PXD019135

PXD019135 is an original dataset announced via ProteomeXchange.

Title	SILAC-based quantitative proteomics implicates SOCS1 in modulating protein constituents of large macromolecular complexes in hepatocytes
Description	Suppressor of Cytokine Signaling 1 (SOCS1) functions as a tumor suppressor in hepatocellular carcinoma by regulating cytokine, growth factor and other signaling pathways. The tumor suppressor functions of SOCS1 are mediated partly via promoting ubiquitination and proteasomal degradation of several signaling proteins. In this study, we used an unbiased approach to characterize SOCS1-mediated changes in the protein profile of hepatocytes. The murine HCC cell line Hepa1-6 transduced with wildtype SOCS1, an SH2 domain mutant or the empty lentiviral vector were grown in Stable Isotopic Labelling of Amino acids in Cell culture (SILAC) media. The cells were stimulated with hepatocyte growth factor or left at steady state. Following cell lysis, proteins were separated on SDS-PAGE gels and peptides extracted by in-gel trypsinization were analyzed by mass spectrometry. Differentially modulated proteins identified and quantified were subjected to pathway enrichment analysis. In total, 3440 proteins were identified in Hepa cells in the presence of SOCS1 at steady state, of which 181 proteins were significantly modulated by SOCS1. The SH2 domain mutation and HGF stimulation increased the number of differentially modulated proteins, which showed only a limited overlap with SOCS1-modulated proteins. Protein interaction network analysis revealed enrichment of SOCS1-modulated proteins within multiprotein complexes such as ubiquitin conjugating enzymes, proteasome, mRNA spliceosome, mRNA exosome and mitochondrial ribosome. Further analysis indicated SOCS1-dependent regulation of the UBE2D ubiquitin conjugating enzymes, which are implicated in growth factor receptor signaling, indirectly via an unknown protein. Given the ubiquitous and highly regulated induction of SOCS1 by diverse cellular stimuli, our findings suggest a fundamental role of SOCS1 in regulating large macromolecular complexes that are important for cellular homeostasis.
HostingRepository	PRIDE
AnnounceDate	2021-02-01
AnnouncementXML	Submission_2021-01-31_22:21:50.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Francois-Michel Boisvert
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	carbamoylated residue; monohydroxylated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2020-05-12 19:00:27	ID requested
⏵ 1	2021-01-31 22:21:50	announced

Dataset with its publication pending

submitter keyword: SOCS1, SILAC, ubiquitination, MET, CBL, proteasome

Subburaj Ilangumaran
contact affiliation	Department of Immunology and Cell Biology Faculty of Medicine and Health Sciences, University of Sherbrooke Canada
contact email	Subburaj.Ilangumaran@Usherbrooke.ca
lab head
Francois-Michel Boisvert
contact affiliation	Université de Sherbrooke
contact email	fm.boisvert@usherbrooke.ca
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD019135
     1. Label: PRIDE project
     2. Name: SILAC-based quantitative proteomics implicates SOCS1 in modulating protein constituents of large macromolecular complexes in hepatocytes