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Koko M, Kyle Satterstrom F, Warrier V, Martin H. Contribution of autosomal rare and de novo variants to sex differences in autism. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.04.13.24305713. [PMID: 38699304 PMCID: PMC11065020 DOI: 10.1101/2024.04.13.24305713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Autism is four times more prevalent in males than females. To study whether this reflects a difference in genetic predisposition attributed to autosomal rare variants, we evaluated the sex differences in effect size of damaging protein-truncating and missense variants on autism predisposition in 47,061 autistic individuals, then compared effect sizes between individuals with and without cognitive impairment or motor delay. Although these variants mediated differential likelihood of autism with versus without motor or cognitive impairment, their effect sizes on the liability scale did not differ significantly by sex exome-wide or in genes sex-differentially expressed in the cortex. Although de novo mutations were enriched in genes with male-biased expression in the fetal cortex, the liability they conferred did not differ significantly from other genes with similar loss-of-function intolerance and sex-averaged cortical expression. In summary, autosomal rare coding variants confer similar liability for autism in females and males.
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Affiliation(s)
- Mahmoud Koko
- Human Genetics, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - F. Kyle Satterstrom
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | | | - Varun Warrier
- Department of Psychiatry, Autism Research Centre, University of Cambridge, Cambridge, Cambridgeshire, CB2 8AH, UK
| | - Hilary Martin
- Human Genetics, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
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2
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McIntyre CL, Boucher TQ, Scheerer NE, Gurm M, Iarocci G. Brief Report: Alexithymia Trait Severity, Not Autistic Trait Severity, Relates to Caregiver Reactions to Autistic Children's Negative Emotions. J Autism Dev Disord 2023; 53:4100-4106. [PMID: 35437678 DOI: 10.1007/s10803-022-05494-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2022] [Indexed: 10/18/2022]
Abstract
Alexithymia impacts an individual's ability to recognize and understand emotions and frequently co-occurs with autism. This study investigated the relationship between children's alexithymia, autistic traits, and caregiver reactions to their child's negative emotions. Caregivers of 54 autistic and 51 non-autistic children between the ages of 7 and 12 years rated their child's alexithymia and autistic trait severity and their reactions to their child's negative emotions. Caregivers of autistic children reported greater supportive reactions and fewer restrictive/controlling reactions to their child's negative emotions when their child had more alexithymia traits. This study extends previous research by demonstrating that caregivers of autistic children with co-occurring alexithymia traits represent a specific subgroup of caregivers that respond more positively to their child's negative emotions.
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Affiliation(s)
- Cassia L McIntyre
- Department of Psychology, Simon Fraser University, 8888 University Drive, V5A 1S6, Burnaby, BC, Canada.
| | - Troy Q Boucher
- Department of Psychology, Simon Fraser University, 8888 University Drive, V5A 1S6, Burnaby, BC, Canada
| | - Nichole E Scheerer
- Department of Psychology, Simon Fraser University, 8888 University Drive, V5A 1S6, Burnaby, BC, Canada
- The Brain and Mind Institute, University of Western Ontario, 1151 Richmond Street, N6A 3K7, London, ON, Canada
| | - Mandeep Gurm
- Department of Psychology, Simon Fraser University, 8888 University Drive, V5A 1S6, Burnaby, BC, Canada
| | - Grace Iarocci
- Department of Psychology, Simon Fraser University, 8888 University Drive, V5A 1S6, Burnaby, BC, Canada
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Dong L, Wang Y, Wang X, Luo T, Zhou Q, Zhao G, Li B, Xia L, Xia K, Li J. Interactions of genetic risks for autism and the broad autism phenotypes. Front Psychiatry 2023; 14:1110080. [PMID: 37102084 PMCID: PMC10123509 DOI: 10.3389/fpsyt.2023.1110080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 03/07/2023] [Indexed: 04/28/2023] Open
Abstract
Background Common polygenic risk and de novo variants (DNVs) capture a small proportion of autism spectrum disorder (ASD) liability, and ASD phenotypic heterogeneity remains difficult to explain. Integrating multiple genetic factors contribute to clarifying the risk and clinical presentation of ASD. Methods In our study, we investigated the individual and combined effects of polygenic risk, damaging DNVs (including those in ASD risk genes), and sex among 2,591 ASD simplex families in the Simons Simplex Collection. We also explored the interactions among these factors, along with the broad autism phenotypes of ASD probands and their unaffected siblings. Finally, we combined the effects of polygenic risk, damaging DNVs in ASD risk genes, and sex to explain the total liability of ASD phenotypic spectrum. Results Our findings revealed that both polygenic risk and damaging DNVs contribute to an increased risk for ASD, with females exhibiting higher genetic burdens than males. ASD probands that carry damaging DNVs in ASD risk genes showed reduced polygenic risk. The effects of polygenic risk and damaging DNVs on autism broad phenotypes were inconsistent; probands with higher polygenic risk exhibited improvement in some behaviors, such as adaptive/cognitive behaviors, while those with damaging DNVs exhibited more severe phenotypes. Siblings with higher polygenic risk and damaging DNVs tended to have higher scores on broader autism phenotypes. Females exhibited more severe cognitive and behavioral problems compared to males among both ASD probands and siblings. The combination of polygenic risk, damaging DNVs in ASD risk genes, and sex explained 1-4% of the total liability of adaptive/cognitive behavior measurements. Conclusion Our study revealed that the risk for ASD and the autism broad phenotypes likely arises from a combination of common polygenic risk, damaging DNVs (including those in ASD risk genes), and sex.
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Affiliation(s)
- Lijie Dong
- Bioinformatics Center and National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Centre for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Yijing Wang
- Bioinformatics Center and National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Centre for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Xiaomeng Wang
- Bioinformatics Center and National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Centre for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Tengfei Luo
- Bioinformatics Center and National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Centre for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Qiao Zhou
- Bioinformatics Center and National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Guihu Zhao
- Bioinformatics Center and National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Bin Li
- Bioinformatics Center and National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Lu Xia
- Bioinformatics Center and National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Centre for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
- *Correspondence: Lu Xia,
| | - Kun Xia
- Bioinformatics Center and National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Kun Xia,
| | - Jinchen Li
- Bioinformatics Center and National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Centre for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Jinchen Li,
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Integrative Functional Genomic Analysis in Multiplex Autism Families from Kazakhstan. DISEASE MARKERS 2022; 2022:1509994. [PMID: 36199823 PMCID: PMC9529466 DOI: 10.1155/2022/1509994] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 08/21/2022] [Accepted: 09/06/2022] [Indexed: 12/14/2022]
Abstract
The study of extended pedigrees containing autism spectrum disorder- (ASD-) related broader autism phenotypes (BAP) offers a promising approach to the search for ASD candidate variants. Here, a total of 650,000 genetic markers were tested in four Kazakhstani multiplex families with ASD and BAP to obtain data on de novo mutations (DNMs), common, and rare inherited variants that may contribute to the genetic risk for developing autistic traits. The variants were analyzed in the context of gene networks and pathways. Several previously well-described enriched pathways were identified, including ion channel activity, regulation of synaptic function, and membrane depolarization. Perhaps these pathways are crucial not only for the development of ASD but also for ВАР. The results also point to several additional biological pathways (circadian entrainment, NCAM and BTN family interactions, and interaction between L1 and Ankyrins) and hub genes (CFTR, NOD2, PPP2R2B, and TTR). The obtained results suggest that further exploration of PPI networks combining ASD and BAP risk genes can be used to identify novel or overlooked ASD molecular mechanisms.
