<p>Leukotrienes are arachidonic acid derivatives long known for their inflammatory properties and their involvement with a number of human diseases, most notably asthma. Recently, leukotriene-based inflammation has also been implicated in atherosclerosis: ALOX5AP and LTA4H, two genes in the leukotriene biosynthesis pathway, have been associated with various cardiovascular disease (CVD) phenotypes. To assess the role of the leukotriene pathway in CVD pathogenesis, we performed genetic association studies of ALOX5AP and LTA4H in a non-familial data set of early onset coronary artery disease. Our results support a modest role for the leukotriene pathway in atherosclerosis pathogenesis, reveal important genomic interactions within the pathway, and suggest the importance of using pathway-based modeling for evaluating the genomics of atherosclerosis susceptibility. Motivated by this need, we investigated the statistical properties of a class of matrix-based statistics to assess epistasis. We simulated multiple two-variant disease models with haplotypes to gain an understanding of pathway interactions in terms of correlation patterns. Our goal was to detect an interaction between multiple disease-causing variants by means of their linkage disequlibrium (LD) patterns with other haplotype markers. The simulated models can be summarized into three categories: 1. No epistasis in the presence of marginal effects and LD; 2. Epistasis in the presence of LD and no marginal effects; and 3. Epistasis in the presence marginal effects and LD. We then assessed previously introduced single-gene methods that compare whole matrices of Single Nucleotide Polymorphism (SNP) LD between two samples. These methods include comparing two sets of principal components, a sum-of-squared-differences comparing pairwise LD, and a contrast test that controls for background LD. We also considered a partial least-square (PLS) approach for modeling gene-gene interactions. Our results indicate that these measures can be used to assess epistasis as well as marginal effects under certain disease models. Understanding and quantifying whole-gene variation and association to disease using multiple SNPs remains a difficult task. Providing a single statistical measure per gene will facilitate combining multiple types of genomic data at a gene-level and will serve as an alternative approach to assess epistasis in genome-wide association studies. The matrix-based measures can also be used in pathway ascertainment tools that require scores on a gene-level.</p> / Dissertation

A metamorfose em insetos é um dos mais complexos e belos eventos biológicos conhecidos, dirigido por sucessivas alterações morfo-fisiológicas. Este intricado processo é coordenado por componentes moleculares como ecdisteroides (20E) e hormônio juvenil (HJ), fatores de transcrição e microRNAs (miRNAs). Os miRNAs regulam a expressão de genes-alvo, que por sua vez orquestram alterações fisiológicas e anatômicas necessárias para o completo desenvolvimento do organismo. Apesar do enorme esforço, os circuitos genéticos e endócrinos que regulam a metamorfose em insetos sociais, como a abelha Apis mellifera, estão longe de serem completamente esclarecidos. Os miRNAs são importantes componentes da maquinaria celular e parecem ser ubíquos no controle de processos biológicos. Desvendar novas interações miRNA-mRNAs alvo envolvidas com a metamorfose e a regulação das cascatas de 20E e HJ lançará uma luz sobre esse complexo evento. Em nosso estudo nós investigamos os papéis de miR-34, miR-281, miR-252a e miR-252b, conhecidos como reguladores da metamorfose em insetos, no modelo A. mellifera. Todos estes miRNAs revelaram alto grau de conservação filogenética, bem como responderam ao tratamento com 20E, sofrendo flutuações na abundância de transcritos. Usando as informações disponíveis e nossos bancos de dados, nós identificamos interações envolvendo estes miRNAs e genes participantes nas cascatas de HJ e 20E: ultraspiracle (Usp), fushi tarazu-transcription factor 1 (ftz-f1), ecdysone receptor (EcR), calponin (chd64), insulin receptor 2 (inr2), e Krüppel homolog 1 (Krh1). A predição das interações miRNA-mRNAs alvo revelou que os receptores de ecdisteroides EcR e Usp, bem como o fator de transcrição ftz-f1 são alvos importantes dos miRNAs estudados, apresentando sítios para os quatros miRNAs investigados. Observamos também que os seis genes codificadores de proteína são putativamente alvejados por miR-34. Por meio do ensaio da luciferase, pudemos validar as interações entre miR-34 e os alvos Kr-h1, chd64 e inr2; miR-252a e os alvos ftz-f1 e EcR; miR-252b e os alvos chd64 e ftz-f1; miR-281 e os alvos ftz-f1, EcR e Usp. A investigação dos perfis de expressão dos miRNAs ao longo do desenvolvimento larval (L3-PP3) e pupal (Pw), contrastados com os perfis de seus respectivos alvos, apontou muitos casos de relações positivas miRNA-mRNA. Estes resultados complementaram os resultados de validação, e expuseram a regulação exercida pelo miRNA sobre seus alvos. Juntos, os nossos resultados apontam para novas interações miRNA-mRNAs, envolvidas com a metamorfose em A. mellifera. As regulações por nós propostas e validadas bem como suas caracterizações e relações com os hormônios reguladores da metamorfose, são inéditas e acrescentam muito ao conhecimento sobre a regulação da metamorfose em A. mellifera. Nesse contexto, nossa pesquisa definitivamente contribui para uma melhor compreensão dos eventos moleculares envolvidos com a metamorfose de abelhas. / Insect metamorphosis is one of the most complex and beautiful of known biological events; it consists of successive morphological and physiological alterations. This intricate process is coordinated by various molecular components, including ecdysteroids (20E), juvenile hormone (JH), transcription factors and microRNAs (miRNAs). The miRNAs regulate gene expression, which in turn orchestrates physiological and anatomical changes necessary for successful insect ontogeny. Despite enormous efforts, the endocrine and genetic circuits