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Neuhaus E, Rea H, Jones E, Benavidez H, Miles C, Whiting A, Johansson M, Eayrs C, Kurtz-Nelson EC, Earl R, Bernier RA, Eichler EE. Shared and divergent mental health characteristics of ADNP-, CHD8- and DYRK1A-related neurodevelopmental conditions. J Neurodev Disord 2024; 16:15. [PMID: 38622540 PMCID: PMC11017562 DOI: 10.1186/s11689-024-09532-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 04/01/2024] [Indexed: 04/17/2024] Open
Abstract
BACKGROUND Neurodevelopmental conditions such as intellectual disability (ID) and autism spectrum disorder (ASD) can stem from a broad array of inherited and de novo genetic differences, with marked physiological and behavioral impacts. We currently know little about the psychiatric phenotypes of rare genetic variants associated with ASD, despite heightened risk of psychiatric concerns in ASD more broadly. Understanding behavioral features of these variants can identify shared versus specific phenotypes across gene groups, facilitate mechanistic models, and provide prognostic insights to inform clinical practice. In this paper, we evaluate behavioral features within three gene groups associated with ID and ASD - ADNP, CHD8, and DYRK1A - with two aims: (1) characterize phenotypes across behavioral domains of anxiety, depression, ADHD, and challenging behavior; and (2) understand whether age and early developmental milestones are associated with later mental health outcomes. METHODS Phenotypic data were obtained for youth with disruptive variants in ADNP, CHD8, or DYRK1A (N = 65, mean age = 8.7 years, 40% female) within a long-running, genetics-first study. Standardized caregiver-report measures of mental health features (anxiety, depression, attention-deficit/hyperactivity, oppositional behavior) and developmental history were extracted and analyzed for effects of gene group, age, and early developmental milestones on mental health features. RESULTS Patterns of mental health features varied by group, with anxiety most prominent for CHD8, oppositional features overrepresented among ADNP, and attentional and depressive features most prominent for DYRK1A. For the full sample, age was positively associated with anxiety features, such that elevations in anxiety relative to same-age and same-sex peers may worsen with increasing age. Predictive utility of early developmental milestones was limited, with evidence of early language delays predicting greater difficulties across behavioral domains only for the CHD8 group. CONCLUSIONS Despite shared associations with autism and intellectual disability, disruptive variants in ADNP, CHD8, and DYRK1A may yield variable psychiatric phenotypes among children and adolescents. With replication in larger samples over time, efforts such as these may contribute to improved clinical care for affected children and adolescents, allow for earlier identification of emerging mental health difficulties, and promote early intervention to alleviate concerns and improve quality of life.
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Affiliation(s)
- Emily Neuhaus
- Department of Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, WA, USA.
- Center On Child Health, Behavior, and Development, Seattle Children's Research Institute, Seattle, WA, USA.
| | - Hannah Rea
- Department of Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Elizabeth Jones
- Department of Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Hannah Benavidez
- Department of Psychology, University of Washington, Seattle, WA, USA
| | - Conor Miles
- Department of Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Alana Whiting
- Department of Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Margaret Johansson
- Department of Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Curtis Eayrs
- Department of Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Rachel Earl
- Department of Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Raphael A Bernier
- Department of Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
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2
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Tabbaa M, Levitt P. Chd8 haploinsufficiency impacts rearing experience in C57BL/6 mice. GENES, BRAIN, AND BEHAVIOR 2024; 23:e12892. [PMID: 38560770 PMCID: PMC10982810 DOI: 10.1111/gbb.12892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/14/2024] [Accepted: 03/05/2024] [Indexed: 04/04/2024]
Abstract
Mutations in CHD8 are one of the highest genetic risk factors for autism spectrum disorder. Studies in mice that investigate underlying mechanisms have shown Chd8 haploinsufficient mice display some trait disruptions that mimic clinical phenotypes, although inconsistencies have been reported in some traits across different models on the same strain background. One source of variation across studies may be the impact of Chd8 haploinsufficiency on maternal-offspring interactions. While differences in maternal care as a function of Chd8 genotype have not been studied directly, a previous study showed that pup survival was reduced when reared by Chd8 heterozygous dams compared with wild-type (WT) dams, suggesting altered maternal care as a function of Chd8 genotype. Through systematic observation of the C57BL/6 strain, we first determined the impact of Chd8 haploinsufficiency in the offspring on WT maternal care frequencies across preweaning development. We next determined the impact of maternal Chd8 haploinsufficiency on pup care. Compared with litters with all WT offspring, WT dams exhibited less frequent maternal behaviors toward litters consisting of offspring with mixed Chd8 genotypes, particularly during postnatal week 1. Dam Chd8 haploinsufficiency decreased litter survival and increased active maternal care also during postnatal week 1. Determining the impact of Chd8 haploinsufficiency on early life experiences provides an important foundation for interpreting offspring outcomes and determining mechanisms that underlie heterogeneous phenotypes.
