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From Gene Identification and Functional Characterization to Genome Editing Approaches for Inherited Retinal Disorders Elise Orhan Le Gac De Lansalut

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From gene identification and functional characterization to genome editing approaches for inherited retinal disorders Elise Orhan Le Gac de Lansalut To cite this version: Elise Orhan Le Gac de Lansalut. From gene identification and functional characterization to genome editing approaches for inherited retinal disorders. Genetics. Université Pierre et Marie Curie - Paris VI, 2015. English. NNT : 2015PA066218. tel-01261327 HAL Id: tel-01261327 https://tel.archives-ouvertes.fr/tel-01261327 Submitted on 26 Jan 2016 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Université Pierre et Marie Curie Ecole doctorale Physiologie, Physiopathologie et Thérapeutique (ED394) Institut de la Vision, Département de génétique, Equipe S6 Audo-Zeitz From gene identification and functional characterization to genome editing approaches for inherited retinal disorders Par Elise Orhan Le Gac de Lansalut Thèse de doctorat en génétique Dirigée par Isabelle Audo et Christina Zeitz Présentée et soutenue publiquement le 16 septembre 2015 Devant un jury composé de : Pr José-Alain Sahel, Professeur, Président du jury Dr Valeria Marigo, Professeur Attaché, Rapporteur Pr Stephan Neuhauss, Professeur, Rapporteur Dr Patrick Benoit, Directeur de Projet International, Examinateur Dr Alain Carrié, MCU-PH, Examinateur Dr Christina Zeitz, CR1, Co-directrice de thèse Dr Isabelle Audo, MCU-PH, Directrice de thèse A ma famille Acknowledgments - Remerciements Since I had the great opportunity to go on a PhD in an outstanding international environment, I would like to address all my best acknowledgements in different languages. Not that I am that polyglot, but just to notify how I loved working on these conditions. First of all, I would like to warmly thank all the jury members to make me the honour and pleasure to review and evaluate the work of these last past years. I am really happy to have the opportunity to present my work in its - almost - integrity. The fruitful and kind discussions I had with absolutely all of you when I met you helped me a lot and I am really grateful that you accepted to judge my work. Je voudrais vous adresser mes plus chaleureux remerciements Pr Sahel pour votre accueil à l’Institut de la Vision et votre soutien durant toutes ces années. Les conditions de travail qui nous sont offertes à l’Institut sont exceptionnelles et vos précieux conseils m’ont énormément aidé lors de ma thèse. Je vous remercie donc pour ce cadre motivant et rassurant, mais également de me faire l’honneur de présider mon jury de thèse. J’aimerais également te remercier Isabelle d’avoir été ma directrice de thèse, faisant de moi ta première doctorante en Sciences! Ton intelligence, ta perspicacité, ton dévouement envers les patients m’ont beaucoup inspirée depuis mon arrivée à l’Institut, et ce n’est probablement pas une coïncidence si je me suis décidée à faire une thèse dans l’équipe A-Z. Merci également de m’avoir accordée une grande autonomie pratiquement dès mon arrivée, de m’avoir toujours permis de me former auprès des spécialistes, de m’avoir permis de communiquer à de nombreuses reprises mes résultats, et de m’avoir laissée gérer dans leur globalité mes multiples projets. Tu m’as permis de me former, personnellement, à devenir « project manager » et c’est probablement l’un des plus beaux cadeaux que tu m’ais fait pour ma carrière. Ich würde gerne auch dir danken Christina, da du meine andere Doktorarbeits Direktorin warst. Merci d’avoir été ma co-directrice et de m’avoir permis de travailler sur ton « hobby », le CSNB, qui est du coup devenu le mien aussi. Merci pour toutes les opportunités de formation, communication, apprentissage de nouvelles techniques que tu m’as donné. Merci également de m’avoir appris à écrire. Tes relectures, critiques constructives sur la façon de formuler les choses lors de la rédaction des articles, grants, abstracts et autres rapports m’ont appris à formuler les choses et me seront tout particulièrement précieux pour mon avenir. Je voudrais également remercier les membres de mon équipe, en commençant tout naturellement par mes deux super copines Kinga et Marie-Elise ! Merci les filles de m’avoir réservé un tel accueil au labo ! Votre amitié, nos fous-rires, vos conseils, votre bienveillance m’ont été hyper précieux et m’ont immédiatement rendu le labo hyper agréable ! Je suis très heureuse qu’ont ait gardé cela après vos départs, et je voudrais vous remercier pour tout ce que vous m’avez toutes deux apportée, autant au niveau professionnel que personnel. Dziękuję & mersi bras ! Un grand merci également à toi Aline pour ton amitié, pour nos sorties Zenzoo-ciné, pour toutes nos conversations qui m’ont permis de m’évader et pour toutes celles qui m’ont rassurée et m’ont permis de m’épanouir. Ton amitié m’est précieuse et j’espère réellement qu’on gardera le contact après ma thèse. Merci également à tous les autres membres de mon équipe : obrigado Miguel et merci Thomas for your friendships and your helps in mouse phenotyping, xièxie Bingqian, merci à Christelle a été ma partenaire dans les longues manipes de vivo, mais aussi à tout les autres membres de l’équipe : Elise, Fiona, Christel, Marion, Cécile mais aussi Aurore, Vanessa, Said. Je voudrais également te remercier Deniz, pour ton amitié et ta bienveillance. Üstün başarıların, iyi niyetli candan yaklaşımın ve daima pozitif tavrınla sana özenmemek mümkün değil, dostluğun ve desteğin benim için çok değerli. Tekrar teşekkür ederim, iyiki varsın. Un grand merci également à toi Olivier pour ta bienveillance, ton aide scientifique et technique, et tous tes conseils qui m’ont été particuluièrement précieux tout le long de ma thèse. J’ai beaucoup appris à ton contact et je te remercie de m’avoir réservé tout ce temps. Merci également Kim pour tout tes conseils et ta bienveillance, de m’avoir guidée à de nombreuses reprises, probablement sans même réellement t’en rendre compte. I would like also to thank you people of the best office ever, for your kindness, support, friendship, and for all the drinks & partys of course! Grazie Stefania & Cataldo! Gracias Marcela & Oriol! Merci Najate, thanks Abhishek! Thanks also to all the 4th floor friends from development department which made the long days easier, and the evenings happier and funnier! Thanks for your friendship & all your invitations to partys & drinks (I am sure you recognized yourself easily on these 2 last words). Merci également à toutes les personnes qui m’ont aidé à toutes les différentes étapes de ma thèse pour leur bienveillance et gentillesse. Travailler avec vous ou encore juste vous voir au quotidien a été un véritable plaisir. Je pense tout particulièrement à Manu, Julie, Léa, Quenol, André, Stéphane, Valérie, Serge, Thierry, Géraldine, Caroline, Yvrick, Mélissa et Romain. Enfin, je finis bien évidemment par ceux qui me sont les plus chers : un grand merci à ma famille et mes amis pour avoir été toujours là, et pour m’avoir toujours encouragée. Merci Özlem, Murat, Nâme, Julie, Matthias, Ridwan, Mathilde, Damien, Sabrina, Thomas, Guillaume, Clara, et tout ceux que j’oublie.. Un grand merci à toute ma famille Le Gac de Lansalut pour vos encouragements, et tout spécialement à Yann et mamie qui m’ont poussé à tenter l’aventure. Un très grand merci à toute la plus formidable et aimante des familles : ma famille Orhan, pour avoir toujours cru en moi, m’avoir encouragée, soutenue, supportée, divertie, et surtout pour votre amour et soutien inconditionnels. Canım annecim, canım babacım, bütün başarılarımız sizin desteğiniz, fedakarlıklarınız ve sevginiz sayesinde, size ne kadar teşekkür etsem azdır. Canim kardeşlerim Raziye, Selma ve Yasemin, size de aynı şekilde daima yanımda yer aldığınız, sürekli desteklediğiniz, ve tabii ki güzel kalpleriniz ve sevginiz için sonsuz teşekkür ederim. Eniştelerim İlkan ve Gürhan size de teşekkür ederim. Ve canım bebişlerimiz Kaan ve Can hayatımıza kattığınız renk, getirdiğiniz sevgi, neşe ve gülücükler için size de ayrıca teşekkür ederim. Enfin, je tiens à remercier celui qui a enduré tout cela, s’est enthousiasmé avec moi, m’a soutenue, conseillée et chouchoutée lorsque c’était nécessaire : mon mari Emmanuel (Manu pour les amis). Merci mon chéri de m’avoir encouragée à faire cette thèse et soutenue dans les moments délicats. Te voir si fier, si impliqué, capable de parler de mon sujet de thèse (et de mes résultats !), et te voir réaliser une véritable veille scientifique autour de mon projet m’ont tout particulièrement portée, merci pour ton implication et ton soutien de tout les jours. Table of contents List of figures and tables ............................................................................................................ 4 List of abbreviations ................................................................................................................... 6 Introduction .............................................................................................................................. 10 A. Preamble .......................................................................................................................
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  • Ligand-Specific Transcriptional Mechanisms Underlie Aryl Hydrocarbon Receptor-Mediated Developmental Toxicity of Oxygenated Pahs