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Timperio AM, Gevi F, Cucinotta F, Ricciardello A, Turriziani L, Scattoni ML, Persico AM. Urinary Untargeted Metabolic Profile Differentiates Children with Autism from Their Unaffected Siblings. Metabolites 2022; 12:metabo12090797. [PMID: 36144201 PMCID: PMC9503174 DOI: 10.3390/metabo12090797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/16/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022] Open
Abstract
Autism Spectrum Disorder (ASD) encompasses a clinical spectrum of neurodevelopmental conditions that display significant heterogeneity in etiology, symptomatology, and severity. We previously compared 30 young children with idiopathic ASD and 30 unrelated typically-developing controls, detecting an imbalance in several compounds belonging mainly to the metabolism of purines, tryptophan and other amino acids, as well as compounds derived from the intestinal flora, and reduced levels of vitamins B6, B12 and folic acid. The present study describes significant urinary metabolomic differences within 14 pairs, including one child with idiopathic ASD and his/her typically-developing sibling, tightly matched by sex and age to minimize confounding factors, allowing a more reliable identification of the metabolic fingerprint related to ASD. By using a highly sensitive, accurate and unbiased approach, suitable for ensuring broad metabolite detection coverage on human urine, and by applying multivariate statistical analysis, we largely replicate our previous results, demonstrating a significant perturbation of the purine and tryptophan pathways, and further highlight abnormalities in the “phenylalanine, tyrosine and tryptophan” pathway, essentially involving increased phenylalanine and decreased tyrosine levels, as well as enhanced concentrations of bacterial degradation products, including phenylpyruvic acid, phenylacetic acid and 4-ethylphenyl-sulfate. The outcome of these within-family contrasts consolidates and extends our previous results obtained from unrelated individuals, adding further evidence that these metabolic imbalances may be linked to ASD rather than to environmental differences between cases and controls. It further underscores the excess of some gut microbiota-derived compounds in ASD, which could have diagnostic value in a network model differentiating the metabolome of autistic and unaffected siblings. Finally, it points toward the existence of a “metabolic autism spectrum” distributed as an endophenotype, with unaffected siblings possibly displaying a metabolic profile intermediate between their autistic siblings and unrelated typically-developing controls.
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Affiliation(s)
- Anna Maria Timperio
- Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy
- Correspondence: (A.M.T.); (A.M.P.)
| | - Federica Gevi
- Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy
| | - Francesca Cucinotta
- Interdepartmental Program “Autism 0-90”, “G. Martino” University Hospital, 98124 Messina, Italy
- IRCCS Centro Neurolesi “Bonino-Pulejo”, 98124 Messina, Italy
| | - Arianna Ricciardello
- Interdepartmental Program “Autism 0-90”, “G. Martino” University Hospital, 98124 Messina, Italy
- Villa Miralago, 21050 Cuasso al Monte, Italy
| | - Laura Turriziani
- Interdepartmental Program “Autism 0-90”, “G. Martino” University Hospital, 98124 Messina, Italy
| | - Maria Luisa Scattoni
- Research Coordination and Support Service, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Antonio M. Persico
- Child & Adolescent Neuropsychiatry Program, Modena University Hospital & Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, 41121 Modena, Italy
- Correspondence: (A.M.T.); (A.M.P.)
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Veatch OJ, Mazzotti DR, Schultz RT, Abel T, Michaelson JJ, Brodkin ES, Tunc B, Assouline SG, Nickl-Jockschat T, Malow BA, Sutcliffe JS, Pack AI. Calculating genetic risk for dysfunction in pleiotropic biological processes using whole exome sequencing data. J Neurodev Disord 2022; 14:39. [PMID: 35751013 PMCID: PMC9233372 DOI: 10.1186/s11689-022-09448-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 06/08/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Numerous genes are implicated in autism spectrum disorder (ASD). ASD encompasses a wide-range and severity of symptoms and co-occurring conditions; however, the details of how genetic variation contributes to phenotypic differences are unclear. This creates a challenge for translating genetic evidence into clinically useful knowledge. Sleep disturbances are particularly prevalent co-occurring conditions in ASD, and genetics may inform treatment. Identifying convergent mechanisms with evidence for dysfunction that connect ASD and sleep biology could help identify better treatments for sleep disturbances in these individuals. METHODS To identify mechanisms that influence risk for ASD and co-occurring sleep disturbances, we analyzed whole exome sequence data from individuals in the Simons Simplex Collection (n = 2380). We predicted protein damaging variants (PDVs) in genes currently implicated in either ASD or sleep duration in typically developing children. We predicted a network of ASD-related proteins with direct evidence for interaction with sleep duration-related proteins encoded by genes with PDVs. Overrepresentation analyses of Gene Ontology-defined biological processes were conducted on the resulting gene set. We calculated the likelihood of dysfunction in the top overrepresented biological process. We then tested if scores reflecting genetic dysfunction in the process were associated with parent-reported sleep duration. RESULTS There were 29 genes with PDVs in the ASD dataset where variation was reported in the literature to be associated with both ASD and sleep duration. A network of 108 proteins encoded by ASD and sleep duration candidate genes with PDVs was identified. The mechanism overrepresented in PDV-containing genes that encode proteins in the interaction network with the most evidence for dysfunction was cerebral cortex development (GO:0,021,987). Scores reflecting dysfunction in this process were associated with sleep durations; the largest effects were observed in adolescents (p = 4.65 × 10-3). CONCLUSIONS Our bioinformatic-driven approach detected a biological process enriched for genes encoding a protein-protein interaction network linking ASD gene products with sleep duration gene products where accumulation of potentially damaging variants in individuals with ASD was associated with sleep duration as reported by the parents. Specifically, genetic dysfunction impacting development of the cerebral cortex may affect sleep by disrupting sleep homeostasis which is evidenced to be regulated by this brain region. Future functional assessments and objective measurements of sleep in adolescents with ASD could provide the basis for more informed treatment of sleep problems in these individuals.
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Affiliation(s)
- Olivia J Veatch
- Department of Psychiatry and Behavioral Sciences, Medical Center, University of Kansas, Kansas City, KS, USA.
| | - Diego R Mazzotti
- Division of Medical Informatics, Department of Internal Medicine, Medical Center, University of Kansas, Kansas City, KS, USA
| | - Robert T Schultz
- Center for Autism Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ted Abel
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute, University of Iowa, Iowa City, Iowa, USA
| | | | - Edward S Brodkin
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Birkan Tunc
- Center for Autism Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Susan G Assouline
- Belin-Blank Center for Gifted Education and Talent Development, University of Iowa, Iowa City, Iowa, USA
| | | | - Beth A Malow
- Division of Sleep Medicine, Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - James S Sutcliffe
- Department of Molecular Physiology and Biophysics, Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA
| | - Allan I Pack
- Division of Sleep Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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The Role of Genetics, Epigenetics, and the Environment in ASD: A Mini Review. EPIGENOMES 2022; 6:epigenomes6020015. [PMID: 35735472 PMCID: PMC9222497 DOI: 10.3390/epigenomes6020015] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 06/12/2022] [Accepted: 06/16/2022] [Indexed: 01/21/2023] Open
Abstract
According to recent findings, variances in autism spectrum disorder (ASD) risk factors might be determined by several factors, including molecular genetic variants. Accumulated evidence has also revealed the important role of biological and chemical pathways in ASD aetiology. In this paper, we assess several reviews with regard to their quality of evidence and provide a brief outline of the presumed mechanisms of the genetic, epigenetic, and environmental risk factors of ASD. We also review some of the critical literature, which supports the basis of each factor in the underlying and specific risk patterns of ASD. Finally, we consider some of the implications of recent research regarding potential molecular targets for future investigations.