that regulate metamorphosis in social insects, such as honey bees (Apis mellifera), are far from being completely elucidated. The miRNAs are a substantial component of this molecular machinery and seem to be ubiquitously involved in the control of biological processes. Disclosing new miRNA-target interactions involved in metamorphosis and in the regulation of 20E and JH cascades can shed light on these poorly understood events. In this study, we provide new pieces to this puzzle. We investigated the roles of miR-34, miR-281, miR-252a and miR-252b, known to be important regulators of insect metamorphosis, in the A. mellifera model. All of these miRNAs revealed a high degree of phylogenetic conservation and responded to treatment with 20E, which altered transcript abundance. Using available information and our databases, we identified interactions involving these miRNAs and the component genes of JH and 20E pathways: ultraspiracle (Usp), fushi tarazu-transcription factor 1 (ftz-f1), ecdysone receptor (EcR), calponin (chd64), insulin receptor 2 (inr2), and Krüppel homolog 1 (Kr-h1). Prediction of miRNA-target interactions revealed that the ecdysteroid receptors EcR and Usp and the transcription factor ftz-f1 are highly targeted by miRNAs involved in metamorphosis; they presented binding sites for all four miRNAs. We also observed that all six-protein coding genes are putatively targeted by miR-34. Using the luciferase assay, we were able to validate the interactions of miR-34 with the targets Krh1, chd64 and inr2; miR-252a with the targets ftz-f1 and EcR; miR-252b with the targets chd64 and ftz-f1; and miR-281 with the targets ftz-f1, EcR and Usp. Investigation of miRNA expression profiles during larval (L3-PP3) and pupal (Pw) development, as a function of the profiles of their respective targets, demonstrated many cases of positive miRNA-mRNA relationships. These results complemented the validation results, showing how the miRNAs regulate their targets. In conclusion, we identified various previously unknown miRNA-mRNA interactions involved in the metamorphosis of A. mellifera. The regulatory pathways proposed and validated by us, as well as their characterizations and relationships with metamorphosis regulator hormones, are unique and add to the understanding of the regulation of metamorphosis in A. mellifera. In this context, our research contributes to a better understanding of the molecular events involved in honey bee metamorphosis.

Background: Although lifestyle modification is the cornerstone of GDM management, the evidence base on which dietary recommendations to prevent GDM is diverse and has not been synthesized in a consistent fashion. Objectives: The overall objective of this thesis is to assess the relationship of diet patterns, foods, and nutrients with GDM risk. Specifically, we seek to: 1) Quantify the relationship between dietary factors and GDM and metabolic disorders of pregnancy; 2) Compare the effects of dietary factors on markers of glycemic control, such as fasting glucose, fasting insulin, HbA1c, and the homeostatic model assessment for insulin resistance (HOMA-IR); 3) Assess the association and interaction between carbohydrate quality, and genetic load on the risk of developing GDM using data from 2 prospective birth cohort studies. Methods: We follow the approach set by the Cochrane Group’s Handbook for Systematic Review of Interventions to conduct meta-analyses and assess the quality of the evidence using the GRADE (Grading of Recommendations, Assessment, Development and Evaluation) approach. We analyze prospective cohort data of 2,504 women from the CHILD and START studies, which enrolled women of White-Caucasian and South Asian ethnicity. We quantify carbohydrate quality by deriving the glycemic index and load (GL), and total and added sugar intake. We construct a gene score using 102 loci that were previously associated with type 2 diabetes in genome-wide association studies. Results: 1) The meta-analysis identified high-quality evidence that red meat increases GDM risk; however, most associations of foods and nutrients with GDM and other metabolic disorders of pregnancy are of low-quality; 2) The network meta-analysis identified that most dietary interventions given with gestational weight gain advice will lower fasting glucose; 3) In South Asians, a high GL coupled with a high genetic load increased GDM risk six fold, but a high total sugar intake in the presence of a high genetic load reduced GDM risk. This paradoxical finding may be explained by a high correlation between total sugars and other healthy foods. Conclusions: Few valid associations between dietary factors and GDM risk exist. GL and total sugars may modify the genetic risk of GDM in South Asians but not in White-Caucasians. Further research is needed to determine effective interventions that can assist women in adopting healthier eating habits during pregnancy. / Thesis / Doctor of Philosophy (PhD) / Gestational diabetes mellitus (GDM) is glucose intolerance that first appears during pregnancy. Although lifestyle modification is the cornerstone of GDM management, dietary recommendations for GDM prevention are sparse. The overarching objective of this thesis is to describe the relationships between diets, foods, and nutrients and GDM and metabolic disorders of pregnancy and to understand whether carbohydrate quality can modify a genetic predisposition to diabetes. In the systematic literature reviews, high-quality evidence showed that red meat increases GDM risk. Moderate-quality evidence showed that several dietary factors also influence the risk of GDM and metabolic disorders of pregnancy, but most of the existing evidence is of low-quality. More high-quality studies are needed before dietary interventions can be implemented In our genetic study, we observed that carbohydrate quality may modify the genetic risk of diabetes in South Asians but not in White-Caucasians and conclude that carbohydrate quality may provide only a limited assessment of overall diet quality.

