Des anomalies biochimiques de la voie sérotonine-N-acétylsérotonine-mélatonine ont été observées dans les Troubles du Spectre Autistique (TSA) et la prématurité. Cependant, les mécanismes moléculaires de régulation de cette voie et les causes des anomalies biochimiques observées dans ces maladies sont encore mal connus. Afin de mieux comprendre les bases génétiques de la voie sérotonine-N-acétylsérotonine-mélatonine, nous avons utilisé une approche de génétique quantitative au travers de deux populations d’étude indépendantes, dans lesquelles des paramètres de cette voie ont été mesurés. Ces deux cohortes, composées d’une part de plus de 250 familles avec autisme et plus de 300 témoins et d’autre part, de 183 nouveau-nés dont 93 nés très prématurés, incluent ainsi des individus présentant deux situations pathologiques différentes associées à des anomalies de cette voie. Une première étude de la voie sérotonine-N-acétylsérotonine-mélatonine dans les familles avec TSA a permis d’obtenir des estimations de l’héritabilité au sens strict, allant de 0,22 pour la mélatonine à 0,72 pour la N-acétylsérotonine (NAS). Des études d’association portant dans un premier temps sur une liste de 812 gènes candidats pour la régulation de la voie sérotonine-NAS-mélatonine et dans un second temps sur tout le génome, n’ont pas permis d’identifier des variants significativement associés aux traits biochimiques. Cependant, des études d’association par gènes ont permis d’identifier trois nouveaux gènes candidats (IL21R, JMJD7 et MAPKBP1) pour la régulation de cette voie dans les familles avec TSA ainsi qu’un nouveau gène (RAET1G) dans la cohorte de nouveau-nés prématurés et témoins. Enfin une étude biochimique des phénol-sulfotransférases (PST) dans les familles avec TSA a mis en évidence une faible activité enzymatique chez 29% des patients en comparaison avec les témoins (5ème percentile). Le séquençage et le génotypage du nombre de copies des gènes de la famille SULT1A1 n’ont pas permis d’identifier des variations génétiques associées aux TSA, à l’activité PST, ou aux taux de sérotonine et de mélatonine. En conclusion, ces résultats confirment la complexité de l’architecture génétique de la voie sérotonine-NAS-mélatonine. D’autre part, ils ont permis de mettre en évidence une héritabilité élevée de cette voie et d’identifier de nouveaux gènes candidats pour comprendre la diversité inter-individuelle de cette voie chez les personnes avec TSA, les enfants prématurés et la population générale. / Biochemical abnormalities of the serotonin-N-acetylserotonin-melatonin pathway have been reported in many clinical conditions such as Autism Spectrum Disorders and preterm birth. However, molecular mechanisms underlying this pathway regulation, as well as the causes of these biochemical abnormalities remain largely unknown. The aim of this study was thus to characterize the genetic basis of the serotonin-N-acetylserotonin-melatonin pathway. To do so, we used a quantitative genetic approach in two independent populations that were previously biochemically explored for this pathway. One cohort consisted of more than 250 families with ASD and more than 300 controls and the other was composed of 183 infants including 93 very preterm newborns. Both cohorts included individuals with clinical conditions associated with disruptions of the serotonin-N-acetylserotonin-melatonin pathway. Narrow sense heritability analysis of this pathway showed relatively high estimates, ranging from 0.22 for melatonin to 0.72 for N-acetyserotonin (NAS). First, candidate-gene association studies including 812 genes related to the serotonin-NAS-melatonin pathway, then genome-wide association studies were conducted. These analyses did not identify any variant associated at the genome-wide significance level. However, a gene-based approach identified three new candidate genes (IL21R, JMJD7 and MAPKBP1) for the regulation of the pathway in families with ASD as well as one gene (RAET1G) in the cohort of preterm and term newborns. Finally, a biochemical exploration of the phenol-sulfotransferases (PST) in families with ASD revealed a decreased enzyme activity in 29% of patients compared with controls (5th percentile). SULT1A1-4 genes were then sequenced and copy number variants (CNV) were genotyped. No genetic variant could be significantly associated with PST activity, melatonin and serotonin levels, or ASD status. In conclusion, these results confirm the complexity of serotonin-NAS-melatonin pathway genetic architecture. Furthermore, this study revealed high heritability of this pathway and identified new candidate genes to understand the inter-individual variability of this pathway in ASD, preterm birth and the general population.