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Affiliation(s)
- Manal Tabbaa
- Children's Hospital Los AngelesThe Saban Research InstituteLos AngelesCaliforniaUSA
- Keck School of Medicine of the University of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Pat Levitt
- Children's Hospital Los AngelesThe Saban Research InstituteLos AngelesCaliforniaUSA
- Keck School of Medicine of the University of Southern CaliforniaLos AngelesCaliforniaUSA
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Astorkia M, Liu Y, Pedrosa EM, Lachman HM, Zheng D. Molecular and network disruptions in neurodevelopment uncovered by single cell transcriptomics analysis of CHD8 heterozygous cerebral organoids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.27.559752. [PMID: 37808768 PMCID: PMC10557718 DOI: 10.1101/2023.09.27.559752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
About 100 genes have been associated with significantly increased risks of autism spectrum disorders (ASD) with an estimate of ~1000 genes that may be involved. The new challenge now is to investigate the molecular and cellular functions of these genes during neural and brain development, and then even more challenging, to link the altered molecular and cellular phenotypes to the ASD clinical manifestations. In this study, we use single cell RNA-seq analysis to study one of the top risk gene, CHD8, in cerebral organoids, which models early neural development. We identify 21 cell clusters in the organoid samples, representing non-neuronal cells, neural progenitors, and early differentiating neurons at the start of neural cell fate commitment. Comparisons of the cells with one copy of the CHD8 knockout and their isogenic controls uncover thousands of differentially expressed genes, which are enriched with function related to neural and brain development, with genes and pathways previously implicated in ASD, but surprisingly not for Schizophrenia and intellectual disability risk genes. The comparisons also find cell composition changes, indicating potential altered neural differential trajectories upon CHD8 reduction. Moreover, we find that cell-cell communications are affected in the CHD8 knockout organoids, including the interactions between neural and glial cells. Taken together, our results provide new data for understanding CHD8 functions in the early stages of neural lineage development and interaction.
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Affiliation(s)
- Maider Astorkia
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Yang Liu
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Erika M. Pedrosa
- Department of Psychiatry and Behavioral Science, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Herbert M. Lachman
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Psychiatry and Behavioral Science, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Neurology, Albert Einstein College of Medicine, Bronx, NY, USA
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4
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St John M, Tripathi T, Morgan AT, Amor DJ. To speak may draw on epigenetic writing and reading: Unravelling the complexity of speech and language outcomes across chromatin-related neurodevelopmental disorders. Neurosci Biobehav Rev 2023; 152:105293. [PMID: 37353048 DOI: 10.1016/j.neubiorev.2023.105293] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/11/2023] [Accepted: 06/20/2023] [Indexed: 06/25/2023]
Abstract
Speech and language development are complex neurodevelopmental processes that are incompletely understood, yet current evidence suggests that speech and language disorders are prominent in those with disorders of chromatin regulation. This review aimed to unravel what is known about speech and language outcomes for individuals with chromatin-related neurodevelopmental disorders. A systematic literature search following PRISMA guidelines was conducted on 70 chromatin genes, to identify reports of speech/language outcomes across studies, including clinical reports, formal subjective measures, and standardised/objective measures. 3932 studies were identified and screened and 112 were systematically reviewed. Communication impairment was core across chromatin disorders, and specifically, chromatin writers and readers appear to play an important role in motor speech development. Identification of these relationships is important because chromatin disorders show promise as therapeutic targets due to the capacity for epigenetic modification. Further research is required using standardised and formal assessments to understand the nuanced speech/language profiles associated with variants in each gene, and the influence of chromatin dysregulation on the neurobiology of speech and language development.
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Affiliation(s)
- Miya St John
- Speech and Language, Murdoch Children's Research Institute, Parkville, VIC, Australia; Department of Audiology and Speech Pathology, University of Melbourne, VIC, Australia.
| | - Tanya Tripathi
- Neurodisability and Rehabilitation, Murdoch Children's Research Institute, Parkville, VIC, Australia.
| | - Angela T Morgan
- Speech and Language, Murdoch Children's Research Institute, Parkville, VIC, Australia; Department of Audiology and Speech Pathology, University of Melbourne, VIC, Australia; Speech Genomics Clinic, Royal Children's Hospital, Parkville, VIC, Australia.
| | - David J Amor
- Neurodisability and Rehabilitation, Murdoch Children's Research Institute, Parkville, VIC, Australia; Speech Genomics Clinic, Royal Children's Hospital, Parkville, VIC, Australia; Department of Paediatrics, University of Melbourne, VIC, Australia.
