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Background: Tourette syndrome (TS) is a childhood-onset neurodevelopmental disorder of complex genetic architecture and is characterized by multiple motor tics and at least one vocal tic persisting for more than 1 year. Methods: We performed a genome-wide meta-analysis integrating a novel TS cohort with previously published data, resulting in a sample size of 6133 individuals with TS and 13,565 ancestry-matched control participants. Results: We identified a genome-wide significant locus on chromosome 5q15. Integration of expression quantitative trait locus, Hi-C (high-throughput chromosome conformation capture), and genome-wide association study data implicated the NR2F1 gene and associated long noncoding RNAs within the 5q15 locus. Heritability partitioning identified statistically significant enrichment in brain tissue histone marks, while polygenic risk scoring of brain volume data identified statistically significant associations with right and left thalamus volumes and right putamen volume. Conclusions: Our work presents novel insights into the neurobiology of TS, thereby opening up new directions for future studies.

Η διδακτορική μου διατριβή επικεντρώνεται στις υπολογιστικές μεθόδους και τα σύνολα εντολών για την ανάλυση διαφορετικών τύπων γονιδιωματικών, μεταγραφικών και επιγονιδιωματικών δεδομένων με στόχο την κατανόηση της αιτιολογίας του συνδρόμου Gilles de la Tourette (GTS), μιας ψυχιατρικής διαταραχής πολύπλοκου υποβάθρου. Οι εξελίξεις στις τεχνολογίες μικροσυστοιχιών έχουν καταστήσει δυνατή την ανάλυση του γονιδιώματος μεγάλων ομάδων ασθενών παράγοντας τεράστιο όγκο δεδομένων. Η ανάλυση του μεγάλου όγκου δεδομένων από τις τεχνολογίες μικροσυστοιχιών πρέπει να αντιμετωπίσει ένα ευρύ φάσμα προβλημάτων, που εκτείνονται από το βασικό έλεγχο ποιότητας έως τα πολύπλοκα μοντέλα συσχέτισης. Η ανάλυση τέτοιων δεδομένων μεγάλου όγκου υποβάλλονται σε αυστηρό ποιοτικό έλεγχο τόσο σε επίπεδο παραλλαγών όσο και επίπεδο δειγμάτων για την εξάλειψη τεχνικών προβλημάτων που μειώνουν τα ψευδώς θετικά αποτελέσματα της συσχέτισης. Εδώ παρουσιάζουμε τις υπολογιστικές μεθόδους και τα σύνολα εντολών που χρησιμοποιούνται για την ανάλυση της γονιδιακής έκφρασης σε επίπεδο ολόκληρου του γονιδιώματος, των μονονουκλεοτιδικών πολυμορφισμών (SNPs), των παραλλαγών αριθμού αντιγράφων (CNVs) και των μελετών δεικτών μεθυλίωσης DNA. Η εφαρμογή των παραπάνω μεθόδων στο GTS ρίχνουν φως στην αιτιολογία της διαταραχής, εμπλέκοντας πολλά υποψήφια γονίδια προδιάθεσης που δικαιολογούν περαιτέρω διερεύνηση.

Background: Tourette Syndrome (TS) is a neurodevelopmental disorder that presents with motor and vocal tics early in childhood. The aim of this study was to investigate genetic variants in the 3' untranslated region (3'UTR) of TS candidate genes with a putative link to microRNA (miRNA) mediated regulation or gene expression. Methods: We used an in silico approach to identify 32 variants in the 3'UTR of 18 candidate genes putatively changing the binding site for miRNAs. In a sample composed of TS cases and controls (n = 290), as well as TS family trios (n = 148), we performed transmission disequilibrium test (TDT) and meta-analysis. Results: We found positive association of rs3750486 in the LIM homeobox 6 (LHX6) gene (p = 0.021) and rs7795011 in the inner mitochondrial membrane peptidase subunit 2 (IMMP2L) gene (p = 0.029) with TS in our meta-analysis. The TDT showed an over-transmission of the A allele of rs1042201 in the arylacetamide deacetylase (AADAC) gene in TS patients (p = 0.029). Conclusion: This preliminary study provides further support for the involvement of LHX6, IMMP2L, and AADAC genes, as well as epigenetic mechanisms, such as altered miRNA mediated gene expression regulation in the etiology of TS.

Purpose of Review Gilles de la Tourette syndrome (TS) is a childhood-onset neurodevelopmental disorder characterized by multiple motor and vocal tics, commonly associated with attention deficit hyperactivity disorder (ADHD), obsessive–compulsive disorder (OCD) and autism spectrum disorders (ASDs). Here, we summarize and discuss evidence pointing to a shared genetic basis among TS, OCD, ADHD and ASD.

