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Cited by 56Metabolomics and Mass Spectrometry StudiesAlzheimer's disease research and treatmentsLipid metabolism and biosynthesis

The Neurolipid Atlas: a lipidomics resource for neurodegenerative diseases

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Feringa, Femke M., Koppes-den Hertog, Sascha J., Wang, Lian Y., Derks, Rico J. E., Kruijff, Iris, Erlebach, Lena, Heijneman, Jorin, Miramontes, Ricardo +19 more·2025·Nature Metabolism
DOI 10.1038/s42255-025-01365-zPMC PMC12552125
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Abstract

Lipid alterations in the brain have been implicated in many neurodegenerative diseases. To facilitate comparative lipidomic research across brain diseases, we establish a data common named the Neurolipid Atlas that we prepopulated with isogenic induced pluripotent stem cell (iPS cell)-derived lipidomics data for different brain diseases. Additionally, the resource contains lipidomics data of human and mouse brain tissue. Leveraging multiple datasets, we demonstrate that iPS cell-derived neurons, microglia and astrocytes exhibit distinct lipid profiles that recapitulate in vivo lipotypes. Notably, the Alzheimer disease (AD) risk gene ApoE4 drives cholesterol ester (CE) accumulation specifically in human astrocytes and we also observe CE accumulation in whole-brain lipidomics from persons with AD. Multiomics interrogation of iPS cell-derived astrocytes revealed that altered cholesterol metabolism has a major role in astrocyte immune pathways such as the immunoproteasome and major histocompatibility complex class I antigen presentation. Our data commons, available online ( https://neurolipidatlas.com/ ), allows for data deposition by the community and provides a user-friendly tool and knowledge base for a better understanding of lipid dyshomeostasis in neurodegenerative diseases.

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  • 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).”

    From APOE genotypes differentially remodel the astrocytic lipid droplet proteome to shape lipid droplet dynamics (2026) · cites this paper as [30]

    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

  • Astrocytic lipid droplets accumulate in an APOE genotype-dependent manner.

    “Astrocytic lipid droplets also accumulate in an APOE genotype-dependent manner.”

    From APOE genotypes differentially remodel the astrocytic lipid droplet proteome to shape lipid droplet dynamics (2026) · cites this paper as [30]

  • 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.”

    From APOE genotypes differentially remodel the astrocytic lipid droplet proteome to shape lipid droplet dynamics (2026) · cites this paper as [30]

  • 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.”

    From APOE genotypes differentially remodel the astrocytic lipid droplet proteome to shape lipid droplet dynamics (2026) · cites this paper as [30]

  • 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).”

    From APOE genotypes differentially remodel the astrocytic lipid droplet proteome to shape lipid droplet dynamics (2026) · cites this paper as [30]

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Authors
Feringa, F. M., Koppes-den Hertog, S. J., Wang, L. Y., Derks, R. J. E., Kruijff, I., Erlebach, L., Heijneman, J., Miramontes, R., Pömpner, N., Blomberg, N., Olivier-Jimenez, D., Johansen, L. E., Cammack, A. J., Giblin, A., Toomey, C. E., Rose, I. V. L., Yuan, H., Ward, M. E., Isaacs, A. M., Kampmann, M., Kronenberg-Versteeg, D., Lashley, T., Thompson, L. M., Ori, A., Mohammed, Y., Giera, M., & van der Kant, R.
Affiliations
  • Amsterdam Neuroscience (NL)
  • Leiden University Medical Center (NL)
  • German Center for Neurodegenerative Diseases (DE)
  • University of California, Irvine (US)
  • Leibniz Institute on Aging - Fritz Lipmann Institute (FLI) (DE)
  • UK Dementia Research Institute (GB)
  • UCL Queen Square Institute of Neurology (GB)
  • University of California, San Francisco (US)
  • National Institutes of Health (US)
Corresponding author
Giera, Martin
ORCID
Venue
Nature Metabolism
Publisher
Springer Science and Business Media LLC
Published
2025-09-22
Volume
7
Issue
10
Pages
2142-2164
ISSN
2522-5812 (ISSN-L)
DOI
10.1038/s42255-025-01365-z
PMC
PMC12552125
OpenAlex
W4414428352
Cited by
56
References
29
Citations by year
2026: 38 · 2025: 16 · 2024: 2
FWCI
14.91
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Metabolism (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nd)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Pure Amsterdam UMC (publishedVersion, cc-by)
  • Informationszentrum Lebenswissenschaften (ZB MED) (submittedVersion, cc-by)
  • PubMed Central (submittedVersion, cc-by-nd)
  • Leiden Repository (Leiden University) (submittedVersion, cc-by)
  • DZNE Pub (submittedVersion, cc-by)
  • VU Research Portal (submittedVersion, other-oa)
  • Leiden Repository (Leiden University) (submittedVersion)
Funders
  • Foundation for the National Institutes of Health (P01 NS084974-06A1, T32NS115706)
  • California Institute for Regenerative Medicine (EDUC4-12812)
  • Alzheimer's Association (2019-AARG-643165, ADSF-21-816750, ADSF-21-831212-C)
  • ZonMw (733050515, 435005033)
  • Nederlandse Organisatie voor Wetenschappelijk Onderzoek (09150172110086)
  • Alzheimer Nederland (WE.03-2019-13, WE-03-2017-09P, WE.15-2019-16)
  • National Institute on Aging (R01AG062359, U01AG072464)
  • National Cancer Institute (P30CA062203)
  • National Institute of Neurological Disorders and Stroke (P01NS084974, T32NS115706, R35NS116872)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Metabolomics and Mass Spectrometry Studies
  • Health Sciences › Medicine › Physiology › Alzheimer's disease research and treatments
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Biochemistry › Lipid metabolism and biosynthesis
Keywords
lipidomics, neurodegenerative diseases, Alzheimer's disease, APOE ε4, cholesterol esters, astrocytes, microglia, cholesterol metabolism, immunoproteasome, MHC class I antigen presentation, data commons

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