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5
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Kurtz-Nelson EC, Rea HM, Petriceks AC, Hudac CM, Wang T, Earl RK, Bernier RA, Eichler EE, Neuhaus E. Characterizing the autism spectrum phenotype in DYRK1A-related syndrome. Autism Res 2023; 16:1488-1500. [PMID: 37497568 PMCID: PMC10530559 DOI: 10.1002/aur.2995] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 07/12/2023] [Indexed: 07/28/2023]
Abstract
Likely gene-disrupting (LGD) variants in DYRK1A are causative of DYRK1A syndrome and associated with autism spectrum disorder (ASD) and intellectual disability (ID). While many individuals with DYRK1A syndrome are diagnosed with ASD, they may present with a unique profile of ASD traits. We present a comprehensive characterization of the ASD profile in children and young adults with LGDs in DYRK1A. Individuals with LGD variants in DYRK1A (n = 29) were compared to children who had ASD with no known genetic cause, either with low nonverbal IQ (n = 14) or average or above nonverbal IQ (n = 41). ASD was assessed using the ADOS-2, ADI-R, SRS-2, SCQ, and RBS-R. Quantitative score comparisons were conducted, as were qualitative analyses of clinicians' behavioral observations. Diagnosis of ASD was confirmed in 85% and ID was confirmed in 89% of participants with DYRK1A syndrome. Individuals with DYRK1A syndrome showed broadly similar social communication behaviors to children with idiopathic ASD and below-average nonverbal IQ, with specific challenges noted in social reciprocity and nonverbal communication. Children with DYRK1A syndrome also showed high rates of sensory-seeking behaviors. Phenotypic characterization of individuals with DYRK1A syndrome may provide additional information on mechanisms contributing to co-occurring ASD and ID and contribute to the identification of genetic predictors of specific ASD traits.
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Affiliation(s)
| | - Hannah M. Rea
- Department of Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, Washington, USA
| | - Aiva C. Petriceks
- Department of Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, Washington, USA
| | - Caitlin M. Hudac
- Department of Psychology, University of South Carolina, Columbia, South Carolina, USA
- Carolina Autism and Neurodevelopment Research Center, Columbia, South Carolina, USA
| | - Tianyun Wang
- Department of Medical Genetics, Center for Medical Genetics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- Neuroscience Research Institute, Peking University; Key Laboratory for Neuroscience, Ministry of Education of China & National Health Commission of China, Beijing, China
- Autism Research Center, Peking University Health Science Center, Beijing, China
| | - Rachel K. Earl
- Department of Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, Washington, USA
| | - Raphael A. Bernier
- Department of Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, Washington, USA
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USA
| | - Emily Neuhaus
- Department of Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, Washington, USA
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6
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Davidson EA, Holingue C, Jimenez-Gomez A, Dallman JE, Moshiree B. Gastrointestinal Dysfunction in Genetically Defined Neurodevelopmental Disorders. Semin Neurol 2023; 43:645-660. [PMID: 37586397 PMCID: PMC10895389 DOI: 10.1055/s-0043-1771460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
Abstract
Gastrointestinal symptoms are common in most forms of neurodevelopment disorders (NDDs) such as in autism spectrum disorders (ASD). The current patient-reported outcome measures with validated questionnaires used in the general population of children without NDDS cannot be used in the autistic individuals. We explore here the multifactorial pathophysiology of ASD and the role of genetics and the environment in this disease spectrum and focus instead on possible diagnostics that could provide future objective insight into the connection of the gut-brain-microbiome in this disease entity. We provide our own data from both humans and a zebrafish model of ASD called Phelan-McDermid Syndrome. We hope that this review highlights the gaps in our current knowledge on many of these profound NDDs and that it provides a future framework upon which clinicians and researchers can build and network with other interested multidisciplinary specialties.
