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Pugsley K, Scherer SW, Bellgrove MA, Hawi Z. Environmental exposures associated with elevated risk for autism spectrum disorder may augment the burden of deleterious de novo mutations among probands. Mol Psychiatry 2022; 27:710-730. [PMID: 34002022 PMCID: PMC8960415 DOI: 10.1038/s41380-021-01142-w] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 04/16/2021] [Accepted: 04/21/2021] [Indexed: 12/11/2022]
Abstract
Although the full aetiology of autism spectrum disorder (ASD) is unknown, familial and twin studies demonstrate high heritability of 60-90%, indicating a predominant role of genetics in the development of the disorder. The genetic architecture of ASD consists of a complex array of rare and common variants of all classes of genetic variation usually acting additively to augment individual risk. The relative contribution of heredity in ASD persists despite selective pressures against the classic autistic phenotype; a phenomenon thought to be explained, in part, by the incidence of spontaneous (or de novo) mutations. Notably, environmental exposures attributed as salient risk factors for ASD may play a causal role in the emergence of deleterious de novo variations, with several ASD-associated agents having significant mutagenic potential. To explore this hypothesis, this review article assesses published epidemiological data with evidence derived from assays of mutagenicity, both in vivo and in vitro, to determine the likely role such agents may play in augmenting the genetic liability in ASD. Broadly, these exposures were observed to elicit genomic alterations through one or a combination of: (1) direct interaction with genetic material; (2) impaired DNA repair; or (3) oxidative DNA damage. However, the direct contribution of these factors to the ASD phenotype cannot be determined without further analysis. The development of comprehensive prospective birth cohorts in combination with genome sequencing is essential to forming a causal, mechanistic account of de novo mutations in ASD that links exposure, genotypic alterations, and phenotypic consequences.
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Affiliation(s)
- Kealan Pugsley
- grid.1002.30000 0004 1936 7857Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Melbourne, VIC Australia
| | - Stephen W. Scherer
- grid.42327.300000 0004 0473 9646The Centre for Applied Genomics and Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada ,grid.17063.330000 0001 2157 2938McLaughlin Centre and Department of Molecular Genetics, University of Toronto, Toronto, ON Canada
| | - Mark A. Bellgrove
- grid.1002.30000 0004 1936 7857Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Melbourne, VIC Australia
| | - Ziarih Hawi
- Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Melbourne, VIC, Australia.
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52
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Català-Solsona J, Miñano-Molina AJ, Rodríguez-Álvarez J. Nr4a2 Transcription Factor in Hippocampal Synaptic Plasticity, Memory and Cognitive Dysfunction: A Perspective Review. Front Mol Neurosci 2021; 14:786226. [PMID: 34880728 PMCID: PMC8645690 DOI: 10.3389/fnmol.2021.786226] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 10/27/2021] [Indexed: 12/26/2022] Open
Abstract
Long-lasting changes of synaptic efficacy are largely mediated by activity-induced gene transcription and are essential for neuronal plasticity and memory. In this scenario, transcription factors have emerged as pivotal players underlying synaptic plasticity and the modification of neural networks required for memory formation and consolidation. Hippocampal synaptic dysfunction is widely accepted to underlie the cognitive decline observed in some neurodegenerative disorders including Alzheimer’s disease. Therefore, understanding the molecular pathways regulating gene expression profiles may help to identify new synaptic therapeutic targets. The nuclear receptor 4A subfamily (Nr4a) of transcription factors has been involved in a variety of physiological processes within the hippocampus, ranging from inflammation to neuroprotection. Recent studies have also pointed out a role for the activity-dependent nuclear receptor subfamily 4, group A, member 2 (Nr4a2/Nurr1) in hippocampal synaptic plasticity and cognitive functions, although the underlying molecular mechanisms are still poorly understood. In this review, we highlight the specific effects of Nr4a2 in hippocampal synaptic plasticity and memory formation and we discuss whether the dysregulation of this transcription factor could contribute to hippocampal synaptic dysfunction, altogether suggesting the possibility that Nr4a2 may emerge as a novel synaptic therapeutic target in brain pathologies associated to cognitive dysfunctions.
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Affiliation(s)
- Judit Català-Solsona
- Departament de Bioquímica i Biologia Molecular, Institut de Neurociències, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain.,Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Alfredo J Miñano-Molina
- Departament de Bioquímica i Biologia Molecular, Institut de Neurociències, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain.,Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - José Rodríguez-Álvarez
- Departament de Bioquímica i Biologia Molecular, Institut de Neurociències, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain.,Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain.,Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, New York, NY, United States
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53
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Dean DD, Agarwal S, Muthuswamy S, Asim A. Brain exosomes as minuscule information hub for Autism Spectrum Disorder. Expert Rev Mol Diagn 2021; 21:1323-1331. [PMID: 34720032 DOI: 10.1080/14737159.2021.2000395] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
INTRODUCTION Autism spectrum disorder (ASD) is a neurodevelopmental disorder initiating in the first three years of life. Early initiation of management therapies can significantly improve the health and quality of life of ASD subjects. Thus, indicating the need for suitable biomarkers for the early identification of ASD. Various biological domains were investigated in the quest for reliable biomarkers. However, most biomarkers are in the preliminary stage, and clinical validation is yet to be defined. Exosome based research gained momentum in various Central Nervous System disorders for biomarker identification. However, the utility and prospect of exosomes in ASD is still underexplored. AREAS COVERED In the present review, we summarized the biomarker discovery current status and the future of brain-specific exosomes in understanding pathophysiology and its potential as a biomarker. The studies reviewed herein were identified via systematic search (dated: June 2021) of PubMed using variations related to autism (ASD OR autism OR Autism spectrum disorder) AND exosomes AND/OR biomarkers. EXPERT OPINION As exosomess are highly relevant in brain disorders like ASD, direct access to brain tissue for molecular assessment is ethically impossible. Thus investigating the brain-derived exosomes would undoubtedly answer many unsolved aspects of the pathogenesis and provide reliable biomarkers.
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Affiliation(s)
- Deepika Delsa Dean
- Deptartment of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences (Sgpgims), Lucknow, India
| | - Sarita Agarwal
- Deptartment of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences (Sgpgims), Lucknow, India
| | | | - Ambreen Asim
- Deptartment of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences (Sgpgims), Lucknow, India
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Steinberg DJ, Aqeilan RI. WWOX-Related Neurodevelopmental Disorders: Models and Future Perspectives. Cells 2021; 10:cells10113082. [PMID: 34831305 PMCID: PMC8623516 DOI: 10.3390/cells10113082] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/28/2021] [Accepted: 11/03/2021] [Indexed: 12/12/2022] Open
Abstract
The WW domain-containing oxidoreductase (WWOX) gene was originally discovered as a putative tumor suppressor spanning the common fragile site FRA16D, but as time has progressed the extent of its pleiotropic function has become apparent. At present, WWOX is a major source of interest in the context of neurological disorders, and more specifically developmental and epileptic encephalopathies (DEEs). This review article aims to introduce the many model systems used through the years to study its function and roles in neuropathies. Similarities and fundamental differences between rodent and human models are discussed. Finally, future perspectives and promising research avenues are suggested.
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55
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Kaiser VB, Talmane L, Kumar Y, Semple F, MacLennan M, FitzPatrick DR, Taylor MS, Semple CA. Mutational bias in spermatogonia impacts the anatomy of regulatory sites in the human genome. Genome Res 2021; 31:1994-2007. [PMID: 34417209 PMCID: PMC8559717 DOI: 10.1101/gr.275407.121] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 08/19/2021] [Indexed: 12/03/2022]
Abstract
Mutation in the germline is the ultimate source of genetic variation, but little is known about the influence of germline chromatin structure on mutational processes. Using ATAC-seq, we profile the open chromatin landscape of human spermatogonia, the most proliferative cell type of the germline, identifying transcription factor binding sites (TFBSs) and PRDM9 binding sites, a subset of which will initiate meiotic recombination. We observe an increase in rare structural variant (SV) breakpoints at PRDM9-bound sites, implicating meiotic recombination in the generation of structural variation. Many germline TFBSs, such as NRF1, are also associated with increased rates of SV breakpoints, apparently independent of recombination. Singleton short insertions (≥5 bp) are highly enriched at TFBSs, particularly at sites bound by testis active TFs, and their rates correlate with those of structural variant breakpoints. Short insertions often duplicate the TFBS motif, leading to clustering of motif sites near regulatory regions in this male-driven evolutionary process. Increased mutation loads at germline TFBSs disproportionately affect neural enhancers with activity in spermatogonia, potentially altering neurodevelopmental regulatory architecture. Local chromatin structure in spermatogonia is thus pervasive in shaping both evolution and disease.
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Affiliation(s)
- Vera B Kaiser
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, The University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, United Kingdom
| | - Lana Talmane
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, The University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, United Kingdom
| | - Yatendra Kumar
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, The University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, United Kingdom
| | - Fiona Semple
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, The University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, United Kingdom
| | - Marie MacLennan
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, The University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, United Kingdom
| | - David R FitzPatrick
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, The University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, United Kingdom
| | - Martin S Taylor
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, The University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, United Kingdom
| | - Colin A Semple
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, The University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, United Kingdom
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NR4A2 expression is not altered in placentas from cases of growth restriction or preeclampsia, but is reduced in hypoxic cytotrophoblast. Sci Rep 2021; 11:20670. [PMID: 34667209 PMCID: PMC8526588 DOI: 10.1038/s41598-021-00192-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 09/29/2021] [Indexed: 11/21/2022] Open
Abstract
Nuclear Receptor Subfamily 4 Group A Member 2 (NR4A2) transcripts are elevated in the circulation of individuals whose pregnancies are complicated by preterm fetal growth restriction (FGR). In this paper, we show that the cases with preeclampsia (PE) have increased circulating NR4A2 transcripts compared to those with normotensive FGR. We aimed to establish whether the dysfunctional placenta mirrors the increase in NR4A2 transcripts and further, to uncover the function of placental NR4A2. NR4A2 expression was detected in preterm and term placental tissue; expressed higher at term. NR4A2 mRNA expression and protein were not altered in placentas from preterm FGR or PE pregnancies. Hypoxia (1% O2 compared to 8% O2) significantly reduced cytotrophoblast NR4A2 mRNA expression, but not placental explant NR4A2 expression. Silencing cytotrophoblast NR4A2 expression under hypoxia (via short interfering (si)RNAs) did not alter angiogenic Placental Growth Factor, nor anti-angiogenic sFlt-1 mRNA expression or protein secretion, but increased expression of cellular antioxidant, oxidative stress, inflammatory, and growth genes. NR4A2 expression was also not altered in a model of tumour necrosis factor-α-induced endothelial dysfunction, or with pravastatin treatment. Further studies are required to identify the origin of the circulating transcripts in pathological pregnancies, and investigate the function of placental NR4A2.
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Eyring KW, Geschwind DH. Three decades of ASD genetics: building a foundation for neurobiological understanding and treatment. Hum Mol Genet 2021; 30:R236-R244. [PMID: 34313757 PMCID: PMC8861370 DOI: 10.1093/hmg/ddab176] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 06/23/2021] [Accepted: 06/24/2021] [Indexed: 02/06/2023] Open
Abstract
Methodological advances over the last three decades have led to a profound transformation in our understanding of the genetic origins of neuropsychiatric disorders. This is exemplified by the study of autism spectrum disorders (ASDs) for which microarrays, whole exome sequencing and whole genome sequencing have yielded over a hundred causal loci. Genome-wide association studies in ASD have also been fruitful, identifying 5 genome-wide significant loci thus far and demonstrating a substantial role for polygenic inherited risk. Approaches rooted in systems biology and functional genomics have increasingly placed genes implicated by risk variants into biological context. Genetic risk affects a finite group of cell-types and biological processes, converging primarily on early stages of brain development (though, the expression of many risk genes persists through childhood). Coupled with advances in stem cell-based human in vitro model systems, these findings provide a basis for developing mechanistic models of disease pathophysiology.
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Affiliation(s)
- Katherine W Eyring
- Neurogenetics Program, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Daniel H Geschwind
- Neurogenetics Program, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Center For Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics and Institute for Precision Health, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
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58
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Marrus N, Turner TN, Forsen E, Bolster D, Marvin A, Whitehouse A, Klinger L, Gurnett CA, Constantino JN. Genetic counseling as preventive intervention: toward individual specification of transgenerational autism risk. J Neurodev Disord 2021; 13:39. [PMID: 34530736 PMCID: PMC8447585 DOI: 10.1186/s11689-021-09389-8] [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: 10/07/2020] [Accepted: 05/11/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Although autism spectrum disorders (ASD) are among the most heritable of all neuropsychiatric syndromes, most affected children are born to unaffected parents. Recently, we reported an average increase of 3-5% over general population risk of ASD among offspring of adults who have first-degree relatives with ASD in a large epidemiologic family sample. A next essential step is to investigate whether there are measurable characteristics of individual parents placing them at higher or lower recurrence risk, as this information could allow more personalized genetic counseling. METHODS We assembled what is to our knowledge the largest collection of data on the ability of four measurable characteristics of unaffected prospective parents to specify risk for autism among their offspring: (1) sub clinical autistic trait burden, (2) parental history of a sibling with ASD, (3) transmitted autosomal molecular genetic abnormalities, and (4) parental age. Leveraging phenotypic and genetic data in curated family cohorts, we evaluate the respective associations between these factors and child outcome when autism is present in the family in the parental generation. RESULTS All four characteristics were associated with elevation in offspring risk; however, the magnitude of their predictive power-with the exception of isolated rare inherited pathogenic variants -does not yet reach a threshold that would typically be considered actionable for reproductive decision-making. CONCLUSIONS Individual specification of risk to offspring of adults in ASD-affected families is not straightforwardly improved by ascertainment of parental phenotype, and it is not yet clear whether genomic screening of prospective parents in families affected by idiopathic ASD is warranted as a clinical standard. Systematic screening of affected family members for heritable pathogenic variants, including rare sex-linked mutations, will identify a subset of families with substantially elevated transmission risk. Polygenic risk scores are only weakly predictive at this time but steadily improving and ultimately may enable more robust prediction either singly or when combined with the risk variables examined in this study.
