which utilizes limma and fdrtools.”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [85] Feng, Z., Fang, P., Zheng, H. & Zhang, X. DEP2: an upgraded comprehensive analysis toolkit for quantitative proteomics data. Bioinformatics 39, https://doi.org/10.1093/bioinformatics/btad526 (2023). source

      The Results section describes DEP2 as a differential-analysis toolkit and says its classical pipeline uses a moderated t-test from limma. Our copy does not mention fdrtools, so it does not support that part of the description. (LLM, conf=0.88)

      Experimental — accuracy not yet measured

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

    Premisecitation

    RUFY2 contains a PI3P-binding FYVE domain, linking it to lipid droplet metabolism, a connection previously established for other FYVE-containing proteins like DFCP1.

    “RUFY2 contains a PI3P-binding FYVE domain, linking it to lipid droplet metabolism, a connection previously established for other FYVE-containing proteins like DFCP167,68.”
    Quote in the paperNot a substantial claim2 of 2 sources checked
    • cites [67] Ismail, V. A. et al. DFCP1 is a regulator of starvation-driven ATGL-mediated lipid droplet lipolysis. J. Lipid Res. 66, 100700 (2025). source
    • cites [68] Lukmantara, I. et al. PI(3)P and DFCP1 regulate the biogenesis of lipid droplets. Mol. Biol. Cell 33, ar131 (2022). source

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

    Premisecitation

    Studies in other model systems have observed impaired autophagy in APOE4 astrocytes and other glia.

    “Studies in other model systems have observed impaired autophagy in APOE4 astrocytes and other glia16,75,76.”
    Quote in the paperNot a substantial claim2 of 3 sources checked
    • cites [16] Windham, I.A. et al. APOE traffics to astrocyte lipid droplets and modulates triglyceride saturation and droplet size. J. Cell Biol. 223, https://doi.org/10.1083/jcb.202305003 (2024). source

      The Introduction describes lipid-metabolism and endocytosis defects in APOE4 glia, while the Discussion reports impaired lipid-droplet turnover in APOE4 astrocytes. Neither passage identifies impaired autophagy; searches for autophagy and related lysosomal terms found no passage addressing that claim. (LLM, conf=0.73)

      Experimental — accuracy not yet measured
    • cites [75] Bassal, R. et al. APOE4 impairs autophagy and Aβ clearance by microglial cells. Inflamm. Res. 74, 61 (2025). source
    • cites [76] Simonovitch, S. et al. Impaired autophagy in APOE4 astrocytes. J. Alzheimers Dis. 51, 915–927 (2016). source

  • May combine two claims.

    Findingown data

    Each APOE genotype exhibited a distinct subset of lipid droplet proteins, with APOE2 containing the highest number of genotype-specific proteins, followed by APOE4 and APOE3.

    “When comparing proteins within the lipid droplet buoyant fractions across genotypes, we found that although the majority of proteins were shared, each genotype exhibited a distinct subset of proteins, with APOE2 containing the highest number of genotype-specific proteins, followed by APOE4 and APOE3 (Fig. 3A and Supplementary Data 11).”
    Quote in the paperSubstantial claim

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

    Findingown data

    Far more subtle differences were detected in phospholipid classes.

    “Far more subtle differences were detected in phospholipid classes (Supplementary Fig. S3A).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    APOE protein is detected on buoyant fractions after oleic acid treatment, and the levels are similar across APOE genotypes.

    “Moreover, we detected APOE protein on buoyant fractions after oleic acid treatment, and the levels were similar across genotypes (Supplementary Fig. S2C).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    RUFY2 co-localized with lipid droplets in iPSC-derived astrocytes but also associates with other organelles, including early endosomes and the Golgi.

    “One such protein is RUFY2, which we confirmed co-localized with lipid droplets in iPSC-derived astrocytes (Fig. 2H), but also associates with other organelles, including early endosomes and the Golgi (Supplementary Fig. S4C).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Human astrocytic lipid droplets exhibit molecular features shared with many cell types and others that are specific to astrocytes.