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Affiliation(s)
| | - Calliope Holingue
- Center for Autism and Related Disorders, Kennedy Krieger Institute, Baltimore, Maryland
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Andres Jimenez-Gomez
- Neuroscience Center, Joe DiMaggio Children’s Hospital, Hollywood, Florida
- Department of Child Neurology, Florida Atlantic University Stiles - Nicholson Brain Institute, Jupiter, Florida
| | - Julia E. Dallman
- Department of Biology, University of Miami, Coral Gables, Miami, Florida
| | - Baharak Moshiree
- Atrium Health, Wake Forest Medical University, Charlotte, North Carolina
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7
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Tabbaa M, Knoll A, Levitt P. Mouse population genetics phenocopies heterogeneity of human Chd8 haploinsufficiency. Neuron 2023; 111:539-556.e5. [PMID: 36738737 PMCID: PMC9960295 DOI: 10.1016/j.neuron.2023.01.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 11/13/2022] [Accepted: 01/11/2023] [Indexed: 02/05/2023]
Abstract
Preclinical models of neurodevelopmental disorders typically use single inbred mouse strains, which fail to capture the genetic diversity and symptom heterogeneity that is common clinically. We tested whether modeling genetic background diversity in mouse genetic reference panels would recapitulate population and individual differences in responses to a syndromic mutation in the high-confidence autism risk gene, CHD8. We measured clinically relevant phenotypes in >1,000 mice from 33 strains, including brain and body weights and cognition, activity, anxiety, and social behaviors, using 5 behavioral assays: cued fear conditioning, open field tests in dark and bright light, direct social interaction, and social dominance. Trait disruptions mimicked those seen clinically, with robust strain and sex differences. Some strains exhibited large effect-size trait disruptions, sometimes in opposite directions, and-remarkably-others expressed resilience. Therefore, systematically introducing genetic diversity into models of neurodevelopmental disorders provides a better framework for discovering individual differences in symptom etiologies.
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Affiliation(s)
- Manal Tabbaa
- Children's Hospital Los Angeles, The Saban Research Institute, Los Angeles, CA 90027, USA; Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA
| | - Allison Knoll
- Children's Hospital Los Angeles, The Saban Research Institute, Los Angeles, CA 90027, USA; Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA
| | - Pat Levitt
- Children's Hospital Los Angeles, The Saban Research Institute, Los Angeles, CA 90027, USA; Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA.
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8
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Villa CE, Cheroni C, Dotter CP, López-Tóbon A, Oliveira B, Sacco R, Yahya AÇ, Morandell J, Gabriele M, Tavakoli MR, Lyudchik J, Sommer C, Gabitto M, Danzl JG, Testa G, Novarino G. CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories. Cell Rep 2022; 39:110615. [PMID: 35385734 DOI: 10.1016/j.celrep.2022.110615] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 11/18/2021] [Accepted: 03/13/2022] [Indexed: 12/13/2022] Open
Abstract
Mutations in the chromodomain helicase DNA-binding 8 (CHD8) gene are a frequent cause of autism spectrum disorder (ASD). While its phenotypic spectrum often encompasses macrocephaly, implicating cortical abnormalities, how CHD8 haploinsufficiency affects neurodevelopmental is unclear. Here, employing human cerebral organoids, we find that CHD8 haploinsufficiency disrupted neurodevelopmental trajectories with an accelerated and delayed generation of, respectively, inhibitory and excitatory neurons that yields, at days 60 and 120, symmetrically opposite expansions in their proportions. This imbalance is consistent with an enlargement of cerebral organoids as an in vitro correlate of patients' macrocephaly. Through an isogenic design of patient-specific mutations and mosaic organoids, we define genotype-phenotype relationships and uncover their cell-autonomous nature. Our results define cell-type-specific CHD8-dependent molecular defects related to an abnormal program of proliferation and alternative splicing. By identifying cell-type-specific effects of CHD8 mutations, our study uncovers reproducible developmental alterations that may be employed for neurodevelopmental disease modeling.