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Affiliation(s)
- Natasha Marrus
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave; Box 8504, St. Louis, MO, 63110, USA.
| | - Tychele N Turner
- Department of Genetics, Washington University School of Medicine, 660 S. Euclid Ave; Box 8108, St. Louis, MO, 63110, USA
| | - Elizabeth Forsen
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave; Box 8504, St. Louis, MO, 63110, USA
| | - Drew Bolster
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave; Box 8504, St. Louis, MO, 63110, USA
| | - Alison Marvin
- Maryland Center for Developmental Disabilities, Kennedy Krieger Institute, PACT Building/Office 121B; 7000 Tudsbury Road, Baltimore, MD, 21244, USA
| | - Andrew Whitehouse
- Telethon Kids Institute, Perth Children's Hospital, 15 Hospital Avenue, Nedlands, WA, 6009, USA
| | - Laura Klinger
- TEACCH Autism Program, Department of Psychiatry, University of North Carolina at Chapel Hill, Campus Box #7180, Chapel Hill, NC, 27599-7180, USA
| | - Christina A Gurnett
- Department of Neurology, Washington University School of Medicine, 660 S. Euclid Ave; Box 8111, St. Louis, MO, 63110, USA
| | - J N Constantino
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave; Box 8504, St. Louis, MO, 63110, USA
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59
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Yoon S, Munoz A, Yamrom B, Lee YH, Andrews P, Marks S, Wang Z, Reeves C, Winterkorn L, Krieger AM, Buja A, Pradhan K, Ronemus M, Baldwin KK, Levy D, Wigler M, Iossifov I. Rates of contributory de novo mutation in high and low-risk autism families. Commun Biol 2021; 4:1026. [PMID: 34471188 PMCID: PMC8410909 DOI: 10.1038/s42003-021-02533-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 08/09/2021] [Indexed: 12/24/2022] Open
Abstract
Autism arises in high and low-risk families. De novo mutation contributes to autism incidence in low-risk families as there is a higher incidence in the affected of the simplex families than in their unaffected siblings. But the extent of contribution in low-risk families cannot be determined solely from simplex families as they are a mixture of low and high-risk. The rate of de novo mutation in nearly pure populations of high-risk families, the multiplex families, has not previously been rigorously determined. Moreover, rates of de novo mutation have been underestimated from studies based on low resolution microarrays and whole exome sequencing. Here we report on findings from whole genome sequence (WGS) of both simplex families from the Simons Simplex Collection (SSC) and multiplex families from the Autism Genetic Resource Exchange (AGRE). After removing the multiplex samples with excessive cell-line genetic drift, we find that the contribution of de novo mutation in multiplex is significantly smaller than the contribution in simplex. We use WGS to provide high resolution CNV profiles and to analyze more than coding regions, and revise upward the rate in simplex autism due to an excess of de novo events targeting introns. Based on this study, we now estimate that de novo events contribute to 52-67% of cases of autism arising from low risk families, and 30-39% of cases of all autism.
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Affiliation(s)
- Seungtai Yoon
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Adriana Munoz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Boris Yamrom
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Yoon-Ha Lee
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Peter Andrews
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Steven Marks
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Zihua Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | | | | | - Abba M Krieger
- Statistics Department, The Wharton School, University of Pennsylvania, Philadelphia, PA, USA
| | - Andreas Buja
- Statistics Department, The Wharton School, University of Pennsylvania, Philadelphia, PA, USA
| | - Kith Pradhan
- Department of Medicine, Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA
| | - Michael Ronemus
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Kristin K Baldwin
- Department of Neuroscience, The Scripps Research Institute, La Jolla, CA, USA
- Department of Genetics and Development, Columbia University, New York, NY, USA
| | - Dan Levy
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Michael Wigler
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Ivan Iossifov
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA.
- New York Genome Center, New York, NY, USA.
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60
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Koire A, Katsonis P, Kim YW, Buchovecky C, Wilson SJ, Lichtarge O. A method to delineate de novo missense variants across pathways prioritizes genes linked to autism. Sci Transl Med 2021; 13:13/594/eabc1739. [PMID: 34011629 DOI: 10.1126/scitranslmed.abc1739] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 03/01/2021] [Indexed: 12/31/2022]
Abstract
Genotype-phenotype relationships shape health and population fitness but remain difficult to predict and interpret. Here, we apply an evolutionary action method to de novo missense variants in whole-exome sequences of individuals with autism spectrum disorder (ASD) to unravel genes and pathways connected to ASD. Evolutionary action predicts the impact of missense variants on protein function by measuring the fitness effect based on phylogenetic distances and substitution odds in homologous gene sequences. By examining de novo missense variants in 2384 individuals with ASD (probands) compared to matched siblings without ASD, we found missense variants in 398 genes representing 23 pathways that were biased toward higher evolutionary action scores than expected by random chance; these pathways were involved in axonogenesis, synaptic transmission, and neurodevelopment. The predicted fitness impact of de novo and inherited missense variants in candidate genes correlated with the IQ of individuals with ASD, even for new gene candidates. Taking an evolutionary action method, we detected those missense variants most likely to contribute to ASD pathogenesis and elucidated their phenotypic impact. This approach could be applied to integrate missense variants across a patient cohort to identify genes contributing to a shared phenotype in other complex diseases.
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Affiliation(s)
- Amanda Koire
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA.,Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA.,Department of Psychiatry, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Panagiotis Katsonis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Young Won Kim
- Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, TX, USA
| | - Christie Buchovecky
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Division of Carrier Screening and Prenatal Testing, SEMA4, Stamford, CT, USA
| | - Stephen J Wilson
- Department of Biochemistry, Baylor College of Medicine, Houston, TX, USA
| | - Olivier Lichtarge
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA. .,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Biochemistry, Baylor College of Medicine, Houston, TX, USA
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61
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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: 30] [Impact Index Per Article: 7.5] [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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62
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Al-Ward H, Liu CY, Liu N, Shaher F, Al-Nusaif M, Mao J, Xu H. Voltage-Gated Sodium Channel β1 Gene: An Overview. Hum Hered 2021; 85:101-109. [PMID: 34038903 DOI: 10.1159/000516388] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/01/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Voltage-gated sodium channels are protein complexes composed of 2 subunits, namely, pore-forming α- and regulatory β-subunits. A β-subunit consists of 5 proteins encoded by 4 genes (i.e., SCN1B-SCN4B). SUMMARY β1-Subunits regulate sodium ion channel functions, including gating properties, subcellular localization, and kinetics. Key Message: Sodium channel β1- and its variant β1B-subunits are encoded by SCN1B. These variants are associated with many human diseases, such as epilepsy, Brugada syndrome, Dravet syndrome, and cancers. On the basis of previous research, we aimed to provide an overview of the structure, expression, and involvement of SCN1B in physiological processes and focused on its role in diseases.
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Affiliation(s)
- Hisham Al-Ward
- Department of Biochemistry and Molecular Biology, Jiamusi University School of Basic Medical Sciences, Jiamusi, China
| | - Chun-Yang Liu
- Department of Biochemistry and Molecular Biology, Ankang University School of Medicine, Ankang, China
| | - Ning Liu
- Department of Biochemistry and Molecular Biology, Jiamusi University School of Basic Medical Sciences, Jiamusi, China
| | - Fahmi Shaher
- Department of Pathophysiology, Jiamusi University School of Basic Medical Sciences, Jiamusi, China
| | - Murad Al-Nusaif
- Department of Neurology, Dalian Medical University, Dalian, China
| | - Jing Mao
- Department of Biochemistry and Molecular Biology, Jiamusi University School of Basic Medical Sciences, Jiamusi, China
| | - Hui Xu
- Department of Biochemistry and Molecular Biology, Jiamusi University School of Basic Medical Sciences, Jiamusi, China
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63
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Overexpression of CD47 is associated with brain overgrowth and 16p11.2 deletion syndrome. Proc Natl Acad Sci U S A 2021; 118:2005483118. [PMID: 33833053 DOI: 10.1073/pnas.2005483118] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Copy number variation (CNV) at the 16p11.2 locus is associated with neuropsychiatric disorders, such as autism spectrum disorder and schizophrenia. CNVs of the 16p gene can manifest in opposing head sizes. Carriers of 16p11.2 deletion tend to have macrocephaly (or brain enlargement), while those with 16p11.2 duplication frequently have microcephaly. Increases in both gray and white matter volume have been observed in brain imaging studies in 16p11.2 deletion carriers with macrocephaly. Here, we use human induced pluripotent stem cells (hiPSCs) derived from controls and subjects with 16p11.2 deletion and 16p11.2 duplication to understand the underlying mechanisms regulating brain overgrowth. To model both gray and white matter, we differentiated patient-derived iPSCs into neural progenitor cells (NPCs) and oligodendrocyte progenitor cells (OPCs). In both NPCs and OPCs, we show that CD47 (a "don't eat me" signal) is overexpressed in the 16p11.2 deletion carriers contributing to reduced phagocytosis both in vitro and in vivo. Furthermore, 16p11.2 deletion NPCs and OPCs up-regulate cell surface expression of calreticulin (a prophagocytic "eat me" signal) and its binding sites, indicating that these cells should be phagocytosed but fail to be eliminated due to elevations in CD47. Treatment of 16p11.2 deletion NPCs and OPCs with an anti-CD47 antibody to block CD47 restores phagocytosis to control levels. While the CD47 pathway is commonly implicated in cancer progression, we document a role for CD47 in psychiatric disorders associated with brain overgrowth.
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Banne E, Abudiab B, Abu-Swai S, Repudi SR, Steinberg DJ, Shatleh D, Alshammery S, Lisowski L, Gold W, Carlen PL, Aqeilan RI. Neurological Disorders Associated with WWOX Germline Mutations-A Comprehensive Overview. Cells 2021; 10:824. [PMID: 33916893 PMCID: PMC8067556 DOI: 10.3390/cells10040824] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 03/30/2021] [Accepted: 04/01/2021] [Indexed: 12/13/2022] Open
Abstract
The transcriptional regulator WW domain-containing oxidoreductase (WWOX) is a key player in a number of cellular and biological processes including tumor suppression. Recent evidence has emerged associating WWOX with non-cancer disorders. Patients harboring pathogenic germline bi-allelic WWOX variants have been described with the rare devastating neurological syndromes autosomal recessive spinocerebellar ataxia 12 (SCAR12) (6 patients) and WWOX-related epileptic encephalopathy (DEE28 or WOREE syndrome) (56 patients). Individuals with these syndromes present with a highly heterogenous clinical spectrum, the most common clinical symptoms being severe epileptic encephalopathy and profound global developmental delay. Knowledge of the underlying pathophysiology of these syndromes, the range of variants of the WWOX gene and its genotype-phenotype correlations is limited, hampering therapeutic efforts. Therefore, there is a critical need to identify and consolidate all the reported variants in WWOX to distinguish between disease-causing alleles and their associated severity, and benign variants, with the aim of improving diagnosis and increasing therapeutic efforts. Here, we provide a comprehensive review of the literature on WWOX, and analyze the pathogenic variants from published and unpublished reports by collecting entries from the ClinVar, DECIPHER, VarSome, and PubMed databases to generate the largest dataset of WWOX pathogenic variants. We estimate the correlation between variant type and patient phenotype, and delineate the impact of each variant, and used GnomAD to cross reference these variants found in the general population. From these searches, we generated the largest published cohort of WWOX individuals. We conclude with a discussion on potential personalized medicine approaches to tackle the devastating disorders associated with WWOX mutations.
