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

Evangelia K. Papachristou, Kamal Kishore, Andrew N. Holding, Kate Harvey, Theodoros I. Roumeliotis, Chandra Sekhar Reddy Chilamakuri, Soleilmane Omarjee, Kee Ming Chia, Alex Swarbrick, Elgene Lim, Florian Markowetz, Matthew Eldridge, Rasmus Siersbaek (), Clive S. D’Santos and Jason S. Carroll ()
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Evangelia K. Papachristou: Cancer Research UK Cambridge Institute, University of Cambridge
Kamal Kishore: Cancer Research UK Cambridge Institute, University of Cambridge
Andrew N. Holding: Cancer Research UK Cambridge Institute, University of Cambridge
Kate Harvey: Garvan Institute of Medical Research, Darlinghurst
Theodoros I. Roumeliotis: Wellcome Trust Sanger Institute
Chandra Sekhar Reddy Chilamakuri: Cancer Research UK Cambridge Institute, University of Cambridge
Soleilmane Omarjee: Cancer Research UK Cambridge Institute, University of Cambridge
Kee Ming Chia: Garvan Institute of Medical Research, Darlinghurst
Alex Swarbrick: Garvan Institute of Medical Research, Darlinghurst
Elgene Lim: Garvan Institute of Medical Research, Darlinghurst
Florian Markowetz: Cancer Research UK Cambridge Institute, University of Cambridge
Matthew Eldridge: Cancer Research UK Cambridge Institute, University of Cambridge
Rasmus Siersbaek: Cancer Research UK Cambridge Institute, University of Cambridge
Clive S. D’Santos: Cancer Research UK Cambridge Institute, University of Cambridge
Jason S. Carroll: Cancer Research UK Cambridge Institute, University of Cambridge

Nature Communications, 2018, vol. 9, issue 1, 1-13

Abstract: 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 (ERα) interactome in breast cancer cells treated with 4-hydroxytamoxifen. Furthermore, we identify endogenous ERα-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.

Date: 2018
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DOI: 10.1038/s41467-018-04619-5

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