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Silverman JL, Thurm A, Ethridge SB, Soller MM, Petkova SP, Abel T, Bauman MD, Brodkin ES, Harony‐Nicolas H, Wöhr M, Halladay A. Reconsidering animal models used to study autism spectrum disorder: Current state and optimizing future. GENES, BRAIN, AND BEHAVIOR 2022; 21:e12803. [PMID: 35285132 PMCID: PMC9189007 DOI: 10.1111/gbb.12803] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 02/18/2022] [Accepted: 02/23/2022] [Indexed: 12/15/2022]
Abstract
Neurodevelopmental disorders (NDDs), including autism spectrum disorder (ASD) and intellectual disability (ID), are pervasive, often lifelong disorders, lacking evidence-based interventions for core symptoms. With no established biological markers, diagnoses are defined by behavioral criteria. Thus, preclinical in vivo animal models of NDDs must be optimally utilized. For this reason, experts in the field of behavioral neuroscience convened a workshop with the goals of reviewing current behavioral studies, reports, and assessments in rodent models. Goals included: (a) identifying the maximal utility and limitations of behavior in animal models with construct validity; (b) providing recommendations for phenotyping animal models; and (c) guidelines on how in vivo models should be used and reported reliably and rigorously while acknowledging their limitations. We concluded by recommending minimal criteria for reporting in manuscripts going forward. The workshop elucidated a consensus of potential solutions to several problems, including revisiting claims made about animal model links to ASD (and related conditions). Specific conclusions included: mice (or other rodent or preclinical models) are models of the neurodevelopmental insult, not specifically any disorder (e.g., ASD); a model that perfectly recapitulates a disorder such as ASD is untenable; and greater attention needs be given to validation of behavioral testing methods, data analysis, and critical interpretation.
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Affiliation(s)
- Jill L. Silverman
- MIND Institute, Department of Psychiatry and Behavioral SciencesUniversity of California Davis School of MedicineSacramentoCaliforniaUSA
| | - Audrey Thurm
- Neurodevelopmental and Behavioral Phenotyping ServiceNational Institute of Mental HealthBethesdaMarylandUSA
| | - Sarah B. Ethridge
- Neurodevelopmental and Behavioral Phenotyping ServiceNational Institute of Mental HealthBethesdaMarylandUSA
| | - Makayla M. Soller
- MIND Institute, Department of Psychiatry and Behavioral SciencesUniversity of California Davis School of MedicineSacramentoCaliforniaUSA
| | - Stela P. Petkova
- MIND Institute, Department of Psychiatry and Behavioral SciencesUniversity of California Davis School of MedicineSacramentoCaliforniaUSA
| | - Ted Abel
- Department of Neuroscience and PharmacologyIowa Neuroscience Institute, University of IowaIowa CityIowaUSA
| | - Melissa D. Bauman
- MIND Institute, Department of Psychiatry and Behavioral SciencesUniversity of California Davis School of MedicineSacramentoCaliforniaUSA
| | - Edward S. Brodkin
- Department of PsychiatryPerelman School of Medicine at the University of Pennsylvania, Translational Research LaboratoryPhiladelphiaPennsylvaniaUSA
| | - Hala Harony‐Nicolas
- Seaver Autism Center for Research and TreatmentIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Markus Wöhr
- Faculty of Psychology and Educational Sciences, Research Unit Brain and Cognition, Laboratory of Biological PsychologySocial and Affective Neuroscience Research Group, KU LeuvenLeuvenBelgium,Leuven Brain InstituteKU LeuvenLeuvenBelgium,Faculty of Psychology, Experimental and Biological Psychology, Behavioral NeurosciencePhilipps‐University of MarburgMarburgGermany,Center for Mind, Brain, and BehaviorPhilipps‐University of MarburgMarburgGermany
| | - Alycia Halladay
- Autism Science FoundationUSA,Department of Pharmacology and ToxicologyRutgers UniversityPiscatawayNew JerseyUSA
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Maltman N, Friedman L, Lorang E, Sterling A. Brief Report: Linguistic Mazes and Perseverations in School-Age Boys with Fragile X Syndrome and Autism Spectrum Disorder and Relationships with Maternal Maze Use. J Autism Dev Disord 2022; 52:897-907. [PMID: 33768421 PMCID: PMC8463634 DOI: 10.1007/s10803-021-04981-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/11/2021] [Indexed: 02/03/2023]
Abstract
Autism spectrum disorder (ASD) and fragile X syndrome (FXS) are neurodevelopmental disorders with overlapping pragmatic language impairments. Prior work suggests pragmatic language differences may run in families. This study examined specific pragmatic difficulties (i.e., linguistic mazes and perseverations) in boys (9-18 years) with idiopathic ASD (n = 26) and FXS+ASD (n = 29), and relationships with maternal maze use. Language samples were obtained separately for boys and mothers. Nonparametric analyses suggested that boys largely did not differ in their rates of mazes, but that boys with FXS+ASD exhibited more perseverations. Mazes were correlated between fragile X dyads. Maternal mazes were correlated with child perseverations among idiopathic ASD dyads. These findings have implications for the etiological significance of ASD-related language phenotypes.
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Affiliation(s)
- Nell Maltman
- Waisman Center, University of Wisconsin-Madison, Madison, USA.
| | - Laura Friedman
- Waisman Center, University of Wisconsin-Madison, Madison, USA
- Department of Communication Sciences and Disorders, University of Wisconsin-Madison, Madison, USA
| | - Emily Lorang
- Waisman Center, University of Wisconsin-Madison, Madison, USA
- Department of Communication Sciences and Disorders, University of Wisconsin-Madison, Madison, USA
| | - Audra Sterling
- Waisman Center, University of Wisconsin-Madison, Madison, USA
- Department of Communication Sciences and Disorders, University of Wisconsin-Madison, Madison, USA
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10
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Klei L, McClain LL, Mahjani B, Panayidou K, De Rubeis S, Grahnat ACS, Karlsson G, Lu Y, Melhem N, Xu X, Reichenberg A, Sandin S, Hultman CM, Buxbaum JD, Roeder K, Devlin B. How rare and common risk variation jointly affect liability for autism spectrum disorder. Mol Autism 2021; 12:66. [PMID: 34615521 PMCID: PMC8495987 DOI: 10.1186/s13229-021-00466-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 09/02/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Genetic studies have implicated rare and common variations in liability for autism spectrum disorder (ASD). Of the discovered risk variants, those rare in the population invariably have large impact on liability, while common variants have small effects. Yet, collectively, common risk variants account for the majority of population-level variability. How these rare and common risk variants jointly affect liability for individuals requires further study. METHODS To explore how common and rare variants jointly affect liability, we assessed two cohorts of ASD families characterized for rare and common genetic variations (Simons Simplex Collection and Population-Based Autism Genetics and Environment Study). We analyzed data from 3011 affected subjects, as well as two cohorts of unaffected individuals characterized for common genetic variation: 3011 subjects matched for ancestry to ASD subjects and 11,950 subjects for estimating allele frequencies. We used genetic scores, which assessed the relative burden of common genetic variation affecting risk of ASD (henceforth "burden"), and determined how this burden was distributed among three subpopulations: ASD subjects who carry a potentially damaging variant implicated in risk of ASD ("PDV carriers"); ASD subjects who do not ("non-carriers"); and unaffected subjects who are assumed to be non-carriers. RESULTS Burden harbored by ASD subjects is stochastically greater than that harbored by control subjects. For PDV carriers, their average burden is intermediate between non-carrier ASD and control subjects. Both carrier and non-carrier ASD subjects have greater burden, on average, than control subjects. The effects of common and rare variants likely combine additively to determine individual-level liability. LIMITATIONS Only 305 ASD subjects were known PDV carriers. This relatively small subpopulation limits this study to characterizing general patterns of burden, as opposed to effects of specific PDVs or genes. Also, a small fraction of subjects that are categorized as non-carriers could be PDV carriers. CONCLUSIONS Liability arising from common and rare risk variations likely combines additively to determine risk of any individual diagnosed with ASD. On average, ASD subjects carry a substantial burden of common risk variation, even if they also carry a rare PDV affecting risk.
