Browsing by Author "Oliveira, G."
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- A 3.2 Mb deletion on 18q12 in a patient with childhood autism and high-grade myopiaPublication . Gilling, M.; Lauritsen, M.B.; Møller, M.; Henriksen, K.F.; Vicente, A.M.; Oliveira, G.; Cintin, C.; Eiberg, H.; Andersen, P.S.; Mors, O.; Rosenberg, T.; Brøndum-Nielsen, K.; Cotterill, R.M.; Lundsteen, C.; Ropers, H.H.; Ullmann, R.; Bache, I.; Tümer, Z.; Tommerup, N.Autism spectrum disorders (ASDs) are a heterogeneous group of disorders with unknown aetiology. Even though ASDs are suggested to be among the most heritable complex disorders, only a few reproducible mutations leading to susceptibility for ASD have been identified. In an attempt to identify ASD susceptibility genes through chromosome rearrangements, we investigated a female patient with childhood autism and high-grade myopia, and an apparently balanced de novo translocation, t(5;18)(q34;q12.2). Further analyses revealed a 3.2 Mb deletion encompassing 17 genes at the 18q break point and an additional deletion of 1.27 Mb containing two genes on chromosome 4q35. Q-PCR analysis of 14 of the 17 genes deleted on chromosome 18 showed that 11 of these genes were expressed in the brain, suggesting that haploinsufficiency of one or more genes may have contributed to the childhood autism phenotype of the patient. Identification of multiple genetic changes in this patient with childhood autism agrees with the most frequently suggested genetic model of ASDs as complex, polygenic disorders.
- Analysis of the neuroligin 3 and 4 genes in autism and other neuropsychiatric patientsPublication . Yan, J.; Oliveira, G.; Coutinho, A.; Yang, C.; Feng, J.; Katz, C.; Sram, J.; Bockholt, A.; Jones, I.R.; Craddock, N.; Cook Jr, E.H.; Vicente, A.M.; Sommer, S.S.
- ASD prevalence study across Europe: developing a school-based screening approach in the ASDEU projectPublication . García Primo, P.; Schendel, D.; Partner, E.; Rasga, C.; Café, C.; Rogé, B.; Arnaud, C.; Saemundsen, E.; Muratori, F.; Narzisi, A.; Boilson, A.; Oliveira, G.; Fuentes, J.; Poustka, L.; Scattonni, M.L.; Gissler, M.; Sweeny, M.R.; Budisteanu, M.; Kawa, R.; Canal-Bedia, R.; Stefanov, R.; Van Bakel, M.E.; Vicente, A.M.; Posada, M.Objectives: The main objective of the present work is to describe the strategy of the Autism Spectrum Disorder in the European Union (ASDEU) project to estimate the prevalence of ASD in school-aged children (7-9 years) across Europe. The focus of the presentation is on the novel field study strategy and aims to be a reflection on what we have learned regarding standardization of study methods across sites, what has worked well and what could be done differently in the future.
- Association of the alpha4 integrin subunit gene (ITGA4) with autismPublication . Correia, C.; Coutinho, A.M.; Almeida, J.; Lontro, R.; Lobo, C.; Miguel, T.S.; Martins, M.; Gallagher, L.; Conroy, J.; Gill, M.; Oliveira, G.; Vicente, A.M.In the present work, we provide further evidence for the involvement of the integrin alpha-4 precursor gene (ITGA4) in the etiology of autism, by replicating previous findings of a genetic association with autism in various independent populations. The ITGA4 gene maps to the autism linkage region on 2q31-33 and is therefore a plausible positional candidate. We tested eight single nucleotide polymorphisms (SNPs) in the ITGA4 gene region for association with autism in a sample of 164 nuclear families. Evidence for association was found for the rs155100 marker (P = 0.019) and for a number of specific marker haplotypes containing this SNP (0.00053 < P < 0.022). alpha4 integrins are known to play a key role in neuroinflammatory processes, which are hypothesized to contribute to autism. In this study, an association was found between the ITGA4 rs1449263 marker and levels of a serum autoantibody directed to brain tissue, which was previously shown to be significantly more frequent in autistic patients than in age-matched controls in our population. This result suggests that the ITGA4 gene could be involved in a neuroimmune process thought to occur in autistic patients and, together with previous findings, offers a new perspective on the role of integrins in the etiology of autism to which little attention has been paid so far.
