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Additional file 2: Fig. S1 MDM2 inhibition activates p53 and reduces tumour proliferation in vitro and in vivo. A. Full gel and blot scans for the Western blots shown in Fig. 1b. Total protein was visualised using BioRad stain-free imaging technology according to the manufacturer’s instructions. B. Analysis of cell cycle phase using flow cytometry to quantify propidium iodide staining of genomic DNA shows significant alterations to cell cycle phase distribution in p53wt models consistent with arrest in both G1 and G2 after incubation for 48 hours with 1μM NVP-CGM097. Red = G1 (bottom), blue = S (middle), green = G2/M (top). Statistical significance from χ2 test using the vehicle treated profile as the expected value is indicated. C. NVP-CGM097 (50mg/kg daily, red) significantly inhibited tumour volumes compared to vehicle (2% DMSO daily, green) at endpoint. Final tumour volumes were compared using two-tailed T test to determine significance. D. Representative images of Ki-67 quantification of endpoint tumours in Qupath software showing the classification of different tissue compartments: tumour (red and blue), stroma (green), and necrosis (black); and detection of Ki-67 negative and positive tumour cells. A single classifier was applied to all tumour sections. Fig. S2. NVP-CGM097 treatment causes gene expression changes in cell cycle and p53 pathways in vitro. A. Multidimensional scaling (MDS) plot showing the level of sample similarity between MCF-7 cell lines treated with vehicle, NVP-CGM097, fulvestrant and combination therapy (NVP-CGM097 plus fulvestrant). B. Venn diagram showing the overlap between differentially expressed genes (adjusted p-value < 0.05- and 2-fold change) induced by treatment in MCF-7 cell lines. C. KEGG pathway analysis using RNA-Seq transcriptomic data shows a significant negative enrichment of Cell Cycle regulation in MCF-7 cell lines following 48 hours of treatment with 1μM NVP-CGM097 and positive enrichment of p53 Signalling Pathway. D. KEGG enrichment analysis showing p53 Signalling Pathway activation in MCF-7 cell lines following treatment with NVP-CGM097. Fig. S3 Enrichment analysis of significant differentially expressed genes against curated gene sets. Fig. S4 MDM2 inhibition induces changes in gene and protein expression associated with the cell cycle in endocrine resistant models in vitro and in vivo. A. Incucyte analysis of cell numbers of parental MCF-7 cells (blue) and MCF-7 FasR cells (red) over time after treatment with 100 nM fulvestrant. Vehicle treated parental MCF-7 cell growth (grey) is shown for comparison. B. Full gel images for the Western blots shown in Fig. 4c. C. Quantification of ER staining in the nucleus and cytoplasm of three independent replicates per arm from PDX model Gar15-13 following 10 days of treatment with vehicle (2% DMSO daily, green), NVP-CGM097 (50mg/kg daily, red), fulvestrant (5 mg weekly, blue) or the combination of fulvestrant and NVP-CGM097 (purple). Tumours treated with fulvestrant alone or in combination had significantly reduced ER staining in both cellular compartments compared to tumours not treated with fulvestrant. Tumour cell identification and ER quantification were performed in QuPath software. D. Heat map of significant downregulated genes from the E2F Targets and G2/M Checkpoint gene sets in the Gar1513 PDX model. E. Normalised log2 expression levels of significant p53 target genes in in the Gar1513 PDX model induced by NVP-CGM097 (red), fulvestrant (blue) and the combination of NVP-CGM097 and fulvestrant (purple), averaged by condition, associated with cell cycle, apoptosis and senescence. Fig. S5. MDM2 inhibition in combination with CDK4/6 inhibition synergistically downregulates cell cycle markers in vitro. A. MDS plot of MCF-7 cell lines treated for 48 h with Vehicle (0.01% DMSO), 1 μM NVP-CGM097, 500 nM palbociclib, or the combination of NVP-CGM097 and palbociclib. B. Venn diagram showing the overlap between differentially expressed genes (adjusted p-value

Estrogen receptor positive (ER+) breast cancer constitutes 70% of all breast cancers and anti-ER therapies such as aromatase inhibitors and tamoxifen represent the main therapeutic strategies in the treatment of this disease. Unfortunately, up to 30% of all primary ER+ tumours will ultimately develop endocrine-resistance and progress on ER-targeted therapies resulting in disease-related morbidity. As a result, there is an urgent medical need for novel therapeutic strategies capable of managing endocrine-resistant breast cancer. Androgen receptor (AR) is expressed in up to 90% of ER+ breast cancers. AR functions as a tumour suppressor in primary ER+ breast cancer and high AR positivity is strongly associated with a favourable patient outcome in the ER+ setting. However, the role of AR in endocrine-resistant breast tumours is highly controversial with data supporting both oncogenic and tumour suppressive functions reported in the literature. Here I have used different modulatory approaches on in vitro and in vivo preclinical models to dissect the functions of AR and determine the best approach to target AR in endocrine-resistant breast cancer. I use an siRNA-mediated approach to knock down AR in cell line models and discover that the basal expression of AR contributes to endocrine-resistance and that loss of AR restores classical ER signalling and reverses endocrine-resistance. However, inhibiting the transcriptional activity of AR with enzalutamide does not recapitulate this effect, suggesting that it is the non-canonical activity of AR which contributes to endocrine-resistance. In contrast, I show that activation of AR by either 5-α dihydrotestosterone (DHT) or selective AR modulator enobosarm in vitro and in patient derived (PDX) models of endocrine-resistance results in significant growth suppression. Mechanistically, this growth-inhibitory effect of AR activation is associated with downregulation of ER signalling. Moreover, I identify AR-regulated genes from the global gene expression of an ER+AR+ endocrine-resistant PDX model treated with DHT and establish a highly prognostic AR gene signature based on primary ER+ patients in the METABRIC dataset. This suggests that activity of AR is tumour-suppressive independent of endocrine-sensitivity. In summary, I demonstrate that activation, not antagonism, is the optimal AR-targeted therapeutic strategy in the management of endocrine-resistant breast cancer.

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.