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Affiliation(s)
- Lambertus Klei
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Lora Lee McClain
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Behrang Mahjani
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Klea Panayidou
- Department of Health Sciences Department, School of Sciences, European University Cyprus, Nicosia, Cyprus
| | - Silvia De Rubeis
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Anna-Carin Säll Grahnat
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Gun Karlsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Yangyi Lu
- Department of Statistics, University of Michigan, Ann Arbor, MI, USA
| | - Nadine Melhem
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Xinyi Xu
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Genebox, Beijing, China
| | - Abraham Reichenberg
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sven Sandin
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Christina M Hultman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Joseph D Buxbaum
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kathryn Roeder
- Department of Statistics, Carnegie Mellon University, Pittsburgh, PA, USA
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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11
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Choi L, An JY. Genetic architecture of autism spectrum disorder: Lessons from large-scale genomic studies. Neurosci Biobehav Rev 2021; 128:244-257. [PMID: 34166716 DOI: 10.1016/j.neubiorev.2021.06.028] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 06/17/2021] [Accepted: 06/17/2021] [Indexed: 12/20/2022]
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder with a strong genetic component. Recently developed genomic technologies, including microarray and next-generation sequencing (NGS), have enabled researchers to genetic analyses aimed at identifying genetic variations associated with ASD and to elucidate the genetic architecture of the disorder. Large-scale microarray, exome sequencing analyses, and robust statistical methods have resulted in successful gene discovery and identification of high-confidence ASD genes from among de novo and inherited variants. Efforts have been made to understand the genetic architecture of ASD using whole-genome sequencing and genome-wide association studies aimed at identifying noncoding mutations and common variants associated with ASD. In addition, the development of systems biology approaches has resulted in the integration of genetic findings with functional genomic datasets, thereby providing a unique insight into the functional convergence of ASD risk genes and their neurobiology. In this review, we summarize the latest findings of ASD genetic studies involving large cohorts and discuss their implications in ASD neurobiology and in clinical practice.
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Affiliation(s)
- Leejee Choi
- School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul, 02841, Republic of Korea; Department of Integrated Biomedical and Life Science, Korea University, Seoul, 02841, Republic of Korea
| | - Joon-Yong An
- School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul, 02841, Republic of Korea; Department of Integrated Biomedical and Life Science, Korea University, Seoul, 02841, Republic of Korea; Transdisciplinary Major in Learning Health Systems, Department of Healthcare Sciences, Graduate School, Korea University, Seoul, 02841, Republic of Korea; BK21FOUR R&E Center for Learning Health Systems, Korea University, Seoul, 02841, Republic of Korea.
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12
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Etiological investigation of genetic cause in autism spectrum disorder. SCIENTIA MEDICA 2021. [DOI: 10.15448/1980-6108.2021.1.39581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
AIMS: The aims of this study were to characterize the etiological investigation of genetic cause in the autism spectrum disorder and to determine the factors related to its identification.METHODS: A retrospective descriptive study, with an analytical component, included children and adolescents with autism spectrum disorder followed in consultation at a level 2 hospital, between November 2017 and October 2019. The following variables were analyzed: age, sex, age at the first consultation, family history, objective examination, cognitive assessment, etiological investigation of genetic cause and etiological diagnosis of genetic cause. Statistical analysis was performed using the SPSS®v23 program (significance level 0.05).RESULTS: We identified 153 children with autism spectrum disorder, of which 48 underwent a genetic cause investigation: 45 performed microarray analysis (15.6% pathogenic); 42 carried out a molecular study of the Fragile X syndrome (one altered); two performed sequencing of the methyl CpG binding protein 2 (MECP2) gene (one altered). The diagnosis of genetic cause was made in 18.8% of the sample. The identification of the etiology of a genetic cause was related to global development delay/ intellectual disability (p = 0.04) and the presence of relevant family history (p = 0.005).CONCLUSIONS: The diagnostic yield of the genetic study was higher in patients with a global development delay /intellectual disability and in patients with relevant family history.
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13
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Searles Quick VB, Wang B, State MW. Leveraging large genomic datasets to illuminate the pathobiology of autism spectrum disorders. Neuropsychopharmacology 2021; 46:55-69. [PMID: 32668441 PMCID: PMC7688655 DOI: 10.1038/s41386-020-0768-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 06/26/2020] [Accepted: 07/06/2020] [Indexed: 12/15/2022]
Abstract
"Big data" approaches in the form of large-scale human genomic studies have led to striking advances in autism spectrum disorder (ASD) genetics. Similar to many other psychiatric syndromes, advances in genotyping technology, allowing for inexpensive genome-wide assays, has confirmed the contribution of polygenic inheritance involving common alleles of small effect, a handful of which have now been definitively identified. However, the past decade of gene discovery in ASD has been most notable for the application, in large family-based cohorts, of high-density microarray studies of submicroscopic chromosomal structure as well as high-throughput DNA sequencing-leading to the identification of an increasingly long list of risk regions and genes disrupted by rare, de novo germline mutations of large effect. This genomic architecture offers particular advantages for the illumination of biological mechanisms but also presents distinctive challenges. While the tremendous locus heterogeneity and functional pleiotropy associated with the more than 100 identified ASD-risk genes and regions is daunting, a growing armamentarium of comprehensive, large, foundational -omics databases, across species and capturing developmental trajectories, are increasingly contributing to a deeper understanding of ASD pathology.
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Affiliation(s)
- Veronica B Searles Quick
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Belinda Wang
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Matthew W State
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94143, USA.
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14
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De novo deleterious variants that may alter the dopaminergic reward pathway are associated with anorexia nervosa. Eat Weight Disord 2020; 25:1643-1650. [PMID: 31664672 DOI: 10.1007/s40519-019-00802-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 10/17/2019] [Indexed: 10/25/2022] Open
Abstract
PURPOSE Anorexia nervosa (AN) is a complex neuropsychiatric disorder presenting with dangerously low body weight, and a deep and persistent fear of gaining weight. Up to now, four genome-wide association studies of AN have been conducted to date and identified only few significant loci. However, both previous studies focused on common variation and on rare exonic variants. Currently, de novo variants are one of the most significant risk factors for neurodevelopmental disorders and psychiatric disorders. METHODS We analyzed by whole exome sequencing a cohort of nine female AN individuals and their parents (mother and father), and focused our analysis on de novo variants. RESULTS Here, we found seven de novo missense variants in potential genes in nine studied AN patients. Four of these genes (CSMD1, CREB3, PTPRD and GAB1) belong to a same signaling pathway involving neuron differentiation and dopamine pathway. CONCLUSIONS This study provides a list of interesting genes such as CSDM1 and CREB3 that are candidates to be involved in the etiology of anorexia nervosa. LEVEL OF EVIDENCE basic research.
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15
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Abstract
Recent advances in understanding the genetic architecture of autism spectrum disorder have allowed for unprecedented insight into its biological underpinnings. New studies have elucidated the contributions of a variety of forms of genetic variation to autism susceptibility. While the roles of de novo copy number variants and single-nucleotide variants-causing loss-of-function or missense changes-have been increasingly recognized and refined, mosaic single-nucleotide variants have been implicated more recently in some cases. Moreover, inherited variants (including common variants) and, more recently, rare recessive inherited variants have come into greater focus. Finally, noncoding variants-both inherited and de novo-have been implicated in the last few years. This work has revealed a convergence of diverse genetic drivers on common biological pathways and has highlighted the ongoing importance of increasing sample size and experimental innovation. Continuing to synthesize these genetic findings with functional and phenotypic evidence and translating these discoveries to clinical care remain considerable challenges for the field.