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Affiliation(s)
- Ehud Banne
- The Genetic Institute, Kaplan Medical Center, Hebrew University-Hadassah Medical School, Rehovot 76100, Israel;
- The Rina Mor Genetic Institute, Wolfson Medical Center, Holon 58100, Israel
| | - Baraa Abudiab
- The Concern Foundation Laboratories, The Lautenberg Center for Immunology and Cancer Research, Department of Immunology and Cancer Research-IMRIC, Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel; (B.A.); (S.A.-S.); (D.J.S.); (S.R.R.); (D.S.)
| | - Sara Abu-Swai
- The Concern Foundation Laboratories, The Lautenberg Center for Immunology and Cancer Research, Department of Immunology and Cancer Research-IMRIC, Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel; (B.A.); (S.A.-S.); (D.J.S.); (S.R.R.); (D.S.)
| | - Srinivasa Rao Repudi
- The Concern Foundation Laboratories, The Lautenberg Center for Immunology and Cancer Research, Department of Immunology and Cancer Research-IMRIC, Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel; (B.A.); (S.A.-S.); (D.J.S.); (S.R.R.); (D.S.)
| | - Daniel J. Steinberg
- The Concern Foundation Laboratories, The Lautenberg Center for Immunology and Cancer Research, Department of Immunology and Cancer Research-IMRIC, Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel; (B.A.); (S.A.-S.); (D.J.S.); (S.R.R.); (D.S.)
| | - Diala Shatleh
- The Concern Foundation Laboratories, The Lautenberg Center for Immunology and Cancer Research, Department of Immunology and Cancer Research-IMRIC, Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel; (B.A.); (S.A.-S.); (D.J.S.); (S.R.R.); (D.S.)
| | - Sarah Alshammery
- Faculty of Medicine and Health, School of Medical Sciences and Discipline of Child and Adolescent Health, The University of Sydney, Westmead 2145, NSW, Australia; (S.A.); (W.G.)
| | - Leszek Lisowski
- Translational Vectorology Research Unit, Children’s Medical Research Institute, The University of Sydney, Westmead 2145, NSW, Australia;
- Laboratory of Molecular Oncology and Innovative Therapies, Military Institute of Medicine, 04-141 Warsaw, Poland
| | - Wendy Gold
- Faculty of Medicine and Health, School of Medical Sciences and Discipline of Child and Adolescent Health, The University of Sydney, Westmead 2145, NSW, Australia; (S.A.); (W.G.)
- Molecular Neurobiology Research Laboratory, Kids Research, Children’s Hospital at Westmead and The Children’s Medical Research Institute, Westmead 2145, NSW, Australia
- Kids Neuroscience Centre, Kids Research, Children’s Hospital at Westmead, Westmead 2145, NSW, Australia
| | - Peter L. Carlen
- Krembil Research Institute, University Health Network and Department of Medicine, Physiology and BME, University of Toronto, Toronto, ON M5T 1M8, Canada;
| | - Rami I. Aqeilan
- The Concern Foundation Laboratories, The Lautenberg Center for Immunology and Cancer Research, Department of Immunology and Cancer Research-IMRIC, Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel; (B.A.); (S.A.-S.); (D.J.S.); (S.R.R.); (D.S.)
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65
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Moreno-De-Luca D, Martin CL. All for one and one for all: heterogeneity of genetic etiologies in neurodevelopmental psychiatric disorders. Curr Opin Genet Dev 2021; 68:71-78. [PMID: 33773394 DOI: 10.1016/j.gde.2021.02.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 02/19/2021] [Accepted: 02/26/2021] [Indexed: 12/27/2022]
Abstract
Alexandre Dumas' famous phrase All for One and One for All recapitulates our current understanding of the genomic architecture of neurodevelopmental psychiatric disorders (NPD), like autism Spectrum disorder, bipolar disorder, and schizophrenia. Many rare genomic variants of large effect size have been identified; all of them together can explain a significant proportion of NPD. In parallel, one rare genomic variant can cause all of the above NPD. Finally, common genomic variants of individually small effect size can be combined to further explain risk for NPD. How do we reconcile different genomic variants accounting for one clinical diagnosis, and different clinical diagnoses arising from a single genomic variant? Here, we discuss a framework to understand genetic and clinical heterogeneity in NPD.
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Affiliation(s)
- Daniel Moreno-De-Luca
- Genomic Psychiatry Consultation Service, Verrecchia Clinic for Children with Autism and Developmental Disabilities, Bradley Hospital, Providence, RI, United States; Division of Child and Adolescent Psychiatry, Department of Psychiatry and Human Behavior, Warren Alpert Medical School of Brown University, Providence, RI, United States.
| | - Christa Lese Martin
- Autism & Developmental Medicine Institute, Geisinger, Danville, PA, United States; Genomic Medicine Institute, Geisinger, Danville, PA, United States.
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66
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Comparison of the diagnostic yield of aCGH and genome-wide sequencing across different neurodevelopmental disorders. NPJ Genom Med 2021; 6:25. [PMID: 33767182 PMCID: PMC7994713 DOI: 10.1038/s41525-021-00188-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 02/26/2021] [Indexed: 02/07/2023] Open
Abstract
Most consensus recommendations for the genetic diagnosis of neurodevelopmental disorders (NDDs) do not include the use of next generation sequencing (NGS) and are still based on chromosomal microarrays, such as comparative genomic hybridization array (aCGH). This study compares the diagnostic yield obtained by aCGH and clinical exome sequencing in NDD globally and its spectrum of disorders. To that end, 1412 patients clinically diagnosed with NDDs and studied with aCGH were classified into phenotype categories: global developmental delay/intellectual disability (GDD/ID); autism spectrum disorder (ASD); and other NDDs. These categories were further subclassified based on the most frequent accompanying signs and symptoms into isolated forms, forms with epilepsy; forms with micro/macrocephaly and syndromic forms. Two hundred and forty-five patients of the 1412 were subjected to clinical exome sequencing. Diagnostic yield of aCGH and clinical exome sequencing, expressed as the number of solved cases, was compared for each phenotype category and subcategory. Clinical exome sequencing was superior than aCGH for all cases except for isolated ASD, with no additional cases solved by NGS. Globally, clinical exome sequencing solved 20% of cases (versus 5.7% by aCGH) and the diagnostic yield was highest for all forms of GDD/ID and lowest for Other NDDs (7.1% versus 1.4% by aCGH) and ASD (6.1% versus 3% by aCGH). In the majority of cases, diagnostic yield was higher in the phenotype subcategories than in the mother category. These results suggest that NGS could be used as a first-tier test in the diagnostic algorithm of all NDDs followed by aCGH when necessary.
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67
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Stevens SR, Rasband MN. Ankyrins and neurological disease. Curr Opin Neurobiol 2021; 69:51-57. [PMID: 33485190 DOI: 10.1016/j.conb.2021.01.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/06/2021] [Accepted: 01/08/2021] [Indexed: 12/11/2022]
Abstract
Ankyrins are scaffolding proteins widely expressed throughout the nervous system. Ankyrins recruit diverse membrane proteins, including ion channels and cell adhesion molecules, into specialized subcellular membrane domains. These domains are stabilized by ankyrins interacting with the spectrin cytoskeleton. Ankyrin genes are highly associated with a number of neurological disorders, including Alzheimer's disease, schizophrenia, autism spectrum disorders, and bipolar disorder. Here, we discuss ankyrin function and their role in neurological disease. We propose mutations in ankyrins contribute to disease through two primary mechanisms: 1) altered neuronal excitability by disrupting ion channel clustering at key excitable domains, and 2) altered neuronal connectivity via impaired stabilization of membrane proteins.
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Affiliation(s)
- Sharon R Stevens
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Matthew N Rasband
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA.
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68
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Gandawijaya J, Bamford RA, Burbach JPH, Oguro-Ando A. Cell Adhesion Molecules Involved in Neurodevelopmental Pathways Implicated in 3p-Deletion Syndrome and Autism Spectrum Disorder. Front Cell Neurosci 2021; 14:611379. [PMID: 33519384 PMCID: PMC7838543 DOI: 10.3389/fncel.2020.611379] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 12/15/2020] [Indexed: 01/06/2023] Open
Abstract
Autism spectrum disorder (ASD) is characterized by impaired social interaction, language delay and repetitive or restrictive behaviors. With increasing prevalence, ASD is currently estimated to affect 0.5–2.0% of the global population. However, its etiology remains unclear due to high genetic and phenotypic heterogeneity. Copy number variations (CNVs) are implicated in several forms of syndromic ASD and have been demonstrated to contribute toward ASD development by altering gene dosage and expression. Increasing evidence points toward the p-arm of chromosome 3 (chromosome 3p) as an ASD risk locus. Deletions occurring at chromosome 3p result in 3p-deletion syndrome (Del3p), a rare genetic disorder characterized by developmental delay, intellectual disability, facial dysmorphisms and often, ASD or ASD-associated behaviors. Therefore, we hypothesize that overlapping molecular mechanisms underlie the pathogenesis of Del3p and ASD. To investigate which genes encoded in chromosome 3p could contribute toward Del3p and ASD, we performed a comprehensive literature review and collated reports investigating the phenotypes of individuals with chromosome 3p CNVs. We observe that high frequencies of CNVs occur in the 3p26.3 region, the terminal cytoband of chromosome 3p. This suggests that CNVs disrupting genes encoded within the 3p26.3 region are likely to contribute toward the neurodevelopmental phenotypes observed in individuals affected by Del3p. The 3p26.3 region contains three consecutive genes encoding closely related neuronal immunoglobulin cell adhesion molecules (IgCAMs): Close Homolog of L1 (CHL1), Contactin-6 (CNTN6), and Contactin-4 (CNTN4). CNVs disrupting these neuronal IgCAMs may contribute toward ASD phenotypes as they have been associated with key roles in neurodevelopment. CHL1, CNTN6, and CNTN4 have been observed to promote neurogenesis and neuronal survival, and regulate neuritogenesis and synaptic function. Furthermore, there is evidence that these neuronal IgCAMs possess overlapping interactomes and participate in common signaling pathways regulating axon guidance. Notably, mouse models deficient for these neuronal IgCAMs do not display strong deficits in axonal migration or behavioral phenotypes, which is in contrast to the pronounced defects in neuritogenesis and axon guidance observed in vitro. This suggests that when CHL1, CNTN6, or CNTN4 function is disrupted by CNVs, other neuronal IgCAMs may suppress behavioral phenotypes by compensating for the loss of function.
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Affiliation(s)
- Josan Gandawijaya
- University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - Rosemary A Bamford
- University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - J Peter H Burbach
- Department of Translational Neuroscience, Brain Center Rudolf Magnus, University Medical Center Utrecht and Utrecht University, Utrecht, Netherlands
| | - Asami Oguro-Ando
- University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
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69
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Aldaz CM, Hussain T. WWOX Loss of Function in Neurodevelopmental and Neurodegenerative Disorders. Int J Mol Sci 2020; 21:E8922. [PMID: 33255508 PMCID: PMC7727818 DOI: 10.3390/ijms21238922] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 11/17/2020] [Accepted: 11/20/2020] [Indexed: 01/13/2023] Open
Abstract
The WWOX gene was initially discovered as a putative tumor suppressor. More recently, its association with multiple central nervous system (CNS) pathologies has been recognized. WWOX biallelic germline pathogenic variants have been implicated in spinocerebellar ataxia type 12 (SCAR12; MIM:614322) and in early infantile epileptic encephalopathy (EIEE28; MIM:616211). WWOX germline copy number variants have also been associated with autism spectrum disorder (ASD). All identified germline genomic variants lead to partial or complete loss of WWOX function. Importantly, large-scale genome-wide association studies have also identified WWOX as a risk gene for common neurodegenerative conditions such as Alzheimer's disease (AD) and multiple sclerosis (MS). Thus, the spectrum of CNS disorders associated with WWOX is broad and heterogeneous, and there is little understanding of potential mechanisms at play. Exploration of gene expression databases indicates that WWOX expression is comparatively higher in the human cerebellar cortex than in other CNS structures. However, RNA in-situ hybridization data from the Allen Mouse Brain Atlas show that specific regions of the basolateral amygdala (BLA), the medial entorhinal cortex (EC), and deep layers of the isocortex can be singled out as brain regions with specific higher levels of Wwox expression. These observations are in close agreement with single-cell RNA-seq data which indicate that neurons from the medial entorhinal cortex, Layer 5 from the frontal cortex as well as GABAergic basket cells and granule cells from cerebellar cortex are the specific neuronal subtypes that display the highest Wwox expression levels. Importantly, the brain regions and cell types in which WWOX is most abundantly expressed, such as the EC and BLA, are intimately linked to pathologies and syndromic conditions in turn associated with this gene, such as epilepsy, intellectual disability, ASD, and AD. Higher Wwox expression in interneurons and granule cells from cerebellum points to a direct link to the described cerebellar ataxia in cases of WWOX loss of function. We now know that total or partial impairment of WWOX function results in a wide and heterogeneous variety of neurodegenerative conditions for which the specific molecular mechanisms remain to be deciphered. Nevertheless, these observations indicate an important functional role for WWOX in normal development and function of the CNS. Evidence also indicates that disruption of WWOX expression at the gene or protein level in CNS has significant deleterious consequences.
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Affiliation(s)
- C. Marcelo Aldaz
- Department of Epigenetics and Molecular Carcinogenesis, Science Park, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA;
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70
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Andrew DR, Moe ME, Chen D, Tello JA, Doser RL, Conner WE, Ghuman JK, Restifo LL. Spontaneous motor-behavior abnormalities in two Drosophila models of neurodevelopmental disorders. J Neurogenet 2020; 35:1-22. [PMID: 33164597 DOI: 10.1080/01677063.2020.1833005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Mutations in hundreds of genes cause neurodevelopmental disorders with abnormal motor behavior alongside cognitive deficits. Boys with fragile X syndrome (FXS), a leading monogenic cause of intellectual disability, often display repetitive behaviors, a core feature of autism. By direct observation and manual analysis, we characterized spontaneous-motor-behavior phenotypes of Drosophila dfmr1 mutants, an established model for FXS. We recorded individual 1-day-old adult flies, with mature nervous systems and prior to the onset of aging, in small arenas. We scored behavior using open-source video-annotation software to generate continuous activity timelines, which were represented graphically and quantitatively. Young dfmr1 mutants spent excessive time grooming, with increased bout number and duration; both were rescued by transgenic wild-type dfmr1+. By two grooming-pattern measures, dfmr1-mutant flies showed elevated repetitions consistent with perseveration, which is common in FXS. In addition, the mutant flies display a preference for grooming posterior body structures, and an increased rate of grooming transitions from one site to another. We raise the possibility that courtship and circadian rhythm defects, previously reported for dfmr1 mutants, are complicated by excessive grooming. We also observed significantly increased grooming in CASK mutants, despite their dramatically decreased walking phenotype. The mutant flies, a model for human CASK-related neurodevelopmental disorders, displayed consistently elevated grooming indices throughout the assay, but transient locomotory activation immediately after placement in the arena. Based on published data identifying FMRP-target transcripts and functional analyses of mutations causing human genetic neurodevelopmental disorders, we propose the following proteins as candidate mediators of excessive repetitive behaviors in FXS: CaMKIIα, NMDA receptor subunits 2A and 2B, NLGN3, and SHANK3. Together, these fly-mutant phenotypes and mechanistic insights provide starting points for drug discovery to identify compounds that reduce dysfunctional repetitive behaviors.
