Students projects


Disentangling Androgen Receptor signaling in Estrogen Receptor-positive Breast Cancer

Steroid hormone receptors are ligand-activated transcription factors that play a pivotal role in breast development and carcinogenesis. While it is well established that estrogen receptor α (ERα) signaling is a major proliferative axis in hormone receptor-positive breast cancers and is targeted pharmacologically, endocrine resistance is a frequent clinical problem and new therapeutic strategies are therefore urgently needed. Interestingly, 90% of hormone receptor-positive breast cancers co-express androgen receptor (AR), but its contribution to breast carcinogenesis remains unclear. We aim to comprehensively dissect the androgen receptor signaling in breast cancer by performing genetic and pharmacological perturbation of AR pathway in patient-derived xenografts and cell lines. The student will perform in vitro and ex vivo experiments to investigate the molecular mechanisms underlying AR action, by taking advantage of both basic and advanced analytical techniques.


  1. Sflomos, G., Dormoy, V., Metsalu, T., Jeitziner, R., Battista, L., Scabia, V., Raffoul, W., Delaloye, J.-F., et al. (2016) ‘A Preclinical Model for ERα-Positive Breast Cancer Points to the Epithelial Microenvironment as Determinant of Luminal Phenotype and Hormone Response’, Cancer Cell. Cell Press, 29(3), pp. 407–422. doi: 10.1016/J.CCELL.2016.02.002.
  2. Fiche, M., Scabia, V., Aouad, P., Battista, L., Treboux, A., Stravodimou, A., … Brisken, C. (2019). Intraductal patient-derived xenografts of estrogen receptor α-positive breast cancer recapitulate the histopathological spectrum and metastatic potential of human lesions. The Journal of Pathology, 247(3), 287–292.

Interested students are welcome to contact :  [email protected]

Compilation of a consensus catalogue of hormone receptor binding regions for breast cancer

Nuclear hormone receptors play an important role in breast cancer development and progression. Key players include estrogen, progesterone and androgen receptors. These transcription factors are recruited to target genomic regions via direct binding to cognate DNA motifs or by indirect mechanism involving cooperativity with other transcription factors such as FOXA1 and GATA3. Due to this fact, hormone responsive regulatory regions often contain multiple binding motifs, and protein binding site profiles revealed by ChIP-seq show extensive colocalization of different factors in the same regions. To support ChIP-seq data analysis, we propose to compile a consensus catalogue of 2000 to 5000 recurrent hormone receptor binding regions in breast cancer tissues. Such a catalogue will serve as a unified framework to quantify ChIP-seq data in a similar way as a gene catalogue serves to quantify RNA-seq data. The purpose is to provide a computational framework that will enable unbiased comparison and smooth integration of breast cancer ChIP-seq data from diverse studies. The catalogue will be based on a representative collection of quality-controlled ChIP-seq data from normal breast tissue, surgically removed tumors, patient-derived xenografts and cancer cell lines. Work on this project will leverage software on data resources developed at EPFL, including the ChIP-Seq tools, the MGA data repository, the Breast Cancer Hub, and quality control indicators from a recent motif benchmarking study. 


  1. Ambrosini G, Dreos R, Kumar S, Bucher P. The ChIP-Seq tools and web server: a resource for analyzing ChIP-seq and other types of genomic data. BMC Genomics. 2016 Nov 18;17(1):938. doi: 10.1186/s12864-016-3288-8. PMID: 27863463; PMCID: PMC5116162.
  2. Dreos R, Ambrosini G, Groux R, Périer RC, Bucher P. MGA repository: a curated data resource for ChIP-seq and other genome annotated data. Nucleic Acids Res. 2018 Jan 4;46(D1):D175-D180. doi: 10.1093/nar/gkx995. PMID: 29069466; PMCID: PMC5753388.
  3. Ambrosini G, Vorontsov I, Penzar D, Groux R, Fornes O, Nikolaeva DD, Ballester B, Grau J, Grosse I, Makeev V, Kulakovskiy I, Bucher P. Insights gained from a comprehensive all-against-all transcription factor binding motif benchmarking study. Genome Biol. 2020 May 11;21(1):114. doi: 10.1186/s13059-020-01996-3. PMID: 32393327; PMCID: PMC7212583.
  4. Ross-Innes CS, Stark R, Teschendorff AE, Holmes KA, Ali HR, Dunning MJ, Brown GD, Gojis O, Ellis IO, Green AR, Ali S, Chin SF, Palmieri C, Caldas C, Carroll JS. Differential oestrogen receptor binding is associated with clinical outcome in breast cancer. Nature. 2012 Jan 4;481(7381):389-93. doi: 10.1038/nature10730. PMID: 22217937; PMCID: PMC3272464.
  5. Severson TM, Kim Y, Joosten SEP, Schuurman K, van der Groep P, Moelans CB, Ter Hoeve ND, Manson QF, Martens JW, van Deurzen CHM, Barbe E, Hedenfalk I, Bult P, Smit VTHBM, Linn SC, van Diest PJ, Wessels L, Zwart W. Characterizing steroid hormone receptor chromatin binding landscapes in male and female breast cancer. Nat Commun. 2018 Feb 2;9(1):482. doi: 10.1038/s41467-018-02856-2. PMID: 29396493; PMCID: PMC5797120.

