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A quantitative mass spectrometry-based approach to monitor the dynamics of endogenous chromatin-associated protein complexes

Abstract

Understanding the dynamics of endogenous protein-protein interactions in complex networks is pivotal in deciphering disease mechanisms. To enable the in-depth analysis of protein interactions in chromatin-associated protein complexes, we have previously developed a method termed RIME (Rapid Immunoprecipitation Mass spectrometry of Endogenous proteins). Here, we present a quantitative multiplexed method (qPLEX-RIME), which integrates RIME with isobaric labelling and tribrid mass spectrometry for the study of protein interactome dynamics in a quantitative fashion with increased sensitivity. Using the qPLEX-RIME method, we delineate the temporal changes of the Estrogen Receptor alpha (ERalpha) interactome in breast cancer cells treated with 4-hydroxytamoxifen. Furthermore, we identify endogenous ERalpha-associated proteins in human Patient-Derived Xenograft tumours and in primary human breast cancer clinical tissue. Our results demonstrate that the combination of RIME with isobaric labelling offers a powerful tool for the in-depth and quantitative characterisation of protein interactome dynamics, which is applicable to clinical samples.

Type Journal
ISBN 2041-1723 (Electronic) 2041-1723 (Linking)
Authors Papachristou, E. K.; Kishore, K.; Holding, A. N.; Harvey, K.; Roumeliotis, T. I.; Chilamakuri, C. S. R.; Omarjee, S.; Chia, K. M.; Swarbrick, A.; Lim, E.; Markowetz, F.; Eldridge, M.; Siersbaek, R.; D'Santos, C. S.; Carroll, J. S.
Responsible Garvan Author A/Prof Alex Swarbrick
Publisher Name Nature Communications
Published Date 2018-06-13
Published Volume 9
Published Issue 1
Published Pages 2311
Status Always Electronic
DOI 10.1038/s41467-018-04619-5
URL link to publisher's version https://www.ncbi.nlm.nih.gov/pubmed/29899353
OpenAccess link to author's accepted manuscript version https://publications.gimr.garvan.org.au/open-access/14672