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

Author

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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
    St Vincent’s Clinical School, UNSW)

  • Elgene Lim

    (Garvan Institute of Medical Research, Darlinghurst
    St Vincent’s Clinical School, UNSW)

  • 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)

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.

Suggested Citation

  • 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, 2018. "A quantitative mass spectrometry-based approach to monitor the dynamics of endogenous chromatin-associated protein complexes," Nature Communications, Nature, vol. 9(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-04619-5
    DOI: 10.1038/s41467-018-04619-5
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    Cited by:

    1. Maurizio Mangolini & Alba Maiques-Diaz & Stella Charalampopoulou & Elena Gerhard-Hartmann & Johannes Bloehdorn & Andrew Moore & Giorgia Giachetti & Junyan Lu & Valar Nila Roamio Franklin & Chandra Sek, 2022. "Viral transduction of primary human lymphoma B cells reveals mechanisms of NOTCH-mediated immune escape," Nature Communications, Nature, vol. 13(1), pages 1-21, December.
    2. Dominik Beck & Honghui Cao & Feng Tian & Yizhou Huang & Miao Jiang & Han Zhao & Xiaolu Tai & Wenqian Xu & Hansen J. Kosasih & David J. Kealy & Weiye Zhao & Samuel J. Taylor & Timothy A. Couttas & Gaox, 2024. "PU.1 eviction at lymphocyte-specific chromatin domains mediates glucocorticoid response in acute lymphoblastic leukemia," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
    3. Jacob Gordon & Fleur L. Chapus & Elizabeth G. Viverette & Jason G. Williams & Leesa J. Deterding & Juno M. Krahn & Mario J. Borgnia & Joseph Rodriguez & Alan J. Warren & Robin E. Stanley, 2022. "Cryo-EM reveals the architecture of the PELP1-WDR18 molecular scaffold," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    4. Jieqiong Zhang & Zhenhua Hu & Hwa Hwa Chung & Yun Tian & Kah Weng Lau & Zheng Ser & Yan Ting Lim & Radoslaw M. Sobota & Hwei Fen Leong & Benjamin Jieming Chen & Clarisse Jingyi Yeo & Shawn Ying Xuan T, 2023. "Dependency of NELF-E-SLUG-KAT2B epigenetic axis in breast cancer carcinogenesis," Nature Communications, Nature, vol. 14(1), pages 1-21, December.

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