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Affiliation(s)
- David R Andrew
- Department of Neurology, University of Arizona Health Sciences, Tucson, AZ, USA.,Center for Insect Science, University of Arizona, Tucson, AZ, USA.,Department of Biological Sciences, Lycoming College, Williamsport, PA, USA
| | - Mariah E Moe
- Department of Neurology, University of Arizona Health Sciences, Tucson, AZ, USA
| | - Dailu Chen
- Department of Neurology, University of Arizona Health Sciences, Tucson, AZ, USA
| | - Judith A Tello
- Department of Neurology, University of Arizona Health Sciences, Tucson, AZ, USA.,Graduate Interdisciplinary Program in Neuroscience, University of Arizona, Tucson, AZ, USA
| | - Rachel L Doser
- Department of Neurology, University of Arizona Health Sciences, Tucson, AZ, USA
| | - William E Conner
- Department of Biology, Wake Forest University, Winston-Salem, NC, USA
| | - Jaswinder K Ghuman
- Department of Psychiatry, University of Arizona Health Sciences, Tucson, AZ, USA
| | - Linda L Restifo
- Department of Neurology, University of Arizona Health Sciences, Tucson, AZ, USA.,Center for Insect Science, University of Arizona, Tucson, AZ, USA.,Graduate Interdisciplinary Program in Neuroscience, University of Arizona, Tucson, AZ, USA.,BIO5 Interdisciplinary Research Institute, University of Arizona, Tucson, AZ, USA
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71
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Ní Ghrálaigh F, Gallagher L, Lopez LM. Autism spectrum disorder genomics: The progress and potential of genomic technologies. Genomics 2020; 112:5136-5142. [DOI: 10.1016/j.ygeno.2020.09.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/01/2020] [Accepted: 09/08/2020] [Indexed: 12/27/2022]
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72
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Trevis KJ, Brown NJ, Green CC, Lockhart PJ, Desai T, Vick T, Anderson V, Pua EPK, Bahlo M, Delatycki MB, Scheffer IE, Wilson SJ. Tracing Autism Traits in Large Multiplex Families to Identify Endophenotypes of the Broader Autism Phenotype. Int J Mol Sci 2020; 21:E7965. [PMID: 33120939 PMCID: PMC7663259 DOI: 10.3390/ijms21217965] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/14/2020] [Accepted: 10/21/2020] [Indexed: 12/11/2022] Open
Abstract
Families comprising many individuals with Autism Spectrum Disorders (ASD) may carry a dominant predisposing mutation. We implemented rigorous phenotyping of the "Broader Autism Phenotype" (BAP) in large multiplex ASD families using a novel endophenotype approach for the identification and characterisation of distinct BAP endophenotypes. We evaluated ASD/BAP features using standardised tests and a semi-structured interview to assess social, intellectual, executive and adaptive functioning in 110 individuals, including two large multiplex families (Family A: 30; Family B: 35) and an independent sample of small families (n = 45). Our protocol identified four distinct psychological endophenotypes of the BAP that were evident across these independent samples, and showed high sensitivity (97%) and specificity (82%) for individuals classified with the BAP. Patterns of inheritance of identified endophenotypes varied between the two large multiplex families, supporting their utility for identifying genes in ASD.
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Affiliation(s)
- Krysta J. Trevis
- Department of Medicine, Austin Health, The University of Melbourne, Heidelberg, VIC 3084, Australia; (K.J.T.); (C.C.G.); (T.D.); (E.P.K.P.); (I.E.S.)
- Melbourne School of Psychological Sciences, The University of Melbourne, Parkville, VIC 3010, Australia;
| | - Natasha J. Brown
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia; (N.J.B.); (M.B.D.)
- Barwon Health, Geelong, VIC 3220, Australia;
| | - Cherie C. Green
- Department of Medicine, Austin Health, The University of Melbourne, Heidelberg, VIC 3084, Australia; (K.J.T.); (C.C.G.); (T.D.); (E.P.K.P.); (I.E.S.)
- Melbourne School of Psychological Sciences, The University of Melbourne, Parkville, VIC 3010, Australia;
- Department of Psychology and Counselling, School of Psychology and Public Health, La Trobe University, Bundoora, VIC 3086, Australia
| | - Paul J. Lockhart
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia;
- Department of Paediatrics, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Tarishi Desai
- Department of Medicine, Austin Health, The University of Melbourne, Heidelberg, VIC 3084, Australia; (K.J.T.); (C.C.G.); (T.D.); (E.P.K.P.); (I.E.S.)
- Melbourne School of Psychological Sciences, The University of Melbourne, Parkville, VIC 3010, Australia;
| | - Tanya Vick
- Barwon Health, Geelong, VIC 3220, Australia;
| | - Vicki Anderson
- Melbourne School of Psychological Sciences, The University of Melbourne, Parkville, VIC 3010, Australia;
- Psychological Service, The Royal Children’s Hospital, Parkville, VIC 3052, Australia
- Clinical Sciences Research, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia
| | - Emmanuel P. K. Pua
- Department of Medicine, Austin Health, The University of Melbourne, Heidelberg, VIC 3084, Australia; (K.J.T.); (C.C.G.); (T.D.); (E.P.K.P.); (I.E.S.)
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia;
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Martin B. Delatycki
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia; (N.J.B.); (M.B.D.)
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia;
- Department of Paediatrics, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Ingrid E. Scheffer
- Department of Medicine, Austin Health, The University of Melbourne, Heidelberg, VIC 3084, Australia; (K.J.T.); (C.C.G.); (T.D.); (E.P.K.P.); (I.E.S.)
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia; (N.J.B.); (M.B.D.)
- Clinical Sciences Research, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia
- The Florey Institute of Neuroscience and Mental Health, Parkville, VIC 3052, Australia
| | - Sarah J. Wilson
- Department of Medicine, Austin Health, The University of Melbourne, Heidelberg, VIC 3084, Australia; (K.J.T.); (C.C.G.); (T.D.); (E.P.K.P.); (I.E.S.)
- Melbourne School of Psychological Sciences, The University of Melbourne, Parkville, VIC 3010, Australia;
- The Florey Institute of Neuroscience and Mental Health, Parkville, VIC 3052, Australia
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73
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Look duration at the face as a developmental endophenotype: elucidating pathways to autism and ADHD. Dev Psychopathol 2020; 32:1303-1322. [DOI: 10.1017/s0954579420000930] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
AbstractIdentifying developmental endophenotypes on the pathway between genetics and behavior is critical to uncovering the mechanisms underlying neurodevelopmental conditions. In this proof-of-principle study, we explored whether early disruptions in visual attention are a unique or shared candidate endophenotype of autism spectrum disorder (ASD) and attention-deficit/hyperactivity disorder (ADHD). We calculated the duration of the longest look (i.e., peak look) to faces in an array-based eye-tracking task for 335 14-month-old infants with and without first-degree relatives with ASD and/or ADHD. We leveraged parent-report and genotype data available for a proportion of these infants to evaluate the relation of looking behavior to familial (n = 285) and genetic liability (using polygenic scores, n = 185) as well as ASD and ADHD-relevant temperament traits at 2 years of age (shyness and inhibitory control, respectively, n = 272) and ASD and ADHD clinical traits at 6 years of age (n = 94).Results showed that longer peak looks at the face were associated with elevated polygenic scores for ADHD (β = 0.078, p = .023), but not ASD (β = 0.002, p = .944), and with elevated ADHD traits in mid-childhood (F(1,88) = 6.401, p = .013, $\eta _p^2$=0.068; ASD: F (1,88) = 3.218, p = .076), but not in toddlerhood (ps > 0.2). This pattern of results did not emerge when considering mean peak look duration across face and nonface stimuli. Thus, alterations in attention to faces during spontaneous visual exploration may be more consistent with a developmental endophenotype of ADHD than ASD. Our work shows that dissecting paths to neurodevelopmental conditions requires longitudinal data incorporating polygenic contribution, early neurocognitive function, and clinical phenotypic variation.
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Integrative genomics identifies a convergent molecular subtype that links epigenomic with transcriptomic differences in autism. Nat Commun 2020; 11:4873. [PMID: 32978376 PMCID: PMC7519165 DOI: 10.1038/s41467-020-18526-1] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 08/27/2020] [Indexed: 01/06/2023] Open
Abstract
Autism spectrum disorder (ASD) is a phenotypically and genetically heterogeneous neurodevelopmental disorder. Despite this heterogeneity, previous studies have shown patterns of molecular convergence in post-mortem brain tissue from autistic subjects. Here, we integrate genome-wide measures of mRNA expression, miRNA expression, DNA methylation, and histone acetylation from ASD and control brains to identify a convergent molecular subtype of ASD with shared dysregulation across both the epigenome and transcriptome. Focusing on this convergent subtype, we substantially expand the repertoire of differentially expressed genes in ASD and identify a component of upregulated immune processes that are associated with hypomethylation. We utilize eQTL and chromosome conformation datasets to link differentially acetylated regions with their cognate genes and identify an enrichment of ASD genetic risk variants in hyperacetylated noncoding regulatory regions linked to neuronal genes. These findings help elucidate how diverse genetic risk factors converge onto specific molecular processes in ASD.
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75
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Chanwigoon S, Piwluang S, Wichadakul D. inCNV: An Integrated Analysis Tool for Copy Number Variation on Whole Exome Sequencing. Evol Bioinform Online 2020; 16:1176934320956577. [PMID: 33029071 PMCID: PMC7520931 DOI: 10.1177/1176934320956577] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 08/13/2020] [Indexed: 12/13/2022] Open
Abstract
The detection of copy number variations (CNVs) on whole-exome sequencing (WES) represents a cost-effective technique for the study of genetic variants. This approach, however, has encountered an obstacle with high false-positive rates due to biases from exome sequencing capture kits and GC contents. Although plenty of CNV detection tools have been developed, they do not perform well with all types of CNVs. In addition, most tools lack features of genetic annotation, CNV visualization, and flexible installation, requiring users to put much effort into CNV interpretation. Here, we present "inCNV," a web-based application that can accept multiple CNV-tool results, then integrate and prioritize them with user-friendly interfaces. This application helps users analyze the importance of called CNVs by generating CNV annotations from Ensembl, Database of Genomic Variants (DGV), ClinVar, and Online Mendelian Inheritance in Man (OMIM). Moreover, users can select and export CNVs of interest including their flanking sequences for primer design and experimental verification. We demonstrated how inCNV could help users filter and narrow down the called CNVs to a potentially novel CNV, a common CNV within a group of samples of the same disease, or a de novo CNV of a sample within the same family. Besides, we have provided in CNV as a docker image for ease of installation (https://github.com/saowwapark/inCNV).
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Affiliation(s)
- Saowwapark Chanwigoon
- Software Engineering Program, Department of Computer Engineering, Faculty of Engineering, Chulalongkorn University, Bangkok, Thailand
| | - Sakkayaphab Piwluang
- Software Engineering Program, Department of Computer Engineering, Faculty of Engineering, Chulalongkorn University, Bangkok, Thailand
| | - Duangdao Wichadakul
- Department of Computer Engineering, Faculty of Engineering, Chulalongkorn University, Bangkok, Thailand
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76
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Matoba N, Liang D, Sun H, Aygün N, McAfee JC, Davis JE, Raffield LM, Qian H, Piven J, Li Y, Kosuri S, Won H, Stein JL. Common genetic risk variants identified in the SPARK cohort support DDHD2 as a candidate risk gene for autism. Transl Psychiatry 2020; 10:265. [PMID: 32747698 PMCID: PMC7400671 DOI: 10.1038/s41398-020-00953-9] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 07/22/2020] [Indexed: 12/13/2022] Open
Abstract
Autism spectrum disorder (ASD) is a highly heritable neurodevelopmental disorder. Large genetically informative cohorts of individuals with ASD have led to the identification of a limited number of common genome-wide significant (GWS) risk loci to date. However, many more common genetic variants are expected to contribute to ASD risk given the high heritability. Here, we performed a genome-wide association study (GWAS) on 6222 case-pseudocontrol pairs from the Simons Foundation Powering Autism Research for Knowledge (SPARK) dataset to identify additional common genetic risk factors and molecular mechanisms underlying risk for ASD. We identified one novel GWS locus from the SPARK GWAS and four significant loci, including an additional novel locus from meta-analysis with a previous GWAS. We replicated the previous observation of significant enrichment of ASD heritability within regulatory regions of the developing cortex, indicating that disruption of gene regulation during neurodevelopment is critical for ASD risk. We further employed a massively parallel reporter assay (MPRA) and identified a putative causal variant at the novel locus from SPARK GWAS with strong impacts on gene regulation (rs7001340). Expression quantitative trait loci data demonstrated an association between the risk allele and decreased expression of DDHD2 (DDHD domain containing 2) in both adult and prenatal brains. In conclusion, by integrating genetic association data with multi-omic gene regulatory annotations and experimental validation, we fine-mapped a causal risk variant and demonstrated that DDHD2 is a novel gene associated with ASD risk.