    “Our analyses reveal that human astrocytic lipid droplets exhibit molecular features shared with many cell types and others that are specific to astrocytes.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    ATGLi showed a measurable and significant change in lipid droplet degradation in astrocytes after a 72 h treatment, maintained up to 96 h without re-adding the drug.

    “We observed that ATGLi showed a measurable and significant change in lipid droplet degradation in astrocytes after a 72 h treatment, that was maintained up to 96 h without re-adding the drug (Supplementary Fig. S7D, E).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Of the 265-protein proteome, 72% of proteins had been previously identified in other datasets, and 28% were newly identified in this study.

    “Of our iPSC-derived astrocyte lipid droplet-associated proteome (265 proteins, Supplementary Data 7), 72% of proteins had been previously identified in other datasets. The remaining 28% of proteins were newly identified in this study (Fig. 2G).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    The APOE2 lipid droplet-associated protein ADK was elevated in APOE2-carriers, while the APOE4 lipid droplet-associated proteins RAB8A and MYO1E were enriched in APOE4-carriers.

    “For instance, the APOE2 lipid droplet-associated protein ADK (linked to toxin response) was elevated in APOE2-carriers, while the APOE4 lipid droplet-associated proteins RAB8A and MYO1E (involved in intracellular trafficking) were enriched in APOE4-carriers (Supplementary Data 14).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Oleic acid treatment decreases both intracellular and secreted APOE levels compared to vehicle control treatment.

    “We observed that oleic acid treatment decreases both intracellular (Supplementary Fig. S2A, B) and secreted APOE levels (Supplementary Fig. S2D–G) compared to vehicle control treatment.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    APOE2 astrocytes exhibited a trend towards reduced lipid droplets while APOE4 astrocytes did not after prolonged starvation.

    “We observed that APOE2 astrocytes exhibited a trend towards reduced lipid droplets while APOE4 astrocytes did not (Supplementary Fig. S8Q).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Lipid droplets in APOE2 astrocytes undergo efficient autophagic turnover, whereas those in APOE4 astrocytes resist degradation.

    “Lipid droplets in APOE2 astrocytes undergo efficient autophagic turnover, whereas those in APOE4 astrocytes resist degradation.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Under vehicle-treated conditions, lipid droplet accumulation varied across the two isogenic iPSC-derived astrocyte sets, with genotype-dependent differences more apparent in KOLF2.1J-derived astrocytes than in BIONi037-derived astrocytes.

    “Under vehicle-treated conditions, lipid droplet accumulation varied across the two isogenic iPSC-derived astrocyte sets, with genotype-dependent differences more apparent in the KOLF2.1J-derived astrocytes (Fig. 1B, C) than in the BIONi037-derived astrocytes (Supplementary Fig. S1E, F).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    RUFY2 is a newly identified lipid droplet-associated protein involved in endosomal trafficking.

    “We identified new lipid droplet-associated proteins like RUFY2, a protein involved in endosomal trafficking.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Both APOE4 and APOE2 astrocytes accumulate more lipid droplets than APOE3, but the molecular features of lipid droplets are different.

    “Although both APOE4 and APOE2 astrocytes accumulate more lipid droplets than APOE3, the molecular features of lipid droplets are different.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    APOE4 lipid droplets accumulate stalled lipophagy adapter proteins and display impaired lipophagy compared to APOE2 lipid droplets.

    “APOE4 lipid droplets accumulate stalled lipophagy adapter proteins and display impaired lipophagy compared to APOE2 lipid droplets, suggesting that the autophagy-mediated turnover of lipid droplets differentiates risk and protective APOE genotypes.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    iPSC-derived astrocytes harboring different APOE genotypes have distinct lipid droplet-associated proteomes that align with transcriptomic patterns in human post-mortem brains.

