Post-GWAS Investigations for discovering pleiotropic gene effects in cardiovascular diseases Alex-Ander Aldasoro To cite this version: Alex-Ander Aldasoro. Post-GWAS Investigations for discovering pleiotropic gene effects in cardio- vascular diseases. Human health and pathology. Université de Lorraine, 2017. English. NNT : 2017LORR0247. tel-01868508 HAL Id: tel-01868508 https://tel.archives-ouvertes.fr/tel-01868508 Submitted on 5 Sep 2018 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. AVERTISSEMENT Ce document est le fruit d'un long travail approuvé par le jury de soutenance et mis à disposition de l'ensemble de la communauté universitaire élargie. Il est soumis à la propriété intellectuelle de l'auteur. Ceci implique une obligation de citation et de référencement lors de l’utilisation de ce document. D'autre part, toute contrefaçon, plagiat, reproduction illicite encourt une poursuite pénale. Contact : [email protected] LIENS Code de la Propriété Intellectuelle. articles L 122. 4 Code de la Propriété Intellectuelle. articles L 335.2- L 335.10 http://www.cfcopies.com/V2/leg/leg_droi.php http://www.culture.gouv.fr/culture/infos-pratiques/droits/protection.htm Ecole Doctorale BioSE (Biologie- Santé- Environnement) Thèse Présentée et soutenue publiquement pour l’obtention du titre de DOCTEUR DE l’UNIVERSITE DE LORRAINE Mention: « Sciences de la Vie et de la Santé » Par: Alex-Ander Aldasoro Post-GWAS Investigations for discovering pleiotropic gene effects in cardiovascular diseases Le 19 Décembre 2017 Membres du jury: Rapporteurs: Mme. Belgin SÜSLEYİCİ Professor, Marmara University, Istanbul, Turkey M. Nikolaos DRAKOULIS Professor, National & Kapodistrian University of Athens, Greece Examinateurs: Mme. Sophie VISVIKIS-SIEST DR1, INSERM U1122 ; IGE-PCV, Universite de Lorraine, Nancy, France – (Thesis Director) Mme. Ndeye Coumba NDIAYE MCU, Faculté de Pharmacie, Université de Lorraine, Nancy, France – (Thesis co-Director) M. Christian DINA IR CNRS, INSERM UMR 915, Université de Nantes, France Mme. Nathalie THILLY PUPH, EA 4360 APEMAC, Université de Lorraine, Nancy, France M. Dwaine R. VANCE PhD, Randox Laboratories, Co-Antrim, United Kingdom Université de Lorraine - UMR INSERM U1122; IGE-PCV - Faculté de Pharmacie - 30, rue Lionnois - 54000 Nancy - France Acknowledgements This thesis is a result of hard work of investigations and experimentations that would not be possible without a number of persons that need to be thanked: Firstly, I would like to express my sincere gratitude to my director of thesis, Dr. Sophie Visvikis-Siest, for the confidence that she have shown me from the beginning of our collaboration three years ago and for accepting the direction of my thesis. Also, because of her contagious and endless motivation for always going further, and for all the hours invested in leading my thesis. Equally, my most sincere thanks must go to Dr. Ndeye Coumba Ndiaye, without her immense knowledge and teachings in genetic epidemiology this thesis would be not possible. Also, I would like to thank her for the patience she given me and for her continuously wise advice. Her guidance has helped me to advance my research and the writing of this thesis. To the members of my jury, I would like to express my profound appreciation. You honor me by accepting to judge my work. To Randox Laboratories Ltd, and the “Agence Nationale de la Recherche, programme d’Investissements d’avenir” and the Operational Programme FEDER-FSE Lorraine et Massif des Vosges 2014-2020 for their help in the realisation of the projects. My sincere thanks also go to Dr. Maria Stathopoulou, who has always been there when I needed her, and for Dr. Sebastién Dade, who also helped me to broaden my researches. To Prof. Gerard Siest, whose experienced advice and lifelong dedication to science will always be a source of inspiration and motivation to me. I would also like to thank all of my fellow lab-mates for making the three years of my PhD Thank !