<p>The estrogen receptor(ER) is a master transcriptional regulator of the breast where it plays key roles in the development and maintenance of normal breast epithelium but is also critical to the growth of luminal breast cancers. ER is also a well-defined molecular therapeutic target and anti-estrogens, such as tamoxifen, are used clinically to inhibit the mitogenic activity of ER and delay disease progression. However, despite the initial benefits to tamoxifen therapy, nearly one third of luminal breast cancer tumors eventually become resistant, limiting the therapeutic utility the drug. Mechanisms of resistance can be attributed to circumvention of ER and reliance on alternative growth pathways, or through upregulation of pathways that converge with ER to allow reactivation. Understanding the molecular determinants of resistance is a critical endeavor that demands attention in order to shape new drug developments and extend the therapeutic efficacy of anti-estrogens.</p><p> A major challenge in elucidating mechanisms of resistance is in understanding the complexities of the ER signaling program in respect to receptor occupancy and the coordinated relationship with chromatin architecture and collaborating transcription factors. This work therefore integrates the relationship between accessible chromatin, as measured by DNase-Seq, with ER occupancy and ER-mediated transcription in an in vivo derived tamoxifen resistant cell line (TamR) and a comparator group of two closely related tamoxifen sensitive cell lines. Cumulatively, these data demonstrate an enhanced role for FOXA1 in tamoxifen resistance. Specifically, FOXA1 occupancy is greatly enriched at differential DNase hypersensitive loci in TamR cells, and FOXA1 target genes are dramatically upregulated. Furthermore, expression of these target genes can be restored to MCF7 levels with siRNA directed against FOXA1. The TamR cells also have increased ER occupancy at FOXA1 overlapping sites, where ER is engaged to chromatin in a ligand-independent manner and results in enhanced activation of nearby target genes that can be repressed with the pure anti-estrogen, ICI. The increased role of FOXA1 is not due to an increase in total protein levels however and instead is manifested through increased activity. </p><p>Other clinical associations of resistance have been elucidated for which there is little to no mechanistic evidence currently available. HOXB13 has been shown to associate with tamoxifen therapy failure from differential microarray expression profiling of patients who relapsed compared to those that remained disease-free at the five year follow-up. The outcome of our studies reveals HOXB13 to downregulate GATA3 levels, which in turn leads to loss of ER function and parallel activation of inflammatory pathways. </p><p>The present study also makes use of publicly available clinical datasets to generate an integrative database of 4885 patients from 25 independent studies. Furthermore, analytical methods and functions were also developed to allow efficient use and application of the data. Access to the breast cancer meta-set and functions are made available to end users via a web interface, GeneAnalytics. Together, the breast cancer meta-set and associated access through the GeneAnalytics web sites provides novel opportunities for researchers to integrate functional studies with tumor derived expression data to further our understanding of cancer related processes.</p><p>Collectively, our findings demonstrate that the ER signaling program is modified as tumors progress to resistance by an increased role of FOXA1 to facilitate ER binding and reprogramming, and by HOXB13 to suppress the actions of ER and promote inflammatory pathways. These mechanisms highlight distinct methods of resistance and provide rational for new therapeutic approaches to extend the utility of current anti-estrogens.</p> / Dissertation

Les cancers du sein sont divisés en sous types définis par leur histologie, leur prolifération et l’expression du récepteur aux œstrogènes ER. Notre étude porte sur le gène FOXA1 dans le sous-type luminal caractérisé par des cellules bien différenciées, peu prolifératives et exprimant fortement les protéines FOXA1 et ER. Des études suggèrent que FOXA1 est impliqué dans le développement de la glande mammaire, dans la différenciation et la prolifération des cellules mammaires. Dans ce cadre, mon projet de thèse s’articulait autour de trois points ; développer un Knock-In au niveau du gène FOXA1, identifier le rôle de FOXA1 dans la différenciation mammaire et enfin rechercher le rôle des facteurs ER et FOXA1 dans la résistance à l’hormonothérapie. De nombreux tests d’intégration ciblée ont été réalisés à l’aide de différentes matrices de recombinaison et de nucléases spécifiques, les ZFNs. Aucune intégration ciblée n’a finalement été observée. Nous avons montré qu’en fonction du contexte cellulaire, FOXA1 jouait différents rôles dans la différenciation cellulaire et l’expression de la molécule d’adhérence E-Cadhérine. Ces résultats suggèrent que FOXA1 influence l’agressivité tumorale suivant le contexte cellulaire. Nous avons également identifié une amplification d’ER et de FOXA1 dans les cellules tumorales résistantes à l’hormonothérapie par une étude génomique. Les tests in vitro ont montré que la surexpression de FOXA1 augmenterait bien la résistance au fulvestrant mais la surexpression d’ER aurait l’effet inverse, suggérant l’implication d’autres facteurs. De futures recherches nous permettront d’identifier ces facteurs et de préciser les rôles de FOXA1 et d’ER dans la différenciation luminale, l’agressivité tumorale et dans la réponse cellulaire à l’hormonothérapie / Breast cancers are divided into subtypes defined by their histology, proliferation and expression of estrogen receptor ER. Our study focuses on the FOXA1 gene in the luminal subtype characterized by well-differentiated cells, low proliferative and strongly expressing FOXA1 protein and ER. Studies suggest that FOXA1 is involved in the mammary gland development and in the differentiation and proliferation of mammary cells. In this context, my thesis project was structured around three points, develop a knock-in at the FOXA1 gene, identify the role of FOXA1 in mammary differentiation and finally explore the role of ER and FOXA1 in resistance to hormone therapy. Many targeted integration tests were performed using different matrix of recombination and specific nucleases, the ZFNs. No direct integration was finally observed. We showed that depending on the cell context, FOXA1 played different roles in cell differentiation and expression of E-cadherin, an adhesion molecule. These results suggest that FOXA1 influence tumor aggressiveness depending on the cell context. We also identified amplification of ER and FOXA1 in tumor cell resistant to hormone therapy by a genomic study. Surprisingly, in vitro tests showed that overexpression of FOXA1 increased resistance to fulvestrant whereas overexpression of ER would have the opposite effect, suggesting the involvement of other factors. Future research will allow us to identify these factors and to clarify the roles of ER and FOXA1 in luminal differentiation, tumor aggressiveness and response to hormone therapy.

