A statistical methodology to select covariates in high-dimensional data under dependence. Application to the classification of genetic profiles in oncology

We propose a new methodology for selecting and ranking covariates associated with a variable of interest in a context of high-dimensional data under dependence but few observations. The methodology successively intertwines the clustering of covariates, decorrelation of covariates using Factor Latent Analysis, selection using aggregation of adapted methods and finally ranking. Simulations study shows the interest of the decorrelation inside the different clusters of covariates. We first apply our method to transcriptomic data of 37 patients with advanced non-small-cell lung cancer who have received chemotherapy, to select the transcriptomic covariates that explain the survival outcome of the treatment. Secondly, we apply our method to 79 breast tumor samples to define patient profiles for a new metastatic biomarker and associated gene network in order to personalize the treatments

A statistical methodology to select covariates in high-dimensional data under dependence. Application to the classification of genetic profiles in oncology

International audienceWe propose a new methodology for selecting and ranking covariates associated with a variable of interest in a context of high-dimensional data under dependence but few observations. The methodology successively intertwines the clustering of covariates, decorrelation of covariates using Factor Latent Analysis, selection using aggregation of adapted methods and finally ranking. Simulations study shows the interest of the decorrelation inside the different clusters of covariates. We first apply our method to transcriptomic data of 37 patients with advanced non-small-cell lung cancer who have received chemotherapy, to select the transcriptomic covariates that explain the survival outcome of the treatment. Secondly, we apply our method to 79 breast tumor samples to define patient profiles for a new metastatic biomarker and associated gene network in order to personalize the treatments

Une exposition à de faibles doses d'alkylphénols entraine des altérations de épithélium mammaires et des défauts transgénérationnels mais n'augmente pas le potentiel tumorigénique des cellules cancéreuses mammaires

International audienceFetal and neonatal exposure to long chain alkylphenols has been suspected to promote breast developmental disorders and consequently to increase breast cancer risk. However, disease predisposition from developmental exposures remains unclear. In this work, human MCF-10A mammary epithelial cells were exposed in vitro to a low dose of a realistic [4-nonylphenol+4-tert-octylphenol] mixture. Transcriptome and cell phenotype analyses combined to functional and signaling network modeling indicated that long chain alkylphenols triggered enhanced proliferation, migration ability and apoptosis resistance and shed light on the underlying molecular mechanisms which involved the human estrogen receptor variant ERα36. A male mouse inherited transgenerational model of exposure to 3 environmentally relevant doses of the alkylphenol mix was set up in order to determine whether and how it would impact on mammary gland architecture. Mammary glands from F3 progeny obtained after intrabuccal chronic exposure of C57BL/6J P0 pregnant mice followed by F1 to F3 male inheritance displayed an altered histology which correlated with the phenotypes observed in vitro in human mammary epithelial cells. Since cellular phenotypes are similar in vivo and in vitro and involve the unique ERα36 human variant, such consequences of alkylphenol exposure could be extrapolated from mouse model to human. However, transient alkylphenol treatment combined to ERα36 overexpression in mammary epithelial cells were not sufficient to trigger tumorigenesis in xenografted Nude mice. Therefore, it remains to be determined if low dose alkylphenol transgenerational exposure and subsequent abnormal mammary gland development could account for an increased breast cancer susceptibility

Transgenerational effects of ERalpha36 over-expression on mammary gland development and molecular phenotype: clinical perspective for breast cancer risk and therapy.

International audienceGrowing source of evidence suggests that exposure to estrogen mimicking agents is a risk factor for breast cancer onset and progression. Long chain alkylphenols are man made compounds still present in household products, industrial and agricultural processes, leading to a global environmental and human contamination. These molecules are known to exert estrogen -like activities through binding to classical estrogen receptors. Recently, we have demonstrated that a realistic mixture of 4 tert - octylphenol and 4 - nonylphenol can stimulate proliferation and modulate epigenetic status of testicular cancer germ cells through a rapid, Estrogen Receptor alpha 36 (ERα36) -dependent non genomic pathway (Ajj et al, 2013; doi: 10.1371/journal.pone.0061758). In a retrospective study of breast tumor samples, we also validated ERα36 expression as a reliable prognostic factor for cancer progression from an estrogen dependent prolifera tive tumor toward an estrogen dispensable metastatic disease (Chamard - Jovenin et al, 2015; doi: 10.1186/s12918 - 015 - 0178 - 7). Since high ERα36 expression enhances expression of migration/invasion markers in breast tumors, we addressed the question of its involvement in response to alkylphenol exposure in vitro (MCF -10A mammary epithelial cell line and MCF -7 estrogen -sensitive cancer cells) and in vivo ( C57BL mice). A male inherited transgenerational model of exposure to environmentally relevant doses of an alkylphenol mix was set up in C57BL/6J mice to determine whether and how it impacts on mammary gland morphogenesis. Human mammary epithelial MCF -10A cells were exposed to similar doses to decipher the molecular mechanisms involved by a combination of transcriptomic study, cell phenotype analyses, functional and signaling network modeling. The relevance of mouse phenotype extrapolation to human risk is discussed. Mouse mammary gland exposed transgenerationally to the alkylphenol mix displayed a neoplastic -like histology. This phenotype was correlated with the enhanced proliferation, migration ability and apoptosis resistance observed in vitro on human mammary epithelial cells and mediated by the estrogen receptor variant ERα36. Since cellular phenotypes are similar in vivo and in vitro and involve the unique ERα36 human variant , such consequences of alkylphenol exposure could be extrapolated from mouse model to human. Low dose alkylphenol transgenerational exposure could promote abnormal mammary gland development and subsequently increase the risk of breast cancer at ageing

