Multi cell line analysis of lysosomal proteomes reveals unique features and novel lysosomal proteins
Open accessPreprint — published as 10.1016/j.mcpro.2023.100509
Abstract
Lysosomes play a key role in the regulation of cellular metabolism and are increasingly recognized as highly active and diverse organelles which are involved in a large variety of processes. Their essential role is exemplified by the detrimental consequences of lysosomal malfunction, which can result in lysosomal storage disorders, neurodegenerative diseases, and cancer. Using lysosome enrichment and mass spectrometry, we investigated the lysosomal proteomes of six common cell lines. We provide first evidence for cell-type specific differences of lysosomes on a large scale, showing highly variable levels of distinct lysosomal proteins within one cell type, while others are highly conserved among cell lines. Using stable isotope labelling and bimodal distribution analysis, we identify high confidence lysosomal proteins for each cell line. Multi cell line correlation of these data reveals potential novel lysosomal proteins, and we confirm lysosomal localization for five candidates. All data are available via ProteomeXchange with identifier PXD020600.
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CRISPR-Cas9 screens suggested autophagy to partially mediate mepacrine effects in CML cells, as supported by enrichment of lysosomal genes, such as SLC12A9 and SPSN1, as sensitization hits to mepacrine.
“Our CRISPR-Cas9 screens suggested autophagy to partially mediate mepacrine effects in CML cells, as supported by the enrichment of lysosomal genes, such as SLC12A929 and SPSN1,30 as sensitization hits to mepacrine.”
From Integrated drug profiling and CRISPR screening identify BCR::ABL1-independent vulnerabilities in chronic myeloid leukemia (2024) · cites this paper as [29]
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- Authors
- Akter, F., Ponnaiyan, S., Kögler-Mohrbacher, B., Bleibaum, F., Damme, M., Renard, B. Y., & Winter, D.
- Affiliations
- University of Bonn (DE)
- Robert Koch Institute (DE)
- Christian-Albrechts-Universität zu Kiel (DE)
- Corresponding author
- Winter, Dominic
- ORCID
- Venue
- Molecular & Cellular Proteomics
- Publisher
- openRxiv
- Published
- 2020-12-21
- Volume
- 22
- Issue
- 3
- Pages
- 100509-100509
- ISSN
- 1535-9476 (ISSN-L)
- PMC
- PMC10025164
- OpenAlex
- W4320480857
- Cited by
- 55
- References
- 98
- Citations by year
- 2026: 11 · 2025: 16 · 2024: 13 · 2023: 5 · 2022: 7 · 2021: 3
- FWCI
- 4.15
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- Molecular & Cellular Proteomics (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Publication server of the Robert Koch Institute (Robert Kock Institute) (submittedVersion, cc-by)
- Greater South Information System
- Funders
- Deutscher Akademischer Austauschdienst
- Deutsche Forschungsgemeinschaft (FOR 2625)
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Health Sciences › Medicine › Epidemiology › Autophagy in Disease and Therapy
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Cellular transport and secretion
- Keywords
- lysosomal proteome, lysosomal proteins, lysosomal storage disease, neurodegenerative diseases, cancer, HEK293 cells, HeLa, SH-SY5Y cells, mouse embryonic fibroblasts
- MeSH terms
- Animals, Humans, Lysosomes, Mammals, Neuroblastoma, Proteins, Proteome, NIH 3T3 Cells, Mice, HEK293 Cells
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