Tic disorders are moderately heritable common psychiatric disorders that can be highly troubling, both in childhood and in adulthood. In this study, we report results obtained in the first epigenome-wide association study (EWAS) of tic disorders. The subjects are participants in surveys at the Netherlands Twin Register (NTR) and the NTR biobank project. Tic disorders were measured with a self-report version of the Yale Global Tic Severity Scale Abbreviated version (YGTSS-ABBR), included in the 8th wave NTR data collection (2008). DNA methylation data consisted of 411,169 autosomal methylation sites assessed by the Illumina Infinium HumanMethylation450 BeadChip Kit (HM450k array). Phenotype and DNA methylation data were available in 1,678 subjects (mean age = 41.5). No probes reached genome-wide significance (p < 1.2 × 10−7). The strongest associated probe was cg15583738, located in an intergenic region on chromosome 8 (p = 1.98 × 10−6). Several of the top ranking probes (p < 1 × 10−4) were in or nearby genes previously associated with neurological disorders (e.g., GABBRI, BLM, and ADAM10), warranting their further investigation in relation to tic disorders. The top significantly enriched gene ontology (GO) terms among higher ranking methylation sites included anatomical structure morphogenesis (GO:0009653, p = 4.6 × 10−15) developmental process (GO:0032502, p = 2.96 × 10−12), and cellular developmental process (GO:0048869, p = 1.96 × 10−12). Overall, these results provide a first insight into the epigenetic mechanisms of tic disorders. This first study assesses the role of DNA methylation in tic disorders, and it lays the foundations for future work aiming to unravel the biological mechanisms underlying the architecture of this disorder.

The Neolithic populations, which colonized Europe approximately 9,000 y ago, presumably migrated from Near East to Anatolia and from there to Central Europe through Thrace and the Balkans. An alternative route would have been island hopping across the Southern European coast. To test this hypothesis, we analyzed genome-wide DNA polymorphisms on populations bordering the Mediterranean coast and from Anatolia and mainland Europe. We observe a striking structure correlating genes with geography around the Mediterranean Sea with characteristic east to west clines of gene flow. Using population network analysis, we also find that the gene flow from Anatolia to Europe was through Dodecanese, Crete, and the Southern European coast, compatible with the hypothesis that a maritime coastal route was mainly used for the migration of Neolithic farmers to Europe.

Gilles de la Tourette syndrome (GTS) is a neuropsychiatric disorder characterized by multiple motor and vocal tics. GTS is a complex disorder, with environmental factors and several genes involved. Although variations within a few genes such as AADAC, NRXN1, SLITRK1, HDC, and IMMP2L have been tentatively associated with GTS (in a small number of patients), the causative genes underlying GTS pathophysiology remain unknown. In a previous genome-wide association study (GWAS) a single nucleotide polymorphism (SNP, rs2060546) near the Netrin-4 (NTN4 - MIM 610401) gene was shown to be associated with GTS [odds ratio (OR) = 1.7; p-value = 5.8 × 10-7] thus warranting further investigations. As NTN4 is one of the axon guidance molecules expressed in the central nervous system and it interacts with the encoded proteins of SLIT and WNT genes guiding the growth cone toward its target, it is an attractive candidate susceptibility gene for GTS. In this study we attempted to replicate the association of rs2060546 with GTS by genotyping a Danish cohort of 240 GTS patients and 1006 healthy controls. Our results did not reveal an association (OR = 1.363; p-value = 0.3329) in the Danish cohort alone, which may be due to the small sample size. However, a meta-analysis including the present cohort and a total of 1316 GTS patients and 5023 controls from the GTS GWAS Replication Initiative (GGRI) and the first GTS-GWAS yielded a significant signal (OR = 3.74; p-value = 0.00018) and same direction of effect in the three cohorts. Thus, our study strengthens the evidence of the possible involvement of NTN4 in GTS etiology, suggesting that further studies in even larger samples and functional studies are warranted to investigate the role of this region in GTS pathogenesis.

Contains fulltext : 168171.pdf (Publisher’s version ) (Open Access) Gilles de la Tourette Syndrome (GTS) is characterized by the presence of multiple motor and phonic tics with a fluctuating course of intensity, frequency, and severity. Up to 90% of patients with GTS present with comorbid conditions, most commonly attention-deficit/hyperactivity disorder (ADHD), and obsessive-compulsive disorder (OCD), thus providing an excellent model for the exploration of shared etiology across disorders. TS-EUROTRAIN (FP7-PEOPLE-2012-ITN, Grant Agr.No. 316978) is a Marie Curie Initial Training Network (http://ts-eurotrain.eu) that aims to elucidate the complex etiology of the onset and clinical course of GTS, investigate the neurobiological underpinnings of GTS and related disorders, translate research findings into clinical applications, and establish a pan-European infrastructure for the study of GTS. This includes the challenges of (i) assembling a large genetic database for the evaluation of the genetic architecture with high statistical power; (ii) exploring the role of gene-environment interactions including the effects of epigenetic phenomena; (iii) employing endophenotype-based approaches to understand the shared etiology between GTS, OCD, and ADHD; (iv) establishing a developmental animal model for GTS; (v) gaining new insights into the neurobiological mechanisms of GTS via cross-sectional and longitudinal neuroimaging studies; and (vi) partaking in outreach activities including the dissemination of scientific knowledge about GTS to the public. Fifteen partners from academia and industry and 12 PhD candidates pursue the project. Here, we aim to share the design of an interdisciplinary project, showcasing the potential of large-scale collaborative efforts in the field of GTS. Our ultimate aims are to elucidate the complex etiology and neurobiological underpinnings of GTS, translate research findings into clinical applications, and establish Pan-European infrastructure for the study of GTS and associated disorders.