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Affiliation(s)
- Nana Matoba
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Dan Liang
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Huaigu Sun
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Nil Aygün
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jessica C McAfee
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jessica E Davis
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Quantitative and Computational Biology Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Huijun Qian
- Department of Statistics and Operations Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Joseph Piven
- Department of Psychiatry and the Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Yun Li
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Sriam Kosuri
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Quantitative and Computational Biology Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Hyejung Won
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
| | - Jason L Stein
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
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77
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Genç Ö, An JY, Fetter RD, Kulik Y, Zunino G, Sanders SJ, Davis GW. Homeostatic plasticity fails at the intersection of autism-gene mutations and a novel class of common genetic modifiers. eLife 2020; 9:55775. [PMID: 32609087 PMCID: PMC7394548 DOI: 10.7554/elife.55775] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 06/07/2020] [Indexed: 01/08/2023] Open
Abstract
We identify a set of common phenotypic modifiers that interact with five independent autism gene orthologs (RIMS1, CHD8, CHD2, WDFY3, ASH1L) causing a common failure of presynaptic homeostatic plasticity (PHP) in Drosophila. Heterozygous null mutations in each autism gene are demonstrated to have normal baseline neurotransmission and PHP. However, PHP is sensitized and rendered prone to failure. A subsequent electrophysiology-based genetic screen identifies the first known heterozygous mutations that commonly genetically interact with multiple ASD gene orthologs, causing PHP to fail. Two phenotypic modifiers identified in the screen, PDPK1 and PPP2R5D, are characterized. Finally, transcriptomic, ultrastructural and electrophysiological analyses define one mechanism by which PHP fails; an unexpected, maladaptive up-regulation of CREG, a conserved, neuronally expressed, stress response gene and a novel repressor of PHP. Thus, we define a novel genetic landscape by which diverse, unrelated autism risk genes may converge to commonly affect the robustness of synaptic transmission.
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Affiliation(s)
- Özgür Genç
- Department of Biochemistry and Biophysics Kavli Institute for Fundamental Neuroscience University of California, San Francisco, San Francisco, United States
| | - Joon-Yong An
- Department of Psychiatry UCSF Weill Institute for Neurosciences University of California, San Francisco, San Francisco, United States.,School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul, Republic of Korea
| | - Richard D Fetter
- Department of Biochemistry and Biophysics Kavli Institute for Fundamental Neuroscience University of California, San Francisco, San Francisco, United States
| | - Yelena Kulik
- Department of Biochemistry and Biophysics Kavli Institute for Fundamental Neuroscience University of California, San Francisco, San Francisco, United States
| | - Giulia Zunino
- Department of Biochemistry and Biophysics Kavli Institute for Fundamental Neuroscience University of California, San Francisco, San Francisco, United States
| | - Stephan J Sanders
- Department of Psychiatry UCSF Weill Institute for Neurosciences University of California, San Francisco, San Francisco, United States
| | - Graeme W Davis
- Department of Biochemistry and Biophysics Kavli Institute for Fundamental Neuroscience University of California, San Francisco, San Francisco, United States
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78
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Ashitha SNM, Ramachandra NB. Integrated Functional Analysis Implicates Syndromic and Rare Copy Number Variation Genes as Prominent Molecular Players in Pathogenesis of Autism Spectrum Disorders. Neuroscience 2020; 438:25-40. [DOI: 10.1016/j.neuroscience.2020.04.051] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 01/05/2023]
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79
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Lyall K, Song L, Botteron K, Croen LA, Dager SR, Fallin MD, Hazlett HC, Kauffman E, Landa R, Ladd-Acosta C, Messinger DS, Ozonoff S, Pandey J, Piven J, Schmidt RJ, Schultz RT, Stone WL, Newschaffer CJ, Volk HE. The Association Between Parental Age and Autism-Related Outcomes in Children at High Familial Risk for Autism. Autism Res 2020; 13:998-1010. [PMID: 32314879 PMCID: PMC7396152 DOI: 10.1002/aur.2303] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 03/20/2020] [Accepted: 03/24/2020] [Indexed: 12/19/2022]
Abstract
Advanced parental age is a well-replicated risk factor for autism spectrum disorder (ASD), a neurodevelopmental condition with a complex and not well-defined etiology. We sought to determine parental age associations with ASD-related outcomes in subjects at high familial risk for ASD. A total of 397 younger siblings of a child with ASD, drawn from existing prospective high familial risk cohorts, were included in these analyses. Overall, we did not observe significant associations of advanced parental age with clinical ASD diagnosis, Social Responsiveness Scale, or Vineland Adaptive Behavior Scales scores. Instead, increased odds of ASD were found with paternal age < 30 years (adjusted odds ratio [AOR] = 2.83 and 95% confidence intervals [CI] = 1.14-7.02). Likewise, younger age (<30 years) for both parents was associated with decreases in Mullen Scales of Early Learning early learning composite (MSEL-ELC) scores (adjusted β = -9.62, 95% CI = -17.1 to -2.15). We also found significant increases in cognitive functioning based on MSEL-ELC scores with increasing paternal age (adjusted β associated with a 10-year increase in paternal age = 5.51, 95% CI = 0.70-10.3). Results suggest the potential for a different relationship between parental age and ASD-related outcomes in families with elevated ASD risk than has been observed in general population samples. Autism Res 2020, 13: 998-1010. © 2020 International Society for Autism Research, Wiley Periodicals, Inc. LAY SUMMARY: Previous work suggests that older parents have a greater likelihood of having a child with autism. We investigated this relationship in the younger siblings of families who already had a child with autism. In this setting, we found a higher likelihood of autism, as well as poorer cognitive scores, in the siblings with younger fathers, and higher cognitive scores in the siblings with older parents. These results suggest that parental age associations may differ based on children's familial risk for autism.
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Affiliation(s)
- Kristen Lyall
- AJ Drexel Autism Institute, Drexel University, Philadelphia, Pennsylvania, USA
| | - Lanxin Song
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Kelly Botteron
- Department of Psychiatry, Washington University, St Louis, Missouri, USA
| | - Lisa A Croen
- Kaiser Permanente Division of Research, Oakland, California, USA
| | - Stephen R Dager
- Department of Radiology, University of Washington, Seattle, Washington, USA
| | - M Daniele Fallin
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Heather C Hazlett
- Department of Psychiatry, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Elizabeth Kauffman
- AJ Drexel Autism Institute, Drexel University, Philadelphia, Pennsylvania, USA
| | - Rebecca Landa
- Department of Psychiatry and Behavioral Sciences, Center for Autism and Related Disorders, Kennedy Krieger Institute, Johns Hopkins University, Baltimore, Maryland, USA
| | - Christine Ladd-Acosta
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | | | - Sally Ozonoff
- MIND Institute, Department of Psychiatry and Behavioral Sciences, University of California Davis, Sacramento, California, USA
| | - Juhi Pandey
- Center for Autism Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Joseph Piven
- Department of Psychiatry, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Rebecca J Schmidt
- Department of Public Health, University of California Davis, Davis, California, USA
- MIND Institute, University of California Davis, Sacramento, California, USA
| | - Robert T Schultz
- Center for Autism Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Wendy L Stone
- Department of Psychology, University of Washington, Seattle, Washington, USA
| | - Craig J Newschaffer
- College of Health and Human Development, Pennsylvania State University, State College, Pennsylvania, USA
| | - Heather E Volk
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
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80
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LaBianca S, LaBianca J, Pagsberg AK, Jakobsen KD, Appadurai V, Buil A, Werge T. Copy Number Variants and Polygenic Risk Scores Predict Need of Care in Autism and/or ADHD Families. J Autism Dev Disord 2020; 51:276-285. [DOI: 10.1007/s10803-020-04552-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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81
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De novo variants of NR4A2 are associated with neurodevelopmental disorder and epilepsy. Genet Med 2020; 22:1413-1417. [PMID: 32366965 PMCID: PMC7394879 DOI: 10.1038/s41436-020-0815-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 04/16/2020] [Accepted: 04/17/2020] [Indexed: 11/08/2022] Open
Abstract
PURPOSE This study characterizes the clinical and genetic features of nine unrelated patients with de novo variants in the NR4A2 gene. METHODS Variants were identified and de novo origins were confirmed through trio exome sequencing in all but one patient. Targeted RNA sequencing was performed for one variant to confirm its splicing effect. Independent discoveries were shared through GeneMatcher. RESULTS Missense and loss-of-function variants in NR4A2 were identified in patients from eight unrelated families. One patient carried a larger deletion including adjacent genes. The cases presented with developmental delay, hypotonia (six cases), and epilepsy (six cases). De novo status was confirmed for eight patients. One variant was demonstrated to affect splicing and result in expression of abnormal transcripts likely subject to nonsense-mediated decay. CONCLUSION Our study underscores the importance of NR4A2 as a disease gene for neurodevelopmental disorders and epilepsy. The identified variants are likely causative of the seizures and additional developmental phenotypes in these patients.
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82
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A framework for an evidence-based gene list relevant to autism spectrum disorder. Nat Rev Genet 2020; 21:367-376. [PMID: 32317787 DOI: 10.1038/s41576-020-0231-2] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/17/2020] [Indexed: 02/06/2023]
Abstract
Autism spectrum disorder (ASD) is often grouped with other brain-related phenotypes into a broader category of neurodevelopmental disorders (NDDs). In clinical practice, providers need to decide which genes to test in individuals with ASD phenotypes, which requires an understanding of the level of evidence for individual NDD genes that supports an association with ASD. Consensus is currently lacking about which NDD genes have sufficient evidence to support a relationship to ASD. Estimates of the number of genes relevant to ASD differ greatly among research groups and clinical sequencing panels, varying from a few to several hundred. This Roadmap discusses important considerations necessary to provide an evidence-based framework for the curation of NDD genes based on the level of information supporting a clinically relevant relationship between a given gene and ASD.
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83
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Casamassa A, Ferrari D, Gelati M, Carella M, Vescovi AL, Rosati J. A Link between Genetic Disorders and Cellular Impairment, Using Human Induced Pluripotent Stem Cells to Reveal the Functional Consequences of Copy Number Variations in the Central Nervous System-A Close Look at Chromosome 15. Int J Mol Sci 2020; 21:ijms21051860. [PMID: 32182809 PMCID: PMC7084702 DOI: 10.3390/ijms21051860] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/02/2020] [Accepted: 03/05/2020] [Indexed: 12/28/2022] Open
Abstract
Recent cutting-edge human genetics technology has allowed us to identify copy number variations (CNVs) and has provided new insights for understanding causative mechanisms of human diseases. A growing number of studies show that CNVs could be associated with physiological mechanisms linked to evolutionary trigger, as well as to the pathogenesis of various diseases, including cancer, autoimmune disease and mental disorders such as autism spectrum disorders, schizophrenia, intellectual disabilities or attention-deficit/hyperactivity disorder. Their incomplete penetrance and variable expressivity make diagnosis difficult and hinder comprehension of the mechanistic bases of these disorders. Additional elements such as co-presence of other CNVs, genomic background and environmental factors are involved in determining the final phenotype associated with a CNV. Genetically engineered animal models are helpful tools for understanding the behavioral consequences of CNVs. However, the genetic background and the biology of these animal model systems have sometimes led to confusing results. New cellular models obtained through somatic cellular reprogramming technology that produce induced pluripotent stem cells (iPSCs) from human subjects are being used to explore the mechanisms involved in the pathogenic consequences of CNVs. Considering the vast quantity of CNVs found in the human genome, we intend to focus on reviewing the current literature on the use of iPSCs carrying CNVs on chromosome 15, highlighting advantages and limits of this system with respect to mouse model systems.
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Affiliation(s)
- Alessia Casamassa
- Cellular Reprogramming Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, Viale dei Cappuccini 1, 71013 San Giovanni Rotondo, Foggia, Italy;
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania Luigi Vanvitelli, Viale Abramo Lincoln 5, 81100 Caserta, Italy
| | - Daniela Ferrari
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy;
| | - Maurizio Gelati
- Fondazione IRCCS Casa Sollievo della Sofferenza, Viale dei Cappuccini 1, 71013 San Giovanni Rotondo, Foggia, Italy; (M.G.); (M.C.)
| | - Massimo Carella
- Fondazione IRCCS Casa Sollievo della Sofferenza, Viale dei Cappuccini 1, 71013 San Giovanni Rotondo, Foggia, Italy; (M.G.); (M.C.)
| | - Angelo Luigi Vescovi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy;
- Fondazione IRCCS Casa Sollievo della Sofferenza, Viale dei Cappuccini 1, 71013 San Giovanni Rotondo, Foggia, Italy; (M.G.); (M.C.)