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Affiliation(s)
- Carlo Emanuele Villa
- Department of Experimental Oncology, IEO, European Institute of Oncology, IRCCS, 20139 Milan, Italy; Human Technopole, Viale Rita Levi Montalcini 1, 20157 Milan, Italy
| | - Cristina Cheroni
- Department of Experimental Oncology, IEO, European Institute of Oncology, IRCCS, 20139 Milan, Italy; Human Technopole, Viale Rita Levi Montalcini 1, 20157 Milan, Italy; Department of Oncology and Hemato-oncology, University of Milan, 20122 Milan, Italy
| | - Christoph P Dotter
- Institute of Science and Technology (IST) Austria, 3400 Klosterneuburg, Austria
| | - Alejandro López-Tóbon
- Department of Experimental Oncology, IEO, European Institute of Oncology, IRCCS, 20139 Milan, Italy; Human Technopole, Viale Rita Levi Montalcini 1, 20157 Milan, Italy; Department of Oncology and Hemato-oncology, University of Milan, 20122 Milan, Italy
| | - Bárbara Oliveira
- Institute of Science and Technology (IST) Austria, 3400 Klosterneuburg, Austria
| | - Roberto Sacco
- Institute of Science and Technology (IST) Austria, 3400 Klosterneuburg, Austria
| | - Aysan Çerağ Yahya
- Institute of Science and Technology (IST) Austria, 3400 Klosterneuburg, Austria
| | - Jasmin Morandell
- Institute of Science and Technology (IST) Austria, 3400 Klosterneuburg, Austria
| | - Michele Gabriele
- Department of Experimental Oncology, IEO, European Institute of Oncology, IRCCS, 20139 Milan, Italy
| | - Mojtaba R Tavakoli
- Institute of Science and Technology (IST) Austria, 3400 Klosterneuburg, Austria
| | - Julia Lyudchik
- Institute of Science and Technology (IST) Austria, 3400 Klosterneuburg, Austria
| | - Christoph Sommer
- Institute of Science and Technology (IST) Austria, 3400 Klosterneuburg, Austria
| | | | - Johann G Danzl
- Institute of Science and Technology (IST) Austria, 3400 Klosterneuburg, Austria
| | - Giuseppe Testa
- Department of Experimental Oncology, IEO, European Institute of Oncology, IRCCS, 20139 Milan, Italy; Human Technopole, Viale Rita Levi Montalcini 1, 20157 Milan, Italy; Department of Oncology and Hemato-oncology, University of Milan, 20122 Milan, Italy.
| | - Gaia Novarino
- Institute of Science and Technology (IST) Austria, 3400 Klosterneuburg, Austria.
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9
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Arnett AB, Wang T, Eichler EE, Bernier RA. Reflections on the genetics-first approach to advancements in molecular genetic and neurobiological research on neurodevelopmental disorders. J Neurodev Disord 2021; 13:24. [PMID: 34148555 PMCID: PMC8215789 DOI: 10.1186/s11689-021-09371-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 05/28/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Neurodevelopmental disorders (NDDs), including autism spectrum disorder (ASD) and intellectual disability (ID), are common diagnoses with highly heterogeneous phenotypes and etiology. The genetics-first approach to research on NDDs has led to the identification of hundreds of genes conferring risk for ASD, ID, and related symptoms. MAIN BODY Although relatively few individuals with NDDs share likely gene-disruptive (LGD) mutations in the same gene, characterization of overlapping functions, protein networks, and temporospatial expression patterns among these genes has led to increased understanding of the neurobiological etiology of NDDs. This shift in focus away from single genes and toward broader gene-brain-behavior pathways has been accelerated by the development of publicly available transcriptomic databases, cell type-specific research methods, and sequencing of non-coding genomic regions. CONCLUSIONS The genetics-first approach to research on NDDs has advanced the identification of critical protein function pathways and temporospatial expression patterns, expanding the impact of this research beyond individuals with single-gene mutations to the broader population of patients with NDDs.
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Affiliation(s)
- Anne B Arnett
- Department of Psychiatry and Behavioral Sciences, University of Washington, CHDD, Box 357920, Seattle, WA, 98195, USA.
- Department of Psychiatry and Behavioral Medicine, Seattle Children's Hospital, Seattle, WA, USA.
| | - Tianyun Wang
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Raphael A Bernier
- Department of Psychiatry and Behavioral Sciences, University of Washington, CHDD, Box 357920, Seattle, WA, 98195, USA
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10
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Coll-Tané M, Gong NN, Belfer SJ, van Renssen LV, Kurtz-Nelson EC, Szuperak M, Eidhof I, van Reijmersdal B, Terwindt I, Durkin J, Verheij MMM, Kim CN, Hudac CM, Nowakowski TJ, Bernier RA, Pillen S, Earl RK, Eichler EE, Kleefstra T, Kayser MS, Schenck A. The CHD8/CHD7/Kismet family links blood-brain barrier glia and serotonin to ASD-associated sleep defects. SCIENCE ADVANCES 2021; 7:7/23/eabe2626. [PMID: 34088660 PMCID: PMC8177706 DOI: 10.1126/sciadv.abe2626] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 04/19/2021] [Indexed: 05/11/2023]
Abstract
Sleep disturbances in autism and neurodevelopmental disorders are common and adversely affect patient's quality of life, yet the underlying mechanisms are understudied. We found that individuals with mutations in CHD8, among the highest-confidence autism risk genes, or CHD7 suffer from disturbed sleep maintenance. These defects are recapitulated in Drosophila mutants affecting kismet, the sole CHD8/CHD7 ortholog. We show that Kismet is required in glia for early developmental and adult sleep architecture. This role localizes to subperineurial glia constituting the blood-brain barrier. We demonstrate that Kismet-related sleep disturbances are caused by high serotonin during development, paralleling a well-established but genetically unsolved autism endophenotype. Despite their developmental origin, Kismet's sleep architecture defects can be reversed in adulthood by a behavioral regime resembling human sleep restriction therapy. Our findings provide fundamental insights into glial regulation of sleep and propose a causal mechanistic link between the CHD8/CHD7/Kismet family, developmental hyperserotonemia, and autism-associated sleep disturbances.