The latter part of the reproductive growth phase in chickpea (<i>Cicer arietinum</i> L.) often coincides with declining temperature and wet conditions in western Canada, in sharp contrast to many other growing environments. This exacerbates the indeterminate nature of the crop, leading to excessive canopy development, and subsequently resulting in delayed maturity. The objectives of this study were to: i) determine the genetic relationships of short internode, double podding and early flowering traits with earliness of crop maturity; ii) determine the genetic control of major earliness traits in chickpea; iii) assess the patterns of post-flowering dry matter accumulation and partitioning to reproductive parts as related to earliness. <p>The results showed that double podding significantly reduced the number of days taken to maturity, under the conditions where this trait was sufficiently expressed. The best double podding genotypes, i.e. those with 1535% of the podded nodes bearing double pods, were about one week earlier than their single podding counterparts and standard checks. A physiological study revealed that the double podding parental genotype 272-2 partitioned a relatively greater proportion (about 58%) of the total dry matter to pods compared to 4254% in the single podding genotypes. Double podding increased the total number of pods set, and thus the increased demand for assimilates may have precluded further production of stems and leaves, resulting in an earlier transition of reproductive growth to physiological maturity. Days to flowering was positively associated with days to maturity, and partial path analysis revealed that days to flowering contributed to days to maturity indirectly via days to first pod maturity. Days to flowering explained 32% of the variation in days to first pod maturity. However, the short internode trait had an undesirable effect, in that all the short internode segregants were too late to mature. <p>Genetic studies revealed that days to flowering was determined by two major genes plus polygenes in chickpea in the short-season temperate environment of western Canada. The two major genes control over 65% of the phenotypic variation. Also, the additive component of genetic variance was significant for days to first podding, days to first pod maturity, reproductive period, and days to maturity; which is desirable for development of superior inbred cultivars of chickpea. These key phenological traits are interrelated but could be manipulated separately in the breeding process. Additional gain in earliness of crop maturity may be achieved through combined selection for these traits.

The latter part of the reproductive growth phase in chickpea (<i>Cicer arietinum</i> L.) often coincides with declining temperature and wet conditions in western Canada, in sharp contrast to many other growing environments. This exacerbates the indeterminate nature of the crop, leading to excessive canopy development, and subsequently resulting in delayed maturity. The objectives of this study were to: i) determine the genetic relationships of short internode, double podding and early flowering traits with earliness of crop maturity; ii) determine the genetic control of major earliness traits in chickpea; iii) assess the patterns of post-flowering dry matter accumulation and partitioning to reproductive parts as related to earliness. <p>The results showed that double podding significantly reduced the number of days taken to maturity, under the conditions where this trait was sufficiently expressed. The best double podding genotypes, i.e. those with 1535% of the podded nodes bearing double pods, were about one week earlier than their single podding counterparts and standard checks. A physiological study revealed that the double podding parental genotype 272-2 partitioned a relatively greater proportion (about 58%) of the total dry matter to pods compared to 4254% in the single podding genotypes. Double podding increased the total number of pods set, and thus the increased demand for assimilates may have precluded further production of stems and leaves, resulting in an earlier transition of reproductive growth to physiological maturity. Days to flowering was positively associated with days to maturity, and partial path analysis revealed that days to flowering contributed to days to maturity indirectly via days to first pod maturity. Days to flowering explained 32% of the variation in days to first pod maturity. However, the short internode trait had an undesirable effect, in that all the short internode segregants were too late to mature. <p>Genetic studies revealed that days to flowering was determined by two major genes plus polygenes in chickpea in the short-season temperate environment of western Canada. The two major genes control over 65% of the phenotypic variation. Also, the additive component of genetic variance was significant for days to first podding, days to first pod maturity, reproductive period, and days to maturity; which is desirable for development of superior inbred cultivars of chickpea. These key phenological traits are interrelated but could be manipulated separately in the breeding process. Additional gain in earliness of crop maturity may be achieved through combined selection for these traits.