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Affiliation(s)
- Caroline M Dias
- Division of Developmental Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA; .,Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts 02115, USA; .,Department of Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts 02115, USA; .,Department of Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Department of Neurology, Harvard Medical School, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
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16
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A brief report: de novo copy number variants in children with attention deficit hyperactivity disorder. Transl Psychiatry 2020; 10:135. [PMID: 32398668 PMCID: PMC7217839 DOI: 10.1038/s41398-020-0821-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 04/06/2020] [Accepted: 04/21/2020] [Indexed: 01/09/2023] Open
Abstract
Recent case-control genetic studies of attention deficit hyperactivity disorder (ADHD) have implicated common and rare genetic risk alleles, highlighting the polygenic and complex aetiology of this neurodevelopmental disorder. Studies of other neurodevelopmental disorders, such as autism spectrum disorder (ASD), Tourette disorder, developmental delay/intellectual disability and schizophrenia indicate that identification of specific risk alleles and additional insights into disorder biology can be gained by studying non-inherited de novo variation. In this study, we aimed to identify large de novo copy number variants (CNVs) in children with ADHD. Children with a confirmed diagnosis of ADHD and their parents were genotyped and included in this sample. We used PennCNV to call large (>200 kb) CNVs and identified those calls that were present in the proband and absent in both biological parents. In 305 parent-offspring trios, we detected 14 de novo CNVs in 13 probands, giving a mutation rate of 4.6% and a per individual rate of 4.3%. This rate is higher than published reports in controls and similar to those observed for ASD, schizophrenia and Tourette disorder. We also identified de novo mutations at four genomic loci (15q13.1-13.2 duplication, 16p13.11 duplication, 16p12.2 deletion and 22q11.21 duplication) that have previously been implicated in other neurodevelopmental disorders, two of which (16p13.11 and 22q11.21) have also been implicated in case-control ADHD studies. Our study complements ADHD case-control genomic analyses and demonstrates the need for larger parent-offspring trio genetic studies to gain further insights into the complex aetiology of ADHD.
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17
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Cukier HN, Griswold AJ, Hofmann NK, Gomez L, Whitehead PL, Abramson RK, Gilbert JR, Cuccaro ML, Dykxhoorn DM, Pericak-Vance MA. Three Brothers With Autism Carry a Stop-Gain Mutation in the HPA-Axis Gene NR3C2. Autism Res 2020; 13:523-531. [PMID: 32064789 DOI: 10.1002/aur.2269] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 11/20/2019] [Accepted: 01/06/2020] [Indexed: 12/30/2022]
Abstract
Whole exome sequencing and copy-number variant analysis was performed on a family with three brothers diagnosed with autism. Each of the siblings shares an alteration in the nuclear receptor subfamily 3 group C member 2 (NR3C2) gene that is predicted to result in a stop-gain mutation (p.Q919X) in the mineralocorticoid receptor (MR) protein. This variant was maternally inherited and provides further evidence for a connection between the NR3C2 and autism. Interestingly, the NR3C2 gene encodes the MR protein, a steroid hormone-regulated transcription factor that acts in the hypothalamic-pituitary-adrenal axis and has been connected to stress and anxiety, both of which are features often seen in individuals with autism. Autism Res 2020, 13: 523-531. © 2020 International Society for Autism Research, Wiley Periodicals, Inc. LAY SUMMARY: Given the complexity of the genetics underlying autism, each gene contributes to risk in a relatively small number of individuals, typically less than 1% of all autism cases. Whole exome sequencing of three brothers with autism identified a rare variant in the nuclear receptor subfamily 3 group C member 2 gene that is predicted to strongly interfere with its normal function. This gene encodes the mineralocorticoid receptor protein, which plays a role in how the body responds to stress and anxiety, features that are often elevated in people diagnosed with autism. This study adds further support to the relevance of this gene as a risk factor for autism.
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Affiliation(s)
- Holly N Cukier
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida.,Department of Neurology, University of Miami Miller School of Medicine, Miami, Florida.,Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida
| | - Anthony J Griswold
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida.,Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida
| | - Natalia K Hofmann
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida
| | - Lissette Gomez
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida
| | - Patrice L Whitehead
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida
| | - Ruth K Abramson
- University of South Carolina School of Medicine, Columbia, South Carolina
| | - John R Gilbert
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida.,Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida
| | - Michael L Cuccaro
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida.,Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida
| | - Derek M Dykxhoorn
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida.,Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida
| | - Margaret A Pericak-Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida.,Department of Neurology, University of Miami Miller School of Medicine, Miami, Florida.,Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida
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18
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Saitow F, Takumi T, Suzuki H. Change in serotonergic modulation contributes to the synaptic imbalance of neuronal circuit at the prefrontal cortex in the 15q11-13 duplication mouse model of autism. Neuropharmacology 2019; 165:107931. [PMID: 31901366 DOI: 10.1016/j.neuropharm.2019.107931] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 12/25/2019] [Accepted: 12/30/2019] [Indexed: 10/25/2022]
Abstract
The prefrontal cortex (PFC) has been extensively studied in autism spectrum disorder (ASD) in an attempt to understand the deficits in executive and other higher brain functions related to sociability and emotion. Disruption of the excitatory/inhibitory (E/I) balance of cortical circuits is thought to underlie the pathophysiology of ASD. Recently, we showed that 15q dup mice (a model for ASD with human chromosome 15q11-13 paternal duplication) exhibit disruption of the E/I balance in layer 2/3 pyramidal neurons of the somatosensory cortex due to a decrease in the number of inhibitory synapses. However, whether there is a pathological abnormality in E/I balance in the PFC of 15q dup mice remains unknown. In this study, we found that 15q dup facilitates the activity-induced LTP of glutamate synapses onto layer 5 pyramidal neurons by shifting the E/I balance to an excitatory state, which this was associated with differences in synaptic glutamatergic and GABAergic inputs onto GABAergic fast-spiking interneurons (FSINs). Furthermore, we found that FSIN excitability was well-modulated and regulated by the constitutive activation of 5-HT2 receptors in PFC microcircuits. These results provide new insights into the cellular mechanisms underlying maintenance of optimal E/I balance in the PFC.
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Affiliation(s)
- Fumihito Saitow
- Department of Pharmacology, Nippon Medical School, Tokyo, 113-8602, Japan.
| | - Toru Takumi
- RIKEN Center for Brain Science, Wako, Saitama, 351-0198, Japan
| | - Hidenori Suzuki
- Department of Pharmacology, Nippon Medical School, Tokyo, 113-8602, Japan
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19
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Glinton KE, Elsea SH. Untargeted Metabolomics for Autism Spectrum Disorders: Current Status and Future Directions. Front Psychiatry 2019; 10:647. [PMID: 31551836 PMCID: PMC6746843 DOI: 10.3389/fpsyt.2019.00647] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 08/12/2019] [Indexed: 12/20/2022] Open
Abstract
Autism spectrum disorders (ASDs) are a group of neurodevelopment disorders characterized by childhood onset deficits in social communication and interaction. Although the exact etiology of most cases of ASDs is unknown, a portion has been proposed to be associated with various metabolic abnormalities including mitochondrial dysfunction, disorders of cholesterol metabolism, and folate abnormalities. Targeted biochemical testing like plasma amino acid and acylcarnitine profiles have demonstrated limited utility in helping to diagnose and manage such patients. Untargeted metabolomics has emerged, however, as a promising tool in screening for underlying biochemical abnormalities and managing treatment and as a means of investigating possible novel biomarkers for the disorder. Here, we review the principles and methodology behind untargeted metabolomics, recent pilot studies utilizing this technology, and areas in which it may be integrated into the care of children with this disorder in the future.