    Ligand-Specific Transcriptional Mechanisms Underlie Aryl Hydrocarbon Receptor-Mediated Developmental Toxicity of Oxygenated Pahs

    Ligand-specific transcriptional mechanisms underlie aryl hydrocarbon receptor-mediated developmental toxicity of oxygenated PAHs Goodale, B.C.* †, La Du, J. *, Tilton, S.C.* ‡, Sullivan, C.M.* §, Bisson, W.H. *, Waters, K.M. ‡ and Tanguay, R.L.* *Department of Environmental and Molecular Toxicology, the Environmental Health Sciences Center, Oregon State University, Corvallis, OR, 97330 †Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, 604 Remsen Bldg., Hanover, NH 03755 ‡Computational Biology and Bioinformatics, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99354 §Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, 97330 Corresponding author: Robert Tanguay, Ph.D., Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97330. Email: [email protected] Abstract Polycyclic aromatic hydrocarbons (PAHs) are priority environmental contaminants that exhibit mutagenic, carcinogenic, proinflammatory and teratogenic properties. Oxygen-substituted PAHs (OPAHs) are formed during combustion processes and via phototoxidation and biological degradation of parent (unsubstituted) PAHs. Despite their prevalence both in contaminated industrial sites and in urban air, OPAH mechanisms of action in biological systems are relatively understudied. Like parent PAHs, OPAHs exert structure-dependent mutagenic activities and activation of the aryl hydrocarbon receptor (AHR) and cytochrome p450 metabolic pathway (CYP1A). Four-ring OPAHs 1,9-benz-10-anthrone (BEZO) and benz(a)anthracene-7,12-dione (7,12-B[a]AQ) cause morphological aberrations and induce markers of oxidative stress in developing zebrafish with similar potency, but only 7,12-B[a]AQ induces robust Cyp1a protein expression. We investigated the role of the AHR in mediating the toxicity of BEZO and 7,12-B[a]AQ, and found that knockdown of AHR2 rescued developmental effects caused by both compounds.