Les récepteurs nucléaires aux œstrogènes, ERα66 et ERβ1, sont les principaux médiateurs des effets des œstrogènes. Ces hormones régulent le développement physiologique de la glande mammaire mais participent aussi à la progression du cancer sein. L’expression d’ERα66 est d’ailleurs utilisée dans la classification moléculaire des tumeurs mammaires afin d’orienter la stratégie thérapeutique. Depuis son clonage, le variant des récepteurs alpha aux œstrogènes, ERα36, a été principalement décrit dans la littérature pour son rôle dans la progression des tumeurs mammaires et dans l’acquisition de résistances aux anti-œstrogènes comme le Tamoxifène. Si une forte expression d’ERα36 dans les cellules cancéreuses mammaires apparaît nettement comme un facteur de mauvais pronostic, peu de données sont disponibles concernant son rôle dans le développement de la glande mammaire saine. C’est pourquoi le premier objectif de ce travail était de déterminer le rôle d’ERα36 dans le développement physiologique de cette glande. Grâce à une approche pluridisciplinaire, incluant des études in vivo sur un modèle de souris transgéniques MMTV-ERα36 et des études in vitro et in silico sur des cellules épithéliales mammaires immortalisées, nous avons montré que l’expression d’ERα36 perturbe le phénotype des cellules épithéliales mammaires et conduit à l’apparition d’altérations structurales des canaux mammaires à l’âge adulte. De plus, nous avons mis en évidence que les alkylphénols, qui sont des perturbateurs endocriniens œstrogèno-mimétiques, stimulent l’expression endogène de ce variant dans les cellules MCF-10A et augmentent leurs capacités migratoires sans pour autant amplifier les effets d’ERα36 sur l’histologie des canaux mammaires. En parallèle, afin de mieux comprendre l’implication d’ERα36 au moment de l’initiation et de la progression tumorale, nous avons étudié les modalités de régulation de l’expression de ce variant dans les cellules cancéreuses mammaires. Les résultats obtenus indiquent que l’expression d’ERα36 est positivement corrélée au statut de méthylation de sa région promotrice et que l’ARNm codant ce variant est la cible d’hsa-miR136-5p. Enfin, le dernier objectif de ce travail était de développer une approche visant à identifier in silico de nouveaux partenaires d’ERα36. L’ensemble de ce travail s’inscrit dans une démarche de raffinement de la classification moléculaire actuelle des tumeurs mammaires en y ajoutant une composante associée à l’expression d’ERα36. / The estrogen nuclear receptors, represented by the canonical forms ERα66 and ERβ1, are the main mediators of the estrogenic effects in mammals. These hormones, which regulate the physiological development of the mammary gland, participate in the initiation and progression of breast cancer. In fact, ERα66 expression is a key molecular classifier of breast tumors used in order to guide the therapeutic strategies toward hormonotherapy. However, in 30% of cases, therapeutic failures are observed, which highlights the importance of identifying new biomarkers. The estrogen receptor variant, ERα36, has been cloned in 2005 and mainly described in the literature to be involved in the progression of mammary tumors and in the acquired resistance to anti-estrogen drugs, such as Tamoxifen. Even if a high expression of ERα36 in breast cancer cells appears to be associated with a poor prognosis, few data are available concerning its role in the normal development of the mammary gland. Therefore, the aim of this work was to determine the role of ERα36 in the physiological development of the mammary gland. Thanks to a multidisciplinary approach, that combines in vivo studies on MMTV-ERα36 transgenic mice, and in vitro and in silico studies on immortalized normal epithelial mammary cells (MCF-10A), we showed that ERα36 expression is sufficient to disturb the mammary epithelial cells phenotype, leading to the emergence of structural alterations of mammary ducts at adulthood. Moreover, we showed that exposure to the estrogen mimicking compounds alkylphenols stimulates the endogenous expression of this variant in MCF-10A cells, and increases their migratory ability. Then, in order to get a better understanding of ERα36 contribution to tumor initiation and/or progression, we studied classical and epigenetic regulation of this variant expression in breast cancer cells. Our results show that ERα36 expression is positively correlated with the methylation status of its promoter region, and that the ERα36 mRNA is the target of the microRNA, has-miR-136-5p. Finally, the last aim of this work was to develop a bioinformatic approach in order to study the ERα36 partners. To summarize, all of this work falls within a need of the current breast tumor molecular classification refinement by adding a component related with ERα36 expression.