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Affiliation(s)
- Kevin E. Glinton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Sarah H. Elsea
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
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20
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Aspromonte MC, Bellini M, Gasparini A, Carraro M, Bettella E, Polli R, Cesca F, Bigoni S, Boni S, Carlet O, Negrin S, Mammi I, Milani D, Peron A, Sartori S, Toldo I, Soli F, Turolla L, Stanzial F, Benedicenti F, Marino-Buslje C, Tosatto SCE, Murgia A, Leonardi E. Characterization of intellectual disability and autism comorbidity through gene panel sequencing. Hum Mutat 2019; 40:1346-1363. [PMID: 31209962 DOI: 10.1002/humu.23822] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 05/18/2019] [Accepted: 05/27/2019] [Indexed: 12/22/2022]
Abstract
Intellectual disability (ID) and autism spectrum disorder (ASD) are clinically and genetically heterogeneous diseases. Recent whole exome sequencing studies indicated that genes associated with different neurological diseases are shared across disorders and converge on common functional pathways. Using the Ion Torrent platform, we developed a low-cost next-generation sequencing gene panel that has been transferred into clinical practice, replacing single disease-gene analyses for the early diagnosis of individuals with ID/ASD. The gene panel was designed using an innovative in silico approach based on disease networks and mining data from public resources to score disease-gene associations. We analyzed 150 unrelated individuals with ID and/or ASD and a confident diagnosis has been reached in 26 cases (17%). Likely pathogenic mutations have been identified in another 15 patients, reaching a total diagnostic yield of 27%. Our data also support the pathogenic role of genes recently proposed to be involved in ASD. Although many of the identified variants need further investigation to be considered disease-causing, our results indicate the efficiency of the targeted gene panel on the identification of novel and rare variants in patients with ID and ASD.
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Affiliation(s)
- Maria C Aspromonte
- Molecular Genetics of Neurodevelopment, Department of Woman and Child Health, University of Padova, C.so Stati Uniti, 4, Padova, Italy.,Fondazione Istituto di Ricerca Pediatrica, Città della Speranza, Padova, Italy
| | - Mariagrazia Bellini
- Molecular Genetics of Neurodevelopment, Department of Woman and Child Health, University of Padova, C.so Stati Uniti, 4, Padova, Italy.,Fondazione Istituto di Ricerca Pediatrica, Città della Speranza, Padova, Italy
| | | | - Marco Carraro
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Elisa Bettella
- Molecular Genetics of Neurodevelopment, Department of Woman and Child Health, University of Padova, C.so Stati Uniti, 4, Padova, Italy.,Fondazione Istituto di Ricerca Pediatrica, Città della Speranza, Padova, Italy
| | - Roberta Polli
- Molecular Genetics of Neurodevelopment, Department of Woman and Child Health, University of Padova, C.so Stati Uniti, 4, Padova, Italy.,Fondazione Istituto di Ricerca Pediatrica, Città della Speranza, Padova, Italy
| | - Federica Cesca
- Molecular Genetics of Neurodevelopment, Department of Woman and Child Health, University of Padova, C.so Stati Uniti, 4, Padova, Italy.,Fondazione Istituto di Ricerca Pediatrica, Città della Speranza, Padova, Italy
| | - Stefania Bigoni
- Medical Genetics Unit, Ospedale Universitario S. Anna, Ferrara, Italy
| | - Stefania Boni
- Medical Genetics Unit, San Martino Hospital, Belluno, Italy
| | - Ombretta Carlet
- Epilepsy and Child Neurophysiology Unit, Scientific Institute IRCCS E. Medea, Treviso, Italy
| | - Susanna Negrin
- Epilepsy and Child Neurophysiology Unit, Scientific Institute IRCCS E. Medea, Treviso, Italy
| | - Isabella Mammi
- Medical Genetics Unit, Dolo General Hospital, Venezia, Italy
| | - Donatella Milani
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, University of Milano, Milan, Italy
| | - Angela Peron
- Child Neuropsychiatry Unit, Epilepsy Center, Department of Health Sciences, Santi Paolo-Carlo Hospital, University of Milano, Milano, Italy.,Division of Medical Genetics, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah
| | - Stefano Sartori
- Paediatric Neurology Unit, Department of Woman and Child Health, University Hospital of Padova, Padova, Italy
| | - Irene Toldo
- Paediatric Neurology Unit, Department of Woman and Child Health, University Hospital of Padova, Padova, Italy
| | - Fiorenza Soli
- Medical Genetics Department, APSS Trento, Trento, Italy
| | - Licia Turolla
- Medical Genetics Unit, Local Health Authority, Treviso, Italy
| | - Franco Stanzial
- Genetic Counseling Service, Department of Pediatrics, Regional Hospital of Bolzano, Bolzano, Italy
| | - Francesco Benedicenti
- Genetic Counseling Service, Department of Pediatrics, Regional Hospital of Bolzano, Bolzano, Italy
| | | | - Silvio C E Tosatto
- Department of Biomedical Sciences, University of Padova, Padova, Italy.,Institute of Neuroscience, National Research Council, Padova, Italy
| | - Alessandra Murgia
- Molecular Genetics of Neurodevelopment, Department of Woman and Child Health, University of Padova, C.so Stati Uniti, 4, Padova, Italy.,Fondazione Istituto di Ricerca Pediatrica, Città della Speranza, Padova, Italy
| | - Emanuela Leonardi
- Molecular Genetics of Neurodevelopment, Department of Woman and Child Health, University of Padova, C.so Stati Uniti, 4, Padova, Italy.,Fondazione Istituto di Ricerca Pediatrica, Città della Speranza, Padova, Italy
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21
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Coll-Tané M, Krebbers A, Castells-Nobau A, Zweier C, Schenck A. Intellectual disability and autism spectrum disorders 'on the fly': insights from Drosophila. Dis Model Mech 2019; 12:dmm039180. [PMID: 31088981 PMCID: PMC6550041 DOI: 10.1242/dmm.039180] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Intellectual disability (ID) and autism spectrum disorders (ASD) are frequently co-occurring neurodevelopmental disorders and affect 2-3% of the population. Rapid advances in exome and genome sequencing have increased the number of known implicated genes by threefold, to more than a thousand. The main challenges in the field are now to understand the various pathomechanisms associated with this bewildering number of genetic disorders, to identify new genes and to establish causality of variants in still-undiagnosed cases, and to work towards causal treatment options that so far are available only for a few metabolic conditions. To meet these challenges, the research community needs highly efficient model systems. With an increasing number of relevant assays and rapidly developing novel methodologies, the fruit fly Drosophila melanogaster is ideally positioned to change gear in ID and ASD research. The aim of this Review is to summarize some of the exciting work that already has drawn attention to Drosophila as a model for these disorders. We highlight well-established ID- and ASD-relevant fly phenotypes at the (sub)cellular, brain and behavioral levels, and discuss strategies of how this extraordinarily efficient and versatile model can contribute to 'next generation' medical genomics and to a better understanding of these disorders.
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Affiliation(s)
- Mireia Coll-Tané
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Alina Krebbers
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Anna Castells-Nobau
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Christiane Zweier
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Annette Schenck
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
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22
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Lo YC, Chen YJ, Hsu YC, Chien YL, Gau SSF, Tseng WYI. Altered frontal aslant tracts as a heritable neural basis of social communication deficits in autism spectrum disorder: A sibling study using tract-based automatic analysis. Autism Res 2018; 12:225-238. [PMID: 30548800 DOI: 10.1002/aur.2044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 09/12/2018] [Accepted: 10/21/2018] [Indexed: 01/08/2023]
Abstract
Investigating social behaviors and brain structural alterations in unaffected siblings of individuals with autism spectrum disorder (ASD) may help identify intermediate phenotypes of social communication deficits in ASD. This study hypothesized that such intermediate phenotypes could be identified in white matter tracts of the social communication model that exhibited reduced tract integrity and associations with social communication deficits. Boys with ASD (N = 30), unaffected male siblings (N = 27), and typically developing (TD) boys (N = 30) underwent clinical evaluation and MRI scanning. Group differences in generalized fractional anisotropy (GFA) values, a white matter integrity index derived from diffusion MRI data, and the relationships of GFA with the Social Responsiveness Scale (SRS) scores and the Child Behavior Checklist (CBCL/4-18) scores were investigated. Significant differences were found in the GFA values of the frontal aslant tract (FAT) among the three groups, with the decreasing order of GFA from TD to siblings to ASD. The GFA values of the FAT were associated with the social communication scores (on the SRS) in the sibling group, and those of the superior longitudinal fasciculus III were associated with the social problems scores (on the CBCL/4-18) in the boys with ASD. Due to the altered tract integrity and association with social communication deficits in the unaffected siblings of individuals with ASD, the FAT might be a heritable neural basis for social communication deficits of ASD. Autism Res 2019, 12: 225-238 © 2018 International Society for Autism Research, Wiley Periodicals, Inc. LAY SUMMARY: Autism spectrum disorder (ASD) is a group of highly heritable disorders with social communication deficits as one of the core symptoms. This study aimed to identify a neural trait of social communication deficits in individuals with ASD. We investigated brain structural alterations and their associations with social communication scores in unaffected siblings of individuals with ASD. The siblings' frontal aslant tract was found to be impaired, and this tract showed a significant association with the social communication scores. Our findings support that the frontal aslant tract might be a potential neural trait of social communication deficits in ASD.
