Dataset Information

Novel binding partners of nucleolar HIF1A in hypoxic breast cancer cells

ABSTRACT: Solid tumors such as breast cancer have intratumoral regions of low oxygen tension, which influence a vast array of cellular responses. Hypoxia-Inducible Factor 1-alpha (HIF1α) represents the principal transcription factor orchestrating cellular responses to hypoxic conditions, mediating the regulation of genes implicated in oxygen homeostasis. The nucleolus is central stress response hub in the cell, as such we sought to identify novel binding partners of HIF1α in the nucleolar compartment during hypoxic stress.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Epithelial Cell, Cell Culture

DISEASE(S): Breast Cancer

SUBMITTER: Brandon Metge

LAB HEAD: Lalita Samant

PROVIDER: PXD053134 | Pride | 2025-07-15

REPOSITORIES: Pride

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			Action	DRS
	Mudpit_jm_20230329_Orbi1_Samant_T47DHypo_HIF1aIP_1.mzid.gz	Mzid
	Mudpit_jm_20230329_Orbi1_Samant_T47DHypo_HIF1aIP_1.mzid_Mudpit_jm_20230329_Orbi1_Samant_T47DHypo_HIF1aIP_1.MGF	Mzid
	Mudpit_jm_20230329_Orbi1_Samant_T47DNorm_HIF1aIP_1.mzid.gz	Mzid
	Mudpit_jm_20230329_Orbi1_Samant_T47DNorm_HIF1aIP_1.mzid_Mudpit_jm_20230329_Orbi1_Samant_T47DNorm_HIF1aIP_1.MGF	Mzid
	Mudpit_jm_QEHFx_06172022_RSamant_1315HIF1alP8h_H_Abonly__F061656_.mzid.gz	Mzid

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Project description:Measuring the properties of endogenous cell proteins, such as expression level, subcellular localization and turnover rates, on a whole proteome level remains a major challenge in the post-genome era. Quantitative methods for measuring mRNA expression do not reliably predict corresponding protein levels and provide little or no information on other protein properties. Here we describe a combined pulse-labelling, spatial proteomics and data analysis strategy to characterize the expression, localization, synthesis, degradation and turnover rates of endogenously expressed, untagged human proteins in different subcellular compartments. Using quantitative mass spectrometry and SILAC, a total of 80,098 peptides from 8,041 HeLa proteins were quantified, and their spatial distribution between the cytoplasm, nucleus and nucleolus determined and visualised using specialised software tools developed in PepTracker. Using information from ion intensities and rates of change in isotope ratios, protein abundance levels and protein synthesis, degradation and turnover rates were calculated for the whole cell and for the respective cytoplasmic, nuclear and nucleolar compartments. Expression levels of endogenous HeLa proteins varied by up to seven orders of magnitude. The average turnover rate for HeLa proteins was approximately 20 hours. Turnover rate did not correlate with either molecular weight or net charge, but did correlate with abundance, with highly abundant proteins showing longer than average half-lives. Fast turnover proteins had overall a higher frequency of PEST motifs than slow turnover proteins but no general correlation was observed between amino or carboxy terminal amino acid identities and turnover rates. A subset of proteins was identified that exist in pools with different turnover rates depending on their subcellular localization. This strongly correlated with subunits of large, multi-protein complexes, suggesting a general mechanism whereby their assembly is controlled in a different subcellular location to their main site of function.

Dataset Information

Novel binding partners of nucleolar HIF1A in hypoxic breast cancer cells

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