Lifelong testicular differentiation in Pleurodeles waltl (Amphibia, Caudata)

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Hormones stéroïdes et perturbateurs endocriniens dans le développement gonadique et la cancérogenèse

Au cours de mon doctorat puis de mes différents stages post-doctoraux, j'ai développé des approches de physiologie et génomique comparatives pour identifier et caractériser des médiateurs moléculaires impliqués dans le contrôle de la prolifération des cellules eucaryotes en réponse aux variations de l'environnement. Je me suis également attachée, dans des modèles biologiques divers, à replacer les mécanismes moléculaires et cellulaires étudiés dans un contexte plus général de physiologie de l'organisme. Depuis ma nomination en tant que Maître de Conférences à l'Université Nancy 1, je me suis focalisée sur l'influence des hormones stéroïdes sur la prolifération et la différenciation normale ou pathologique des cellules germinales. Le projet de recherche que je souhaite développer s'articule autour de 3 mots-clefs : tumeurs hormono-sensibles, perturbateurs endocriniens, voie non conventionnelle de signalisation oestrogénique. Le premier axe renferme un projet concernant les effets d'un mélange d'alkylphénols sur l'initiation et la progression tumorale dans un modèle de cancer testiculaire d'origine germinale puis de cancer mammaire, in vitro et in vivo. Le but est de caractériser le rôle éventuel de ERa36 dans ces processus afin de valider cette forme du récepteur des oestrogènes comme marqueur d'exposition aux perturbateurs endocriniens dans les cellules hormono-. Le second axe s'inscrit dans un objectif à plus long terme qui sera de valider ERa36 comme marqueur prédictif de réponse aux traitements anti-tumoraux dans les cancers hormono-sensibles et en particulier dans le cancer du sein

Influence de l'acide rétinoïque et des stéroïdes sexuels sur l'entrée en méiose des cellules germinales et la prolifération des cellules de tumeurs testiculaires d'origine germinale

Au cours de cette thèse, nous nous sommes intéressés à la différenciation normale et pathologique des cellules germinales (CGs). Dans une première partie, la différenciation normale a été étudiée chez l'amphibien urodèle Pleurodeles waltl. L'acide rétinoïque (AcR) est impliqué dans l'induction de l'entrée en méiose des cellules germinales (CGs) chez les amniotes (Bowles et al., 2006 ; Smith et al., 2008). Nous avons voulu savoir si l'AcR était aussi impliqué dans ce processus chez le pleurodèle. Nous avons montré que l'expression de PwDmc1 (marqueur de méiose), survient plus précocement dans les gonades femelles (avant la métamorphose) que dans les gonades mâles (après la métamorphose). In vitro, l'application d'AcR sur des gonades mâles et femelles en culture organotypique ainsi que l'inhibition de la dégradation de l'AcR endogène induisent l'entrée en méiose des CGs. Nous avons également montré que la balance synthèse/dégradation l'AcR endogène est modulée par les hormones stéroïdes. Les mécanismes de différenciation des CGs décrits chez les mammifères semblent donc conservés chez les urodèles. La seconde partie de la thèse s'inscrit dans le contexte de la différenciation pathologique des CGs.De nombreuses études ont montré qu'une exposition in utero à des xénobiotiques pouvait provoquer des altérations de la différenciation des CGs. Ces cellules altérées restent en dormance pendant l'enfance. A la puberté, elles prolifèrent et donnent naissance aux tumeurs testiculaires, suggérant que le développement de ces tumeurs est hormono-sensible (McIntyre et al., 2008). Nous avons étudié les effets des hormones stéroïdes sur la prolifération des cellules séminomateuses humaines TCam2. L'oestradiol et la testostérone stimulent leur prolifération ainsi que l'expression d'une isoforme tronquée du récepteur alpha des oestrogènes ER[alpha]36. Ce récepteur est induit par la voie GPER-AMPc/PKA et semble nécessaire à l'expression du récepteur à l'EGF. Il pourrait donc constituer une cible thérapeutique potentielle.Retinoic acid (RA) is involved in germ cells meiosis onset (CGs) in amniotes (Bowles et al., 2006 ; Smith et al., 2008). The aim of the first part of our study was to determine if RA is able to induce meiosis entry in the urodele amphibian Pleurodeles waltl. Our data on PwDmc1 (meiosis marker) expression indicate an earlier meiosis onset in females compared with males depending on RA biosynthesis. In vitro, the treatment of male and female gonads with RA induces an earlier meiosis entry in both sexes. Moreover, we have shown that RA biosynthesis is regulated by steroid hormones. Therefore, the mechanisms which trigger GCs differentiation in mammals might be conserved in urodeles. Many studies indicated that in utero xenobiotic exposure is able to induce alterations in GCs differentiation. These neoplasic cells enter in a period of dormancy until after puberty where they proliferate and the testicular tumours emerge. This prepubertal dormancy suggests that the testicular cancer development is hormone sensitive (McIntyre et al., 2008). In the second part we studied the effects of steroid hormones on the proliferation of the seminoma cell line TCam2. Our results indicate that estradiol and testosterone can induce the proliferation of this cell line and the expression of ER[alpha]36, a truncated form of estrogen receptor alpha. This expression is stimulated by GPER-cAMP/PKA signalisation pathway and activates EGFR expression. ER[alpha]36 could be a potential therapeutic target.NANCY1-Bib. numérique (543959902) / SudocSudocFranceF