Le projet gnomAD montre l’importance de ne pas avoir qu’un seul génome humain de référence !

International audienc

Identification de facteurs génétiques impliqués dans les troubles du spectre autistique et de la dyslexie

Les troubles du spectre autistique (TSA) touchent approximativement 1% de la population générale. Ces troubles se caractérisent par un déficit de la communication sociale, ainsi que des comportements stéréotypés et des intérêts restreints. Plusieurs gènes impliqués dans le déterminisme des TSA ont été identifiés, comme par exemple les gènes NLGN3-4X, NRXN1-3 et SHANK1-3. Au cours des années précédentes, les TSA ont été considérés comme un ensemble complexe de troubles monogéniques. Cependant, les études récentes du génome complet suggèrent la présence de gènes modificateurs ( multiple hits model ). La dyslexie est caractérisée par un trouble dans l apprentissage de la lecture et de l écriture qui touche 5- 15% de la population générale. Les facteurs génétiques impliqués restent pour l instant inconnus car seuls des gènes ou loci candidats ont été identifiés. Mon projet de thèse avait pour objectif de poursuivre l identification des facteurs génétiques impliqués dans les TSA et de découvrir un premier facteur génétique pour la dyslexie. Pour cela, deux types de populations ont été étudiés : d une part des patients atteints de TSA (N>600) provenant de France, de Suède et des Iles Faroe, d autre part des patients atteints de dyslexie (N>200) provenant de France, en particulier une famille de 11 personnes atteintes sur 3 générations. J ai utilisé à la fois la technologie des puces à ADN Illumina (600 K et 5M) et le séquençage complet du génome humain pour effectuer des analyses de liaison et d association. Pour les TSA, grâce aux analyses de CNVs, j ai pu identifier des gènes candidats pour l autisme et confirmer l association de plusieurs gènes synaptiques avec l autisme. En particulier, l étude d une population de 30 patients des îles Faroe a pu confirmer l implication des gènes NLGN1 et NRXN1 dans l autisme et identifier un nouveau gène candidat IQSEC3. En parallèle, j ai exploréPRRT2 localisé en 16p11.2. PRRT2 code pour un membre du complexe SNARE synaptique qui permet la libération des vésicules synaptiques. Je n ai pas pu mettre en évidence d association avec les TSA, mais j ai montré que ce gène important pour certaines maladies neurologiques était sous pression de sélection différente selon les populations. Pour la dyslexie, j ai effectué une analyse de liaison (méthode des lod-scores) pour une grande famille de 11 individus atteints sur trois générations. Cette étude a permis d identifier CNTNAP2 comme un gène de vulnérabilité à la dyslexie. Cette découverte est importante car ce même gène est aussi associé aux TSA. Par contre, aucune des 20 variations rares découvertes par le séquençage complet du génome n est localisée dans les parties codantes du gène. Plusieurs variations localisées dans des régions régulatrices sont candidates. En conclusion, les résultats de ma thèse ont permis d identifier des gènes candidats pour les TSA, de confirmer le rôle des gènes synaptiques dans ce trouble, de montrer pour la première fois grâce à une analyse de liaison le rôle de CNTNAP2 dans la dyslexie.Autism spectrum disorders (ASD) affect 1% of the general population. These disorders are characterized by deficits in social communication as well as stereotyped behaviors and restricted interests. Several genes involved in the determination of ASD have been identified, such as NLGN3-4, NRXN1-3 and SHANK1-3. In the previous years, ASD have been considered as a complex set of monogenic disorders. Recent studies on the complete genome nevertheless suggest the presence of modifier genes ("multiple hits model"). Dyslexia is characterized by difficulties in learning to read and write. It affects 5-15 % of the general population. Genetic factors involved remain unknown. Only candidate genes or loci have been identified. My thesis had two main objectives: pursuing the identification of genetic factors involved in ASD, and discovering a first genetic factor for dyslexia. I therefore studied two types of populations: on the one hand a group of patients with ASD (N > 600) from France, Sweden and the Faroe Islands, and on the other hand another group of patients with dyslexia (N > 200) from France, and more specifically a family of 11 people followed over 3 generations. I used both Illumina microarrays technology (600K and 5M) and the complete human genome sequencing to conduct linkage and association analyses. Regarding ASD, CNVs (copy number variants) analyses allowed me to confirm the association of several synaptic genes with autism and to identify new candidate genes. In particular, the study of a population of 30 patients from the Faroe Islands confirmed the involvement of NLGN1 and NRXN1 genes in autism and identified a new candidate gene, IQSEC3. At the same time, I explored PRRT2 located in 16p11.2. PRRT2 encodes a member of the synaptic SNARE complex that allows the release of synaptic vesicles. I have not been able to demonstrate any association with ASD, but I showed that this gene, which is important for some neurological diseases, was under different selection pressures according to the population considered. Regarding dyslexia, I realized a linkage analysis (lod-score method) for a large family of 11 individuals, with three generations affected. This study identified the CNTNAP2 gene as a vulnerability factor for dyslexia. This finding is important because this gene is also associated with ASD. Nevertheless, none of the 20 rare variations discovered by whole genome sequencing is localized in the coding parts of the gene. Only several variations localized in regulatory regions are robust candidates. To conclude, my findings enabled the identification of new candidate genes for ASD, the confirmation of the role of synaptic genes in this disorder, and the highlight for the first time of the role of CNTNAP2 in dyslexia through linkage analysis.PARIS5-Bibliotheque electronique (751069902) / SudocSudocFranceF