Avec 59 000 nouveaux cas en 2017, le cancer du sein est le cancer le plus fréquemment diagnostiqué chez les femmes françaises, et pose un réel problème de santé publique en France, mais aussi au niveau mondial. Il est bien établi que la complexité de la carcinogenèse implique des modifications épigénétiques profondes qui contribuent au processus du développement tumoral. La dérégulation des marques d'histones acétylées H3 et H4 font partie de ces modifications. L'acétylation et la désacétylation des protéines sont des modifications posttraductionnelles majeures qui régulent l'expression des gènes liés au cancer et à l'activité d'une myriade d'oncoprotéines. Ainsi, une activité désacétylase aberrante peut alors favoriser ou supprimer la tumorigenèse dans différents types de cancers humains, y compris le cancer du sein. La désacétylase SIRT1 et l’acétyltransférase TIP60 sont 2 enzymes épigénétiques antagonistes qui sont impliquées dans l'apoptose, la régulation des gènes, la stabilité génomique, la réparation de l'ADN, et le développement du cancer. Dans le cadre de cette thèse, nous avons étudié la dérégulation des profils d’acétylation des histones H3 et H4 dans les différents sous-types moléculaires du cancer du sein, et investigué l’implication de SIRT1 et de TIP60 dans la progression tumorale de cancer du sein. Tout d’abord, nous avons signalé les rôles de SIRT1 et de TIP60 comme des biomarqueurs pronostiques potentiels en révélant leurs expressions différentielles en fonction de l’agressivité du cancer. Ensuite, nous avons montré leur régulation épigénétique différentielle des cibles histones en fonction du sous-type moléculaire, ainsi que leur modulation de la marque activatrice H3K4ac. En outre, l’inhibition de ces 2 enzymes par des Épidrogues s’est avérée comme une stratégie efficace dans le traitement du cancer. Ces travaux mettent en relief alors, SIRT1 et TIP60 comme des cibles thérapeutiques potentielles du cancer sporadique du sein. / With 59,000 new cases in 2017, breast cancer is the most frequently diagnosed cancer among French women, and poses a real public health problem in France, but also worldwide. It is well established that the complexity of carcinogenesis involves profound epigenetic deregulations that contribute to the tumorigenesis process. Deregulated H3 and H4 acetylated histone marks are amongst those alterations. Acetylation and deacetylation are major post-translational protein modifications that regulate gene expression and the activity of a myriad of oncoproteins. Aberrant deacetylase activity can promote or suppress tumorigenesis in different types of human cancers, including breast cancer. The deacetylase SIRT1 and the acetyltransferase TIP60 are 2 antagonistic epigenetic enzymes that are well implicated in apoptosis, gene regulation, genomic stability, DNA repair, and cancer development. In this manuscript, we identified the dysregulation of the histones H3 and H4 acetylation profiles in different molecular subtypes of sporadic breast cancer, and investigated the involvement of SIRT1 and TIP60 in breast tumorigenesis. First, we highlighted the roles of SIRT1 and TIP60 as potential prognostic biomarkers by revealing their differential expression patterns depending on breast cancer aggressiveness. Then, we demonstrated their differential epigenetic regulation of histone targets according to molecular subtype, and revealed their modulation of the H3K4ac epigenetic marker. Moreover, Epi-drugs mediated inhibition of these 2 enzymes has proven to be an effective strategy in the treatment of cancer. Thus, this work highlights the potential use of SIRT1 and TIP60 as epigenetic therapeutic targets for sporadic breast cancer.

