Evidence map›Paper›PMID 41103078›Full record

ArticleAutophagy2025

Lysosomal proteomics reveals mechanisms of neuronal APOE4-associated lysosomal dysfunction.

Einar K Krogsaeter, Justin McKetney, Leopoldo Valiente-Banuet, Angelica Marquez, Alexandra Willis, Zeynep Cakir, Erica Stevenson, Gwendolyn M Jang, Antara Rao, Emmy Li and 7 more

Abstract read
In one paragraph

Article in Autophagy, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.

0numbers the graph read from it
0cells of the map it votes in
15citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

15 citing papers in PubMed.

  1. Review
  2. Article
  3. Review
  4. Review
  5. Compartmental pH regulation in cancer and antitumor immunity: therapeutic opportunities and challenges.Apoptosis : an international journal on programmed cell death · 2026
    Review
  6. APOE4 disrupts the central dogma by arresting neuronal proteome dynamics.bioRxiv : the preprint server for biology · 2026
    Article
  7. Review
  8. Lysosomal homeostasis at the crossroads of neurodegeneration.The Journal of clinical investigation · 2026
    Review
  9. Article
  10. Review
  11. Article
  12. Review
  13. Review
  14. Article
  15. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

17 authors.

Einar K KrogsaeterGladstone Data Science and Biotechnology Institute, The J. David Gladstone Institutes, San Francisco, USA.ORCID 0000-0001-8232-5498
Justin McKetneyGladstone Data Science and Biotechnology Institute, The J. David Gladstone Institutes, San Francisco, USA.ORCID 0000-0002-2405-8288
Leopoldo Valiente-BanuetDepartment of Neurology, David Geffen School of Medicine, University of California, Los Angeles, USA.ORCID 0009-0007-8157-5488
Angelica MarquezGladstone Data Science and Biotechnology Institute, The J. David Gladstone Institutes, San Francisco, USA.
Alexandra WillisGladstone Data Science and Biotechnology Institute, The J. David Gladstone Institutes, San Francisco, USA.
Zeynep CakirGladstone Data Science and Biotechnology Institute, The J. David Gladstone Institutes, San Francisco, USA.
Erica StevensonGladstone Data Science and Biotechnology Institute, The J. David Gladstone Institutes, San Francisco, USA.ORCID 0000-0001-7853-1854
Gwendolyn M JangGladstone Data Science and Biotechnology Institute, The J. David Gladstone Institutes, San Francisco, USA.ORCID 0000-0001-7806-9874
Antara RaoGladstone Institute of Neurological Disease, The J. David Gladstone Institutes, San Francisco, USA.ORCID 0000-0002-1269-018X
Emmy LiInstitute for Neurodegenerative Diseases, University of California, San Francisco, USA.
Anton ZhouGladstone Institute of Neurological Disease, The J. David Gladstone Institutes, San Francisco, USA.
Anjani AttiliInstitute for Neurodegenerative Diseases, University of California, San Francisco, USA.
Timothy S ChangDepartment of Neurology, David Geffen School of Medicine, University of California, Los Angeles, USA.ORCID 0000-0002-9225-9874
Martin KampmannInstitute for Neurodegenerative Diseases, University of California, San Francisco, USA.ORCID 0000-0002-3819-7019
Yadong HuangGladstone Institute of Neurological Disease, The J. David Gladstone Institutes, San Francisco, USA.ORCID 0000-0002-5871-4589
Nevan J KroganGladstone Data Science and Biotechnology Institute, The J. David Gladstone Institutes, San Francisco, USA.ORCID 0000-0003-4902-337X
Danielle L SwaneyGladstone Data Science and Biotechnology Institute, The J. David Gladstone Institutes, San Francisco, USA.ORCID 0000-0001-6119-6084