Étude biochimique et génétique des anomalies de la voie sérotonine-mélatonine comme facteurs de vulnérabilité à l autisme

Les troubles du spectre autistique (TSA) sont définis par l association de troubles des interactions sociales, de troubles du langage et de comportements stéréotypés et intérêts restreints. Cette entité recouvre en réalité des situations cliniques très hétérogènes, tant par le spectre de sévérité des symptômes que par la variété des comorbidités et signes associés. Si l étiologie génétique semble prépondérante, les mécanismes moléculaires impliqués semblent complexes et hétérogènes, et les associations génotype-phénotype inconstantes. Une stratégie possible pour décomposer cette hétérogénéité clinique et génétique consiste à s appuyer sur des endophénotypes, ou phénotypes intermédiaires, pour définir des catégories plus homogènes sur le plan physiopathologique. Parmi les nombreux endophénotypes biologiques décrits dans les TSA, l augmentation de la sérotonine sanguine est l un des mieux documentés, mais les mécanismes en sont encore inconnus. Des déficits en mélatonine (qui est un dérivé de la sérotonine) ont également été rapportés par plusieurs études. L objectif de cette thèse était de caractériser les anomalies de la voie sérotonine-mélatonine dans les TSA, et d en étudier les mécanismes et les corrélats cliniques. L exploration exhaustive de la voie sérotonine-mélatonine à partir de prélèvements sanguins dans une grande cohorte de plus de 200 patients avec TSA et leurs apparentés a permis d estimer la prévalence de l hypersérotoninémie dans les TSA à 45%, et celle du déficit en mélatonine à environ 60%. Cette étude a mis en évidence des anomalies du catabolisme de la sérotonine ainsi que des anomalies de la synthèse de la mélatonine, et a ainsi permis de proposer des mécanismes biochimiques à ces deux endophénotypes. Les anomalies de synthèse de la mélatonine, qui pourraient s accompagner d une augmentation de la N-acétylsérotonine, ont été confirmées sur des échantillons de glandes pinéales et de tractus gastro-intestinal (sources majeures de mélatonine et de sérotonine de l organisme) issus de patients avec TSA. Les gènes impliqués dans la synthèse de la mélatonine (gènes codant pour les enzymes AANAT et ASMT) ont été étudiés dans les TSA, ainsi que dans des pathologies neurodéveloppementales connexes. Les anomalies de la synthèse de mélatonine pourraient être associées aux troubles du sommeil, fréquents chez les patients avec TSAAutism Spectrum Disorders (ASD) are defined by three core symptoms: social interaction impairments, language impairments, and stereotyped behavior and restricted interests. Beyond this definition lie extremely diverse clinical situations, in terms of symptoms severity as well as comorbidities and associated features. The aetiology of ASD is considered to be mostly genetic, but the molecular mechanisms involved seem to be complex and heterogeneous, and the genotype-phenotype associations elusive. One possible strategy for decomposing the clinical and genetic complexity is to focus on endophenotypes, or intermediate phenotypes, to define more homogeneous pathophysiological categories. Among many biological endophenotypes reported in ASD, the increase of blood serotonin is well documented but still unexplained. Deficits in melatonin (which chemically derives from serotonin) have also been described. The aim of this work was to characterize the impairments of the serotonin-melatonin pathway in ASD, and to address their mechanisms and clinical correlates. Based on a comprehensive assessment of the serotonin-melatonin pathway from blood samples in a large cohort of 200 patients with ASD and their relatives, the prevalence of hyperserotonemia in ASD was estimated to be 45%, and that of melatonin deficit about 60%. Impairments of serotonin catabolism were shown, as well as impairments of melatonin synthesis, thus providing biochemical mechanisms for both endophenotypes. Abnormal melatonin synthesis, which may involve an increase in N-acetylserotonin, was confirmed on pineal gland and gastro-intestinal tract samples (i.e. the major sources of melatonin and serotonin) from patients with ASD. The genes involved in melatonin synthesis (coding for AANAT and ASMT enzymes) were studied in ASD and in related neurodevelopmental disorders. Abnormal melatonin synthesis may be associated with sleep disorders, frequently observed in patients with ASDPARIS5-Bibliotheque electronique (751069902) / SudocSudocFranceF

Screening, intervention and outcome in autism and other developmental disorders: the role of randomized controlled trials