Widely effective treatment for alcohol use disorder is not yet available, because the exact biological mechanisms that underlie this disorder are not completely understood. One way to gain a better understanding of these mechanisms is to examine the genetic frameworks that contribute to the risk for developing this disorder. This dissertation examines genetic association data in combination with gene expression networks in the brain to identify functional groups of genes associated with alcohol consumption and dependence. The first study took advantage of the behavioral complexity of human samples, and experimental capabilities provided by mouse models, by co-analyzing gene expression networks in the mesolimbocortical system of acute alcohol-treated mice and human genetic alcohol dependence association data. This study successfully identified ethanol-responsive gene expression networks with overrepresentation of genes suggestively associated with alcohol dependence in an independent human sample, indicating that gene expression networks in mouse models are informative for identifying mechanistic networks relevant to the risk for developing dependence. The second study aimed to identify quantitative trait loci for voluntary alcohol drinking behaviors under an intermittent ethanol access paradigm, in the genetically complex Diversity Outbred mice. After determining high heritability for alcohol consumption and dependence amongst the progenitor strains, we identified several specific genetic loci associated with these traits. One locus replicated results from a human association study of alcohol consumption, and provided insight to the potentially contributing genes. Finally, we identified alcohol consumption-correlated gene expression networks in the prefrontal cortex of these mice. We also mapped quantitative trait loci for network expression levels, some of which overlapped with the behavioral loci, indicating that the functions represented by these modules mediate the relationship between the genotypes in that region and drinking behaviors. Overall, our studies revealed neuroplastic and ubiquitin-related genes pathways involved in alcohol consumption in mice and humans, and that likely contribute to the risk for developing dependence.

Pubertal timing displays wide, normally distributed variation in a healthy population of sexually maturing adolescents. However, like many complex traits, factors contributing to the variation are not well understood. Epigenetic regulation may contribute to some of the population variation. The role that epigenetics, specifically DNA methylation and histone acetylation, may play in regulating pubertal timing was investigated in C57BL/6 female mice: investigating whether population variation in pubertal timing among inbred mice could be explained by environmental factors; whether perturbing the epigenome using a histone deacetylase inhibitor or methyl-donor would alter pubertal timing; and examining genome-wide methylation patterns in hypothalami of early versus late maturing mice. Results demonstrate that measurable micro-environmental factors have only negligible effects on pubertal timing; pubertal timing was significantly altered by administration of epigenetic modifying agents; differences in methylation patterns are subtle. This initial evidence supports the involvement of epigenetic mechanisms in regulating pubertal timing.

Pubertal timing displays wide, normally distributed variation in a healthy population of sexually maturing adolescents. However, like many complex traits, factors contributing to the variation are not well understood. Epigenetic regulation may contribute to some of the population variation. The role that epigenetics, specifically DNA methylation and histone acetylation, may play in regulating pubertal timing was investigated in C57BL/6 female mice: investigating whether population variation in pubertal timing among inbred mice could be explained by environmental factors; whether perturbing the epigenome using a histone deacetylase inhibitor or methyl-donor would alter pubertal timing; and examining genome-wide methylation patterns in hypothalami of early versus late maturing mice. Results demonstrate that measurable micro-environmental factors have only negligible effects on pubertal timing; pubertal timing was significantly altered by administration of epigenetic modifying agents; differences in methylation patterns are subtle. This initial evidence supports the involvement of epigenetic mechanisms in regulating pubertal timing.