- Autism Spectrum Disorder: gene variants involved in the nonsense-mediated mRNA decay pathwayPublication . Marques, Ana Rita; Martiniano, H.; Santos, J.X.; Vilela, J.; Rasga, C.; Oliveira, G.; Romão, L.; Vicente, A.M.No abstract available
- Autism Spectrum Disorder: gene variants involved in the nonsense-mediated mRNA decay pathwayPublication . Marques, Ana Rita; Martiniano, Hugo; Santos, J.X.; Vilela, Joana; Asif, M.; Rasga, C.; Oliveira, G.; Romão, Luísa; Vicente, AstridGenetic factors account for 50-80% of the familial risk of Autism Spectrum Disorder (ASD), but most of the genetic determinants are still unknown and a role for other regulatory mechanisms is likely. The nonsense-mediated decay (NMD) pathway is essential to control mRNA quality and has an important role in the regulation of the transcriptome. Mutations in genes involved in the NMD pathway, such as the UPF3B gene, a core component of this pathway, were previously linked to ASD. In this study we explored the potential role of NMD factors in ASD. We generated a list of 153 genes involved in the NMD pathway using AmiGO, Reactome and a systematic literature review. To identify potentially pathogenic variants in the NMD genes, we analyzed whole exome sequencing data (WES) data from 1338 ASD subjects. We also searched for Copy Number Variants (CNVs) targeting NMD genes in ASD patients (n=3570) and checked their frequency in controls (n=9649). We identified 43 high impact variants in 28 NMD genes, including the UPF3B and ACE, two genes previously implicated in ASD. Importantly, 11 were novel candidate genes that carry loss-of-function and missense (deleterious and damaging) variants with a frequency of 1 to 5% in this ASD dataset. Additionally, 5 NMD genes were found to be targeted by CNVs in 12 ASD subjects but none of the controls. The discovery of 33 NMD genes that are intriguing candidates for ASD in large patient genomic datasets provides evidence supporting the involvement of the NMD pathway in ASD pathophysiology.
- Brief report: High frequency of biochemical markers for mitochondrial dysfunction in autism: no association with the mitochondrial aspartate/glutamate carrier SLC25A12 genePublication . Correia, C.; Coutinho, A.M.; Diogo, L.; Grazina, M.; Marques, C.; Miguel, T.; Ataíde, A.; Almeida, J.; Borges, L.; Oliveira, C.; Oliveira, G.; Vicente, A.M.In the present study we confirm the previously reported high frequency of biochemical markers of mitochondrial dysfunction, namely hyperlactacidemia and increased lactate/pyruvate ratio, in a significant fraction of 210 autistic patients. We further examine the involvement of the mitochondrial aspartate/glutamate carrier gene (SLC25A12) in mitochondrial dysfunction associated with autism. We found no evidence of association of the SLC25A12 gene with lactate and lactate/pyruvate distributions or with autism in 241 nuclear families with one affected individual. We conclude that while mitochondrial dysfunction may be one of the most common medical conditions associated with autism, variation at the SLC25A12 gene does not explain the high frequency of mitochondrial dysfunction markers and is not associated with autism in this sample of autistic patients.
- CNVs leading to fusion transcripts in individuals with autism spectrum disorderPublication . Holt, R.; Sykes, N.H.; Conceição, I.C.; Cazier, J.B.; Anney, R.J.; Oliveira, G.; Gallagher, L.; Vicente, A.M.; Monaco, A.P.; Pagnamenta, A.T.There is strong evidence that rare copy number variants (CNVs) have a role in susceptibility to autism spectrum disorders (ASDs). Much research has focused on how CNVs mediate a phenotypic effect by altering gene expression levels. We investigated an alternative mechanism whereby CNVs combine the 5' and 3' ends of two genes, creating a 'fusion gene'. Any resulting mRNA with an open reading frame could potentially alter the phenotype via a gain-of-function mechanism. We examined 2382 and 3096 rare CNVs from 996 individuals with ASD and 1287 controls, respectively, for potential to generate fusion transcripts. There was no increased burden in individuals with ASD; 122/996 cases harbored at least one rare CNV of this type, compared with 179/1287 controls (P=0.89). There was also no difference in the overall frequency distribution between cases and controls. We examined specific examples of such CNVs nominated by case-control analysis and a candidate approach. Accordingly, a duplication involving REEP1-POLR1A (found in 3/996 cases and 0/1287 controls) and a single occurrence CNV involving KIAA0319-TDP2 were tested. However, no fusion transcripts were detected by RT-PCR. Analysis of additional samples based on cell line availability resulted in validation of a MAPKAPK5-ACAD10 fusion transcript in two probands. However, this variant was present in controls at a similar rate and is unlikely to influence ASD susceptibility. In summary, although we find no evidence that fusion-gene generating CNVs lead to ASD susceptibility, discovery of a MAPKAPK5-ACAD10 transcript with an estimated frequency of ∼1/200 suggests that gain-of-function mechanisms should be considered in future CNVs studies.
- 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.