    “Together, these findings cement that iPSC-derived astrocytes harboring different APOE genotypes have distinct lipid droplet-associated proteomes that align with transcriptomic patterns in human post-mortem brains.”
    Quote in the paperSubstantial claim

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

    Premisecitation

    SQSTM1/p62 binds ubiquitinated proteins and organelles and recruits them to autophagosomes for degradation.

    “SQSTM1/p62 binds ubiquitinated proteins and organelles and recruits them to autophagosomes for degradation59.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [59] Lamark, T. & Johansen, T. Mechanisms of Selective Autophagy. Annu. Rev. Cell Dev. Biol. 37, 143–169 (2021). source

  • Classified as probably not a substantial claim.

    Interpretationown data

    Characterizing the APOE genotype-specific lipid droplet-associated proteome provides insights on the dynamics of these organelles that can be further validated with cell-based assays.

    “Taken together, we demonstrate that characterizing the APOE genotype-specific lipid droplet-associated proteome provides insights on the dynamics of these organelles that can be further validated with cell-based assays.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    Although both genotypes accumulate significant numbers of lipid droplets, APOE4 lipid droplets are resistant to lipophagy, unlike APOE2.

    “Together, these findings suggest that although both genotypes accumulate significant numbers of lipid droplets, APOE4 lipid droplets are resistant to lipophagy, unlike APOE2.”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim.

    Study design and conductreasoning

    A stringent threshold was chosen to avoid false positives in proteome definition.

    “We chose a stringent threshold to avoid false positives.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    Oleic acid treatment enables isolation of more lipid droplets from the same amount of cell material without substantially altering the proteomic composition of the lipid droplets.

    “This finding gave us confidence that oleic acid treatment enables us to isolate more lipid droplets from the same amount of cell material, without substantially altering the proteomic composition of the lipid droplets.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Study design and conductown data

    The buoyant fraction isolated by sucrose gradient ultracentrifugation from oleic acid-treated iPSC-derived astrocytes is lipid droplet-rich and shows no detectable contamination from lysosomes, mitochondria, and ER.

    “This buoyant fraction was lipid droplet-rich and showed no detectable contamination from other organelles, including lysosomes, mitochondria, and ER (Fig. 1E).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    Lipophagy in APOE4 astrocytes is impaired and cannot be activated by starvation-induced autophagy.

    “This finding suggests that lipophagy in APOE4 astrocytes is impaired and cannot be activated by starvation-induced autophagy.”
    Quote in the paperSubstantial claim

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

    Study design and conductnone given

    No statistical method was used to predetermine sample size, but sample sizes were based on previously published research on iPSC-derived astrocytes.

    “No statistical method was used to predetermine sample size, but sample sizes were based on previously published research on iPSC-derived astrocytes.”
    Quote in the paperNot a substantial claim

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

    Study design and conductnone given

    APOE secreted levels were normalized to total secreted protein levels quantified by immunoblotting in the same conditioned media samples.

    “APOE secreted levels were normalized to total secreted protein levels quantified by immunoblotting in the same conditioned media samples.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Interpretationreasoning

    The higher p-value threshold of 0.1 allows comprehensive account of changes between oleic acid and vehicle (BSA) treatments.

    “It also allows us to comprehensively account for changes between oleic acid and vehicle (BSA) treatments.”
    Quote in the paperSubstantial claim

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

    Study design and conductnone given

    Medium normalization was applied to all samples.

    “Medium normalization was applied to all samples.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Study design and conductnone given

    Proteins that appeared in over half of the mass spectrometry studies in the database were excluded from analyses.

    “Proteins that appeared in over half of the mass spectrometry studies in the database (Supplementary Data 1) were excluded from our analyses.”
    Quote in the paperSubstantial claim

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

    Study design and conductnone given

    Only complete cases were considered in the linear model fitting.

    “Only complete cases were considered.”
    Quote in the paperNot a substantial claim

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

    Study design and conductnone given

    Missing protein values were imputed using a mixed imputation model: randomly missing values were imputed using kNN, and proteins not missing at random (missing in every replicate of a genotype-treatment group) were imputed as 1.

