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Iron response of HepG2 cells - The exon-intron gene structure upstream of the initiation codon predicts translation efficiency

ABSTRACT: Quantitative proteomics of HepG2 cells in response to iron. SILAC 3plex was conducted

OTHER RELATED OMICS DATASETS IN: PRJNA389312

INSTRUMENT(S): LTQ Orbitrap

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Hepatocyte, Cell Culture

SUBMITTER: Chun Shen Lim

LAB HEAD: Chris Brown

PROVIDER: PXD006661 | Pride | 2018-04-23

REPOSITORIES: Pride

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			Action	DRS
	12026__Exp3_S1F1.RAW	Raw
	12026__Exp3_S1F10.RAW	Raw
	12026__Exp3_S1F2.RAW	Raw
	12026__Exp3_S1F3.RAW	Raw
	12026__Exp3_S1F4.RAW	Raw

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Publications

The exon-intron gene structure upstream of the initiation codon predicts translation efficiency.

Lim Chun Shen CS T Wardell Samuel J SJ Kleffmann Torsten T Brown Chris M CM

Nucleic acids research 20180501 9

Introns in mRNA leaders are common in complex eukaryotes, but often overlooked. These introns are spliced out before translation, leaving exon-exon junctions in the mRNA leaders (leader EEJs). Our multi-omic approach shows that the number of leader EEJs inversely correlates with the main protein translation, as does the number of upstream open reading frames (uORFs). Across the five species studied, the lowest levels of translation were observed for mRNAs with both leader EEJs and uORFs (29%). T ...[more]

PMID: 29684192

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2022-11-08 | PXD031924 | Pride

Mass spectrometry (MS) datasets of QKI5 co-immunoprecipitation samples in THP-1 cells

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2021-09-27 | PXD028743 | Pride

Magnitude of ubiquitination determines the fate of activated epidermal growth factor receptor and downstream cellular effects

Project description:Receptor tyrosine kinases (RTK) bind growth factors and are critical for cell proliferation and differentiation. Their dysregulation leads to a loss of growth control, often resulting in cancer. Epidermal growth factor receptor (EGFR) is the prototypic RTK and can bind several ligands exhibiting distinct mitogenic potentials. Whereas the phosphorylation on individual EGFR sites and their roles for downstream signaling have been extensively studied, less is known about ligand-specific ubiquitination events on EGFR, which are crucial for signal attenuation and termination. We used a proteomics-based workflow for absolute quantitation combined with mathematical modelling to unveil potentially decisive ubiquitination events on EGFR from the first 30 seconds to 15 minutes of stimulation. Four ligands were used for stimulation: epidermal growth factor (EGF), heparin-binding-EGF like growth factor, transforming growth factor- and epiregulin. Whereas only little differences in the kinetic profiles of individual ubiquitination sites were observed, the overall amount of modified receptor differed depending on the used ligand, indicating that absolute magnitude of EGFR ubiquitination, and not distinctly regulated ubiquitination sites, is a major determinant for signal attenuation and the subsequent cellular outcomes.

2022-05-31 | PXD019621 | Pride

SILAC Phospho-proteomics: Trypanosoma brucei

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2023-03-11 | PXD034516 | Pride

Triple SILAC based quantitative MS approach to determine Withaferin A regulated proteins in prostate cancer

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2021-07-21 | PXD016759 | Pride

Transfer of Alarmins from Neutrophils to Platelets after Acute Myocardial Infarction

Project description:Platelets are central to the pathophysiology of myocardial infarction (MI). How the platelet proteome is altered during MI is unknown. We sought to describe changes in the platelet proteome at the time of MI and identify potential mechanisms. Platelets from patients experiencing ST-elevation myocardial infarction (STEMI) before and 3 days after treatment (n= 30), and a matched cohort of patients with severe stable coronary artery disease (CAD) prior to and 3 days after coronary artery bypass grafting (CABG, n=25) underwent quantitative proteomic analysis. Elevations of the alarmins S100A8 and S100A9 were detected at the time of STEMI compared with stable CAD (S100A8, FC = 2.00, FDR = 0.05; S100A9, FC = 2.28, FDR = 0.005). During STEMI, S100A8 mRNA and protein levels were correlated in platelets (R = 0.46, p = 0.012). To determine if protein synthesis occurs, activated platelets were incubated with 13C-labelled amino acids for 24 hours and analyzed by mass spectrometry. No incorporation was detected, consistent with the notion that protein synthesis in platelets is not a major contributor to the platelet proteome. Platelet abundance of S100A8 and A9 was strongly correlated with neutrophil abundance at the time of STEMI. When isolated platelets and neutrophils were co-incubated under quiescent and TRAP-6 activated conditions, release of S100A8 from neutrophils resulted in uptake of S100A8 by platelets. Leukocyte-to-platelet protein transfer, rather than protein synthesis, may occur in a thromboinflammatory environment such as STEMI, representing a potential new contributor in the innate immune pathogenesis of STEMI.

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