Funding

Research Education ComponentP30AG062422 · NIA · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Serggio Carlo Lanata · 2019 to 2026
$36.9M
Research Education ComponentP30AG019610 · NIA · SUN HEALTH RESEARCH INSTITUTE · PI GONZALEZ HERNANDEZ, GRACIELA · 2001 to 2020
$32.5M
Project 4: Cross-species Dissection of Cellular Response to APOE Genotype and AD Pathology Using Single-cell Multi-omicsP01AG073082 · NIA · J. DAVID GLADSTONE INSTITUTES · PI MUCKE, LENNART · 2021 to 2025
$23.4M
Uncovering the Genetic Mechanisms of the Chromosome 17q21.31 Tau Haplotype on Neurodegeneration Risk in FTD and PSPU54NS123746 · NINDS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI GOATE, ALISON M · 2021 to 2025
$9.4M
National Brain and Tissue Resource for Parkinson's Disease and Related DisordersU24NS072026 · NINDS · BANNER SUN HEALTH RESEARCH INSTITUTE · PI BEACH, THOMAS G · 2011 to 2015
$7.8M
PREDOCTORAL TRAINING IN DEVELOPMENTAL BIOLOGYT32HD007470 · NICHD · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Todd Nystul · 1994 to 2026
$7.7M
Proteomic and Genetic Approaches Defining Apolipoprotein E4 Neuropathologic MechanismsRF1AG059751 · NIA · J. DAVID GLADSTONE INSTITUTES · PI KROGAN, NEVAN J, MAHLEY, ROBERT W. · 2019 to 2019
$4.7M
Neuronal ApoE Drives Selective Neurodegeneration in Alzheimer's DiseaseR01AG071697 · NIA · J. DAVID GLADSTONE INSTITUTES · PI HUANG, YADONG · 2021 to 2025
$4.1M
Aberrant proteomes in tauopathy: revealing functional consequences via multimodal proteomicsR01AG092454 · NIA · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Martin Kampmann, Danielle L Swaney · 2025 to 2026
$1.6M
PUMAS - A Pipeline program for comMUnity college students Advancing in the SciencesR25HL121037 · NHLBI · J. DAVID GLADSTONE INSTITUTES · PI Sudha Krishnamurthy, Melanie Maria Ott · 2014 to 2026
$1.1M
Rare Genetic Risk and Gene Networks in TauopathyK08AG065519 · NIA · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI CHANG, TIMOTHY S · 2020 to 2024
$887k
Alzheimer's Disease Organelle Proteome Task (ADOPT)-pilot phaseR03AG091095 · NIA · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI WANG, BIAO · 2025 to 2025
$328k
NHLBI NIH HHS R25 HL121037NIA NIH HHS K08 AG065519NIA NIH HHS P01 AG073082NIA NIH HHS P30 AG019610NIA NIH HHS P30 AG062422NIA NIH HHS R01 AG071697NIA NIH HHS R01 AG092454NIA NIH HHS R03 AG091095NIA NIH HHS RF1 AG059751NICHD NIH HHS T32 HD007470NINDS NIH HHS U24 NS072026NINDS NIH HHS U54 NS123746
6 · The paper itself

Abstract

APOE4 is the primary risk factor for Alzheimer disease (AD). Early AD pathological events first affect the neuronal endolysosomal system, which in turn causes neuronal protein aggregation and cell death. Despite the crucial influence of lysosomes upon AD pathophysiology, and that APOE4 localizes to lysosomes, the influence of APOE4 on lysosomal function remains unexplored. We find that expression of APOE4 in neuronal cell lines results in lysosomal alkalinization and impaired lysosomal function. To identify driving factors for these defects, we performed quantitative lysosomal proteome profiling. This revealed that APOE4 expression results in differential regulation of numerous lysosomal proteins, correlating with APOE allele status and disease severity in AD brains. In particular, APOE4 expression results in the depletion of lysosomal LGALS3BP and the accumulation of lysosomal TMED5. We additionally validated that these lysosomal protein changes can be targeted to modulate lysosomal function. Taken together, this work thereby reveals that APOE4 causes widespread lysosomal defects through remodeling the lysosomal proteome, with the lysosomal TMED5 accumulation and LGALS3BP depletion manifesting as lysosomal alkalinization in APOE4 neurons.

Indexed as

Apolipoprotein E4LysosomesNeuronsProteomicsAlzheimer DiseaseAutophagyHumansProteomeApolipoprotein E4ProteomeAlzheimer diseaseAPOE4LGALS3BPLysoIPlysosomespHTMED5

Identifiers

PMID41103078
PMCPMC12758178

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.