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Gene expression profiling and quantitative shotgun proteomics

Gene expression profiling and quantitative shotgun proteomics

The endoplasmic reticulum (ER) is an intracellular organelle that produces all proteins destined to the cell surface, to the extracellular environments and to the organelles of the endocytic and secretory pathways.

In a paper published on February 16th in the Journal of Biological Chemistry, Timothy Bergmann, Ilaria Fregno and Maurizio Molinari from the IRB, an institute affiliated to the Università della Svizzera italiana, describe how human cells respond to ER stresses induced by chemical challenges or by the expression of disease-causing, mutant polypeptides. The study combines gene expression profiling and quantitative shotgun proteomics and has been performed in collaboration with Andrea Rinaldi and Francesco Bertoni (IOR) and Paola Picotti (ETH-Zurich).

The results show that chemically induced ER stress, as studied in the last decades, leads to the full activation of the so called “Unfolded Protein Responses” (UPR), which induce the transcription and translation of several hundred genes and eventually lead to multi compartmental failure and cell death. In contrast, expression of mutant, folding-defective polypeptides leads to the transcriptional and translational induction of a limited subset of UPR target genes, which are part of a supramolecular complex comprising ER chaperones, PDIs, ERAD and cell viability factors. In contrast to cellular responses to chemically induced ER stresses, responses to expression of misfolded proteins do not activate the PERK pathway of the UPR responsible for induction of apoptosis. This work shows that chemically-induced UPR, even if titrated down to induce similar ER stress levels as the expression of misfolded proteins, does not mimic cellular responses to latter. Transcriptional programs activated in response to perturbation of ER homeostasis by misfolded proteins are specific and tightly controlled, in fact only misfolded proteins that sequester a significant amount of BiP induce a UPR signature. All in all, these mechanisms prevent a premature collapse of ER homeostasis and activation of apoptotic programs.

This work was supported by grants from Signora Alessandra, Alpha-ONE Foundation, Foundation for Research on Neurodegenerative Diseases, the Novartis Foundation, Comel and Gelu Foundations, Swiss National Science Foundation (SNF). Maurizio Molinari is supported by a Sinergia grant of the Swiss National Science Foundation.


Chemical stresses fail to mimic the unfolded protein response resulting from luminal load with unfolded polypeptides
T. J. Bergmann, I. Fregno, F. Fumagalli, A. Rinaldi, F. Bertoni, P. J. Boersema, P. Picotti, M. Molinari
in J Biol Chem (2018)

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