We draw attention to a number of important considerations in the arguments about screening and outcome of intervention in children with autism and other developmental disorders. Autism screening in itself never provides a final clinical diagnosis, but may well identify developmental deviations indicative of autism—or of other developmental disorders—that should lead to referral for further clinical assessment. Decisions regarding population or clinic screening cannot be allowed to be based on the fact that prospective longitudinal RCT designs over decades could never be performed in complex developmental disorders. We propose an alternative approach. Early screening for autism and other developmental disorders is likely to be of high societal importance and should be promoted and rigorously evaluated

Shank2 Mutant Mice Display Hyperactivity Insensitive to Methylphenidate and Reduced Flexibility in Social Motivation, but Normal Social Recognition

Mouse models of autism can be used to study evolutionarily conserved mechanisms underlying behavioral abnormalities in social communication and repetitive behaviors. SHANK genes code for synaptic scaffolding proteins at excitatory synapses and mutations in all SHANK genes have been associated with autism. Here, we present three behavioral aspects of the mutant mice deleted for exon 16 in Shank2. First, we treated Shank2 mutant mice with methylphenidate to rescue the hyperactivity. Our failure to do so suggests that the hyperactivity displayed by Shank2 mutant mice is not related to the one displayed by the typical mouse models of hyperactivity, and might be more closely related to manic-like behaviors. Second, by testing the effect of group housing and social isolation on social interest, we highlighted that Shank2 mutant mice lack the typical flexibility to modulate social interest, in comparison with wild-type littermates. Finally, we established a new protocol to test for social recognition in a social context. We used this protocol to show that Shank2 mutant mice were able to discriminate familiar and unknown conspecifics in free interactions. Altogether, these studies shed some light on specific aspects of the behavioral defects displayed by the Shank2 mouse model. Such information could be used to orient therapeutic strategies and to design more specific tests to characterize the complex behavior of mouse models of autism

Definition and clinical variability of SHANK3-related Phelan-McDermid syndrome

Phelan-McDermid syndrome (PMS) is an infrequently described syndrome that presents with a disturbed development, neurological and psychiatric characteristics, and sometimes other comorbidities. As part of the development of European medical guidelines we studied the definition, phenotype, genotype-phenotype characteristics, and natural history of the syndrome. The number of confirmed diagnoses of PMS in different European countries was also assessed and it could be concluded that PMS is underdiagnosed. The incidence of PMS in European countries is estimated to be at least 1 in 30,000. Next generation sequencing, including analysis of copy number variations, as first tier in diagnostics of individuals with intellectual disability will likely yield a larger number of individuals with PMS than presently known. A definition of PMS by its phenotype is at the present not possible, and therefore PMS-SHANK3 related is defined by the presence of SHANK3 haploinsufficiency, either by a deletion involving region 22q13.2–33 or a pathogenic/likely pathogenic variant in SHANK3. In summarizing the phenotype, we subdivided it into that of individuals with a 22q13 deletion and that of those with a pathogenic/likely pathogenic SHANK3 variant. The phenotype of individuals with PMS is variable, depending in part on the deletion size or whether only a variant of SHANK3 is present. The core phenotype in the domains development, neurology, and senses are similar in those with deletions and SHANK3 variants, but individuals with a SHANK3 variant more often are reported to have behavioural disorders and less often urogenital malformations and lymphedema. The behavioural disorders may, however, be a less outstanding feature in individuals with deletions accompanied by more severe intellectual disability. Data available on the natural history are limited. Results of clinical trials using IGF-1, intranasal insulin, and oxytocin are available, other trials are in progress. The present guidelines for PMS aim at offering tools to caregivers and families to provide optimal care to individuals with PMS.</p

Social and non-social autism symptom and trait domains are genetically dissociable

The core diagnostic criteria for autism comprise two symptom domains – social and communication difficulties, and unusually repetitive and restricted behaviour, interests and activities. There is some evidence to suggest that these two domains are dissociable, yet, this hypothesis has not been tested using molecular genetics. We test this using a GWAS of a non-social autistic trait, systemizing (N = 51,564), defined as the drive to analyse and build systems. We demonstrate that systemizing is heritable and genetically correlated with autism. In contrast, we do not identify significant genetic correlations between social autistic traits and systemizing. Supporting this, polygenic scores for systemizing are significantly positively associated with restricted and repetitive behaviour but not with social difficulties in autistic individuals. These findings strongly suggest that the two core domains of autism are genetically dissociable, and point at how to fractionate the genetics of autism

Social and non-social autism symptoms and trait domains are genetically dissociable

Abstract: The core diagnostic criteria for autism comprise two symptom domains – social and communication difficulties, and unusually repetitive and restricted behaviour, interests and activities. There is some evidence to suggest that these two domains are dissociable, though this hypothesis has not yet been tested using molecular genetics. We test this using a genome-wide association study (N = 51,564) of a non-social trait related to autism, systemising, defined as the drive to analyse and build systems. We demonstrate that systemising is heritable and genetically correlated with autism. In contrast, we do not identify significant genetic correlations between social autistic traits and systemising. Supporting this, polygenic scores for systemising are significantly and positively associated with restricted and repetitive behaviour but not with social difficulties in autistic individuals. These findings strongly suggest that the two core domains of autism are genetically dissociable, and point at how to fractionate the genetics of autism