Time Series Proteome Profiling to Study Endoplasmic Reticulum Stress Response

Overview

Journal J Proteome Res

Publisher American Chemical Society

Specialty Biochemistry

Date 2008 Apr 26

PMID 18435558

Citations 16

Authors

Michelle Mintz

Adeline Vanderver

Kristy J Brown

Joseph Lin

Zuyi Wang

Christine Kaneski

Raphael Schiffmann

Kanneboyina Nagaraju

Eric P Hoffman

Yetrib Hathout

Affiliations

Soon will be listed here.

Abstract

Time series profiling is a powerful approach for obtaining information on protein expression dynamics and prevailing biochemical pathways. To date, such information could only be obtained at the mRNA level using mature and highly parallel technologies such as microarray gene expression profiling. The generation of time series data at the protein level has lagged due to the lack of robust and highly reproducible methodologies. Using a combination of SILAC strategy, SDS-PAGE and LC-MS/MS, we demonstrate successful monitoring of expression levels of the same set of proteins across different time points within the ER compartment of human primary fibroblast cells when exposed to ER stress inducers tunicamycin and thapsigargin. Data visualization was facilitated using GeneSpring GX analysis platform that was designed to process Affymetrix microarray data. This software also facilitated the generation of important parameters such as data normalization, calculation of statistical values to extract significant changes in protein expression, and the cross comparison of data sets.

Citing Articles

Utility of Extrapolating Human S1500+ Genes to the Whole Transcriptome: Tunicamycin Case Study.

Mav D, Phadke D, Balik-Meisner M, Merrick B, Auerbach S, Niemeijer M Bioinform Biol Insights. 2020; 14:1177932220952742.

PMID: 33088175 PMC: 7545517. DOI: 10.1177/1177932220952742.

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

Itzhak D, Sacco F, Nagaraj N, Tyanova S, Mann M, Murgia M Dis Model Mech. 2019; 12(11).

PMID: 31628211 PMC: 6899043. DOI: 10.1242/dmm.040741.

Dynamic analysis of proteomic alterations in response to N-linked glycosylation inhibition in a drug-resistant ovarian carcinoma cell line.

Shu J, Dang L, Zhang D, Shah P, Chen L, Zhang H FEBS J. 2019; 286(8):1594-1605.

PMID: 30884134 PMC: 7360092. DOI: 10.1111/febs.14811.

The transcriptional profiles and functional implications of long non-coding RNAs in the unfolded protein response.

Quan H, Fan Q, Li C, Wang Y, Wang L Sci Rep. 2018; 8(1):4981.

PMID: 29563563 PMC: 5862980. DOI: 10.1038/s41598-018-23289-3.

Acute Exposure to Tris(1,3-dichloro-2-propyl) Phosphate (TDCIPP) Causes Hepatic Inflammation and Leads to Hepatotoxicity in Zebrafish.

Liu C, Su G, Giesy J, Letcher R, Li G, Agrawal I Sci Rep. 2016; 6:19045.

PMID: 26743178 PMC: 4705469. DOI: 10.1038/srep19045.

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