Le mélanome cutané est un cancer des cellules de la peau (mélanocytes) qui se situe, en France, au 11e rang des cancers les plus fréquents. Sa mortalité reste élevée lorsqu’il est diagnostiqué à un stade tardif. Ce cancer résulte de nombreux facteurs génétiques, environnementaux et des interactions entre ces facteurs. La susceptibilité génétique à ce cancer recouvre un large spectre de variabilité génétique, depuis des mutations rares conférant un risque élevé jusqu’à des variants fréquents conférant un risque modeste. C’est dans le cadre de l’identification de variants fréquents liés à l’apparition du mélanome et à son pronostic que se situe mon travail de thèse. À ce jour, les études d’associations pangénomiques du mélanome ont identifié des variants fréquents à effets relativement modestes qui expliquent seulement une part de la composante génétique. Les variants fonctionnels au sein des régions identifiées sont le plus souvent inconnus. Les études pangénomiques ont eu principalement recours à des analyses simple-marqueur qui peuvent manquer de puissance pour détecter des variants ayant un effet individuel faible ou interagissant avec d’autres variants. L’objectif principal de ce travail de thèse a été de proposer des stratégies d’analyse multi-marqueurs pour identifier de nouveaux gènes impliqués dans le mélanome et pour caractériser des variants potentiellement fonctionnels au sein des régions du génome associées au mélanome.Pour identifier de nouveaux gènes associés au risque de mélanome et à un facteur pronostique de ce cancer (l’indice de Breslow), nous avons proposé une stratégie d’analyse multi-marqueurs qui intègre une analyse de pathways biologiques basée sur la méthode GSEA (Gene Set Enrichment Analysis) et une analyse d’interactions entre gènes au sein des pathways associés au mélanome. Ces analyses ont été menées dans deux études : l’étude française MELARISK et l’étude américaine du MD Anderson Cancer Center (MDACC), totalisant 2 980 cas et 3 823 témoins. Nous avons identifié une interaction entre les gènes, TERF1 et AFAP1L2, pour le risque de mélanome et une interaction entre les gènes, CDC42 et SCIN, pour l’indice de Breslow. Ces gènes sont particulièrement pertinents sur le plan biologique du fait de leur rôle dans la biologie des télomères pour la première paire de gènes et dans la dynamique des filaments d’actine pour la seconde paire. Afin d’identifier les variants potentiellement fonctionnels au sein des régions du génome mises en évidence par études pangénomiques, nous avons proposé une stratégie de cartographie fine qui repose principalement sur une méthode de régression pénalisée (méthode HyperLasso) appliquée à tous les variants de la région étudiée. Par l’analyse de la région 16q24 qui contient le gène MC1R dont les variants fonctionnels sont connus, nous avons montré que cette stratégie était capable d’identifier ces variants parmi de nombreux variants associés au mélanome dans cette région. Nous avons contribué à identifier cinq nouvelles régions du génome associées au mélanome par méta-analyse d’études pangénomiques réalisées au niveau mondial (43 000 sujets) puis mené une étude de cartographie fine de toutes les régions associées au mélanome, en se basant sur la stratégie proposée et validée dans la région 16q24. Les stratégies d’analyses multi-marqueurs proposées dans le cadre de ce travail de thèse ont permis d’identifier de nouveaux gènes associés au risque de mélanome et à un facteur pronostique de ce cancer et de caractériser les variants génétiques potentiellement fonctionnels au sein des régions du génome identifiées par études pangénomiques. / Cutaneous melanoma is a skin cancer developed from melanocytes. It is the 11th most common cancers in France. Mortality due to melanoma remains high when diagnosed at a late stage. This cancer results from many genetic, environmental factors and interactions between these factors. The genetic susceptibility to melanoma covers a broad spectrum of genetic variation, from rare mutations conferring high risk to common variants conferring low risk. My thesis was conducted in the framework of low-risk variants associated with melanoma occurrence and prognosis. To date, genome-wide association studies (GWAS) of melanoma have identified common variants with relatively modest effects which only explain a part of the genetic component of this cancer. Functional variants at the identified loci are mostly unknown. GWASs have been mainly conducted using single-marker analysis which may be underpowered to detect variants with small effect or interacting with each other. The main objective of this thesis was to propose multi-marker analysis strategies to identify novel genes involved in melanoma and to characterize potentially functional variants in chromosomal regions found associated with melanoma. To identify new genes associated with melanoma risk and a prognostic factor for this cancer (Breslow thickness), we proposed a multi-marker analysis strategy which integrates pathway analysis based on the GSEA (Gene Set Enrichment Analysis) method and gene-gene interaction analysis within melanoma-associated pathways. These analyses were conducted in two studies: the French MELARISK study and the North-American MD Anderson Cancer Center (MDACC) study, with a total of 2,980 cases and 3,823 controls. We identified gene-gene interactions between TERF1 and AFAP1L2 genes for melanoma risk and between CDC42 and SCIN genes for Breslow thickness. These genes are biologically relevant because of their role in telomere biology for the former gene pair and in actin dynamics for the latter pair. To identify potentially functional variants at loci identified by GWAS, we proposed a fine mapping strategy which is mainly based on a penalized regression approach (HyperLasso method) that can be applied to all variants of the region under study. By studying the 16q24 region which harbors the MC1R gene whose functional variants are known, we showed this strategy was able to identify those variants among many variants associated with melanoma in this region. We contributed to the identification of five novel regions associated with melanoma through a worldwide meta-analysis of melanoma GWASs (43,000 subjects) and conducted fine mapping of all melanoma-associated loci using the strategy we proposed and validated in the 16q24 region. The multi-marker strategies proposed in this work have allowed identifying new biologically relevant genes associated with risk of melanoma and a major melanoma prognostic factor and characterizing potentially functional genetic variants within regions identified by GWAS.