- Correspondence: (A.L.V.); (J.R.)
| | - Jessica Rosati
- Cellular Reprogramming Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, Viale dei Cappuccini 1, 71013 San Giovanni Rotondo, Foggia, Italy;
- Correspondence: (A.L.V.); (J.R.)
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84
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Gordovez FJA, McMahon FJ. The genetics of bipolar disorder. Mol Psychiatry 2020; 25:544-559. [PMID: 31907381 DOI: 10.1038/s41380-019-0634-7] [Citation(s) in RCA: 161] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 11/22/2019] [Accepted: 12/11/2019] [Indexed: 12/11/2022]
Abstract
Bipolar disorder (BD) is one of the most heritable mental illnesses, but the elucidation of its genetic basis has proven to be a very challenging endeavor. Genome-Wide Association Studies (GWAS) have transformed our understanding of BD, providing the first reproducible evidence of specific genetic markers and a highly polygenic architecture that overlaps with that of schizophrenia, major depression, and other disorders. Individual GWAS markers appear to confer little risk, but common variants together account for about 25% of the heritability of BD. A few higher-risk associations have also been identified, such as a rare copy number variant on chromosome 16p11.2. Large scale next-generation sequencing studies are actively searching for other alleles that confer substantial risk. As our understanding of the genetics of BD improves, there is growing optimism that some clear biological pathways will emerge, providing a basis for future studies aimed at molecular diagnosis and novel therapeutics.
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Affiliation(s)
- Francis James A Gordovez
- Human Genetics Branch, National Institute of Mental Health Intramural Research Program, Department of Health and Human Services, National Institutes of Health, Bethesda, MD, USA.,College of Medicine, University of the Philippines Manila, 1000, Ermita, Manila, Philippines
| | - Francis J McMahon
- Human Genetics Branch, National Institute of Mental Health Intramural Research Program, Department of Health and Human Services, National Institutes of Health, Bethesda, MD, USA.
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85
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Bacchelli E, Cameli C, Viggiano M, Igliozzi R, Mancini A, Tancredi R, Battaglia A, Maestrini E. An integrated analysis of rare CNV and exome variation in Autism Spectrum Disorder using the Infinium PsychArray. Sci Rep 2020; 10:3198. [PMID: 32081867 PMCID: PMC7035424 DOI: 10.1038/s41598-020-59922-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 01/19/2020] [Indexed: 01/11/2023] Open
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental condition with a complex and heterogeneous genetic etiology. While a proportion of ASD risk is attributable to common variants, rare copy-number variants (CNVs) and protein-disrupting single-nucleotide variants (SNVs) have been shown to significantly contribute to ASD etiology. We analyzed a homogeneous cohort of 127 ASD Italian families genotyped with the Illumina PsychArray, to perform an integrated analysis of CNVs and SNVs and to assess their contribution to ASD risk. We observed a higher burden of rare CNVs, especially deletions, in ASD individuals versus unaffected controls. Furthermore, we identified a significant enrichment of rare CNVs intersecting ASD candidate genes reported in the SFARI database. Family-based analysis of rare SNVs genotyped by the PsychArray also indicated an increased transmission of rare SNV variants from heterozygous parents to probands, supporting a multigenic model of ASD risk with significant contributions of both variant types. Moreover, our study reinforced the evidence for a significant role of VPS13B, WWOX, CNTNAP2, RBFOX1, MACROD2, APBA2, PARK2, GPHN, and RNF113A genes in ASD susceptibility. Finally, we showed that the PsychArray, besides providing useful genotyping data in psychiatric disorders, is a valuable and cost-efficient tool for genic CNV detection, down to 10 kb.
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Affiliation(s)
- Elena Bacchelli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.
| | - Cinzia Cameli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Marta Viggiano
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Roberta Igliozzi
- IRCCS Stella Maris Foundation, Viale del Tirreno 331, 56128, Calambrone, Pisa, Italy
| | - Alice Mancini
- IRCCS Stella Maris Foundation, Viale del Tirreno 331, 56128, Calambrone, Pisa, Italy
| | - Raffaella Tancredi
- IRCCS Stella Maris Foundation, Viale del Tirreno 331, 56128, Calambrone, Pisa, Italy
| | - Agatino Battaglia
- IRCCS Stella Maris Foundation, Viale del Tirreno 331, 56128, Calambrone, Pisa, Italy
| | - Elena Maestrini
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.
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86
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Girault JB, Swanson MR, Meera SS, Grzadzinski RL, Shen MD, Burrows CA, Wolff JJ, Pandey J, John TS, Estes A, Zwaigenbaum L, Botteron KN, Hazlett HC, Dager SR, Schultz RT, Constantino JN, Piven J. Quantitative trait variation in ASD probands and toddler sibling outcomes at 24 months. J Neurodev Disord 2020; 12:5. [PMID: 32024459 PMCID: PMC7003330 DOI: 10.1186/s11689-020-9308-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 01/21/2020] [Indexed: 12/28/2022] Open
Abstract
Background Younger siblings of children with autism spectrum disorder (ASD) are at increased likelihood of receiving an ASD diagnosis and exhibiting other developmental concerns. It is unknown how quantitative variation in ASD traits and broader developmental domains in older siblings with ASD (probands) may inform outcomes in their younger siblings. Methods Participants included 385 pairs of toddler siblings and probands from the Infant Brain Imaging Study. ASD probands (mean age 5.5 years, range 1.7 to 15.5 years) were phenotyped using the Autism Diagnostic Interview-Revised (ADI-R), the Social Communication Questionnaire (SCQ), and the Vineland Adaptive Behavior Scales, Second Edition (VABS-II). Siblings were assessed using the ADI-R, VABS-II, Mullen Scales of Early Learning (MSEL), and Autism Diagnostic Observation Schedule (ADOS) and received a clinical best estimate diagnosis at 24 months using DSM-IV-TR criteria (n = 89 concordant for ASD; n = 296 discordant). We addressed two aims: (1) to determine whether proband characteristics are predictive of recurrence in siblings and (2) to assess associations between proband traits and sibling dimensional outcomes at 24 months. Results Regarding recurrence risk, proband SCQ scores were found to significantly predict sibling 24-month diagnostic outcome (OR for a 1-point increase in SCQ = 1.06; 95% CI = 1.01, 1.12). Regarding quantitative trait associations, we found no significant correlations in ASD traits among proband-sibling pairs. However, quantitative variation in proband adaptive behavior, communication, and expressive and receptive language was significantly associated with sibling outcomes in the same domains; proband scores explained 9–18% of the variation in cognition and behavior in siblings with ASD. Receptive language was particularly strongly associated in concordant pairs (ICC = 0.50, p < 0.001). Conclusions Proband ASD symptomology, indexed by the SCQ, is a predictor of familial ASD recurrence risk. While quantitative variation in social communication and restricted and repetitive behavior were not associated among sibling pairs, standardized ratings of proband language and communication explained significant variation in the same domains in the sibling at 24 months, especially among toddlers with an ASD diagnosis. These data suggest that proband characteristics can alert clinicians to areas of developmental concern for young children with familial risk for ASD.
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Affiliation(s)
- Jessica B Girault
- Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel Hill, Campus Box 3376, Chapel Hill, NC, 27599, USA.
| | - Meghan R Swanson
- Department of Psychology, School of Behavioral and Brain Sciences, University of Texas at Dallas, Richardson, TX, USA
| | - Shoba S Meera
- Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel Hill, Campus Box 3376, Chapel Hill, NC, 27599, USA.,National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Rebecca L Grzadzinski
- Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel Hill, Campus Box 3376, Chapel Hill, NC, 27599, USA
| | - Mark D Shen
- Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel Hill, Campus Box 3376, Chapel Hill, NC, 27599, USA.,Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Jason J Wolff
- Department of Educational Psychology, University of Minnesota, Minneapolis, MN, USA
| | - Juhi Pandey
- Center for Autism Research, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Tanya St John
- Department of Speech and Hearing Science, University of Washington, Seattle, WA, USA
| | - Annette Estes
- Department of Speech and Hearing Science, University of Washington, Seattle, WA, USA
| | | | - Kelly N Botteron
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Heather C Hazlett
- Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel Hill, Campus Box 3376, Chapel Hill, NC, 27599, USA.,Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Stephen R Dager
- Department of Radiology, University of Washington Medical Center, Seattle, WA, USA
| | - Robert T Schultz
- Center for Autism Research, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - John N Constantino
- Division of Child Psychiatry, Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Joseph Piven
- Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel Hill, Campus Box 3376, Chapel Hill, NC, 27599, USA.,Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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87
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Abstract
Autism spectrum disorder (referred to here as autism) is one of several overlapping neurodevelopmental conditions that have variable impacts on different individuals. This variability results from dynamic interactions between biological and non-biological risk factors, which result in increasing differentiation between individuals over time. Although this differentiation continues well into adulthood, the infancy period is when the brain and behavior develop rapidly, and when the first signs and symptoms of autism emerge. This review discusses advances in our understanding of the causal pathways leading to autism and overlapping neurodevelopmental conditions. Research is also mapping trajectories of brain and behavioral development for some risk groups, namely later born siblings of children with autism and/or infants referred because of developmental concerns. This knowledge has been useful in improving early identification and establishing the feasibility of targeted interventions for infant risk groups before symptoms arise. However, key knowledge gaps remain, such as the discovery of protective factors (biological or environmental) that may mitigate the impact of risk. Also, the dynamic mechanisms that underlie the associations between risk factors and outcomes need further research. These include the processes of resilience, which may explain why some individuals at risk for autism achieve better than expected outcomes. Bridging these knowledge gaps would help to provide tools for early identification and intervention that reflect dynamic developmental pathways from risk to outcomes.
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Affiliation(s)
- Mayada Elsabbagh
- Montreal Neurological Institute, Azrieli Centre for Autism Research, McGill University, Montreal, Canada
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88
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McDonald NM, Senturk D, Scheffler A, Brian JA, Carver LJ, Charman T, Chawarska K, Curtin S, Hertz-Piccioto I, Jones EJH, Klin A, Landa R, Messinger DS, Ozonoff S, Stone WL, Tager-Flusberg H, Webb SJ, Young G, Zwaigenbaum L, Jeste SS. Developmental Trajectories of Infants With Multiplex Family Risk for Autism: A Baby Siblings Research Consortium Study. JAMA Neurol 2020; 77:73-81. [PMID: 31589284 PMCID: PMC6784852 DOI: 10.1001/jamaneurol.2019.3341] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 08/18/2019] [Indexed: 01/01/2023]
Abstract
Importance Autism spectrum disorder (ASD) is a neurodevelopmental disorder associated with different genetic etiologies. Prospective examination of familial-risk infants informs understanding of developmental trajectories preceding ASD diagnosis, potentially improving early detection. Objective To compare outcomes and trajectories associated with varying familial risk for ASD across the first 3 years of life. Design, Setting, and Participants This longitudinal, prospective cohort study used data from 11 sites in the Baby Siblings Research Consortium database. Data were collected between 2003 and 2015. Infants who were younger siblings of children with ASD were followed up for 3 years. Analyses were conducted in April 2018. Of the initial 1008 infants from the database, 573 were removed owing to missing necessary data, diagnostic discrepancies, or only having 1 older sibling. Exposures Number of siblings with ASD. Main Outcomes and Measures Outcomes included ASD symptoms, cognitive abilities, and adaptive skills. Diagnosis (ASD or no ASD) was given at 36-month outcome. The no-ASD group was classified as atypical (developmental delays and/or social-communication concerns) or typical for some analyses. Generalized linear mixed models examined developmental trajectories by ASD outcome and familial-risk group. Results In the 435 analyzed participants (age range at outcome, 32-43 months; 246 male [57%]), 355 (82%) were from single-incidence families (1 sibling with ASD and ≥1 sibling without ASD) and 80 (18%) were from multiplex families (≥2 siblings with ASD). There were no significant group differences in major demographics. Children from multiplex families were more likely than those from single-incidence families to be classified as having ASD (29 of 80 [36%] vs 57 of 355 [16%]; 95% CI, 9%-31%; P < .001) and less likely as typical (26 of 80 [33%] vs 201 of 355 [57%]; 95% CI, -36% to -13%; P < .001), with similar rates of atypical classifications (25 of 80 [31%] vs 97 of 355 [27%]; 95% CI, -7% to 15%; P = .49). There were no differences in ASD symptoms between multiplex and single-incidence groups after controlling for ASD outcome (95% CI, -0.02 to 0.20; P = .18). During infancy, differences in cognitive and adaptive abilities were observed based on ASD outcome in the single-incidence group only. At 36 months, the multiplex/no-ASD group had lower cognitive abilities than the single-incidence/no-ASD group (95% CI, -11.89 to -2.20; P = .02), and the multiplex group had lower adaptive abilities than individuals in the single-incidence group after controlling for ASD outcome (95% CI, -9.01 to -1.48; P = .02). Conclusions and Relevance Infants with a multiplex family history of ASD should be monitored early and often and referred for early intervention at the first sign of concern. Direct examination of genetic contributions to neurodevelopmental phenotypes in infants with familial risk for ASD is needed.