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Le traitement systémique adjuvant du cancer du sein infiltrant repose sur la chimiothérapie et l’hormonothérapie. Certains facteurs sont connus pour être pronostiques (âge, taille tumorale, statut ganglionnaire, grade tumoral, emboles vasculaires, statut des récepteurs hormonaux (RH) et de HER2) ou prédictifs de réponse aux traitements (RH et HER2) et influent sur nos décisions thérapeutiques. Cependant, certaines patientes récidivent malgré un traitement complet alors que d’autres vont recevoir un traitement qui aurait pu être évité de par leur bon pronostic « intrinsèque ». Nous avons cherché à identifier dans ce travail d’autres facteurs pronostiques et / ou prédictifs dans le cancer du sein infiltrant en situation néoadjuvante / adjuvante. Premièrement, nous montrons que le type histologique lobulaire, réputé pour être une histologie de cancer du sein de bon pronostic et peu chimiosensible, ne doit pas être un facteur décisionnel quant aux traitements systémiques. En situation adjuvante et concernant la chimiothérapie, la validité et l’utilité cliniques des tests génomiques nécessitent d’être évaluées spécifiquement dans ce sous-groupe. Ensuite, nous avons étudié la validité analytique, la validité clinique et l’utilité clinique de 2 classifications moléculaires des cancers du sein selon PAM50 et l’analyse immunohistochimique de biomarqueurs : récepteur œstrogène, HER2 et Ki67 avec un cut-off à 14%. Selon nos conclusions, il n’y a actuellement pas de données suffisamment robustes pour que ces 2 classifications modifient les décisions de traitement systémique. Nous avons mis en évidence un sous-groupe de tumeurs triples négatives exprimant le récepteur androgène et FOXA1 et se comportant comme des tumeurs luminales. Enfin, nous avons montré sur une large série néoadjuvante que la réponse histologique complète est un critère substitutif de survie pour les tumeurs RH négatifs / The adjuvant systemic treatment of invasive breast cancer is based on chemotherapy and endocrine therapy. Several prognostic factors (age, tumoral size, nodal status, tumoral grade, vascular embols, hormonal receptors (HR), HER2) and predictive factors of response to treatment (HR and HER2) are described and have an impact on our therapeutic decisions. However, recurrences are frequent after a complete treatment and patients could avoid such treatment because of the good “intrinsic” prognosis. In this work, we aimed to identify other prognostic and / or predictive factors for the invasive breast cancer in the neoadjuvant / adjuvant settings. Firstly, we showed that the lobular histology, considered as histology of good prognosis and low chemo sensitive, should not be a decisive factor regarding systemic therapy. In the adjuvant setting, regarding chemotherapy, clinical validity and utility of the genomic tests need to be specifically evaluated in this subgroup. Then, we studied analytical validity, clinical validity and clinical utility of 2 molecular classification of breast cancer: PAM50 and a panel of 3 biomarkers in immunohistochemistry (estrogen receptor, HER2 and Ki-67 with a cut-off of 14%). We concluded that the data were not strong enough and that the therapeutic decisions should not be influenced by these classifications. We identified a subgroup of triple negative breast cancer that express androgen receptor and FOXA1 and which behave like luminal tumors. At last, we showed in a large neoadjuvant population, that the pathological complete response is a surrogate marker of survival in RH negative tumors

Transdifferentiation induces chromatin reconstructions and epigenetic changes that affect gene expression spectum and cause cell remodeling in general. Direct conversion of mature somatic cell line into another mature cell type occures during the transdifferentiation thereby differences betweeen individual germ layers are eliminated. The aim of the master thesis is transdifferentation of mesenchymal cells - mouse embryonic fibroblast into endodermal cells - hepatocytes in vitro, using combination of transcripion factors Hnf4α and Foxa1. Detection of fibroblasts transformation has been initiated immediately after retroviral transduction and final generation of induced hepatocyte culture was confirmed by morphological and function analysis. The population of mouse induced hepatocytes served as a possible model for human liver disease in case of a pacient whose liver proteins could not be detected immunohistochemically. Genome editing of induced hepatocytes was realized by CRISPR/Cas9 technology which is based on cooperation of guideRNA and Cas9 nuclease followed in addition to generation of DNA-specific double strand breaks. These specific breaks in the Tight junction protein 2 gene were repaired via homologous recombination that induced a missense mutation with amino acid changes in the target...

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