H2O2 generated by alveolar macrophages has been linked to the development pulmonary fibrosis, but little is known about its source, mechanism of production and exact role upon alveolar macrophage activation. In this study, we found that alveolar macrophages from asbestosis patients spontaneously produce high levels of H2O2 and have high expression of Cu,Zn-SOD. Cu,Zn-SOD localized to the mitochondrial intermembrane space (IMS) in asbestosis patients and asbestos induced translocation of Cu,Zn-SOD to the IMS. This process was unique to macrophages and dependent on functional mitochondrial respiration. The presence of at least one of the conserved cysteines was required for disulfide bond formation and mitochondrial translocation. These conserved cysteine residues were also necessary for enzyme activation and H2O2 generation. Cu,Zn-SOD-mediated H2O2 generation was inhibited by knockdown of the iron-sulfur protein, Rieske, in complex III. The role of Cu,Zn-SOD was biologically relevant as Cu,Zn-SOD-/- mice generated significantly less H2O2, had less oxidative stress, and were protected from developing pulmonary fibrosis. This protective mechanism is closely related to the alveolar macrophage activation and polarization in Cu,Zn-SOD-/- mice, as they had a dominant pro-inflammatory phenotype. Macrophages not only initiate and accentuate inflammation after tissue injury, but they are also involved in resolution and repair. The pro-inflammatory M1 macrophages have microbicidal and tumoricidal activity, whereas the M2 macrophages are involved in tumor progression and tissue remodeling, and can be pro-fibrotic in certain settings. We demonstrate that overexpression of Cu,Zn-SOD promoted macrophages polarization into an M2 phenotype. Furthermore, overexpression of Cu,Zn-SOD in mice resulted in a pro-fibrotic environment and accelerated the development of pulmonary fibrosis. The mechanism which Cu,Zn-SOD-mediated H2O2 utilizes to modulate macrophage M2 polarization is through redox regulation of a critical cysteine in STAT6. The polarization process, at least partially, was regulated by epigenetic modulation. We show that STAT6 was indispensable for Cu,Zn-SOD-mediated M2 polarization. STAT6 upregulated Jmjd3, a histone H3 lysine 27 demethylase, and initiated M2 gene transcriptional activation. Targeting STAT6 with leflunomide, which can reduce cellular ROS production and inhibit STAT6 phosphorylation, abolished M2 polarization and ameliorated the fibrotic development. Taken together, these observations provide a novel mechanism for the pathogenesis of pulmonary fibrosis whereby the antioxidant enzyme Cu,Zn-SOD plays a paradoxical role. The study highlights the importance of mitochondrial Cu,Zn-SOD and redox signals in macrophage polarization and fibrosis development. These observations demonstrate that the Cu,Zn-SOD-STAT6-Jmjd3 pathway is a novel regulatory mechanism for M2 polarization and that leflunomide is a potential therapeutic agent in the treatment of pulmonary fibrosis.

Les notions selon lesquelles l’exposition environnementale peut être mémorisée et puisse dans des conditions défavorables favoriser l’apparition d’épimutations soulèvent la question d’une possible transmission transgénérationnelle chez l’Homme lorsque les gamètes sont atteints.Afin de répondre à la question du risque de transmission de dérégulation épigénétique (épimutation) chez l’Homme, nous l’avons abordé selon deux axes. Le premier nous a permis d’évaluer le risque de transmission intergénérationnelle chez un patient présentant un syndrome de Silver-Russell (SRS) et nous avons pu démontrer pour la première fois l’efficience de la reprogrammation épigénétique chez l’Homme pour des régions soumises à empreinte : disparition du défaut de méthylation du locus H19/IGF2 causal dans les gamètes du patient ainsi qu’une absence de transmission à sa descendance. Le second nous a conduit à dépister la présence d’épimutations spermatiques à partir de deux modèles : 1/ de pères d’enfants atteints de pathologies liées à l’empreinte parentale et 2/ de patients atteints de cancer testiculaire. Dans les 2 cas, l’analyse par pyroséquençage de leurs spermatozoïdes n’a pas mis en évidence de défaut d’empreinte. Néanmoins, nous avons retrouvé une association entre oligozoospermie et défaut d’empreinte spermatique.Le principal défi des études à venir est d’identifier les mécanismes intervenant dans l’apparition de ces épimutations. Les principales pistes convergent vers les petits ARNs non codants ou certaines régions de l’ADN dont les marques épigénétiques pourraient (au moins partiellement) échapper aux contrôles mis en place lors des phases successives de reprogrammation épigénétique. / The notion that environmental exposure can be memorized and promote epimutation (defined as defects on DNA methylation) raises the question of possible epigenetic transgenerational transmission in humans. To address whether an epimutation could be transmitted in humans, we pursued two axes. First, the evaluation of intergenerational transmission in the family of a Silver-Russell patient has shown, for the first time, the efficiency of epigenetic reprogramming in humans, specifically on imprinted regions. Indeed, no imprinted defect on causal H19/IGF2 locus was detected in the patient’s spermatozoa or in the DNA of his daughter. The second axis was to assess the presence of sperm epimutations 1/ from fathers of children diagnosed with imprinted syndromes and 2/ from men presenting testicular seminoma. Pyrosequencing analyses on imprinted genes did not reveal any alteration of sperm DNA methylation, though we confirmed an association between oligozoospermia and sperm imprinting defects.The next step will be to identify the mechanisms involved in the origin of the sperm epimutation. The main hypotheses converge to small non-coding RNAs or certain DNA regions which escape to controls setting up (at least partially) at the time of epigenetic reprogramming.