Background Tourette Syndrome (TS) is a neurodevelopmental disorder that presents early in childhood and is marked by the appearance of multiple involuntary motor tics and at least one vocal tic. It presents high comorbidity rates with other disorders such as attention deficit hyperactivity disorder (ADHD) and obsessive compulsive disorder (OCD). Despite a strong genetic contribution, the molecular mechanisms behind TS are still uncertain, although multiple lines of evidence suggest involvement of specific candidate genes and corresponding epigenetic mechanisms via miRNA regulators. Methods To date only a few genetic findings have been replicated in TS. Among these the nicotinic acetylcholine receptor alpha 7 subunit (CHRNA7) gene has been recently suggested as candidate susceptibility gene. CHRNA7 is known to regulate a wide variety of developmental and secretory functions, however, the mechanism of its transcriptional regulation is still unclear [1]. Another recent promising finding in TS genetic research is Netrin 4 (NTN4), which belongs to a family of extracellular proteins that direct axon outgrowth and guidance [2]. Several microRNAs have already been associated with neuropsychiatric disorders, but most importantly a few miRNA have also been associated with Tourette Syndrome [3,4].Our goal was to investigate the role of selected candidate genes in a case-control setup along with functional validation involving miRNA regulation in the possible involvement in TS pathogenesis through analysis of 3’UTR regions. Results An OpenArray platform (TaqMan® OpenArray® Genotyping System) was used for the case-control analysis of TS patients (N=564) and healthy controls. Starting from a list of candidate genes previously indicated as possible risk factors for TS, we screened for presence of SNPs in the 3’UTR regulatory regions. This analysis (data retrieved by mirSNP and polymiRTS databases) led to the identification of 32 SNPs which were predicted to change the seed sequence of in silico proposed miRNAs. To proof this concept, we performed functional validation study using a luciferase assay reporter containing 3’ UTR regions of CHRNA7 and NTN4 transfected with their predicted miRNA. Specifically, miRNA-106b and miRNA-198b were identified as the most potent miRNA candidates for regulation of CHRNA7 and NTN4 gene expression. SKNF1 and HEK human cell lines were co-transfected using lipofectamine with the luciferase reporter-3’ UTR construct of CHRNA7 and NTN4 (SwitchGear Genomics) and the corresponding putative miRNAs (miR-106b, miR-198b) along with non-targeting control miRNAs (miR-196b, miR-641b) in the functional validation studies. Discussion In order to increase our understanding of the underlying genetic and epigenetic mechanisms of TS, we aimed to study the possible miRNA regulation processes in TS-related genes, which would help not only to better understand the full genetic architecture of this disorder but also to determine how miRNAs contribute to the complexity of gene regulation in the development of disease. OpenArray analysis identified significant differences among the selected candidates genes (LHX6, iMMP2L) confirming the implication of those genes in TS etiology. In the luciferase assays we characterized the regulatory effect of the predicted miRNAs on the expression candidate genes in a concentration-dependent manner, which showed up to 5-fold change in the relative gene expression levels in case of CHRNA7 and NTN4 thereby proving the concept of our study.

An important challenge in drug discovery and disease prognosis is to predict genes that are preferentially expressed in one or a few tissues, i.e. showing a considerably higher expression in one tissue(s) compared to the others. Although several data sources and methods have been published explicitly for this purpose, they often disagree and it is not evident how to retrieve these genes and how to distinguish true biological findings from those that are due to choice-of-method and/or experimental settings. In this work we have developed a computational approach that combines results from multiple methods and datasets with the aim to eliminate method/study-specific biases and to improve the predictability of preferentially expressed human genes. A rule-based score is used to merge and assign support to the results. Five sets of genes with known tissue specificity were used for parameter pruning and cross-validation. In total we identify 3434 tissue-specific genes. We compare the genes of highest scores with the public databases: PaGenBase (microarray), TiGER (EST) and HPA (protein expression data). The results have 85% overlap to PaGenBase, 71% to TiGER and only 28% to HPA. 99% of our predictions have support from at least one of these databases. Our approach also performs better than any of the databases on identifying drug targets and biomarkers with known tissue-specificity.