La malformation de Chiari type 1 (MCI) est une anomalie congénitale de la jonction cranio-cérébrale fréquente avec une incidence de 1:1280. MCI est caractérisée par la descente des amygdales cérébelleuses à travers le foramen magnum et est souvent associée à la syringomyélie. Les causes de cette maladie semblent être multifactorielles incluant des facteurs génétiques. La MCI est similaire à une malformation fréquente chez la race des Griffon Bruxellois (GB) connue sous le nom de Malformation Chiari-like (MCL). Le modèle canin offre l’avantage d’une forte homogénéité génétique réduisant ainsi la complexité de la maladie et facilitant l’identification d’un locus causatif. Une étude d’association du génome entier sur une cohorte de 56 GB suivie d’une cartographie fine sur une cohorte de 217 GB a identifié un locus fortement associé à la MCL sur le chromosome 2 (22 SNPs, valeur P= 7 x 10-8) avec un haplotype de 1.9 Mb plus fréquent chez les non affectés. Une seconde étude d’association du génome entier sur une cohorte de 113 GB a permis d’identifier un 2 ème locus fortement associé à la MCL sur le chromosome 13 (25 SNPs , valeur P= 3 x 10 -7) avec un haplotype de 4 Mb surreprésenté chez les non affectés. Ces régions candidates constituent la première étape vers l’identification de gènes causatifs pour la MCL. Notre étude offre un point d’entrée vers une meilleure compréhension des mécanismes moléculaires sous-tendant la pathogénèse de la MCI humaine. / Chiari I malformation (CMI) represents a common congenital abnormality of the craniocerebral junction with an estimated incidence of 1 in 1280. CMI is characterized by a descent of the cerebellar tonsils into the foramen magnum, often in association with syringomyelia. The developmental defect in CMI is thought to be the result of an underdeveloped occipital bone and small posterior fossa. The etiology of CMI is thought to be multifactorial involving genetic factors. CMI in humans is similar to a condition in the dog called Chiari-like malformation (CM) that is particularly common in the Griffon Bruxellois (GB) breeds. A genome wide association study on a 56 GB cohort followed by a fine mapping in a 217 GB cohort have identified a locus on chromosome 2 that was strongly associated with CM (22 SNPs, P value= 7 x 10-8). Haploview analysis of this locus identified a haplotype of 1.9 Mb that was more frequent in non-affected dogs. A second genome wide association study in a 113 GB cohort lead to the identification of another locus on chromosome 13 that was strongly associated with CM (25 SNPs , P value= 3 x 10-7). Analysis of this region identified a 4Mb haplotype that was more frequent in non-affected dogs. Our study constitutes the first essential step towards identification of the causative genes in CM. Our study provides an entry point for better understanding of the molecular genetic mechanisms underlying the pathogenesis of human CMI.

