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Proteomic characterisation of Estrogen Receptor (ERα) interactome in breast cancer


Type

Thesis

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Authors

Papachristou, Evangelia 

Abstract

Breast cancer is the most common cancer in women in the western world. It has been shown that estrogen receptor alpha (ERα) contributes to tumour formation in 75% of breast cancer cases and various drugs, such as 4-hydroxytamoxifen (OHT), have been used to inhibit estrogen-induced signals. Studies have highlighted the importance of interactions between ERα and various factors in regulating chromatin binding and gene transcription, underlying estrogen signalling in breast cancer. During the last decade, quantitative mass spectrometry (MS)-based proteomics has become a powerful tool for the study of protein interactions. However, technical challenges have restricted most applications to qualitative observations and the dynamics of protein interactomes have until recently been largely unexplored. Here, we describe the development and application of a quantitative multiplexed method, termed qPLEX-RIME, which integrates RIME with isobaric labelling for the study of protein interactome dynamics in a quantitative fashion with increased sensitivity. Using the qPLEX-RIME method we successfully identified endogenous ERα-associated proteins in human Patient Derived Xenograft (PDX) and primary tumours and we delineated the mechanistic temporal changes of the ERα interactome in MCF7 cells upon OHT treatment. Our pipeline was also successfully applied for the study of other factors, such as CBP, NCOA3 and RNA Polymerase II. The integration of the different interactome datasets, lead to the discovery of a transcription factor, termed ZNF207, that belongs to the zinc finger protein family. In MCF7 cells, ZNF207 interacts with ERα, known ERα interactors and components of the transcription machinery. Knockdown of ZNF207, affected cellular proliferation of various cancer and non-cancer cell models, suggesting a functional role in the majority of cellular contexts. Interactome and chromatin binding assays revealed that ZNF207 is important for the assembly and chromatin binding of the Mediator complex and general transcription factors, whilst RNA-sequencing and proteomic analysis showed a decrease in expression of genes linked to cell cycle followed ZNF207 knockdown. The effect was likely mediated by changes in the chromatin binding of the subunit MED1 and the transcription factor TAF3 to promoters of cell cycle genes. Thus, ZNF207 plays an important role in our model system and was studied in depth in this thesis by integrating various functional assays. Our results demonstrate that qPLEX-RIME offers a powerful tool for the in-depth characterisation of protein interactome dynamics, which is also applicable to clinical samples. Our findings constitute the basis for a deeper mechanistic insight into the dynamics of ERα interaction network and its role in breast cancer along with the discovery of a transcription factor that may play a vital role in the initiation of transcription.

Description

Date

2020-12-01

Advisors

Carroll, Jason

Keywords

proteomics, Estrogen receptor, breast cancer, mass spectrometry, isobaric labelling

Qualification

Doctor of Philosophy (PhD)

Awarding Institution

University of Cambridge
Sponsorship
Cancer Research UK (C14303/A17197)