Worldwide, alcohol is the third leading risk factor for disease burden, while its harmful use leads to 2.5 million deaths every year. Alcohol dependence (AD) is a complex disease, with devastating effects on individuals, families, and society. It is estimated that 76.3 million people worldwide have suffered from alcohol use disorders (AUD), including alcohol abuse and AD. Alcohol withdrawal or alcohol withdrawal symptom (AWS) refers to a cluster of symptoms that may occur when a heavy drinker suddenly stops or significantly reduces their alcohol intake. These symptoms can start as early as 2 h after the last drink, persist for weeks, and range from mild anxiety and shakiness to severe complications, such as seizures and delirium tremens. Family, twin, and adoption studies have indicated that genetic and environmental factors and their interactions contribute to the development of AD and related phenotypes, with a heritability coefficient of more than 0.5 for AD. Whole-genome linkage and candidate gene association studies have successfully identified several chromosome regions and genes that are related to AD and AWS. Furthermore, gene expression analysis, epigenetic studies, and genome-wide association studies (GWAS) have provided regions and loci for AWS. This chapter reviews the recent findings in genetic studies of AWS.

La leucémie lymphoblastique aigüe (LLA) est une maladie génétique complexe. Malgré que cette maladie hématologique soit le cancer pédiatrique le plus fréquent, ses causes demeurent inconnues. Des études antérieures ont démontrées que le risque à la LLA chez l’enfant pourrait être influencé par des gènes agissant dans le métabolisme des xénobiotiques, dans le maintient de l’intégrité génomique et dans la réponse au stress oxydatif, ainsi que par des facteurs environnementaux. Au cours de mes études doctorales, j’ai tenté de disséquer davantage les bases génétiques de la LLA de l’enfant en postulant que la susceptibilité à cette maladie serait modulée, au moins en partie, par des variants génétiques agissant dans deux voies biologiques fondamentales : le point de contrôle G1/S du cycle cellulaire et la réparation des cassures double-brin de l’ADN. En utilisant une approche unique reposant sur l’analyse d’une cohorte cas-contrôles jumelée à une cohorte de trios enfants-parents, j’ai effectué une étude d’association de type gènes/voies biologiques candidats. Ainsi, j’ai évaluer le rôle de variants provenant de la séquence promotrice de 12 gènes du cycle cellulaire et de 7 gènes de la voie de réparation de l’ADN, dans la susceptibilité à la LLA. De tels polymorphismes dans la région promotrice (pSNPs) pourraient perturber la liaison de facteurs de transcription et mener à des différences dans les niveaux d’expression des gènes pouvant influencer le risque à la maladie. En combinant différentes méthodes analytiques, j’ai évalué le rôle de différents mécanismes génétiques dans le développement de la LLA chez l’enfant. J’ai tout d’abord étudié les associations avec gènes/variants indépendants, et des essaies fonctionnels ont été effectués afin d’évaluer l’impact des pSNPs sur la liaison de facteurs de transcription et l’activité promotrice allèle-spécifique. Ces analyses ont mené à quatre publications. Il est peu probable que ces gènes de susceptibilité agissent seuls; j’ai donc utilisé une approche intégrative afin d’explorer la possibilité que plusieurs variants d’une même voie biologique ou de voies connexes puissent moduler le risque de la maladie; ces travaux ont été soumis pour publication. En outre, le développement précoce de la LLA, voir même in utero, suggère que les parents, et plus particulièrement la mère, pourraient jouer un rôle important dans le développement de cette maladie chez l’enfant. Dans une étude par simulations, j’ai évalué la performance des méthodes d’analyse existantes de détecter des effets fœto-maternels sous un design hybride trios/cas-contrôles. J’ai également investigué l’impact des effets génétiques agissant via la mère sur la susceptibilité à la LLA. Cette étude, récemment publiée, fût la première à démontrer que le risque de la leucémie chez l’enfant peut être modulé par le génotype de sa mère. En conclusions, mes études doctorales ont permis d’identifier des nouveaux gènes de susceptibilité pour la LLA pédiatrique et de mettre en évidence le rôle du cycle cellulaire et de la voie de la réparation de l’ADN dans la leucémogenèse. À terme, ces travaux permettront de mieux comprendre les bases génétiques de la LLA, et conduiront au développement d’outils cliniques qui amélioreront la détection, le diagnostique et le traitement de la leucémie chez l’enfant. / Childhood acute lymphoblastic leukemia (ALL) is a complex and heterogeneous genetic disease. Although it is the most common pediatric cancer, its etiology remains poorly understood. Previous studies provided evidence that childhood ALL might originate through the collective contribution of different