Le Syndrome d’Impatiences Musculaires de l’Éveil (SIME) est une maladie neurologique caractérisée par un besoin urgent de bouger les jambes. C’est également l’une des causes les plus fréquentes d’insomnie. C’est une maladie très répandue, avec une prévalence de presque 15 % dans la population générale. Les maladies multifactorielles comme le SIME sont souvent le résultat de l’évolution d’une composante génétique et d’une composante environnementale. Dans le cadre du SIME, les études d’association génomique ont permis l’identification de 4 variants à effet modéré ou faible. Cependant, ces quatre variants n’expliquent qu’une faible partie de la composante génétique de la maladie, ce qui confirme que plusieurs nouveaux variants sont encore à identifier. Le rôle des déséquilibres génomiques (Copy Number Variations ou CNVs) dans le mécanisme génétique du SIME est à ce jour inconnu. Cependant, les CNVs se sont récemment positionnés comme une source d’intérêt majeur de variation génétique potentiellement responsable des phénotypes. En collaboration avec une équipe de Munich, nous avons réalisé deux études CNVs à échelle génomique (biopuces à SNP et hybridation génomique comparée (CGH)) sur des patients SIME d’ascendance germanique. À l’aide d’une étude cas-contrôle, nous avons pu identifier des régions avec une occurrence de CNVs différentes pour les patients SIME, comparés à différents groupes contrôles. L’une de ces régions est particulièrement intéressante, car elle est concordante à la fois avec des précédentes études familiales ainsi qu’avec les récentes études d’associations génomiques. / Restless Legs syndrome (RLS) is a neurological disorder characterized by the urge to move one’s limbs. It is also one of the most frequent causes of insomnia. The prevalence of RLS is estimated to be around 15% in the general population. Complexes disorders like RLS are often the result of the evolution of genetic and environmental components. For RLS, recent Genome Wide Association Study (GWAS) have identified four variants with mild to moderate effects. However, those four variants explain only a small part of the disease heritability and thus, we expect that many new variants are still to be found. The impact of Copy-Number Variation (CNV) in the genetic mechanism of RLS is still unknown. However, many studies have recently position the CNVs as a significant source of genetic variation potentially responsible of phenotypes. In collaboration with a team from Munich, we conducted two genome-wide CNVs studies (Genome Wide SNP chips and Comparative Genomic Hybridization (CGH)) on RLS patients from Germany. Using cases-controls studies, we identified regions with a different occurrence of CNVs for RLS patients, compared to different groups of controls. One of these regions is particularly interesting, as it has already been identified by both linkage and association studies.

Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal

For more than half a decade, lithium has been successfully used to treat bipolar disorder. Worldwide, it is considered the first-line mood stabilizer. Apart from its proven antimanic and prophylactic effects, considerable evidence also suggests an antisuicidal effect in affective disorders. Lithium is also effectively used to augment antidepressant drugs in the treatment of refractory major depressive episodes and prevent relapses in recurrent unipolar depression. In contrast to many psychiatric drugs, lithium has outlasted various pharmacotherapeutic ‘fashions’, and remains an indispensable element in contemporary psychopharmacology. Nevertheless, data from pharmacogenetic studies of lithium are comparatively sparse, and these studies are generally characterized by small sample sizes and varying definitions of response. Here, we present an international effort to elucidate the genetic underpinnings of lithium response in bipolar disorder. Following an initiative by the International Group for the Study of Lithium-Treated Patients (www.IGSLI.org) and the Unit on the Genetic Basis of Mood and Anxiety Disorders at the National Institute of Mental Health,lithium researchers from around the world have formed the Consortium on Lithium Genetics (www.ConLiGen.org) to establish the largest sample to date for genome-wide studies of lithium response in bipolar disorder, currently comprising more than 1,200 patients characterized for response to lithium treatment. A stringent phenotype definition of response is one of the hallmarks of this collaboration. ConLiGen invites all lithium researchers to join its efforts. / Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich.