    “Imputation was carried out using a mixed imputation model where imputation for proteins with randomly missing values were imputed using kNN, and proteins not missing at random (defined as proteins missing in every replicate of a genotype-treatment group) were imputed as 1.”
    Quote in the paperSubstantial claim

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

    Study design and conductnone given

    Vehicle control treatments (DMSO for ATGLi and bafilomycin A1; ultrapure H20 for chloroquine) were included for comparison.

    “Vehicle control treatments (DMSO for ATGLi and bafilomycin A1; ultrapure H20 for chloroquine) were included for comparison.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Interpretationreasoning

    The higher p-value threshold of 0.1 allows for the exclusion of false negatives.

    “This higher p-value allows for the exclusion of false negatives”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim.

    Study design and conductreasoning

    Proteins were identified as differentially abundant between genotypes using an adjusted p-value threshold of < 0.1.

    “with proteins identified as differentially abundant with an adjusted p-value threshold of < 0.1.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S2 (checkable).

    Study design and conductreasoning

    Our findings should be interpreted in the context of lipid-loaded astrocytes.

    “Therefore, our findings should be interpreted in the context of lipid-loaded astrocytes, and future studies will be needed to determine how APOE genotype influences lipid droplet composition and dynamics under additional disease-relevant stresses, including inflammatory, oxidative, and amyloid-associated conditions.”
    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

    Genomic stability of all iPSC lines was characterized by karyotyping or SNP array testing, and all samples were tested to ensure no mycoplasma contamination.

    “Genomic stability of all iPSC lines was characterized by karyotyping or SNP array testing, and all samples were tested to ensure no mycoplasma contamination.”
    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 were excluded from analysis.

    “No data were excluded from analysis.”
    • Also stated in: § Statistics and reproducibility · plain
      “No data was excluded from analysis.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S2 (checkable).

    Interpretationreasoning

    The study sheds light on the diverse and understudied roles of lipid droplets in human astrocytes.

    “Given the centrality of lipid and glial cell dysregulations contributing to neurodegenerative disease, our study sheds light on the diverse and understudied roles of lipid droplets in human astrocytes.”
    Quote in the paperNot a substantial claim

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

    Study design and conductnone given

    Comprehensive targeted lipidomics was accomplished using a flow-injection assay based on lipid class separation by differential mobility spectroscopy and selective multiple reaction monitoring (MRM) targeting individual lipid species (Lipidyzer platform).

    “Comprehensive targeted lipidomics was accomplished using a flow-injection assay based on lipid class separation by differential mobility spectroscopy and selective multiple reaction monitoring (MRM) targeting individual lipid species (Lipidyzer platform).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Study design and conductnone given

    Oleic acid treatment is an artificial lipid-loading condition and does not correspond to a single defined physiological or pathological stimulus.

    “A limitation of this study is that oleic acid treatment is an artificial lipid-loading condition and does not correspond to a single defined physiological or pathological stimulus.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Interpretationreasoning

    APOE isoforms could modulate the lipid droplet protein and lipid content via interactions with proteins and lipids in the ER.

    “Because APOE isoforms are present in the secretory pathway and are lipid-binding proteins, they could modulate the lipid droplet protein and lipid content via interactions with proteins and lipids in the ER.”
    Quote in the paperSubstantial claim
    • Rests on an assumption: APOE isoforms are present in the secretory pathway and are lipid-binding proteins.

  • Classified as probably not a substantial claim.

    Study design and conductnone given

    Proteins present in each replicate of any genotype-treatment group across both cell lines were retained for analysis.

    “Proteins present in each replicate of any genotype-treatment group across both lines were retained”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    APOE genotype alters lipophagy via changes to the lipid droplet-associated proteome and lipophagy disruptions could contribute to APOE4-associated risk.

