Multi cell line comparison of lysosome enriched fractions reveals cell type specific features and novel lysosomal proteins

ABSTRACT: Lysosomes are the main degradative organelles of mammalian cells and are responsible for the breakdown of the majority of cellular macromolecules and the recycling of their building blocks. To accomplish this task, lysosomes contain ~60 hydrolases. Malfunction of these proteins, as well as other proteins responsible for the transport of small molecules or proteins, lead to the accumulation of their respective substrates. This accumulation of substrates results in heavy impairment of lysosomal function leading to ~70 lysosomal storage disorders (LSDs). A better understanding of lysosomal composition is of high importance not only for a better understanding of LSDs, but also for cellular function. Analysis of lysosomes by mass spectrometry-based proteomics presents an attractive approach to allow for a better characterization of lysosomes. In the current study, we investigated the lysosomal proteome from six different cell lines (HEK293, HeLa, HuH-7, SH-SY5Y, MEF and NIH3T3) by lysosome enrichment using SPIONs (superparamagnetic iron oxide nanoparticles) combined with mass spectrometry-based proteomics. Comparison of the individual proteomes revealed cell type specific characteristics in lysosomal protein expression. To allow for the discrimination of lysosomal from unspecific enriched proteins, we included a differentially SILAC (stable isotope labelling by amino acids in cell culture) labelled control sample. Afterwards, lysosomal proteins were identified using a bimodal distribution model. By combination of data from several cell lines, we were able to generate a high confidence list of putative novel lysosomal proteins of which several were confirmed by immunostaining.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (human) Mus Musculus (mouse)

TISSUE(S): Epithelial Cell, Early Embryonic Cell, Fibroblast

SUBMITTER: Fatema Akter  

LAB HEAD: Dominic Winter

PROVIDER: PXD020600 | Pride | 2023-02-21

REPOSITORIES: Pride