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Affiliation(s)
- Mireia Coll-Tané
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, 6525 GA, Nijmegen, Netherlands.
| | - Naihua N Gong
- Departments of Psychiatry and Neuroscience, Chronobiology and Sleep Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Samuel J Belfer
- Departments of Psychiatry and Neuroscience, Chronobiology and Sleep Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lara V van Renssen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, 6525 GA, Nijmegen, Netherlands
| | | | - Milan Szuperak
- Departments of Psychiatry and Neuroscience, Chronobiology and Sleep Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ilse Eidhof
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, 6525 GA, Nijmegen, Netherlands
| | - Boyd van Reijmersdal
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, 6525 GA, Nijmegen, Netherlands
| | - Isabel Terwindt
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, 6525 GA, Nijmegen, Netherlands
| | - Jaclyn Durkin
- Departments of Psychiatry and Neuroscience, Chronobiology and Sleep Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michel M M Verheij
- Department of Cognitive Neuroscience, Centre for Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, Netherlands
| | - Chang N Kim
- Departments of Anatomy and Psychiatry, University of California, San Francisco, CA 94143 USA
| | - Caitlin M Hudac
- Center for Youth Development and Intervention and Department of Psychology, University of Alabama, Tuscaloosa, AL 35487, USA
| | - Tomasz J Nowakowski
- Departments of Anatomy and Psychiatry, University of California, San Francisco, CA 94143 USA
| | - Raphael A Bernier
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98185, USA
| | - Sigrid Pillen
- Center for Sleep Medicine, Kempenhaeghe, Heeze, Netherlands
| | - Rachel K Earl
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98185, 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, USA
| | - Tjitske Kleefstra
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, 6525 GA, Nijmegen, Netherlands
| | - Matthew S Kayser
- Departments of Psychiatry and Neuroscience, Chronobiology and Sleep Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Annette Schenck
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, 6525 GA, Nijmegen, Netherlands.
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11
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Li K, Fang Z, Zhao G, Li B, Chen C, Xia L, Wang L, Luo T, Wang X, Wang Z, Zhang Y, Jiang Y, Pan Q, Hu Z, Guo H, Tang B, Liu C, Sun Z, Xia K, Li J. Cross-Disorder Analysis of De Novo Mutations in Neuropsychiatric Disorders. J Autism Dev Disord 2021; 52:1299-1313. [PMID: 33970367 PMCID: PMC8854168 DOI: 10.1007/s10803-021-05031-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/14/2021] [Indexed: 12/02/2022]
Abstract
The clinical similarity among different neuropsychiatric disorders (NPDs) suggested a shared genetic basis. We catalogued 23,109 coding de novo mutations (DNMs) from 6511 patients with autism spectrum disorder (ASD), 4,293 undiagnosed developmental disorder (UDD), 933 epileptic encephalopathy (EE), 1022 intellectual disability (ID), 1094 schizophrenia (SCZ), and 3391 controls. We evaluated that putative functional DNMs contribute to 38.11%, 34.40%, 33.31%, 10.98% and 6.91% of patients with ID, EE, UDD, ASD and SCZ, respectively. Consistent with phenotype similarity and heterogeneity in different NPDs, they show different degree of genetic association. Cross-disorder analysis of DNMs prioritized 321 candidate genes (FDR < 0.05) and showed that genes shared in more disorders were more likely to exhibited specific expression pattern, functional pathway, genetic convergence, and genetic intolerance.