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Affiliation(s)
- Nicole M. McDonald
- Semel Institute for Neuroscience & Human Behavior, University of California, Los Angeles, Los Angeles
| | - Damla Senturk
- Department of Biostatistics, University of California, Los Angeles, Los Angeles
| | - Aaron Scheffler
- Department of Biostatistics, University of California, Los Angeles, Los Angeles
- now with Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco
| | - Jessica A. Brian
- Holland Bloorview Kids Rehabilitation Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Leslie J. Carver
- Department of Psychology, University of California, San Diego, La Jolla
| | - Tony Charman
- Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London, United Kingdom
| | - Katarzyna Chawarska
- Child Study Center, Yale University School of Medicine, New Haven, Connecticut
| | - Suzanne Curtin
- Department of Psychology, University of Calgary, Calgary, Alberta, Canada
| | - Irva Hertz-Piccioto
- MIND Institute, Department of Public Health Sciences, University of California, Davis, Davis
| | - Emily J. H. Jones
- Centre for Brain & Cognitive Development, Birkbeck, University of London, London, United Kingdom
| | - Ami Klin
- Marcus Autism Center, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta, Georgia
| | - Rebecca Landa
- Center for Autism and Related Disorders, Kennedy Krieger Institute, Baltimore, Maryland
| | - Daniel S. Messinger
- Department of Psychology, University of Miami, Coral Gables, Florida
- Department of Pediatrics, University of Miami, Coral Gables, Florida
- Department of Electrical & Computer Engineering, University of Miami, Coral Gables, Florida
- Department of Music Engineering, University of Miami, Coral Gables, Florida
| | - Sally Ozonoff
- MIND Institute, Department of Psychiatry and Behavioral Sciences, University of California, Davis, Sacramento
| | - Wendy L. Stone
- Department of Psychology, University of Washington, Seattle
| | - Helen Tager-Flusberg
- Department of Psychology & Brain Sciences, Boston University, Boston, Massachusetts
| | - Sara Jane Webb
- Psychiatry and Behavioral Sciences, University of Washington, Seattle
| | - Gregory Young
- MIND Institute, Department of Psychiatry and Behavioral Sciences, University of California, Davis, Sacramento
| | - Lonnie Zwaigenbaum
- Department of Pediatrics, University of Alberta, Edmonton, Alberta, Canada
- Department of Psychiatry, University of Alberta, Edmonton, Alberta, Canada
| | - Shafali S. Jeste
- Semel Institute for Neuroscience & Human Behavior, University of California, Los Angeles, Los Angeles
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89
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Zhao X, Wang S, Hao J, Zhu P, Zhang X, Wu M. A Whole-Exome Sequencing Study of Tourette Disorder in a Chinese Population. DNA Cell Biol 2019; 39:63-68. [PMID: 31855460 DOI: 10.1089/dna.2019.4746] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
To investigate the contribution of de novo variants to Tourette disorder (TD) probands in China. Whole-exome sequencing (WES) conducted on 15 child-parent trios (45 samples) detected 25 coding de novo variants, including 2 de novo Likely Gene Disrupting (LGD) variants and 6 Missense3 variants. The de novo LGD variants were consistently associated with TD risk (Fisher's exact test OR 2.69; p = 0.1952), although statistical significance was not achieved due to the small sample size. We then assessed the relationship between the genetic events and phenotypic data by comparing Yale Global Tic Severity Scale (YGTSS) scores. The TD probands with damaging variants (defined as LGD variants and Mis3 variants) had significantly higher YGTSS scores, suggesting more severe tic symptoms (p = 0.019). We also observed a hit for a damaging compound heterozygous (CH) mutation in CELSR3, a high-confidence TD risk gene, in one of the TD probands. To our knowledge, this is the first study to investigate de novo variants in TD in a Chinese population. Our results showed that de novo LGD variants contributed to TD risk in our cohort and that TD probands with de novo damaging variants have more severe symptoms. Furthermore, our observation of damaging CH mutations in CELSR3 in an individual affected with TD further strengthened the confidence in a role for this gene in TD etiology.
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Affiliation(s)
- Xin Zhao
- Department of Traditional Chinese Medicine, Xinhua Hospital Affiliated to Shanghai Jiatong University School of Medicine, Shanghai, China
| | - Sheng Wang
- Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, California
| | - Juanjuan Hao
- Department of Traditional Chinese Medicine, Xinhua Hospital Affiliated to Shanghai Jiatong University School of Medicine, Shanghai, China
| | - Pengcheng Zhu
- Department of Traditional Chinese Medicine, Xinhua Hospital Affiliated to Shanghai Jiatong University School of Medicine, Shanghai, China
| | - Xin Zhang
- Department of Traditional Chinese Medicine, Xinhua Hospital Affiliated to Shanghai Jiatong University School of Medicine, Shanghai, China
| | - Min Wu
- Department of Traditional Chinese Medicine, Xinhua Hospital Affiliated to Shanghai Jiatong University School of Medicine, Shanghai, China
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90
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D'Abate L, Walker S, Yuen RKC, Tammimies K, Buchanan JA, Davies RW, Thiruvahindrapuram B, Wei J, Brian J, Bryson SE, Dobkins K, Howe J, Landa R, Leef J, Messinger D, Ozonoff S, Smith IM, Stone WL, Warren ZE, Young G, Zwaigenbaum L, Scherer SW. Predictive impact of rare genomic copy number variations in siblings of individuals with autism spectrum disorders. Nat Commun 2019; 10:5519. [PMID: 31801954 PMCID: PMC6892938 DOI: 10.1038/s41467-019-13380-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 10/31/2019] [Indexed: 12/21/2022] Open
Abstract
Identification of genetic biomarkers associated with autism spectrum disorders (ASDs) could improve recurrence prediction for families with a child with ASD. Here, we describe clinical microarray findings for 253 longitudinally phenotyped ASD families from the Baby Siblings Research Consortium (BSRC), encompassing 288 infant siblings. By age 3, 103 siblings (35.8%) were diagnosed with ASD and 54 (18.8%) were developing atypically. Thirteen siblings have copy number variants (CNVs) involving ASD-relevant genes: 6 with ASD, 5 atypically developing, and 2 typically developing. Within these families, an ASD-related CNV in a sibling has a positive predictive value (PPV) for ASD or atypical development of 0.83; the Simons Simplex Collection of ASD families shows similar PPVs. Polygenic risk analyses suggest that common genetic variants may also contribute to ASD. CNV findings would have been pre-symptomatically predictive of ASD or atypical development in 11 (7%) of the 157 BSRC siblings who were eventually diagnosed clinically.
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Affiliation(s)
- L D'Abate
- The Centre for Applied Genomics, Genetics, and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - S Walker
- The Centre for Applied Genomics, Genetics, and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - R K C Yuen
- The Centre for Applied Genomics, Genetics, and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - K Tammimies
- The Centre for Applied Genomics, Genetics, and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.,Center of Neurodevelopmental Disorders at Karolinska Institutet (KIND), Department of Women's and Children's Health, Stockholm, Sweden.,Center for Psychiatry Research, Region Stockholm, Stockholm, Sweden
| | - J A Buchanan
- The Centre for Applied Genomics, Genetics, and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - R W Davies
- The Centre for Applied Genomics, Genetics, and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - B Thiruvahindrapuram
- The Centre for Applied Genomics, Genetics, and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - J Wei
- The Centre for Applied Genomics, Genetics, and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - J Brian
- Autism Research Centre, Bloorview Research Institute and University of Toronto, Toronto, ON, Canada
| | - S E Bryson
- Autism Research Centre, IWK Health Centre and Dalhousie University, Halifax, NS, Canada
| | - K Dobkins
- Department of Psychology, UC San Diego, La Jolla, CA, USA
| | - J Howe
- The Centre for Applied Genomics, Genetics, and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - R Landa
- Center for Autism and Related Disorders, Kennedy Krieger Institute, Baltimore, MD, USA
| | - J Leef
- Autism Research Centre, Bloorview Research Institute and University of Toronto, Toronto, ON, Canada
| | - D Messinger
- Department of Psychology, University of Miami, Coral Gables, FL, USA
| | - S Ozonoff
- MIND Institute, Department of Psychiatry, UC Davis, Davis, CA, USA
| | - I M Smith
- Autism Research Centre, IWK Health Centre and Dalhousie University, Halifax, NS, Canada
| | - W L Stone
- Department of Psychology, University of Washington, Seattle, WA, USA
| | - Z E Warren
- Vanderbilt Kennedy Center Treatment and Research Institute for Autism Spectrum Disorders, Vanderbilt Kennedy Centre, Nashville, TN, USA
| | - G Young
- MIND Institute, Department of Psychiatry, UC Davis, Davis, CA, USA
| | - L Zwaigenbaum
- Autism Research Centre, University of Alberta, Edmonton, AB, Canada
| | - S W Scherer
- The Centre for Applied Genomics, Genetics, and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada. .,McLaughlin Centre, University of Toronto, Toronto, ON, Canada.
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91
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Lévy J, Grotto S, Mignot C, Maruani A, Delahaye-Duriez A, Benzacken B, Keren B, Haye D, Xavier J, Heulin M, Charles E, Verloes A, Dupont C, Pipiras E, Tabet AC. NR4A2 haploinsufficiency is associated with intellectual disability and autism spectrum disorder. Clin Genet 2019; 94:264-268. [PMID: 29770430 DOI: 10.1111/cge.13383] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 05/10/2018] [Accepted: 05/11/2018] [Indexed: 01/15/2023]
Abstract
NR4A2, a member of the nuclear receptor superfamily, is involved in modulation of target gene transcription, regulating several developmental processes such as regulation of cellular homeostasis, neuronal development, inflammation and carcinogenesis. 2q24.1 deletions are extremely rare, and only 1 patient with a de novo deletion encompassing only NR4A2 gene was reported so far. We report 3 additional patients with a de novo deletion encompassing NR4A2: 2 patients have deletions encompassing only NR4A2 gene and 1 patient has a deletion including NR4A2 and the first exon of GPD2. Our patients presented a neurodevelopmental disorder including language impairment, developmental delay, intellectual disability and/or autism spectrum disorder. We suggest that NR4A2 haploinsufficiency is implicated in neurodevelopmental disorder with high penetrance.
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Affiliation(s)
- J Lévy
- Genetics Department, AP-HP, Robert-Debré University Hospital, Paris, France.,INSERM UMR1141, Paris Diderot University, AP-HP, Robert-Debré Hospital, Paris, France
| | - S Grotto
- Genetics Department, AP-HP, Robert-Debré University Hospital, Paris, France
| | - C Mignot
- Genetics Department, AP-HP, Pitié-Salpêtrière Hospital, Paris, France.,Centre de Référence Déficience Intellectuelle de Causes Rares, GRC Université Pierre et Marie Curie « Déficience Intellectuelle et Autisme », Pitié-Salpêtrière Hospital, Paris, France
| | - A Maruani
- Child and Adolescent Psychiatry Department, Robert-Debré Hospital, AP-HP, Paris, France.,Neuroscience Department, Génétique Humaine et Fonction Cognitive Unit, Pasteur Institute, Paris, France
| | - A Delahaye-Duriez
- INSERM UMR1141, Paris Diderot University, AP-HP, Robert-Debré Hospital, Paris, France.,Department of Cytogenetics, Jean-Verdier Hospital, Paris 13 University, Embryology and Histology, AP-HP, Bondy, France.,Division of Brain Sciences, Imperial College Faculty of Medicine, London
| | - B Benzacken
- INSERM UMR1141, Paris Diderot University, AP-HP, Robert-Debré Hospital, Paris, France.,Department of Cytogenetics, Jean-Verdier Hospital, Paris 13 University, Embryology and Histology, AP-HP, Bondy, France
| | - B Keren
- Genetics Department, AP-HP, Pitié-Salpêtrière Hospital, Paris, France
| | - D Haye
- Genetics Department, AP-HP, Pitié-Salpêtrière Hospital, Paris, France
| | - J Xavier
- Department of Child and Adolescent Psychiatry, Pitié-Salpêtrière Hospital, AP-HP, Paris, France
| | - M Heulin
- Unité de Diagnostic et d'Evaluation Pluriprofessionnelle de l'autisme et des troubles apparentés, Etablissement publique de santé de Ville-Evrard, Neuilly Sur Marne, France
| | - E Charles
- Unité de Diagnostic et d'Evaluation Pluriprofessionnelle de l'autisme et des troubles apparentés, Etablissement publique de santé de Ville-Evrard, Neuilly Sur Marne, France
| | - A Verloes
- Genetics Department, AP-HP, Robert-Debré University Hospital, Paris, France.,INSERM UMR1141, Paris Diderot University, AP-HP, Robert-Debré Hospital, Paris, France
| | - C Dupont
- Genetics Department, AP-HP, Robert-Debré University Hospital, Paris, France
| | - E Pipiras
- INSERM UMR1141, Paris Diderot University, AP-HP, Robert-Debré Hospital, Paris, France.,Department of Cytogenetics, Jean-Verdier Hospital, Paris 13 University, Embryology and Histology, AP-HP, Bondy, France
| | - A-C Tabet
- Genetics Department, AP-HP, Robert-Debré University Hospital, Paris, France.,Neuroscience Department, Génétique Humaine et Fonction Cognitive Unit, Pasteur Institute, Paris, France
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92
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Feliciano P, Zhou X, Astrovskaya I, Turner TN, Wang T, Brueggeman L, Barnard R, Hsieh A, Snyder LG, Muzny DM, Sabo A, Gibbs RA, Eichler EE, O’Roak BJ, Michaelson JJ, Volfovsky N, Shen Y, Chung WK. Exome sequencing of 457 autism families recruited online provides evidence for autism risk genes. NPJ Genom Med 2019; 4:19. [PMID: 31452935 PMCID: PMC6707204 DOI: 10.1038/s41525-019-0093-8] [Citation(s) in RCA: 152] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 07/11/2019] [Indexed: 12/30/2022] Open
Abstract
Autism spectrum disorder (ASD) is a genetically heterogeneous condition, caused by a combination of rare de novo and inherited variants as well as common variants in at least several hundred genes. However, significantly larger sample sizes are needed to identify the complete set of genetic risk factors. We conducted a pilot study for SPARK (SPARKForAutism.org) of 457 families with ASD, all consented online. Whole exome sequencing (WES) and genotyping data were generated for each family using DNA from saliva. We identified variants in genes and loci that are clinically recognized causes or significant contributors to ASD in 10.4% of families without previous genetic findings. In addition, we identified variants that are possibly associated with ASD in an additional 3.4% of families. A meta-analysis using the TADA framework at a false discovery rate (FDR) of 0.1 provides statistical support for 26 ASD risk genes. While most of these genes are already known ASD risk genes, BRSK2 has the strongest statistical support and reaches genome-wide significance as a risk gene for ASD (p-value = 2.3e-06). Future studies leveraging the thousands of individuals with ASD who have enrolled in SPARK are likely to further clarify the genetic risk factors associated with ASD as well as allow accelerate ASD research that incorporates genetic etiology.