genes controlling the efficiency of carcinogen metabolism, the capacity of maintaining DNA integrity and the response to oxidative stress, as well as environmental factors. In my doctoral research project I attempted to further dissect the genetic intricacies underlying childhood ALL. I postulated that a child’s susceptibility to ALL may be influenced, in part, by functional sequence variation in genes encoding components of two core biologic pathways: G1/S cell cycle control and DNA double-strand break repair. Using a unique two-tiered study design consisting of both unrelated ALL cases and healthy controls, as well as case-parent trios, I performed a pathway-based candidate-gene association study to investigate the role of sequence variants in the promoter regions of 12 candidate cell cycle genes and 7 DNA repair genes, in modulating ALL risk among children. Polymorphisms in promoter regions (pSNPs) could perturb transcription factor binding and lead to differences in gene expression levels that in turn could modify the risk of disease. To better depict the complex genetic architecture of childhood ALL, I used multiple analytical approaches. First, individual genes/variants were tested for association with disease, while functional in vitro validation was performed to evaluate the impact of the pSNPs on differential transcription factor binding and allele-specific promoter activity. These analyses led to four published articles. Given that these genes are not likely to act alone to confer disease risk I used an integrative approach to explore the possibility that combinations of functionally relevant pSNPs among several components of the same or of interconnected pathways, could contribute to modified childhood ALL risk either through pathway-specific or epistatic effects; this work was recently submitted for publication. Finally, childhood ALL is thought to arise in utero suggesting that the parents, and in particular the mother, may play an important role in shaping disease susceptibility in their offspring. Using simulations, I investigated the performance of existing methods to test for maternal genotype associations using a case-parent trio/case-control hybrid design, and then assessed the impact of maternally-mediated genetic effects on ALL susceptibility among children. This published work was the first to show that the mother’s genotype can indeed influence the risk of leukemia in children, further corroborating the importance of considering parentally-mediated effects in the study of early-onset diseases. In conclusion, my doctoral work lead to the identification of novel genetic susceptibility loci for childhood ALL and provided evidence for the implication of the cell cycle control and DNA repair pathways in leukemogenesis. Better elucidation of the genetic mechanisms underlying the pathogenesis of ALL in children could be of great diagnostic value and provide data to help guide risk-directed therapy and improve disease management and outcome. Ultimately, this study brings us one step closer to unraveling the genetic architecture of childhood ALL and provides a stepping-stone towards disease prevention.

La leucémie lymphoblastique aigüe (LLA) est une maladie génétique complexe. Malgré que cette maladie hématologique soit le cancer pédiatrique le plus fréquent, ses causes demeurent inconnues. Des études antérieures ont démontrées que le risque à la LLA chez l’enfant pourrait être influencé par des gènes agissant dans le métabolisme des xénobiotiques, dans le maintient de l’intégrité génomique et dans la réponse au stress oxydatif, ainsi que par des facteurs environnementaux. Au cours de mes études doctorales, j’ai tenté de disséquer davantage les bases génétiques de la LLA de l’enfant en postulant que la susceptibilité à cette maladie serait modulée, au moins en partie, par des variants génétiques agissant dans deux voies biologiques fondamentales : le point de contrôle G1/S du cycle cellulaire et la réparation des cassures double-brin de l’ADN. En utilisant une approche unique reposant sur l’analyse d’une cohorte cas-contrôles jumelée à une cohorte de trios enfants-parents, j’ai effectué une étude d’association de type gènes/voies biologiques candidats. Ainsi, j’ai évaluer le rôle de variants provenant de la séquence promotrice de 12 gènes du cycle cellulaire et de 7 gènes de la voie de réparation de l’ADN, dans la susceptibilité à la LLA. De tels polymorphismes dans la région promotrice (pSNPs) pourraient perturber la liaison de facteurs de transcription et mener à des différences dans les niveaux d’expression des gènes pouvant influencer le risque à la maladie. En combinant différentes méthodes analytiques, j’ai évalué le rôle de différents mécanismes génétiques dans le développement de la LLA chez l’enfant. J’ai tout d’abord étudié les associations avec gènes/variants indépendants, et des essaies fonctionnels ont été effectués afin d’évaluer l’impact des pSNPs sur la liaison de facteurs de