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Multi cell line analysis of lysosomal proteomes reveals unique features and novel lysosomal proteins

View ORCID ProfileFatema Akter, View ORCID ProfileSrigayatri Ponnaiyan, Bianca Kögler-Mohrbacher, View ORCID ProfileFlorian Bleibaum, View ORCID ProfileMarkus Damme, View ORCID ProfileBernhard Y. Renard, View ORCID ProfileDominic Winter
doi: https://doi.org/10.1101/2020.12.21.423747
Fatema Akter
1Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, 53115 Bonn, Germany
2Department of Pharmacology, Faculty of Veterinary Science, Bangladesh Agricultural University, 2202 Mymensingh, Bangladesh
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  • ORCID record for Fatema Akter
Srigayatri Ponnaiyan
1Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, 53115 Bonn, Germany
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Bianca Kögler-Mohrbacher
3Bioinformatics Unit (MF1), Robert Koch Institute, 13353 Berlin, Germany
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Florian Bleibaum
4Institute for Biochemistry, University of Kiel, 24118 Kiel, Germany
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Markus Damme
4Institute for Biochemistry, University of Kiel, 24118 Kiel, Germany
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Bernhard Y. Renard
3Bioinformatics Unit (MF1), Robert Koch Institute, 13353 Berlin, Germany
5Hasso Plattner Institute, University of Potsdam, 14482 Potsdam, Germany
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Dominic Winter
1Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, 53115 Bonn, Germany
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  • For correspondence: dominic.winter@uni-bonn.de
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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.

Competing Interest Statement

The authors have declared no competing interest.

  • Abbreviations

    SPIONs
    Superparamagnetic Iron Oxide Nanoparticles
    SILAC
    Stable Isotope Labelling of Amino Acids in Cell Culture
    LC-MSMS
    Liquid Chromatography-tandem Mass Spectrometry
    iBAQ
    intensity Based Absolute Quantification
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    Posted December 21, 2020.
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    Multi cell line analysis of lysosomal proteomes reveals unique features and novel lysosomal proteins
    Fatema Akter, Srigayatri Ponnaiyan, Bianca Kögler-Mohrbacher, Florian Bleibaum, Markus Damme, Bernhard Y. Renard, Dominic Winter
    bioRxiv 2020.12.21.423747; doi: https://doi.org/10.1101/2020.12.21.423747
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    Multi cell line analysis of lysosomal proteomes reveals unique features and novel lysosomal proteins
    Fatema Akter, Srigayatri Ponnaiyan, Bianca Kögler-Mohrbacher, Florian Bleibaum, Markus Damme, Bernhard Y. Renard, Dominic Winter
    bioRxiv 2020.12.21.423747; doi: https://doi.org/10.1101/2020.12.21.423747

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