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Affiliation(s)
- Yu-Chun Lo
- Institute of Medical Device and Imaging, National Taiwan University College of Medicine, Taipei, Taiwan.,Ph.D. Program for Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan.,Research Center of Brain and Consciousness, Taipei Medical University, Taipei, Taiwan
| | - Yu-Jen Chen
- Institute of Medical Device and Imaging, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Yung-Chin Hsu
- Institute of Medical Device and Imaging, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Yi-Ling Chien
- Department of Psychiatry, National Taiwan University Hospital and College of Medicine, Taipei, Taiwan
| | - Susan Shur-Fen Gau
- Department of Psychiatry, National Taiwan University Hospital and College of Medicine, Taipei, Taiwan.,Graduate Institute of Brain and Mind Sciences, National Taiwan University, Taipei, Taiwan
| | - Wen-Yih Isaac Tseng
- Institute of Medical Device and Imaging, National Taiwan University College of Medicine, Taipei, Taiwan.,Graduate Institute of Brain and Mind Sciences, National Taiwan University, Taipei, Taiwan.,Department of Medical Imaging, National Taiwan University Hospital, Taipei, Taiwan.,Molecular Imaging Center, National Taiwan University, Taipei, Taiwan
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23
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Alvares GA, Dawson PA, Dissanayake C, Eapen V, Gratten J, Grove R, Henders A, Heussler H, Lawson L, Masi A, Raymond E, Rose F, Wallace L, Wray NR, Whitehouse AJO. Study protocol for the Australian autism biobank: an international resource to advance autism discovery research. BMC Pediatr 2018; 18:284. [PMID: 30149807 PMCID: PMC6112136 DOI: 10.1186/s12887-018-1255-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 08/15/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The phenotypic and genetic heterogeneity of autism spectrum disorder (ASD) presents considerable challenges in understanding etiological pathways, selecting effective therapies, providing genetic counselling, and predicting clinical outcomes. With advances in genetic and biological research alongside rapid-pace technological innovations, there is an increasing imperative to access large, representative, and diverse cohorts to advance knowledge of ASD. To date, there has not been any single collective effort towards a similar resource in Australia, which has its own unique ethnic and cultural diversity. The Australian Autism Biobank was initiated by the Cooperative Research Centre for Living with Autism (Autism CRC) to establish a large-scale repository of biological samples and detailed clinical information about children diagnosed with ASD to facilitate future discovery research. METHODS The primary group of participants were children with a confirmed diagnosis of ASD, aged between 2 and 17 years, recruited through four sites in Australia. No exclusion criteria regarding language level, cognitive ability, or comorbid conditions were applied to ensure a representative cohort was recruited. Both biological parents and siblings were invited to participate, along with children without a diagnosis of ASD, and children who had been queried for an ASD diagnosis but did not meet diagnostic criteria. All children completed cognitive assessments, with probands and parents completing additional assessments measuring ASD symptomatology. Parents completed questionnaires about their child's medical history and early development. Physical measurements and biological samples (blood, stool, urine, and hair) were collected from children, and physical measurements and blood samples were collected from parents. Samples were sent to a central processing site and placed into long-term storage. DISCUSSION The establishment of this biobank is a valuable international resource incorporating detailed clinical and biological information that will help accelerate the pace of ASD discovery research. Recruitment into this study has also supported the feasibility of large-scale biological sample collection in children diagnosed with ASD with comprehensive phenotyping across a wide range of ages, intellectual abilities, and levels of adaptive functioning. This biological and clinical resource will be open to data access requests from national and international researchers to support future discovery research that will benefit the autistic community.
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Affiliation(s)
- Gail A. Alvares
- Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Brisbane, QLD Australia
- Telethon Kids Institute, University of Western Australia, Perth, WA Australia
| | - Paul A. Dawson
- Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Brisbane, QLD Australia
- Mater Research Institute, The University of Queensland, Brisbane, QLD Australia
| | - Cheryl Dissanayake
- Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Brisbane, QLD Australia
- Olga Tennison Autism Research Centre, La Trobe University, Melbourne, VIC Australia
| | - Valsamma Eapen
- Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Brisbane, QLD Australia
- School of Psychiatry, University of New South Wales, Sydney, NSW Australia
- Academic Unit of Child Psychiatry South West Sydney, Ingham Institute, Liverpool Hospital, Sydney, NSW Australia
| | - Jacob Gratten
- Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Brisbane, QLD Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD Australia
| | - Rachel Grove
- Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Brisbane, QLD Australia
- School of Psychiatry, University of New South Wales, Sydney, NSW Australia
| | - Anjali Henders
- Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Brisbane, QLD Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD Australia
| | - Helen Heussler
- Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Brisbane, QLD Australia
- Mater Research Institute, The University of Queensland, Brisbane, QLD Australia
| | - Lauren Lawson
- Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Brisbane, QLD Australia
- Olga Tennison Autism Research Centre, La Trobe University, Melbourne, VIC Australia
| | - Anne Masi
- Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Brisbane, QLD Australia
- School of Psychiatry, University of New South Wales, Sydney, NSW Australia
| | - Emma Raymond
- Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Brisbane, QLD Australia
- Wesley Medical Research, Brisbane, QLD Australia
| | - Felicity Rose
- Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Brisbane, QLD Australia
| | - Leanne Wallace
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD Australia
| | - Naomi R. Wray
- Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Brisbane, QLD Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD Australia
| | - Andrew J. O. Whitehouse
- Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Brisbane, QLD Australia
- Telethon Kids Institute, University of Western Australia, Perth, WA Australia
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24
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Carratala-Marco F, Andreo-Lillo P, Martinez-Morga M, Escamez-Martínez T, Botella-López A, Bueno C, Martinez S. Clinical Phenotypes Associated to Engrailed 2 Gene Alterations in a Series of Neuropediatric Patients. Front Neuroanat 2018; 12:61. [PMID: 30147646 PMCID: PMC6095973 DOI: 10.3389/fnana.2018.00061] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 07/04/2018] [Indexed: 01/10/2023] Open
Abstract
The engrailed homeobox protein (EN) plays an important role in the regionalization of the neural tube. EN distribution regulates the cerebellum and midbrain morphogenesis, as well as retinotectal synaptogenesis. In humans, the EN1 and EN2 genes code for the EN family of transcription factors. Genetic alterations in the expression of EN2 have been related to different neurologic conditions and more particularly to autism spectrum disorders (ASD). We aimed to study and compare the phenotypes of three series of patients: (1) patients with encephalic structural anomalies (ESA) and abnormalities in the genomic (DNA) and/or transcriptomic (RNAm) of EN2 (EN2-g), (2) ESA patients having other gene mutations (OG-g), and (3) ESA patients free of these mutations (NM-g). Subjects and Methods: We have performed a descriptive study on 109 patients who suffer from mental retardation (MR), cerebral palsy (CP), epilepsy (EP), and behavioral disorders (BD), showing also ESA in their encephalic MRI. We studied genomic DNA and transcriptional analysis (cDNA) on EN2 gene (EN2), and in other genes (OG): LIS1, PTAFR, PAFAH1B2, PAFAH1B3, FGF8, PAX2, D17S379, D17S1866, and SMG6 (D17S5), as a routine genetic diagnosis in ESA patients. Results: From 109 patients, fifteen meet the exclusion criteria. From the remaining 94 patients, 12 (12.8%) showed mutations in EN2 (EN2-g), 20 showed mutations in other studied genes (OG-g), and 62 did not showed any mutation (NM-g). All EN2-g patients, suffered from MR, nine EP, seven BD and four CP. The proportions of these phenotypes in EN2-g did not differ from those in the OG-g, but it was significantly higher when comparing EN2-g with NM-g (MR: p = 0.013; EP: p = 0.001; BD: p = 0.0001; CP: p = 0.07, ns). Groups EN2-g and OG-g showed a 100 and a 70% of comorbidity, respectively, being significantly (p = 0.04) greater than NM-group (62.9%). Conclusion: Our series reflects a significant effect of EN2 gene alterations in neurodevelopmental abnormalities associated to ESA. Conversely, although these EN2 related anomalies might represent a predisposition to develop brain diseases, our results did not support direct relationship between EN2 mutations and specific clinical phenotypes.
