Dataset Information

PSL-LCCL: a resource for subcellular protein localization in liver cancer cell line SK_HEP1.

ABSTRACT: The characterization of subcellular protein localization provides a basis for further understanding cellular behaviors. A delineation of subcellular localization of proteins on cytosolic membrane-bound organelles in human liver cancer cell lines (hLCCLs) has yet to be performed. To obtain its proteome-wide view, we isolated and enriched six cytosolic membrane-bound organelles in one of the hLCCLs (SK_HEP1) and quantified their proteins using mass spectrometry. The vigorous selection of marker proteins and a machine-learning-based algorithm were implemented to localize proteins at cluster and neighborhood levels. We validated the performance of the proposed method by comparing the predicted subcellular protein localization with publicly available resources. The profiles enabled investigating the correlation of protein domains with their subcellular localization and colocalization of protein complex members. A subcellular proteome database for SK_HEP1, including (i) the subcellular protein localization and (ii) the subcellular locations of protein complex members and their interactions, was constructed. Our research provides resources for further research on hLCCLs proteomics. Database URL: http://www.igenetics.org.cn/project/PSL-LCCL/.

SUBMITTER: Huang F

PROVIDER: S-EPMC9248857 | biostudies-literature | 2022 Feb

REPOSITORIES: biostudies-literature

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PSL-LCCL: a resource for subcellular protein localization in liver cancer cell line SK_HEP1.

Huang Fang F Tang Xia X Ye Bo B Wu Songfeng S Ding Keyue K

Database : the journal of biological databases and curation 20220201

The characterization of subcellular protein localization provides a basis for further understanding cellular behaviors. A delineation of subcellular localization of proteins on cytosolic membrane-bound organelles in human liver cancer cell lines (hLCCLs) has yet to be performed. To obtain its proteome-wide view, we isolated and enriched six cytosolic membrane-bound organelles in one of the hLCCLs (SK_HEP1) and quantified their proteins using mass spectrometry. The vigorous selection of marker pr ...[more]

PMID: 35134877

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Project description:Accurate knowledge of the intracellular location of proteins is important for numerous areas of biomedical research including assessing fidelity of putative protein-protein interactions, modeling cellular processes at a system-wide level and investigating metabolic and disease pathways. Many proteins have not been localized, or have been incompletely localized, partly because most studies do not account for entire subcellular distribution. Thus, proteins are frequently assigned to one organelle whereas a significant fraction may reside elsewhere. As a step toward a comprehensive cellular map, we used subcellular fractionation with classic balance sheet analysis and isobaric labeling/quantitative mass spectrometry to assign locations to >6000 rat liver proteins. We provide quantitative data and error estimates describing the distribution of each protein among the eight major cellular compartments: nucleus, mitochondria, lysosomes, peroxisomes, endoplasmic reticulum, Golgi, plasma membrane and cytosol. Accounting for total intracellular distribution improves quality of organelle assignments and assigns proteins with multiple locations. Protein assignments and supporting data are available online through the Prolocate website (http://prolocate.cabm.rutgers.edu). As an example of the utility of this data set, we have used organelle assignments to help analyze whole exome sequencing data from an infant dying at 6 months of age from a suspected neurodegenerative lysosomal storage disorder of unknown etiology. Sequencing data was prioritized using lists of lysosomal proteins comprising well-established residents of this organelle as well as novel candidates identified in this study. The latter included copper transporter 1, encoded by SLC31A1, which we localized to both the plasma membrane and lysosome. The patient harbors two predicted loss of function mutations in SLC31A1, suggesting that this may represent a heretofore undescribed recessive lysosomal storage disease gene.

Dataset Information

PSL-LCCL: a resource for subcellular protein localization in liver cancer cell line SK_HEP1.

Publications

PSL-LCCL: a resource for subcellular protein localization in liver cancer cell line SK_HEP1.

Similar Datasets

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