صديق ,journey more pleasant. Thank you Abdel, for being always there for a coffee you Brigitte, for your constant support! Thank you Christine, for your help during the experiments! And finally, thank you Vesna, your good mood and fresh motivation really helps me! Merci a vous tous! Azkenik, mila esker zuri, Laura Dirand, hiru urte baina gehiago iraun duen bidaia zoro hau ez baitzen posible izango zu gabe! Abstract Cardiovascular diseases (CVD) are complex diseases where many environmental and genetic factors are involved. Due to this, their study needs to take into account different risk factors and the interactions between them, in order to reduce their incidence and mortality. Thanks to the breakthroughs of the Hap Map and Human genome projects and the development of GWAS and PheWAS, the genetic etiology of the CVD has been extensively investigated the last two decades. However, there is still a big room of knowledge waiting to be discovered and alternative approaches are needed in order to keep advancing in the pathophysiology of CVD. In this thesis, we propose an integrative approach to discover new genetic associations potentially involved in CVD. We chose previous GWAS hits and we focused on phenotypically homogeneous populations, in order to limit as much as possible the heterogeneity of intermediate phenotypes. We also centred our efforts in studying the pleiotropic and gene-gender interaction effects of the genes selected. Another main goal during this thesis was to defend the implementation of personalized genome-based therapy of the results obtained. By using the above-explained approaches, new pleiotropic effects were discovered in the IL- 6R and ABO genes. Within the IL-6R gene we found an antagonistic pleiotropy of this gene when it relates to CRP and lipid trait levels. We also found new pleiotropic effects within the ABO gene, by independently associating the major rs644234*T allele with increased sE- selectin and HDL levels, and decreased ApoE levels. Detection of pleiotropy is a source of new hypothesis and makes easier the development of new drugs, hence improving prevention and personalized medicine within the CVD. In addition, we studied the gene-gender interaction effects, finding some sex-specific associations in two of the genes studied (ABO and GNB3). Further, we centered our efforts in implementing the results obtained during the thesis at the clinical level, with the aim of ameliorating the genetics of personalized medicine. The SNP rs2234246 within the TREM-1 gene was associated with increased levels of its protein and could be used as a predictor or risk biomarker for different diseases (including CVD). Indeed, and due to the high potential of this polymorphism, we applied a European patent and we are planning to start Phase I clinical trials in patients suffering from Septic Shock and Acute Myocardial Infarction. Also the IL-6R haplotype rs4845628*T/rs4537545*C, which is increasing simultaneously CRP, LDL-C and ApoB levels, could be used in the treatment of personalized medicine. One of the side effects of the drug Tocilizumab, which is targeting the IL-6R gene, is the increase of LDL-C levels in patients, which could lead to a risk of suffering from ischaemic heart disease. In order to prevent these side effects, patients carriers of the haplotype rs4845628*T/rs4537545*C could be treated by analogue drugs or different doses of tocilizumab, which could make the treatment more personalized and hence, more secure and precise. Following the goals and approaches synthetized above, we discovered new associations between genes of interest and intermediate phenotypes that are involved in CVD and other complex diseases. Our results help to better understand how the studied genes are exerting their effects at the molecular level, ultimately affecting the outcome of the individuals suffering from CVD. Our results will hopefully be taken into account in future personalized treatments. Key words: Cardiovascular diseases, Pleiotropy, Gene-gender interactions, Genetic epidemiology, Personalized medicine, Intermediate phenotypes. Résumé Les maladies cardiovasculaires (MCV) sont d’une étiologie complexe et elles sont soumises à de nombreux facteurs environnementaux ainsi que génétiques. Pour pouvoir mieux comprendre leur pathophysiologie et réduire leur incidence et leur mortalité, l’étude des MCV prend en compte beaucoup de facteurs de risques différents en même temps, ainsi que leurs interactions. Les dernières percées technologiques dans le cadre du Projet Génome Humain, ou du Projet HapMap ont permis de développer de nouvelles approches méthodologiques. Les études d’association pangénomiques ou GWAS et les études d’association panphénotypiques ou PheWAS ont révolutionné l’épidémiologie génétique de la dernière décennie. Malgré les succès obtenus, une stagnation de la réduction de la morbidité et de la mortalité CV a rapidement été atteinte ces dernières années, rendant nécessaire l’identification de nouveaux biomarqueurs en utilisant des approches différentes. Cette thèse propose une approche