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Affiliation(s)
- Kuokuo Li
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China.,Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China.,Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, No 218 Jixi Road, Hefei, 230022, Anhui, China.,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Zhenghuan Fang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China
| | - Guihu Zhao
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China
| | - Bin Li
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China
| | - Chao Chen
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China
| | - Lu Xia
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China
| | - Lin Wang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China
| | - Tengfei Luo
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China
| | - Xiaomeng Wang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China
| | - Zheng Wang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China
| | - Yi Zhang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China
| | - Yi Jiang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China
| | - Qian Pan
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China
| | - Zhengmao Hu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China.,Institute of Molecular Precision Medicine, Xiangya Hospital, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China
| | - Hui Guo
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China.,Institute of Molecular Precision Medicine, Xiangya Hospital, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China
| | - Beisha Tang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China.,Institute of Molecular Precision Medicine, Xiangya Hospital, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China
| | - Chunyu Liu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China.,Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Zhongsheng Sun
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China. .,Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, China.
| | - Kun Xia
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China. .,School of Basic Medical Science, Central South University, Changsha, Hunan, China. .,CAS Center for Excellence in Brain Science and Intelligence Technology (CEBSIT), Shanghai, China.
| | - Jinchen Li
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China. .,Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China. .,Institute of Molecular Precision Medicine, Xiangya Hospital, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China.
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12
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Hoffmann A, Spengler D. Single-Cell Transcriptomics Supports a Role of CHD8 in Autism. Int J Mol Sci 2021; 22:3261. [PMID: 33806835 PMCID: PMC8004931 DOI: 10.3390/ijms22063261] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/16/2021] [Accepted: 03/20/2021] [Indexed: 12/16/2022] Open
Abstract
Chromodomain helicase domain 8 (CHD8) is one of the most frequently mutated and most penetrant genes in the autism spectrum disorder (ASD). Individuals with CHD8 mutations show leading symptoms of autism, macrocephaly, and facial dysmorphisms. The molecular and cellular mechanisms underpinning the early onset and development of these symptoms are still poorly understood and prevent timely and more efficient therapies of patients. Progress in this area will require an understanding of "when, why and how cells deviate from their normal trajectories". High-throughput single-cell RNA sequencing (sc-RNAseq) directly quantifies information-bearing RNA molecules that enact each cell's biological identity. Here, we discuss recent insights from sc-RNAseq of CRISPR/Cas9-editing of Chd8/CHD8 during mouse neocorticogenesis and human cerebral organoids. Given that the deregulation of the balance between excitation and inhibition (E/I balance) in cortical and subcortical circuits is thought to represent a major etiopathogenetic mechanism in ASD, we focus on the question of whether, and to what degree, results from current sc-RNAseq studies support this hypothesis. Beyond that, we discuss the pros and cons of these approaches and further steps to be taken to harvest the full potential of these transformative techniques.
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Affiliation(s)
| | - Dietmar Spengler
- Translational Research in Psychiatry, Max Planck Institute of Psychiatry, 80804 Munich, Germany;
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13
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Hoffmann A, Spengler D. Chromatin Remodeler CHD8 in Autism and Brain Development. J Clin Med 2021; 10:366. [PMID: 33477995 PMCID: PMC7835889 DOI: 10.3390/jcm10020366] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/14/2021] [Accepted: 01/14/2021] [Indexed: 12/14/2022] Open
Abstract
Chromodomain Helicase DNA-binding 8 (CHD8) is a high confidence risk factor for autism spectrum disorders (ASDs) and the genetic cause of a distinct neurodevelopmental syndrome with the core symptoms of autism, macrocephaly, and facial dysmorphism. The role of CHD8 is well-characterized at the structural, biochemical, and transcriptional level. By contrast, much less is understood regarding how mutations in CHD8 underpin altered brain function and mental disease. Studies on various model organisms have been proven critical to tackle this challenge. Here, we scrutinize recent advances in this field with a focus on phenotypes in transgenic animal models and highlight key findings on neurodevelopment, neuronal connectivity, neurotransmission, synaptic and homeostatic plasticity, and habituation. Against this backdrop, we further discuss how to improve future animal studies, both in terms of technical issues and with respect to the sex-specific effects of Chd8 mutations for neuronal and higher-systems level function. We also consider outstanding questions in the field including 'humanized' mice models, therapeutic interventions, and how the use of pluripotent stem cell-derived cerebral organoids might help to address differences in neurodevelopment trajectories between model organisms and humans.