Interested students are welcome to contact : [email protected]

Personalized endocrine prevention of hormone receptor-positive breast cancer progression

The majority of breast cancer (BC) cases are hormone receptor-positive (HR+). It is well established that estrogen receptor α (ERα) is a key driver of proliferation in HR+ BC. Nowadays, patients diagnosed with this type of BC are uniformly treated with drugs that inhibit only ERα. However, endocrine resistance and tumor recurrence remain frequent clinical problems, and new therapeutic strategies are needed. Besides ERα, such tumors also express the receptors for progesterone and testosterone, but their role in breast cancer development remains controversial and is currently not used for therapy. Using the mouse intraductal model (MIND), a physiologically relevant in vivo model to study BC, we have preliminary evidence that estrogen (ER), progesterone (PR), and androgen (AR) receptors signaling are deregulated in different ways during breast carcinogenesis in individual patients. That can provide targets for personalized prevention of BC progression, meaning that targeting PR or AR instead of ERα could benefit some patients. To study the signaling of different hormone receptors and to identify new possible targets, the student will use genetic (shRNA) and pharmacological approaches (HR modulators) in in vitro and ex vivo models of different BC cell lines and patient-derived samples. During this project, the student will master the basics of the cell culture approach, molecular biology methods, and immunohistochemistry techniques. 


  1. Sflomos, G., Dormoy, V., Metsalu, T., Jeitziner, R., Battista, L., Scabia, V., Raffoul, W., Delaloye, J.-F., et al. (2016) ‘A Preclinical Model for ERα-Positive Breast Cancer Points to the Epithelial Microenvironment as Determinant of Luminal Phenotype and Hormone Response’, Cancer Cell. Cell Press, 29(3), pp. 407–422. doi: 10.1016/j.ccell.2016.02.002. PMID: 26947176.
  2. Scabia, V., Ayyanan, A., De Martino, F. et al. Estrogen receptor positive breast cancers have patient specific hormone sensitivities and rely on progesterone receptor. Nat Commun 13, 3127 (2022).

Interested students are welcome to contact :

Regulation of metastatic dormancy in hormone receptor-positive breast cancer

Breast cancers (BC) are divided into 4 main subtypes based on their expression of the oestrogen receptor (ER), progesterone receptor (PR) and the Human epidermal growth factor receptor (HER2) (1). ER+ breast cancer patients’ probability of survival decreases 5 – 20 years post-diagnosis due to minimal residual disease and metastatic relapse. This deadly phenomenon is caused by dormant DCCs at metastatic sites that remain undetectable at the time of initial diagnosis until giving rise to overt metastatic disease (2,3). Understanding the kinetics and molecular programmes employed by these DCCs during disease progression is essential for early intervention and prevention of this metastatic latency. In line with metastatic latency in ER+ breast cancer, it has been shown that metastatic cells from low burden tissues (HR+) displayed high expression of epithelial-to-mesenchymal transition (EMT), stem cell and dormancy genes compared to that of high burden tissues (HR-) (4,5). This suggests that cancer cells may undergo EMT and disseminate at early stages of tumour formation and seed as quiescent/dormant cells at metastatic sites for years before initiating secondary disease (6,7). As HR+ breast cancers make up roughly 70% of all breast cancers, late metastatic disease and cancer cell dormancy remains a significant clinical problem that has largely been overlooked by breast cancer researchers. This project aims to identify global regulators of EMT and metastatic dormancy in HR+ breast cancers using the MIND-model.
The student will gain experience with in vitro cell culture, ex vivo models and molecular biology techniques to tackle these questions.


  1. Koboldt DC, Fulton RS, McLellan MD, Schmidt H, Kalicki-Veizer J, McMichael JF, et al. Comprehensive molecular portraits of human breast tumours. Nature. 2012;490(7418):61–70.
  2. Gawrzak S, Rinaldi L, Gregorio S, Arenas EJ, Salvador F, Urosevic J, et al. MSK1 regulates luminal cell differentiation and metastatic dormancy in ER + breast cancer. Nat Cell Biol [Internet]. 2018;20(2):211–21. Available from:
  3. Zhang XHF, Giuliano M, Trivedi M V., Schiff R, Kent Osborne C. Metastasis dormancy in estrogen receptor-positive breast cancer. Clin Cancer Res. 2013;19(23):6389–97.
  4. Lawson DA, Bhakta NR, Kessenbrock K, Prummel KD, Yu Y, Takai K, et al. Single-cell analysis reveals a stem-cell program in human metastatic breast cancer cells. Nature. 2015;526(7571):131–5.
  5. Aouad P, Zhang Y, Stibolt C, Mani SA, Sflomos G, Brisken C. Epithelial-mesenchymal plasticity determines estrogen receptor positive (ER+) breast cancer dormancy and reacquisition of an epithelial state drives awakening. bioRxiv [Internet]. 2021 Jan1;2021.07.22.453458. Available from:
  6. Hosseini H, Obradovic MMS, Hoffmann M, Harper KL, Sosa MS, Werner-Klein M, et al. Early dissemination seeds metastasis in breast cancer. Nature [Internet]. 2016;540(7634):552–8. Available from:
  7. Jiang J, Zheng M, Zhang M, Yang X, Li L, Wang S-S, et al. PRRX1 Regulates Cellular Phenotype Plasticity and Dormancy of Head and Neck Squamous Cell Carcinoma Through miR-642b-3p. Neoplasia. 2019 Feb;21(2):216–29.

