SILAC-based quantitative proteomics using mass spectrometry quantifies endoplasmic reticulum stress in whole HeLa...

Area of Science:

• Cellular Biology
• Proteomics
• Molecular Biology

Background:

• The unfolded protein response (UPR) is crucial for cellular proteostasis, involving complex proteome remodeling.
• Previous comprehensive analyses of the UPR were limited by technological constraints.

Purpose of the Study:

• To comprehensively quantify proteome-wide expression changes during the UPR using advanced proteomics.
• To compare the UPR induced by different chemical stressors (tunicamycin, thapsigargin, DTT).
• To identify novel proteins associated with ER stress and proteostasis disorders.

Main Methods:

• Stable isotope labeling with amino acids in cell culture (SILAC)-based quantitative proteomics.
• Analysis of over 6200 proteins in HeLa cells exposed to varying tunicamycin concentrations.
• Comparative proteomic analysis of tunicamycin, thapsigargin, and DTT induced UPR.

Main Results:

• Quantified proteome-wide expression changes in response to proteostatic stress.
• Identified 38 proteins not previously linked to the UPR, with 15 potentially involved in ER stress remediation.
• Observed limited downregulation of proteins despite CHOP expression, suggesting a minor role for RIDD in cell death.

Conclusions:

• This proteomic dataset serves as a valuable resource for understanding UPR and proteostasis.
• Novel UPR-associated proteins were discovered, potentially contributing to disease pathophysiology.
• The limited impact of RIDD on cell death in this system warrants further investigation.