    “Together with our results, these findings reveal that APOE genotype alters lipophagy via changes to the lipid droplet-associated proteome and that lipophagy disruptions could contribute to APOE4- associated risk.”
    Quote in the paperSubstantial claim
    • Rests on an assumption: APOE2 is protective, APOE3 is neutral, and APOE4 is risk for Alzheimer's disease.

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

    Study design and conductnone given

    Lipidomic data normalized to cell number or sample volume were used for further analysis.

    “For further analysis, lipidomic data normalized to cell number or sample volume were used.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Study design and conductown data

    Proteins were identified as differentially abundant between oleic acid and vehicle (BSA) treated cells if they met a p-value cutoff of < 0.1.

    “Proteins were identified as differentially abundant if they met a p-value cutoff of < 0.1 (Supplementary Data 2).”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim.

    Interpretationreasoning

    The higher p-value threshold of 0.1 accounts for the variability due to cell lines from different humans.

    “and accounts for the variability due to cell lines from different humans.”
    Quote in the paperSubstantial claim

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

    Study design and conductnone given

    directDIA false discovery rate was set to 1%.

    “directDIA false discovery rate set to 1%, protein N-terminal acetylation and methionine oxidation were set as variable modifications and carbamidomethylation of cysteine residues was selected as a fixed modification.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Study design and conductnone given

    The top 2.5% of residual scores over 0 were chosen to identify proteins enriched in the buoyant fraction for each comparison.

    “The top 2.5% of residual scores over 0 were chosen for each comparison (Supplementary Data 5).”
    Quote in the paperSubstantial claim

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

    Study design and conductown data

    Proteins only present in the buoyant fraction were identified by ranking by mean z-score and selecting proteins with a z-score > −1.

    “we ranked the proteins by mean z-score from greatest to least and selected proteins with a z-score of >−1 (Supplementary Data 6).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationreasoning

    The less labile APOE4 lipid droplets are less able to respond and buffer cellular stress and therefore present a liability to cell health when faced with disease-associated stresses.

    “The less labile APOE4 lipid droplets are less able to respond and buffer cellular stress and therefore present a liability to cell health when faced with disease-associated stresses.”
    Quote in the paperSubstantial claim
    • Rests on an assumption: APOE2 is protective, APOE3 is neutral, and APOE4 is risk for Alzheimer's disease.

  • Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based).

    Study design and conductnone given

    Research in this study conforms with all relevant ethical regulations and institutional guidelines at the NIH Intramural Research Program.

    “Research in this study conforms with all relevant ethical regulations and institutional guidelines at the NIH Intramural Research Program.”
    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 could not capture heterogeneity within lipid droplets in a single cell type or genotype.

    “However, our study could not capture heterogeneity within lipid droplets in a single cell type or genotype, which may provide greater insights into organellar function80,81.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Study design and conductnone given

    The purity of buoyant fractions was analyzed by immunoblotting.

    “The purity of buoyant fractions was analyzed by immunoblotting.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S2 (checkable).

    Interpretationnone given

    Understanding APOE genotype-driven differences can illuminate the molecular mechanisms underlying the biology of genetic risk and protection for AD.

    “Moreover, understanding APOE genotype-driven differences can illuminate the molecular mechanisms underlying the biology of genetic risk and protection for AD.”
    Quote in the paperNot a substantial claim
    • Rests on an assumption: APOE2 is protective, APOE3 is neutral, and APOE4 is risk for Alzheimer's disease.

  • May combine two claims.

    Interpretationown data

    The accumulation of lipid droplets is not inherently pathological; rather, impaired dynamics and turnover distinguishes disease risk from protection.

    “When examining the effects of APOE genotype on the composition of lipid droplets, we discovered that the accumulation of lipid droplets is not inherently pathological; rather, their impaired dynamics and turnover distinguishes disease risk from protection.”
    Quote in the paperSubstantial claim
    • Rests on an assumption: APOE2 is protective, APOE3 is neutral, and APOE4 is risk for Alzheimer's disease.

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

    Study design and conductnone given

    Investigators preparing samples were different from those running molecular characterization and those analyzing data for all omics data.

