ERα transcriptional activity drives tumour development and metastasis in more than 70% of breast cancer cases. Tamoxifen is the most widely and successfully used endocrine treatment for pre-menopausal women with ERα positive breast cancer. However, subgroups of patients are resistant to this drug. Investigation into the mechanisms of the endocrine refractory phenotype would therefore open possibilities for novel targeted therapies. One key aspect of ERα gene regulation is its accessibility to compacted chromatin. FOXA1 is a pioneer transcription factor that has the ability to bind to ‘closed’ chromatin and open it up for ERα subsequent binding, thereby creating the regulatory elements that are used by ERα. In this thesis, the dependence of the ERα hormone receptor on FOXA1 is reinforced and the latter is confirmed as a bone fide pioneer transcription factor and a promising drug target in hormone-dependent cancers. Moreover, novel molecular mechanisms of Tamoxifen resistance were investigated using quantitative multiplexed rapid immunoprecipitation mass spectrometry of endogenous proteins (qPLEX-RIME) in multiple in vitro and in vivo breast cancer models. The results showed that the two key proteins ERα and FOXA1 are enriched in the resistant phenotype, together with their newly-identified interactor ETV6. The role of ETV6 in endocrine resistance was confirmed using an independent siRNA screen. In addition, the direct contribution of ETV6 to breast cancer progression was proved by the promoting effects of ETV6 overexpression on colony formation ability of endocrine sensitive cell lines. Furthermore, chromatin immunoprecipitation followed by sequencing (ChIP-seq) analysis revealed that Tamoxifen resistance is associated with a global redistribution of FOXA1, ERα, ETV6- DNA interactions and altered genomic landscape. This differential binding of the three transcription factors also results in compromised transcriptional programmes in endocrine resistance, as assessed by RNA-seq. In addition, inhibition of MAPK pathway reduced breast cancer progression and modulated ETV6-chromatin interactions. Importantly, the clinical significance of ETV6 copy number amplifications was assessed in the METABRIC cohort (Curtis et al., 2012). They correlate with significantly reduced disease-free survival in Luminal B breast cancer subtype, which is the more aggressive ERα positive subtype and is more likely to metastasise. Moreover, by conducting a screen of 1000 FDA-approved drugs, potential candidates for the treatment of hormone-refractory breast cancer were identified. Further in vitro and in vivo validation would consolidate these findings. Taken together, the data presented in this dissertation reinforces FOXA1 independence of hormonal signalling, it identifies ETV6 as a novel ERα and FOXA1 co-factor that drives a more proliferative phenotype and proposes alternative therapies for the endocrine refractory phenotype.