Browsing by Author "Mouga, S."
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- Convergence of genes and cellular pathways dysregulated in autism spectrum disordersPublication . Pinto, D.; Delaby, E.; Merico, D.; Barbosa, M.; Merikangas, A.; Klei, L; Thiruvahindrapuram, B.; Xu, X.; Ziman, R.; Wang, Z.; Vorstman, J.A.; Thompson, A.; Regan, R.; Pilorge, M.; Pellecchia, G.; Pagnamenta, A.T.; Oliveira, B.; Marshall, C.R.; Magalhães, T.R.; Lowe, J.K.; Howe, J.L.; Griswold, A.J.; Gilbert, J.; Duketis, E.; Dombroski, B.A.; De Jonge, M.V.; Cuccaro, M.; Crawford, E.L.; Correia, C.T.; Conroy, J.; Conceição, I.C; Chiocchetti, A.G.; Casey, J.P.; Cai, G.; Cabrol, C.; Bolshakova, N.; Bacchelli, E.; Anney, R.; Gallinger, S.; Cotterchio, M.; Casey, G.; Zwaigenbaum, L.; Wittemeyer, K.; Wing, K.; Wallace, S.; van Engeland, H.; Tryfon, A.; Thomson, S.; Soorya, L.; Rogé, B.; Roberts, W.; Poustka, F.; Mouga, S.; Minshew, N.; McInnes, L.A.; McGrew, S.G.; Lord, C.; Leboyer, M.; Le Couteur, A.S.; Kolevzon, A.; Jiménez González, P.; Jacob, S.; Holt, R.; Guter, S.; Green, J.; Green, A.; Gillberg, C.; Fernandez, B.A.; Duque, F.; Delorme, R.; Dawson, G.; Chaste, P.; Café, C.; Brennan, S.; Bourgeron, T.; Bolton, P.F.; Bölte, S.; Bernier, R.; Baird, G.; Bailey, A.J.; Anagnostou, E.; Almeida, J.; Wijsman, E.M.; Vieland, V.J.; Vicente, A.M.; Schellenberg, G.D.; Pericak-Vance, M.; Paterson, A.D.; Parr, J.R.; Oliveira, G.; Nurnberger, J.I.; Monaco, A.P.; Maestrini, E.; Klauck, S.M.; Hakonarson, H.; Haines, J.L.; Geschwind, D.H.; Freitag, C.M.; Folstein, S.E.; Ennis, S.; Coon, H.; Battaglia, A.; Szatmari, P.; Sutcliffe, J.S.; Hallmayer, J.; Gill, M.; Cook, E.H.; Buxbaum, J.D.; Devlin, B.; Gallagher, L.; Betancur, C.Rare copy-number variation (CNV) is an important source of risk for autism spectrum disorders (ASDs). We analyzed 2,446 ASD-affected families and confirmed an excess of genic deletions and duplications in affected versus control groups (1.41-fold, p = 1.0 × 10(-5)) and an increase in affected subjects carrying exonic pathogenic CNVs overlapping known loci associated with dominant or X-linked ASD and intellectual disability (odds ratio = 12.62, p = 2.7 × 10(-15), ∼3% of ASD subjects). Pathogenic CNVs, often showing variable expressivity, included rare de novo and inherited events at 36 loci, implicating ASD-associated genes (CHD2, HDAC4, and GDI1) previously linked to other neurodevelopmental disorders, as well as other genes such as SETD5, MIR137, and HDAC9. Consistent with hypothesized gender-specific modulators, females with ASD were more likely to have highly penetrant CNVs (p = 0.017) and were also overrepresented among subjects with fragile X syndrome protein targets (p = 0.02). Genes affected by de novo CNVs and/or loss-of-function single-nucleotide variants converged on networks related to neuronal signaling and development, synapse function, and chromatin regulation.