This work is concerned with the genetic basis of normal human pigmentation variation. Specifically, the role of polymorphisms within the solute carrier family 45 member 2 (SLC45A2 or membrane associated transporter protein; MATP) gene were investigated with respect to variation in hair, skin and eye colour ― both between and within populations. SLC45A2 is an important regulator of melanin production and mutations in the gene underly the most recently identified form of oculocutaneous albinism. There is evidence to suggest that non-synonymous polymorphisms in SLC45A2 are associated with normal pigmentation variation between populations. Therefore, the underlying hypothesis of this thesis is that polymorphisms in SLC45A2 will alter the function or regulation of the protein, thereby altering the important role it plays in melanogenesis and providing a mechanism for normal pigmentation variation. In order to investigate the role that SLC45A2 polymorphisms play in human pigmentation variation, a DNA database was established which collected pigmentation phenotypic information and blood samples of more than 700 individuals. This database was used as the foundation for two association studies outlined in this thesis, the first of which involved genotyping two previously-described non-synonymous polymorphisms, p.Glu272Lys and p.Phe374Leu, in four different population groups. For both polymorphisms, allele frequencies were significantly different between population groups and the 272Lys and 374Leu alleles were strongly associated with black hair, brown eyes and olive skin colour in Caucasians. This was the first report to show that SLC45A2 polymorphisms were associated with normal human intra-population pigmentation variation. The second association study involved genotyping several SLC45A2 promoter polymorphisms to determine if they also played a role in pigmentation variation. Firstly, the transcription start site (TSS), and hence putative proximal promoter region, was identified using 5' RNA ligase mediated rapid amplification of cDNA ends (RLM-RACE). Two alternate TSSs were identified and the putative promoter region was screened for novel polymorphisms using denaturing high performance liquid chromatography (dHPLC). A novel duplication (c.–1176_–1174dupAAT) was identified along with other previously described single nucleotide polymorphisms (c.–1721C>G and c.–1169G>A). Strong linkage disequilibrium ensured that all three polymorphisms were associated with skin colour such that the –1721G, +dup and –1169A alleles were associated with olive skin in Caucasians. No linkage disequilibrium was observed between the promoter and coding region polymorphisms, suggesting independent effects. The association analyses were complemented with functional data, showing that the –1721G, +dup and –1169A alleles significantly decreased SLC45A2 transcriptional activity. Based on in silico bioinformatic analysis that showed these alleles remove a microphthalmia-associated transcription factor (MITF) binding site, and that MITF is a known regulator of SLC45A2 (Baxter and Pavan, 2002; Du and Fisher, 2002), it was postulated that SLC45A2 promoter polymorphisms could contribute to the regulation of pigmentation by altering MITF binding affinity. Further characterisation of the SLC45A2 promoter was carried out using luciferase reporter assays to determine the transcriptional activity of different regions of the promoter. Five constructs were designed of increasing length and their promoter activity evaluated. Constitutive promoter activity was observed within the first ~200 bp and promoter activity increased as the construct size increased. The functional impact of the –1721G, +dup and –1169A alleles, which removed a MITF consensus binding site, were assessed using electrophoretic mobility shift assays (EMSA) and expression analysis of genotyped melanoblast and melanocyte cell lines. EMSA results confirmed that the promoter polymorphisms affected DNA-protein binding. Interestingly, however, the protein/s involved were not MITF, or at least MITF was not the protein directly binding to the DNA. In an effort to more thoroughly characterise the functional consequences of SLC45A2 promoter polymorphisms, the mRNA expression levels of SLC45A2 and MITF were determined in melanocyte/melanoblast cell lines. Based on SLC45A2’s role in processing and trafficking TYRP1 from the trans-Golgi network to stage 2 melanosmes, the mRNA expression of TYRP1 was also investigated. Expression results suggested a coordinated expression of pigmentation genes. This thesis has substantially contributed to the field of pigmentation by showing that SLC45A2 polymorphisms not only show allele frequency differences between population groups, but also contribute to normal pigmentation variation within a Caucasian population. In addition, promoter polymorphisms have been shown to have functional consequences for SLC45A2 transcription and the expression of other pigmentation genes. Combined, the data presented in this work supports the notion that SLC45A2 is an important contributor to normal pigmentation variation and should be the target of further research to elucidate its role in determining pigmentation phenotypes. Understanding SLC45A2’s function may lead to the development of therapeutic interventions for oculocutaneous albinism and other disorders of pigmentation. It may also help in our understanding of skin cancer susceptibility and evolutionary adaptation to different UV environments, and contribute to the forensic application of pigmentation phenotype prediction.