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Affiliation(s)
| | - Xueya Zhou
- Department of Systems Biology, Columbia University, New York, NY 10032 USA
| | | | - Tychele N. Turner
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195 USA
| | - Tianyun Wang
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195 USA
| | - Leo Brueggeman
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA 52242 USA
| | - Rebecca Barnard
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239 USA
| | - Alexander Hsieh
- Department of Systems Biology, Columbia University, New York, NY 10032 USA
| | | | - Donna M. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
| | - Aniko Sabo
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195 USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195 USA
| | - Brian J. O’Roak
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239 USA
| | - Jacob J. Michaelson
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA 52242 USA
| | | | - Yufeng Shen
- Department of Systems Biology, Columbia University, New York, NY 10032 USA
| | - Wendy K. Chung
- Simons Foundation, New York, NY 10010 USA
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032 USA
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93
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Ruzzo EK, Pérez-Cano L, Jung JY, Wang LK, Kashef-Haghighi D, Hartl C, Singh C, Xu J, Hoekstra JN, Leventhal O, Leppä VM, Gandal MJ, Paskov K, Stockham N, Polioudakis D, Lowe JK, Prober DA, Geschwind DH, Wall DP. Inherited and De Novo Genetic Risk for Autism Impacts Shared Networks. Cell 2019; 178:850-866.e26. [PMID: 31398340 PMCID: PMC7102900 DOI: 10.1016/j.cell.2019.07.015] [Citation(s) in RCA: 281] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 04/08/2019] [Accepted: 07/11/2019] [Indexed: 02/08/2023]
Abstract
We performed a comprehensive assessment of rare inherited variation in autism spectrum disorder (ASD) by analyzing whole-genome sequences of 2,308 individuals from families with multiple affected children. We implicate 69 genes in ASD risk, including 24 passing genome-wide Bonferroni correction and 16 new ASD risk genes, most supported by rare inherited variants, a substantial extension of previous findings. Biological pathways enriched for genes harboring inherited variants represent cytoskeletal organization and ion transport, which are distinct from pathways implicated in previous studies. Nevertheless, the de novo and inherited genes contribute to a common protein-protein interaction network. We also identified structural variants (SVs) affecting non-coding regions, implicating recurrent deletions in the promoters of DLG2 and NR3C2. Loss of nr3c2 function in zebrafish disrupts sleep and social function, overlapping with human ASD-related phenotypes. These data support the utility of studying multiplex families in ASD and are available through the Hartwell Autism Research and Technology portal.
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Affiliation(s)
- Elizabeth K Ruzzo
- Department of Psychiatry and Biobehavioral Sciences, Semel Institue, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Laura Pérez-Cano
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Jae-Yoon Jung
- Department of Pediatrics, Division of Systems Medicine, Stanford University, Stanford, CA, USA; Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Lee-Kai Wang
- Department of Psychiatry and Biobehavioral Sciences, Semel Institue, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Dorna Kashef-Haghighi
- Department of Pediatrics, Division of Systems Medicine, Stanford University, Stanford, CA, USA; Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Chris Hartl
- Bioinformatics IDP, University of California, Los Angeles, Los Angeles, CA, USA
| | - Chanpreet Singh
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Jin Xu
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Jackson N Hoekstra
- Department of Psychiatry and Biobehavioral Sciences, Semel Institue, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Olivia Leventhal
- Department of Psychiatry and Biobehavioral Sciences, Semel Institue, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Virpi M Leppä
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Michael J Gandal
- Department of Psychiatry and Biobehavioral Sciences, Semel Institue, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Kelley Paskov
- Department of Pediatrics, Division of Systems Medicine, Stanford University, Stanford, CA, USA; Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Nate Stockham
- Department of Pediatrics, Division of Systems Medicine, Stanford University, Stanford, CA, USA; Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Damon Polioudakis
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Jennifer K Lowe
- Department of Psychiatry and Biobehavioral Sciences, Semel Institue, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - David A Prober
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Daniel H Geschwind
- Department of Psychiatry and Biobehavioral Sciences, Semel Institue, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
| | - Dennis P Wall
- Department of Pediatrics, Division of Systems Medicine, Stanford University, Stanford, CA, USA; Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
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94
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Ramos LLP, Monteiro FP, Sampaio LPB, Costa LA, Ribeiro MDO, Freitas EL, Kitajima JP, Kok F. Heterozygous loss of function of NR4A2 is associated with intellectual deficiency, rolandic epilepsy, and language impairment. Clin Case Rep 2019; 7:1582-1584. [PMID: 31428396 PMCID: PMC6693049 DOI: 10.1002/ccr3.2260] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 04/30/2019] [Accepted: 05/05/2019] [Indexed: 11/08/2022] Open
Abstract
Recognition of a de novo mutation in NR4A2 associated with a neurodevelopmental phenotype reinforces its role in 2q23q24 microdeletion syndrome. Using the proband WES data and the probability of loss-of-function intolerance index (pLi) set at 1.0 (highest intolerance constraint), we could target NR4A2 as the candidate gene in this patient.
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Affiliation(s)
| | | | | | | | | | | | | | - Fernando Kok
- Mendelics Genomic AnalysisSao PauloBrazil
- Department of NeurologyUniversity of Sao Paulo School of MedicineSao PauloBrazil
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95
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Affiliation(s)
- Jordan W Smoller
- Department of Psychiatry and Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston; and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Mass
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96
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Genetic mechanisms of regression in autism spectrum disorder. Neurosci Biobehav Rev 2019; 102:208-220. [DOI: 10.1016/j.neubiorev.2019.04.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 02/12/2019] [Accepted: 04/28/2019] [Indexed: 12/17/2022]
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97
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Autism spectrum disorder in a patient with a genomic rearrangement that only involves the EPHA5 gene. Psychiatr Genet 2019; 29:86-90. [DOI: 10.1097/ypg.0000000000000217] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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98
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Lazaro MT, Taxidis J, Shuman T, Bachmutsky I, Ikrar T, Santos R, Marcello GM, Mylavarapu A, Chandra S, Foreman A, Goli R, Tran D, Sharma N, Azhdam M, Dong H, Choe KY, Peñagarikano O, Masmanidis SC, Rácz B, Xu X, Geschwind DH, Golshani P. Reduced Prefrontal Synaptic Connectivity and Disturbed Oscillatory Population Dynamics in the CNTNAP2 Model of Autism. Cell Rep 2019; 27:2567-2578.e6. [PMID: 31141683 PMCID: PMC6553483 DOI: 10.1016/j.celrep.2019.05.006] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 02/20/2019] [Accepted: 04/30/2019] [Indexed: 11/25/2022] Open
Abstract
Loss-of-function mutations in CNTNAP2 cause a syndromic form of autism spectrum disorder in humans and produce social deficits, repetitive behaviors, and seizures in mice. However, the functional effects of these mutations at cellular and circuit levels remain elusive. Using laser-scanning photostimulation, whole-cell recordings, and electron microscopy, we found a dramatic decrease in excitatory and inhibitory synaptic inputs onto L2/3 pyramidal neurons of the medial prefrontal cortex (mPFC) of Cntnap2 knockout (KO) mice, concurrent with reduced spines and synapses, despite normal dendritic complexity and intrinsic excitability. Moreover, recording of mPFC local field potentials (LFPs) and unit spiking in vivo revealed increased activity in inhibitory neurons, reduced phase-locking to delta and theta oscillations, and delayed phase preference during locomotion. Excitatory neurons showed similar phase modulation changes at delta frequencies. Finally, pairwise correlations increased during immobility in KO mice. Thus, reduced synaptic inputs can yield perturbed temporal coordination of neuronal firing in cortical ensembles.
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Affiliation(s)
- Maria T Lazaro
- Interdepartmental Program for Neuroscience, UCLA, Los Angeles, CA, USA; Center for Neurobehavioral Genetics, Semel Institute, UCLA, Los Angeles, CA, USA; Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Jiannis Taxidis
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Integrative Center for Learning and Memory, Brain Research Institute, UCLA, Los Angeles, CA, USA
| | - Tristan Shuman
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Integrative Center for Learning and Memory, Brain Research Institute, UCLA, Los Angeles, CA, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Iris Bachmutsky
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Taruna Ikrar
- Department of Anatomy and Neurobiology, UC Irvine, Irvine, CA, USA
| | - Rommel Santos
- Department of Anatomy and Neurobiology, UC Irvine, Irvine, CA, USA
| | - G Mark Marcello
- Department of Anatomy and Histology, University of Veterinary Medicine, Budapest, Hungary
| | - Apoorva Mylavarapu
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Swasty Chandra
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Allison Foreman
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Rachna Goli
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Duy Tran
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Nikhil Sharma
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Michelle Azhdam
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Hongmei Dong
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Katrina Y Choe
- Center for Neurobehavioral Genetics, Semel Institute, UCLA, Los Angeles, CA, USA
| | - Olga Peñagarikano
- Department of Pharmacology, School of Medicine, University of the Basque Country (UPV/EHU), Vizcaya, Spain; Centro de Investigación Biomédica en Red en Salud Mental (CIBERSAM), Madrid, Spain
| | - Sotiris C Masmanidis
- Integrative Center for Learning and Memory, Brain Research Institute, UCLA, Los Angeles, CA, USA
| | - Bence Rácz
- Department of Anatomy and Histology, University of Veterinary Medicine, Budapest, Hungary
| | - Xiangmin Xu
- Department of Anatomy and Neurobiology, UC Irvine, Irvine, CA, USA
| | - Daniel H Geschwind
- Center for Neurobehavioral Genetics, Semel Institute, UCLA, Los Angeles, CA, USA; Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Center for Autism Research and Treatment, Semel Institute, UCLA, Los Angeles, CA, USA; Intellectual Development and Disabilities Research Center, UCLA, Los Angeles, CA, USA.
| | - Peyman Golshani
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Integrative Center for Learning and Memory, Brain Research Institute, UCLA, Los Angeles, CA, USA; Intellectual Development and Disabilities Research Center, UCLA, Los Angeles, CA, USA; West Los Angeles VA Medical Center, Los Angeles, CA.
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99
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Peter B, Dinu V, Liu L, Huentelman M, Naymik M, Lancaster H, Vose C, Schrauwen I. Exome Sequencing of Two Siblings with Sporadic Autism Spectrum Disorder and Severe Speech Sound Disorder Suggests Pleiotropic and Complex Effects. Behav Genet 2019; 49:399-414. [DOI: 10.1007/s10519-019-09957-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Accepted: 03/18/2019] [Indexed: 12/19/2022]
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100
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Rediscovering the value of families for psychiatric genetics research. Mol Psychiatry 2019; 24:523-535. [PMID: 29955165 PMCID: PMC7028329 DOI: 10.1038/s41380-018-0073-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 01/11/2018] [Accepted: 03/26/2018] [Indexed: 01/09/2023]
Abstract
As it is likely that both common and rare genetic variation are important for complex disease risk, studies that examine the full range of the allelic frequency distribution should be utilized to dissect the genetic influences on mental illness. The rate limiting factor for inferring an association between a variant and a phenotype is inevitably the total number of copies of the minor allele captured in the studied sample. For rare variation, with minor allele frequencies of 0.5% or less, very large samples of unrelated individuals are necessary to unambiguously associate a locus with an illness. Unfortunately, such large samples are often cost prohibitive. However, by using alternative analytic strategies and studying related individuals, particularly those from large multiplex families, it is possible to reduce the required sample size while maintaining statistical power. We contend that using whole genome sequence (WGS) in extended pedigrees provides a cost-effective strategy for psychiatric gene mapping that complements common variant approaches and WGS in unrelated individuals. This was our impetus for forming the "Pedigree-Based Whole Genome Sequencing of Affective and Psychotic Disorders" consortium. In this review, we provide a rationale for the use of WGS with pedigrees in modern psychiatric genetics research. We begin with a focused review of the current literature, followed by a short history of family-based research in psychiatry. Next, we describe several advantages of pedigrees for WGS research, including power estimates, methods for studying the environment, and endophenotypes. We conclude with a brief description of our consortium and its goals.
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