- Copy number variants involving components of the glutamatergic synaptic pathway in ASD patientsPublication . Oliveira, B.A.; Conceição, I.C.; Correia, C.A.; Café, C.; Almeida, J.; Mouga, S.; Duque, F.; Oliveira, G.; Vicente, A.M.Copy Number Variants (CNVs) play an important role in susceptibility to Autism Spectrum Disorders (ASD), in particular when deleting or duplicating genes involved in synaptic structure and function such as glutamatergic synapse genes. Identifying CNVs of etiologic relevance for ASD that include glutamatergic genes may contribute to the understanding of glutamate-related pathogenic mechanisms in this disorder.
- Definition of a putative pathological region in PARK2 associated with autism spectrum disorder through in silico analysis of its functional structurePublication . Conceição, I.C.; Rama, M.M.; Oliveira, B.; Café, C.; Almeida, J.; Mouga, S.; Duque, F.; Oliveira, G.; Vicente, A.M.Objective: The PARK2 gene encodes Parkin, a component of a multiprotein E3 ubiquitin ligase complex that targets substrate proteins for proteasomal degradation. PARK2 mutations are frequently associated with Parkinson’s disease, but structural alterations have also been described in patients with neurodevelopmental disorders (NDD), suggesting a pathological effect ubiquitous to neurodevelopmental and neurodegenerative brain processes. The present study aimed to define the critical regions for NDD within PARK2. Materials and methods: To clarify PARK2 involvement in NDDs, we examined the frequency and location of copy number variants (CNVs) identified in patients from our sample and reported in the literature and relevant databases, and compared with control populations. Results: Overall, the frequency of PARK2 CNVs was higher in controls than in NDD cases. However, closer inspection of the CNV location in PARK2 showed that the frequency of CNVs targeting the Parkin C-terminal, corresponding to the ring-between-ring (RBR) domain responsible for Parkin activity, is significantly higher in NDD cases than in controls. In contrast, CNVs targeting the N-terminal of Parkin, including domains that regulate ubiquitination activity, are very common both in cases and in controls. Conclusion: Although PARK2 may be a pathological factor for NDDs, likely not all variants are pathogenic, and a conclusive assessment of PARK2 variant pathogenicity requires an accurate analysis of their location within the coding region and encoded functional domains.
- Differential diagnosis of Autism Spectrum Disorder (ASD) by CNV detection – can early diagnosis be improved?Publication . Kwiatkowska, K.; Conceição, I.C.; Rodrigues, A.C.; Picanço, I.; Marques, I.; Melo, J.; Ferreira, S.; Café, C.; Almeida, J.; Mouga, S.; Oliveira, G.; Vicente, A.M.Autism Spectum Disorder (ASD) is an impairment in neurodevelopment that can be recognized in the first years of life. Symptoms are diverse and vary in severity, determining prognosis and influencing the integration in the community. ASD is characterized by difficulties in interpersonal interaction, verbal and nonverbal communication, and by uncommon interests, inappropriate and uncontrolled behaviors, and repetitive activities. Specific and early diagnosis allows early and effective intervention that improves learning, communication and social skills of autistic children.
- Expression Profile of Circulating miRNAs in Autism Spectrum DisordersPublication . Rodrigues, A.C.; Conceição, I.C.; Kwiatkowska, K.; Picanço, I.; Café, C.; Almeida, J.; Mouga, S.; Enguita, F.J.; Oliveira, G.; Vicente, A.M.Autism Spectrum Disorder (ASD) is a common disorder with an heterogeneous clinical presentation and unclear etiology. Rare, highly penetrant, variants explain approximately 20% of ASD genetic liability, while common genetic factors of low effect, which combine in affected individuals to reach a pathological threshold, have not yet been identified. Epigenetic factors may additionally modulate the effect of genetic variants. ASD overlaps with other Neurodevelopmental Disorders (NDD), both in clinical aspects and in causative genetic variants, frequently rendering specific diagnosis difficult1,5. Here we hypothesize that, while genetic variants overlap in a large extent between NDDs, epigenetic factors may regulate the expression, activity or function of genetic factors, leading to the characteristic phenotypic presentation that differentiates ASD from other NDDs. To test this hypothesis, we addressed the role of epigenetic factors in ASD, focusing on microRNAs (miRNAs). These small noncoding RNA molecules negatively regulate gene expression, influencing many biological processes and, because they are released from pathological tissues to plasma in disease situations, may constitute useful biomarkers. We thus profiled miRNAs in plasma from ASD patients and patients with other NDDs.