Plus de 170 millions d'individus sont infectés par le VHC dans le monde et 37 millions par le VIH. La coinfection VIH/VHC est fréquente et représente un élément clé de la prise en charge des patients infectés par le VIH. Depuis l'arrivée des HAART, les maladies du foie sont devenues la cause principale de mortalité chez les patients coinfectés VIH/VHC. L'évolution naturelle et le pronostic de l'hépatite C sont plus sévères en cas de coinfection par le VIH du fait d'une fibrose accélérée et d'une évolution rapide vers la cirrhose et ses complications. Certains facteurs accélérant la fibrose hépatique sont clairs aujourd'hui comme: l'absence de recours au traitement anti-VHC, la réplication active du VHC et la consommation excessive d'alcool. De plus, il existe de plus en plus de preuves que les variants génétiques contribuent à la fibrose hépatique chez les patients monoinfectés par le VHC, mais cet aspect a été peu étudié dans la coinfection VIH/VHC.Durant ma thèse, j'ai eu accès aux données d'un échantillon de 494 patients coinfectés génotypés issu de la cohorte ANRS CO13 HEPAVIH. L'histoire naturelle du VIH et du VHC y est renseignée de manière très détaillée et le suivi clinique des patients permet d'avoir des informations précises sur l'état de fibrose hépatique. J'ai pu alors réaliser deux études d'association « génome-entier » pour identifier des polymorphismes associés à la sévérité de la fibrose à l'aide de données complètes de 292 patients. La première étude a mis en évidence une association entre la quantification de l'élasticité hépatique par Fibroscan® et un locus, également répliqué dans la monoinfection par le VHC. Cette association a permis d'identifier deux gènes impliqués dans des mécanismes de maintien de structure et de signalisation cellulaire (CAV3) mais aussi dans la réplication du VHC (RAD18). La seconde étude a identifié deux associations significatives en comparant deux groupes de scores METAVIR (F0F1F2 vs F3F4), en particulier dans le gène CTNND2 qui est impliqué dans un réseau d'interaction associé à des mécanismes moléculaires lié à des maladies hépatiques.Ces deux études sont en cours de publication dans des revues scientifiques internationales à comité de lecture. Ces nouvelles perspectives dans la compréhension des mécanismes de fibrose dans le contexte de la coinfection VIH/VHC pourraient aider à l'identification de nouvelles cibles pour la création de médicaments ou de tests diagnostiques afin d'améliorer les soins des patients. / Over 170 million people worldwide are infected by HCV and 37 million by HIV. Both viruses share the same modes of transmission, and HIV/HCV coinfection is common and represents a key element in the management of patients infected with HIV. Since the appearance of HAART, liver diseases have become the leading cause of death in HIV/HCV coinfected patients. The natural history and prognosis of hepatitis C are more severe in case of coinfection with HIV due to accelerated rate of fibrosis progression and rapid progression to cirrhosis and its complications. Factors accelerating liver fibrosis are known today such as the lack of recourse to anti-HCV treatment, active HCV replication and excessive alcohol consumption. There is increasing evidence that genetic variants contribute to liver fibrosis in HCV monoinfection, but this aspect has been little studied in HIV/HCV coinfection.I have exploited the genotype information from 494 coinfected patients from the cohort ANRS CO13 HEPAVIH. These patients are very-well documented regarding the history of their HIV/HCV infection and are very carefully followed-up, especially regarding the status of liver fibrosis. I have performed two genome-wide association studies to identify polymorphisms associated with the severity of fibrosis from complete data of 292 patients. The first study has dealt with the quantification of liver stiffness by Fibroscan® and an association with the 3p25 region has been identified, also replicated in monoinfection HCV. Two genes involved in cell signaling and structure of holding mechanisms (CAV3) but also in HCV replication (RAD18) appear as good candidates. The second study has unraveled two significant associations by comparing the METAVIR score group (F0F1F2 vs F3F4), especially in the CTNND2 gene implicated in a network of interactions with molecular mechanisms involved in liver diseases.These results are under publications in peer-review international scientific journals. These new insights into the molecular mechanisms of liver fibrosis in patients with HIV/HCV co- infection may help to define new targets for drug development or new diagnostic tests, to improve patient care.