    “Investigators preparing samples were different from those running molecular characterization and those analyzing data for all omics data.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Study design and conductcitation

    The proteomics data from each fraction (cytosolic and buoyant) were filtered, normalized, and imputed using the DEP2 package in R.

    “Spectronaut outputs of each fraction (cytosolic and buoyant) were subjected to filtering, normalization, and imputation using the DEP2 package in R85.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites R85

      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).

    Study design and conductnone given

    Proteins identified by only a single peptide were excluded from the proteomic analysis.

    “Proteins only identified with a single peptide were excluded from analysis.”
    Quote in the paperNot a substantial claim
90 of 90

  • The paper relies on this without support.

    APOE2 is protective, APOE3 is neutral, and APOE4 is risk for Alzheimer's disease.

    “homozygous for the APOE2 (protective), APOE3 (neutral), and APOE4 (risk) genotypes.”

  • The paper relies on this without support.

    APOE isoforms are present in the secretory pathway and are lipid-binding proteins.

    “Because APOE isoforms are present in the secretory pathway and are lipid-binding proteins, they could modulate the lipid droplet protein and lipid content via interactions with proteins and lipids in the ER.”
2 of 2

Self-check

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

  • ATGL inhibitor treatment time does not match the pulse-chase schedule

    Minor

    The methods specify 48 h of pretreatment, a 2 h pulse, and a 42 h chase. These span 92 h, not the stated 96 h; the 18 h and 24 h chases likewise cannot both correspond to 72 h of treatment.

    Reported 96 · recomputed 92

  • Figure 2 protein counts exceed the stated total

    Minor

    The figure legend lists 499 proteins unique to the buoyant fraction and 2807 in the other category, totaling 3306 rather than 3256. The Results text instead gives 449 unique proteins, which does sum to 3256 with 2807.

    Reported 3256 · recomputed 3306

2 of 2

Cites

Flagged first, then by citations

2 of the 92 references couldn’t be matched to a known paper.

Cited by

Sorted by citations

Related

Authors
Cuní-López, C., Root, J. T., Hao, Y., Blomberg, N., Koppes-den Hertog, S. J., Sacks, D., Trujillo, A. E., Ghirlando, R., Kowal, I., Epstein, J., Yang, L. G., Cookson, M. R., Marsan, E., van der Kant, R., Giera, M., Qi, Y. A., & Narayan, P. S.
Affiliations
  • National Institutes of Health (US)
  • Leiden University Medical Center (NL)
Corresponding author
Narayan, Priyanka S.
ORCID
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2026-08-19
Volume
17
Issue
1
ISSN
2041-1723 (ISSN-L)
DOI
10.1038/s41467-026-76565-6
PMC
PMC13582944
OpenAlex
W7203795734
Cited by
0
References
92
FWCI
0.00
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Communications (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • VU Research Portal (publishedVersion, other-oa)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
Funders
  • U.S. Department of Health & Human Services | National Institutes of Health (1ZIADK075158)
  • Chan Zuckerberg Initiative
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Biochemistry › Lipid metabolism and biosynthesis
  • Health Sciences › Medicine › Physiology › Alzheimer's disease research and treatments
  • Health Sciences › Medicine › Epidemiology › Autophagy in Disease and Therapy
Keywords
apolipoprotein E, APOE ε4, APOE2, APOE3, astrocytes, lipid droplets, lipid droplet proteome, lipidome, lipophagy, autophagy, Alzheimer's disease, induced pluripotent stem cell-derived astrocytes, oleic acid, genetic risk factors
MeSH terms
Alzheimer Disease, Apolipoproteins E, Astrocytes, Autophagy, Genotype, Humans, Oleic Acid, Proteome, Lipid Metabolism, Apolipoprotein E3, Apolipoprotein E4, Apolipoprotein E2, Induced Pluripotent Stem Cells, Lipid Droplets

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 2026-11-02.

Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-11-02.

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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