- Expression Profile of Circulating miRNAs in Autism Spectrum Disorders Population samplePublication . Conceição, I.C.; Rodrigues, A.C.; Kwiatkowska, K.; Picanço, I.; Café, C.; Almeida, J.; Mouga, S.; Enguita, F.J.; Oliveira, G.; Vicente, A.M.Autism Spectrum Disorder (ASD) is a common complex disorder, highly heterogeneous and with unclear etiology. While many different rare variants are known to be etiological factors for ASD, they don’t completely explain the genetic variance in this disorder, and common genetic variants could not, thus far, be identified. The possible contribution of epigenetic factors, such as deregulated miRNAs expression, should be addressed. miRNAs are small noncoding RNA molecules that negatively regulate gene expression via degradation or translational repression of their target messenger RNAs. miRNAs play critical roles in several biological processes, and are associated with human pathology. Recent studies have suggested that miRNAs in plasma and serum might be derived from circulating blood cells under healthy conditions, but might be released from pathological tissues during illness. The strong correlation between circulating and tissue miRNAs indicates that circulating miRNAs might be biomarkers for diseases, including central nervous system disorders. We are currently assessing miRNA profiles in plasma from ASD patients and patients with other neurodevelopmental disabilities (eg. psychomotor developmental delay, intellectual disability, etc).
- Recurrent duplications of the annexin A1 gene (ANXA1) in autism spectrum disordersPublication . Correia, C.T.; Conceição, I.C.; Oliveira, B.; Coelho, J.; Sousa, I.; Sequeira, A.F.; Almeida, J.; Café, C.; Duque, F; Mouga, S.; Roberts, W.; Gao, K.; Lowe, J.K.; Thiruvahindrapuram, B.; Walker, S.; Marshall, C.R.; Pinto, D.; Nurnberger, J.I.; Scherer, S.W.; Geschwind, D.H.; Oliveira, G.; Vicente, A.M.Validating the potential pathogenicity of copy number variants (CNVs) identified in genome-wide studies of autism spectrum disorders (ASD) requires detailed assessment of case/control frequencies, inheritance patterns, clinical correlations, and functional impact. Here, we characterize a small recurrent duplication in the annexin A1 (ANXA1) gene, identified by the Autism Genome Project (AGP) study.
- Synaptic Transmission: Looking for Clues to Autism Spectrum Disorders (ASD) Etiology in Copy Number Variants Containing Synaptic GenesPublication . Oliveira, B.A.; Correia, C.A.; Conceição, I.C.; Café, C.; Almeida, J.; Mouga, S.; Duque, F.; Oliveira, G.; Vicente, A.M.Copy Number Variants (CNVs) play an important role in susceptibility to ASD, often mediated by the deletion or duplication of genes involved in synaptic structure and function. Increasing evidence suggests a central role for defects in synaptic structure and function in the pathogenesis of non-syndromic ASD. In this study we tested the hypothesis of an enrichment in CNVs encompassing synaptic transmission genes in ASD