transcription et l’activité promotrice allèle-spécifique. Ces analyses ont mené à quatre publications. Il est peu probable que ces gènes de susceptibilité agissent seuls; j’ai donc utilisé une approche intégrative afin d’explorer la possibilité que plusieurs variants d’une même voie biologique ou de voies connexes puissent moduler le risque de la maladie; ces travaux ont été soumis pour publication. En outre, le développement précoce de la LLA, voir même in utero, suggère que les parents, et plus particulièrement la mère, pourraient jouer un rôle important dans le développement de cette maladie chez l’enfant. Dans une étude par simulations, j’ai évalué la performance des méthodes d’analyse existantes de détecter des effets fœto-maternels sous un design hybride trios/cas-contrôles. J’ai également investigué l’impact des effets génétiques agissant via la mère sur la susceptibilité à la LLA. Cette étude, récemment publiée, fût la première à démontrer que le risque de la leucémie chez l’enfant peut être modulé par le génotype de sa mère. En conclusions, mes études doctorales ont permis d’identifier des nouveaux gènes de susceptibilité pour la LLA pédiatrique et de mettre en évidence le rôle du cycle cellulaire et de la voie de la réparation de l’ADN dans la leucémogenèse. À terme, ces travaux permettront de mieux comprendre les bases génétiques de la LLA, et conduiront au développement d’outils cliniques qui amélioreront la détection, le diagnostique et le traitement de la leucémie chez l’enfant. / Childhood acute lymphoblastic leukemia (ALL) is a complex and heterogeneous genetic disease. Although it is the most common pediatric cancer, its etiology remains poorly understood. Previous studies provided evidence that childhood ALL might originate through the collective contribution of different genes controlling the efficiency of carcinogen metabolism, the capacity of maintaining DNA integrity and the response to oxidative stress, as well as environmental factors. In my doctoral research project I attempted to further dissect the genetic intricacies underlying childhood ALL. I postulated that a child’s susceptibility to ALL may be influenced, in part, by functional sequence variation in genes encoding components of two core biologic pathways: G1/S cell cycle control and DNA double-strand break repair. Using a unique two-tiered study design consisting of both unrelated ALL cases and healthy controls, as well as case-parent trios, I performed a pathway-based candidate-gene association study to investigate the role of sequence variants in the promoter regions of 12 candidate cell cycle genes and 7 DNA repair genes, in modulating ALL risk among children. Polymorphisms in promoter regions (pSNPs) could perturb transcription factor binding and lead to differences in gene expression levels that in turn could modify the risk of disease. To better depict the complex genetic architecture of childhood ALL, I used multiple analytical approaches. First, individual genes/variants were tested for association with disease, while functional in vitro validation was performed to evaluate the impact of the pSNPs on differential transcription factor binding and allele-specific promoter activity. These analyses led to four published articles. Given that these genes are not likely to act alone to confer disease risk I used an integrative approach to explore the possibility that combinations of functionally relevant pSNPs among several components of the same or of interconnected pathways, could contribute to modified childhood ALL risk either through pathway-specific or epistatic effects; this work was recently submitted for publication. Finally, childhood ALL is thought to arise in utero suggesting that the parents, and in particular the mother, may play an important role in shaping disease susceptibility in their offspring. Using simulations, I investigated the performance of existing methods to test for maternal genotype associations using a case-parent trio/case-control hybrid design, and then assessed the impact of maternally-mediated genetic effects on ALL susceptibility among children. This published work was the first to show that the mother’s genotype can indeed influence the risk of leukemia in children, further corroborating the importance of considering parentally-mediated effects in the study of early-onset diseases. In conclusion, my doctoral work lead to the identification of novel genetic susceptibility loci for childhood ALL and provided evidence for the implication of the cell cycle control and DNA repair pathways in leukemogenesis. Better elucidation of the genetic mechanisms underlying the pathogenesis of ALL in children could be of great diagnostic value and provide data to help guide risk-directed therapy and improve disease management and outcome. Ultimately, this study brings us one step closer to unraveling the genetic architecture of childhood ALL and provides a stepping-stone towards disease prevention.