Lentivirus efficiently transduce stem cells, however are notably silenced in embryonic stem cells (ESC). Provirus can be silent, expressing, or variegated when clonal single copy ESCs spawn daughters that revert expression despite containing identical integration sites (IS) indicating epigenetic regulation. In the silent state, variegated provirus are bound by H1 and MeCP2, where H1 compensates for MeCP2 binding in DNA methylation null ESCs, consistent with a model of heterochromatin formation dependent on concentrations of its constituent components. ESC Variegation was hypothesized to result from spreading of nearby heterochromatin. Global IS analysis indicates Variegated IS favour gene deserts, repeat clusters, and LINEs while Expressers prefer gene density with stable modest expression and SINEs. Chromatin data does not support a role for the spread of heterochromatin possibly a consequence of the dynamic/dispersed nature of ESC heterochromatin. Variegation thus may depend on stochastic chromatin regulation by pluripotency factors at proximal genome organizing repeats.

Lentivirus efficiently transduce stem cells, however are notably silenced in embryonic stem cells (ESC). Provirus can be silent, expressing, or variegated when clonal single copy ESCs spawn daughters that revert expression despite containing identical integration sites (IS) indicating epigenetic regulation. In the silent state, variegated provirus are bound by H1 and MeCP2, where H1 compensates for MeCP2 binding in DNA methylation null ESCs, consistent with a model of heterochromatin formation dependent on concentrations of its constituent components. ESC Variegation was hypothesized to result from spreading of nearby heterochromatin. Global IS analysis indicates Variegated IS favour gene deserts, repeat clusters, and LINEs while Expressers prefer gene density with stable modest expression and SINEs. Chromatin data does not support a role for the spread of heterochromatin possibly a consequence of the dynamic/dispersed nature of ESC heterochromatin. Variegation thus may depend on stochastic chromatin regulation by pluripotency factors at proximal genome organizing repeats.

The precise regulation of Major Histocompatibility class II (MHC-II) genes plays an important role in the control of the adaptive immune response. MHC-II genes are expressed constitutively in only a few cell types, but their expression can be induced by the inflammatory response cytokine interferon gamma (INF-γ). The regulation of MHC-II is controlled by a Master Regulator, the class II transactivator (CIITA). Multiple studies have shown that CIITA regulated expression of MHC-II is controlled and induced by INF-γ. It has been also shown that a functional CIITA gene is necessary for the expression of MHC-II genes. CIITA is thus a general regulator of both constitutive and inducible MHC-II expression. Although much is known about the transcription factors necessary for CIITA expression, there is little information as to the epigenetic modifications and the requisite enzymes needed to provide these transcription factors access to DNA. Previous studies in the Greer lab have shown that increased levels of acetylation of histones H3 upon INF-γ stimulation, as does tri-methylation of H3K4 upon prolonged cytokine stimulation. Similar observations were made at early time points post IFN-γ stimulation, where there is an instantaneous increase in the levels of H3K18ac and H3K4me3. In contrast to this, the levels of silencing modifications begin to drop with in the first 20 minutes of IFN-γ stimulation. The binding of STAT1 reaches its peak at about 60 minutes and the first transcripts for the protein start to appear as early as 40 minutes post the cytokines stimulation. Our study is the first to link the rapidly occurring epigenetic changes at the CIITA promoter pIV to EZH2