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Affiliation(s)
| | | | - Marta Martinez-Morga
- Neuroscience Institute UMH-CSIC, CIBERSAM-ISCIII, Alicante, Spain.,IMIB-Arrixaca, University of Murcia, Murcia, Spain
| | | | | | - Carlos Bueno
- Neuroscience Institute UMH-CSIC, CIBERSAM-ISCIII, Alicante, Spain
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25
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Nguyen RL, Medvedeva YV, Ayyagari TE, Schmunk G, Gargus JJ. Intracellular calcium dysregulation in autism spectrum disorder: An analysis of converging organelle signaling pathways. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2018; 1865:1718-1732. [PMID: 30992134 DOI: 10.1016/j.bbamcr.2018.08.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 07/18/2018] [Accepted: 08/02/2018] [Indexed: 12/14/2022]
Abstract
Autism spectrum disorder (ASD) is a group of complex, neurological disorders that affect early cognitive, social, and verbal development. Our understanding of ASD has vastly improved with advances in genomic sequencing technology and genetic models that have identified >800 loci with variants that increase susceptibility to ASD. Although these findings have confirmed its high heritability, the underlying mechanisms by which these genes produce the ASD phenotypes have not been defined. Current efforts have begun to "functionalize" many of these variants and envisage how these susceptibility factors converge at key biochemical and biophysical pathways. In this review, we discuss recent work on intracellular calcium signaling in ASD, including our own work, which begins to suggest it as a compelling candidate mechanism in the pathophysiology of autism and a potential therapeutic target. We consider how known variants in the calcium signaling genomic architecture of ASD may exert their deleterious effects along pathways particularly involving organelle dysfunction including the endoplasmic reticulum (ER), a major calcium store, and the mitochondria, a major calcium ion buffer, and theorize how many of these pathways intersect.
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Affiliation(s)
- Rachel L Nguyen
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA; UCI Center for Autism Research and Translation, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Yuliya V Medvedeva
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA; UCI Center for Autism Research and Translation, School of Medicine, University of California, Irvine, Irvine, CA, USA; Department of Neurology, University of California, Irvine, Irvine, CA, USA
| | - Tejasvi E Ayyagari
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA; UCI Center for Autism Research and Translation, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Galina Schmunk
- UCI Center for Autism Research and Translation, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - John Jay Gargus
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA; UCI Center for Autism Research and Translation, School of Medicine, University of California, Irvine, Irvine, CA, USA; Department of Pediatrics, Section of Human Genetics and Genomics, University of California, Irvine, Irvine, CA, USA.
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26
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Epigenetic and Cellular Diversity in the Brain through Allele-Specific Effects. Trends Neurosci 2018; 41:925-937. [PMID: 30098802 DOI: 10.1016/j.tins.2018.07.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 06/29/2018] [Accepted: 07/10/2018] [Indexed: 01/18/2023]
Abstract
The benefits of diploidy are considered to involve masking partially recessive mutations and increasing genetic diversity. Here, we review new studies showing evidence for diverse allele-specific expression and epigenetic states in mammalian brain cells, which suggest that diploidy expands the landscape of gene regulatory and expression programs in cells. Allele-specific expression has been thought to be restricted to a few specific classes of genes. However, new studies show novel genomic imprinting effects that are brain-region-, cell-type- and age-dependent. In addition, novel forms of random monoallelic expression that impact many autosomal genes have been described in vitro and in vivo. We discuss the implications for understanding the benefits of diploidy, and the mechanisms shaping brain development, function, and disease.
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27
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Rogozin IB, Gertz EM, Baranov PV, Poliakov E, Schaffer AA. Genome-Wide Changes in Protein Translation Efficiency Are Associated with Autism. Genome Biol Evol 2018; 10:1902-1919. [PMID: 29986017 PMCID: PMC6086092 DOI: 10.1093/gbe/evy146] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2018] [Indexed: 01/05/2023] Open
Abstract
We previously proposed that changes in the efficiency of protein translation are associated with autism spectrum disorders (ASDs). This hypothesis connects environmental factors and genetic factors because each can alter translation efficiency. For genetic factors, we previously tested our hypothesis using a small set of ASD-associated genes, a small set of ASD-associated variants, and a statistic to quantify by how much a single nucleotide variant (SNV) in a protein coding region changes translation speed. In this study, we confirm and extend our hypothesis using a published set of 1,800 autism quartets (parents, one affected child and one unaffected child) and genome-wide variants. Then, we extend the test statistic to combine translation efficiency with other possibly relevant variables: ribosome profiling data, presence/absence of CpG dinucleotides, and phylogenetic conservation. The inclusion of ribosome profiling abundances strengthens our results for male-male sibling pairs. The inclusion of CpG information strengthens our results for female-female pairs, giving an insight into the significant gender differences in autism incidence. By combining the single-variant test statistic for all variants in a gene, we obtain a single gene score to evaluate how well a gene distinguishes between affected and unaffected siblings. Using statistical methods, we compute gene sets that have some power to distinguish between affected and unaffected siblings by translation efficiency of gene variants. Pathway and enrichment analysis of those gene sets suggest the importance of Wnt signaling pathways, some other pathways related to cancer, ATP binding, and ATP-ase pathways in the etiology of ASDs.
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Affiliation(s)
- Igor B Rogozin
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, Maryland
| | - E Michael Gertz
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, Maryland
| | - Pasha V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Eugenia Poliakov
- National Eye Institute, NIH, Laboratory of Retinal Cell and Molecular Biology, Bethesda, Maryland
| | - Alejandro A Schaffer
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, Maryland
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28
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Neural Glycosylphosphatidylinositol-Anchored Proteins in Synaptic Specification. Trends Cell Biol 2017; 27:931-945. [PMID: 28743494 DOI: 10.1016/j.tcb.2017.06.007] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Revised: 06/27/2017] [Accepted: 06/29/2017] [Indexed: 12/15/2022]
Abstract
Glycosylphosphatidylinositol (GPI)-anchored proteins are a specialized class of lipid-associated neuronal membrane proteins that perform diverse functions in the dynamic control of axon guidance, synaptic adhesion, cytoskeletal remodeling, and localized signal transduction, particularly at lipid raft domains. Recent studies have demonstrated that a subset of GPI-anchored proteins act as critical regulators of synapse development by modulating specific synaptic adhesion pathways via direct interactions with key synapse-organizing proteins. Additional studies have revealed that alteration of these regulatory mechanisms may underlie various brain disorders. In this review, we highlight the emerging role of GPI-anchored proteins as key synapse organizers that aid in shaping the properties of various types of synapses and circuits in mammals.
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