Ce travail concerne le comportement de retrait relationnel du jeune enfant, sa mesure et sa validité prédictive sur la qualité du développement précoce dans ses différentes dimensions. Il représente la première synthèse de l'histoire du concept de retrait relationnel du jeune enfant, de ses liens avec les modèles animaux, avec le modèle paradigmatique du "Still Face" et de la réparation, de la dys-synchronie comme facteur majeur de la psychopathologie précoce. Le comportement de retrait relationnel prend ses racines dans la physiologie, comme mode privilégié de régulation par le bébé de l'interaction, dans une échelle micro interactive. D'une façon plus clinique et sur une échelle temporelle plus longue, il apparaît comme un mode de défense majeur face à la violation des attentes du bébé dans l'interaction. On l'observe donc de façon privilégiée dans la dépression maternelle post natale mais aussi dans toutes les circonstances psychopathologiques qui affectent les capacités parentales (par exemple et de façon très nette dans les situations de conflit et violences conjugales). Le retrait relationnel peut également être lié à des difficultés de traitement de l'information sensorielle par le bébé, à des difficultés de communication sociale, à une douleur intense prolongée, et dans la prématurité ou dans certains syndromes génétiques à une association de ces facteurs liés à l'enfant. Ce travail retrace les débuts de la construction d'un outil de mesure du retrait relationnel précoce, dans la mesure où cet outil n'existait pas en tant que tel, alors que le retrait relationnel apparaît comme un signal d'alarme important, témoignant de la difficulté du bébé de jouer le jeu relationnel à hauteur de ses capacités développementales, que ce soit pour des causes liées à lui-même, à la relation avec ses caregivers, ou aux deux. Ce travail s'ouvre par une histoire de la psychiatrie du bébé et de l'avènement de la psychopathologie développementale, car on note l'importance du symptôme retrait dans cette histoire, qu'il s'agisse de l'autisme (Kanner) ou de la dépression ou de la carence précoces (Spitz), puis un historique de concept de retrait relationnel précoce : contexte clinique modèles animaux, biologie, la Construction et validation de l'échelle Alarme Détresse bébé (ADBB à 8 items) puis celle de la m-ADBB à 5 items, puis par la Psychopathologie du retrait relationnel durable, et Les développements et les applications de l'échelle ADBB : m-ADBB, effets à terme du retrait, études longitudinales, la prématurité comme analyseur du développement, dépistage précoce de l'autisme et enfin les projets en cours et trois projets actuels, autour du dépistage de l'autisme, autour de l'étude des différentes analyses factorielles et de la validation de la m-ADBB, et autour des pistes génétiques et épigénétiques du comportement de retrait. Il présente les résultats des études contrôlées et publiées avec l'ADBB, en particulier celles liées à la cohorte française d'étude des facteurs de risque et de résilience du développement précoce (étude périnatale EDEN). Le comportement clinique de retrait relationnel apparaît comme le résultat d'une interaction gène environnement, basée sur la susceptibilité génétique au comportement de retrait. Celle-ci apparaît liée au système allélique 5-HTTPR. Sur le plan cognitif, la question se pose du retrait comme pari, comme choix dans une situation d'incertitude. Les études de suivi des enfants en retrait montrent l'impact sur diverses dimensions du développement, langage, intersubjectivité, régulation émotionnelle, avec la question d'une période sensible. Ceci souligne l'importance du dépistage de ce comportement en vue d'une intervention précoce adaptée à sa cause. / This work deals with social withdrawal behavior in infants, its measure and its conceptual validity, its predictive value on early development within its several dimensions. This is the first synthesis on the history of the concept of withdrawal in infant, of its links with animal models, with the still face experimental paradigm, as well as with the repair process and with interactional dys- syssynchrony as a major process in early psychopathology. Social withdrawal behavior has its roots in physiology, as privileged way used by the infant to regulate the input within the parent infant interaction, within a micro temporal scale. On a longer temporal and more clinical scale, withdrawal behavior appears as a major defense maneuver when the baby is faced with major violations of his her expectations within the relationship. It is therefore observed in a privileged way in maternal post-natal depression, but also in all circumstances which hamper parental capacities, as conjugal violence and conflict may do for instance. Social withdrawal behavior may be as well linked with difficulties in processing sensorial input in the child, or difficulties in social communication and synchrony, or be due to an intense and sustained pain, or be linked with some genetic disorder or with some association of these factors. This work retraces the construction of a scale to asses social withdrawal behavior in infants, since no such tool existed at the time, although social withdrawal behavior appears to be an important alarm signal, showing the inability of the child to play the relational game as his her developmental level allow him or her to do, be it for causes related to himself or herself, for relational causes of because of both. This work opens on a history of the development of child psychiatry and of the coming of ages of infant development. Social withdrawal behavior took a large place at the onset of this history, with the description of autism by Kanner and anaclitic depression by Spitz. Then a history of the concept of social relational withdrawal, and of the construction of the alarm distress scale (8 item) the of the short version (5 item m-ADBB), then the studies on long term effects of social withdrawal on development. We then review the application of the scale on early diagnosis of autism, on the several factor analysis with several samples, and of the several epigenetic and genetic pathways of the social withdrawal behavior. This work reviews the results of several controlled studies with the ADBB, particularly those from the perinatal French EDEN cohort. Social withdrawal behavior appears as the result of a gene interaction, based on the genetic c susceptibility for social withdrawal behavior, possibly liked with the 5-HTPPR allele system. On a cognitive level, the issue is raised of social withdrawal behavior as a choice of a risk taking position in an uncertain situation. Follow up studies show the impact of the social withdrawal behavior on several dimensions of early development, i.e. language, early development of intersubjectivity or emotional regulation.