Interested students are welcome to contact : [email protected]

Understanding hormone signaling through topological data analysis

Breast cancer (BC) is the most commonly diagnosed cancer in the world [1]. Over 70% of breast cancer cases are estrogen receptor (ER) positive. It is well established that the main proliferative driver of this BC subtype is the ER signaling. Therefore, ER+ BC patients are treated with endocrine therapies. However, one common occurrence is the development of resistance to such therapies. We aim to understand the hormone signaling pathways in ER+ BC patients by using data obtained through next generation sequencing technologies in hormone treated patient-derived xenografts and use this knowledge to better tailor treatment for ER+ BC patients. The student will learn current techniques to analyse RNA-seq data and will also further develop one topological tool [2] to analyse such data. The student will also learn R, how to write R packages and deploy them to bioconductor.
Minimum requirements are a strong understanding of linear algebra and knowledge of a programming language (it can be any, not necessarily R).


  2. Two-Tier Mapper, an unbiased topology-based clustering method for enhanced global gene expression analysis, _Bioinformatics_, Volume 35, Issue 18, 15 September 2019, Pages 3339–3347,

Interested students are welcome to contact : [email protected]

Suggested Projects

1. Rethinking of Hormonal Therapies in ILC Progression

Invasive lobular carcinoma (ILC) is the most common breast cancer ‘‘special type’’ and is mainly driven by the loss of E-cadherin expression. ILC responds poorly to chemotherapy and tamoxifen and is the histological subtype strongly associated with ovarian hormone usage, especially estrogens e.g., Ethinylestradiol (EE) and progestogens (e.g., medroxyprogesterone acetate). Since it has been impossible to establish xenografts from ILC cell lines and patient samples, the mechanisms underlying the characteristic biology have been challenging to address. We have recently shown that the microenvironment is critical for ER+ tumor engraftment, which is enabled by injection into the mouse milk ducts, including ILCs. We aim to address the latter biological feature of ILC by assessing the effect of different ovarian hormones in ILC breast cancer cell lines and patients’ cells in vivo and in ex vivo models of ILC. The student will master basic and advanced molecular biology methods and become familiar with in vivo and ex vivo analysis.



2. Dissecting the Molecular Mechanisms of Endocrine Therapy Resistance

In clinics, endocrine resistance is increasingly observed following treatment with anti-estrogen therapies and aromatase inhibitors (AI). Using the intraductal transplantation method for ER+ breast cancers, we will model the clinical scenario by treating mice engrafted intraductally with either ER-positive cells MCF7 and ILC MDA-MB-134 and SUM44 with anti-estrogen therapies (tamoxifen, fulvestrant, and estrogen deprivation) to model the responses of invasive breast cancer of no special type and invasive lobular carcinomas, respectively.

We will perform transcriptomics, proteomics, and genomics analyses of the residual tumors and compare them with naïve treated xenografted tumors. We will perform endocrine treatment studies in patient-derived xenografts generated from freshly isolated breast tumors to confirm our findings. The student will master basic and advanced molecular biology methods and become familiar with in vivo and ex vivo analysis.



  1. PMID: 34771558 –
  2. PMID: 17081916 –
  3. PMID: 32508307 –
  4. PMID: 29563191 –
  5. PMID: 26977876 –
  6. PMID: 26947176 –
  7. PMID: 26241069 –

Interested students are welcome to contact :  [email protected]


Optimizing an ex vivo assay for testing hormone and drug response in hormone-sensitive breast cancer

Breast cancer is a leading cause of cancer-related mortality for women worldwide (1). Endocrine therapy is of significant therapeutic value for hormone receptor-positive breast tumors that represent 70% of breast cancer cases (2). However, current standard endocrine therapies are largely based on pathological breast cancer features, and the outcomes are consequently affected by patient-to-patient heterogeneity. To provide tailored endocrine therapy, we propose a biomaterial-based 3D system to test hormone and drug sensitivity of patient-derived xenografts and patient tumor biopsies. The student will learn to manipulate and encapsulate tumors in biomaterials, and assess gene and protein expression using molecular biology and immunohistochemistry techniques, respectively.


  1. Friedenreich CM. Physical activity and breast cancer: Review of the epidemiologic evidence and biologic mechanisms. Vol. 188, Recent Results in Cancer Research. Springer, Berlin, Heidelberg; 2011. p. 125–39.
  2. Harbeck N, Gnant M. Breast cancer. Vol. 389, The Lancet. 2017

Interested students are welcome to contact : [email protected]