- The impact of the metabotropic glutamate receptor and other gene family interaction networks on autismPublication . Hadley, D.; Wu, Z.L.; Kao, C.; Kini, A.; Mohamed-Hadley, A.; Thomas, K.; Vazquez, L.; Qiu, H.; Mentch, F.; Pellegrino, R.; Kim, C.; Connolly, J.; Glessner, J.; Hakonarson, H.; Pinto, D.; Merikangas, A.; Klei, L.; Vorstman, J.A.; Thompson, A.; Regan, R.; Pagnamenta, A.T.; Oliveira, B.; Magalhaes, T.R.; Gilbert, J.; Duketis, E.; De Jonge, M.V.; Cuccaro, M.; Correia, C.T.; Conroy, J.; Conceição, I.C.; Chiocchetti, A.G.; Casey, J.P.; Bolshakova, N.; Bacchelli, E.; Anney, R.; Zwaigenbaum, L.; Wittemeyer, K.; Wallace, S.; Engeland, Hv; Soorya, L.; Rogé, B.; Roberts, W.; Poustka, F.; Mouga, S.; Minshew, N.; McGrew, S.G.; Lord, C.; Leboyer, M.; Le Couteur, A.S.; Kolevzon, A.; Jacob, S.; Guter, S.; Green, J.; Green, A.; Gillberg, C.; Fernandez, B.A.; Duque, F.; Delorme, R.; Dawson, G.; Café, C.; Brennan, S.; Bourgeron, T.; Bolton, P.F.; Bölte, S.; Bernier, R.; Baird, G.; Bailey, A.J.; Anagnostou, E.; Almeida, J.; Wijsman, E.M.; Vieland, V.J.; Vicente, A.M.; Schellenberg, G.D.; Pericak-Vance, M.; Paterson, A.D.; Parr, J.R.; Oliveira, G.; Almeida, J.; Café, C.; Mouga, S.; Correia, C.; Nurnberger, J.I.; Monaco, A.P.; Maestrini, E.; Klauck, S.M.; Hakonarson, H.; Haines, J.L.; Geschwind, D.H.; Freitag, C.M.; Folstein, S.E.; Ennis, S.; Coon, H.; Battaglia, A.; Szatmari, P.; Sutcliffe, J.S.; Hallmayer, J.; Gill, M.; Cook, E.H.; Buxbaum, J.D.; Devlin, B.; Gallagher, L.; Betancur, C.; Scherer, S.W.Although multiple reports show that defective genetic networks underlie the aetiology of autism, few have translated into pharmacotherapeutic opportunities. Since drugs compete with endogenous small molecules for protein binding, many successful drugs target large gene families with multiple drug binding sites. Here we search for defective gene family interaction networks (GFINs) in 6,742 patients with the ASDs relative to 12,544 neurologically normal controls, to find potentially druggable genetic targets. We find significant enrichment of structural defects (P≤2.40E-09, 1.8-fold enrichment) in the metabotropic glutamate receptor (GRM) GFIN, previously observed to impact attention deficit hyperactivity disorder (ADHD) and schizophrenia. Also, the MXD-MYC-MAX network of genes, previously implicated in cancer, is significantly enriched (P≤3.83E-23, 2.5-fold enrichment), as is the calmodulin 1 (CALM1) gene interaction network (P≤4.16E-04, 14.4-fold enrichment), which regulates voltage-independent calcium-activated action potentials at the neuronal synapse. We find that multiple defective gene family interactions underlie autism, presenting new translational opportunities to explore for therapeutic interventions.
- Use of machine leaning approaches to explore genetic and phenotypic associations for Autism Spectrum DisorderPublication . Asif, M.; Conceição, I.C.; Machado, C.; Pereira, P.; Café, C.; Almeida, J.; Mouga, S.; Oliveira, G.; Couto, F.; Vicente, A.M.Introduction: Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder of high complexity ASD is characterized by impaired social interaction and communication and by stereotyped behaviors, and a high heterogeneity in clinical presentation. It is hypothesized that such complex heterogeneous phenotypic behaviors are associated with genetic factors. To further dissect the complex correlations between phenotype and genotype in ASD, in the current study we used powerful machine learning algorithms, like decision trees, to integrate clinical information from diagnostic instruments like the ADI-R and the ADOS as well as adaptive behavior and cognitive scales (VABS and WISC) with genetic data (Copy Number Variants, CNVs). ASD traits in parents were assessed using specific tools SRS and PSPQ.