BACKGROUND: Fetal growth is a complex process which depends on nutrient and oxygen availability and transport from the mother to the fetus across the placenta. This involves hormones and growth factors as well as maternal and fetal genes. The failure of the fetus to reach his or her full potential for growth is called Intrauterine Growth Restriction (IUGR) and implies risks for adverse short‐ and long‐ term outcomes. Imprinted genes are a specific subset of genes that display, in mammals and flowering plants, monoallelic expression depending on the parental origin of the allele. The regulation of imprinted expression depends on epigenetic mechanisms, a subset of heritable marks that have the ability to regulate DNA functions without altering its sequence. Imprinted genes tend to cluster in the genome due to coordinated regulation through Imprinting Control Centers, usually in the form of Differentially Methylated Regions between the paternally and maternally inherited alleles. Studies in both animals and humans as well as imprinting syndromes have uncovered a role for this group of genes in prenatal growth. Two imprinted genes (PLAGL1 and HYMAI) have been described in the 6q24 locus. Genetic and epigenetic defects in this region relate to the Transient Neonatal Diabetes Mellitus 1 phenotype, including severe growth restriction. We aimed to study the involvement of this region in non‐syndromic IUGR. PARTICIPANTS AND METHODS: One hundred placental samples from a cohort of healthy term singletons, fetal tissues from fifty‐four first trimester terminations and one hundred placental samples from healthy and complicated pregnancies of different gestational ages were used to analyze the role of the 6q24 region in normal fetal growth and IUGR, respectively. Relevant clinical data was obtained after informed consent. The methylation status of the 6q24 CpG islands was studied by array technology and bisulfite sequencing in normal term placenta and in first trimester fetal tissues. Methylation levels in the PLAGL1 DMR in healthy and IUGR placentas were compared by pyrosequencing. Allelic origin of expression was assessed by heterozygous DNA/cDNA SNP analysis. Levels of expression of imprinted transcripts were analyzed by qRT‐PCR. RESULTS: PLAGL1 P1, HYMAI and two newly described PLAGL1 isoforms (P3 and P4) were the only transcripts subjected to genomic imprinting in the investigated 6q24 region. Correspondingly, the CpG island associated to the P1 promoter was the only differentially methylated region. There was no correlation between PLAGL1 expression in the placenta and fetal size in uneventful pregnancies. In placentas from IUGR gestations, expression of HYMAI was significantly higher than in those from normally grown fetuses. Levels of expression of PLAGL1 were lower in IUGR and correlated positively and significantly with the presence of IUGR in placentas from girls, but not boys. These changes in expression were not mediated by Loss of Imprinting or abnormalities in the levels of methylation of the promoter‐associated DMR, but possibly by a change in regulatory posttranscriptional mechanisms, as suggested by the loss of correlation of PLAGL1 P1 and HYMAI expression in IUGR. CONCLUSIONS: Imprinted expression in the 6q24 region is limited to the PLAGL1/HYMAI locus, maybe due to demarcation of this region by CTCF boundaries. Intrauterine Growth Restriction is associated to abnormalities in expression of PLAGL1 and HYMAI in the placenta, which are not due to LOI or methylation changes.

Ctcf is a "master regulator" of the genome that plays a role in a variety of gene regulatory functions as well as in genome architecture. Evidence from studying the epigenetic process of X-chromosome inactivation suggests that, in certain cases, Ctcf might carry out its functions through interacting with RNA. Using mouse embryonic stem (ES) cells and a modified protocol for UV-crosslinking and immunoprecipitation followed by high-throughput sequencing (CLIP-seq), Ctcf is found to interact with a multitude of transcripts genome-wide, both protein-coding mRNA (or noncoding transcripts therein) as well as many long-noncoding RNA (lncRNA). Examples of the latter include both well-characterized species from imprinted loci and previously unannotated transcripts from intergenic space. RNA binding targets of Ctcf are validated by a variety of biochemical methods, and Ctcf is found to interact with RNA through its C-terminal domain, distinct from its DNA-binding zinc-finger domain. Ctcf chromatin immunoprecipitation (ChIP)-seq done in parallel reveals distinct but correlated binding of Ctcf to DNA and RNA. In addition, allelic analysis of Ctcf ChIP pattern reveals significant differences between Ctcf binding to the presumptive inactive and active X chromosomes. Together, the current work reveals a further layer of complexity to Ctcf biology by implicating a role for Ctcf-RNA interactions in its recruitment to genomic binding sites.

No description available.