Lysosomal proteomics reveals mechanisms of neuronal apoE4associated lysosomal dysfunction

Einar K Krogsaeter; Justin McKetney; Angelica Marquez; Zeynep Cakir; Erica Stevenson; Gwendolyn M Jang; Antara Rao; Anton Zhou; Yadong Huang; Nevan J Krogan; Danielle L Swaney

doi:10.1101/2023.10.02.560519

Lysosomal proteomics reveals mechanisms of neuronal apoE4associated lysosomal dysfunction

bioRxiv [Preprint]. 2023 Oct 2:2023.10.02.560519. doi: 10.1101/2023.10.02.560519.

Authors

Einar K Krogsaeter^{1

2

3

4}, Justin McKetney^{1

2

3

4}, Angelica Marquez^{1

2

3}, Zeynep Cakir^{1

2

3}, Erica Stevenson^{1

2

3}, Gwendolyn M Jang^{1

2

3}, Antara Rao^{5

6}, Anton Zhou⁵, Yadong Huang^{5

6

7

8

9

10}, Nevan J Krogan^{1

2

3}, Danielle L Swaney^{1

2

3}

Affiliations

¹ Gladstone Data Science and Biotechnology Institute, The J. David Gladstone Institutes, San Francisco, California, USA.
² Quantitative Bioscience Institute, University of California, San Francisco, California, USA.
³ Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA.
⁴ These authors contributed equally.
⁵ Gladstone Institute of Neurological Disease, The J. David Gladstone Institutes, San Francisco, USA.
⁶ Developmental and Stem Cell Biology Graduate Program, University of California, San Francisco, USA.
⁷ Neuroscience Graduate Program, University of California, San Francisco, USA.
⁸ Gladstone Center for Translational Advancement, Gladstone Institutes, San Francisco, USA.
⁹ Biomedical Sciences Graduate Program, University of California, San Francisco, USA.
¹⁰ Departments of Neurology and Pathology, University of California, San Francisco, USA.

Abstract

ApoE4 is the primary risk factor for Alzheimer's Disease. While apoE is primarily expressed by astrocytes, AD pathology including endosomal abnormalities and mitochondrial dysfunction first occurs in neurons. Lysosomes are poised at the convergence point between these features. We find that apoE4-expressing cells exhibit lysosomal alkalinization, reduced lysosomal proteolysis, and impaired mitophagy. To identify driving factors for this lysosomal dysfunction, we performed quantitative lysosomal proteome profiling. This revealed that apoE4 expression results in lysosomal depletion of Lgals3bp and accumulation of Tmed5 in both Neuro-2a cells and postmitotic human neurons. Modulating the expression of both proteins affected lysosomal function, with Tmed5 knockdown rescuing lysosomal alkalinization in apoE4 cells, and Lgals3bp knockdown causing lysosomal alkalinization and reduced lysosomal density in apoE3 cells. Taken together, our work reveals that apoE4 exerts gain-of-toxicity by alkalinizing the lysosomal lumen, pinpointing lysosomal Tmed5 accumulation and Lgals3bp depletion as apoE4-associated drivers for this phenotype.

Keywords: APOE4; Alzheimer’s Disease; Lgals3bp; Lysosomes; Proteomics; pH.

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Preprint

Abstract

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