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Affiliation(s)
| | - Dietmar Spengler
- Department of Translational Research in Psychiatry, Max-Planck Institute of Psychiatry, 80804 Munich, Germany;
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14
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Transcriptional subtyping explains phenotypic variability in genetic subtypes of autism spectrum disorder. Dev Psychopathol 2021; 32:1353-1361. [PMID: 32912353 DOI: 10.1017/s0954579420000784] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Autism spectrum disorder (ASD) is a common neurodevelopmental disorder characterized by deficits in social communication and presence of restricted, repetitive behaviors, and interests. However, individuals with ASD vary significantly in their challenges and abilities in these and other developmental domains. Gene discovery in ASD has accelerated in the past decade, and genetic subtyping has yielded preliminary evidence of utility in parsing phenotypic heterogeneity through genomic subtypes. Recent advances in transcriptomics have provided additional dimensions with which to refine genetic subtyping efforts. In the current study, we investigate phenotypic differences among transcriptional subtypes defined by neurobiological spatiotemporal co-expression patterns. Of the four transcriptional subtypes examined, participants with mutations to genes typically expressed highly in all brain regions prenatally, and those with differential postnatal cerebellar expression relative to other brain regions, showed lower cognitive and adaptive skills, higher severity of social communication deficits, and later acquisition of speech and motor milestones, compared to those with mutations to genes highly expressed during the postnatal period across brain regions. These findings suggest higher-order characterization of genetic subtypes based on neurobiological expression patterns may be a promising approach to parsing phenotypic heterogeneity among those with ASD and related neurodevelopmental disorders.
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15
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Vaisfeld A, Spartano S, Gobbi G, Vezzani A, Neri G. Chromosome 14 deletions, rings, and epilepsy genes: A riddle wrapped in a mystery inside an enigma. Epilepsia 2020; 62:25-40. [PMID: 33205446 DOI: 10.1111/epi.16754] [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: 06/24/2020] [Revised: 10/16/2020] [Accepted: 10/16/2020] [Indexed: 11/29/2022]
Abstract
The ring 14 syndrome is a rare condition caused by the rearrangement of one chromosome 14 into a ring-like structure. The formation of the ring requires two breakpoints and loss of material from the short and long arms of the chromosome. Like many other chromosome syndromes, it is characterized by multiple congenital anomalies and developmental delays. Typical of the condition are retinal anomalies and drug-resistant epilepsy. These latter manifestations are not found in individuals who are carriers of comparable 14q deletions without formation of a ring (linear deletions). To find an explanation for this apparent discrepancy and gain insight into the mechanisms leading to seizures, we reviewed and compared literature cases of both ring and linear deletion syndrome with respect to both their clinical manifestations and the role and function of potentially epileptogenic genes. Knowledge of the epilepsy-related genes in chromosome 14 is an important premise for the search of new and effective drugs to combat seizures. Current clinical and molecular evidence is not sufficient to explain the known discrepancies between ring and linear deletions.
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Affiliation(s)
- Alessandro Vaisfeld
- Institute of Genomic Medicine, Catholic University School of Medicine, Rome, Italy
| | - Serena Spartano
- Institute of Genomic Medicine, Catholic University School of Medicine, Rome, Italy
| | - Giuseppe Gobbi
- Residential Center for Rehabilitation Luce Sul Mare, Rimini, Italy
| | - Annamaria Vezzani
- Department of Neuroscience, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Milano, Italy
| | - Giovanni Neri
- Institute of Genomic Medicine, Catholic University School of Medicine, Rome, Italy.,J.C. Self Research Institute, Greenwood Genetic Center, Greenwood, SC, USA
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16
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Kurtz-Nelson EC, Tham SW, Ahlers K, Cho D, Wallace AS, Eichler EE, Bernier RA, Earl RK. Brief Report: Associations Between Self-injurious Behaviors and Abdominal Pain Among Individuals with ASD-Associated Disruptive Mutations. J Autism Dev Disord 2020; 51:3365-3373. [PMID: 33175317 DOI: 10.1007/s10803-020-04774-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/27/2020] [Indexed: 12/27/2022]
Abstract
Self-injurious behaviors (SIB) are elevated in autism spectrum disorder (ASD) and related genetic disorders, but the genetic and biological mechanisms that contribute to SIB in ASD are poorly understood. This study examined rates and predictors of SIB in 112 individuals with disruptive mutations to ASD-risk genes. Current SIB were reported in 30% of participants and associated with poorer cognitive and adaptive skills. History of severe abdominal pain predicted higher rates of SIB and SIB severity after controlling for age and adaptive behavior; individuals with a history of severe abdominal pain were eight times more likely to exhibit SIB than those with no history. Future research is needed to examine associations between genetic risk, pain, and SIB in this population.
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Affiliation(s)
- Evangeline C Kurtz-Nelson
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, Washington, USA
| | - See Wan Tham
- Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, Washington, USA.,Seattle Children's Research Institute, Seattle, Washington, USA
| | - Kaitlyn Ahlers
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, Washington, USA
| | - Daniel Cho
- Seattle Children's Autism Center, Seattle, Washington, USA
| | - Arianne S Wallace
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, Washington, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA.,Howard Hughes Medical Institute, Seattle, Washington, USA
| | - Raphael A Bernier
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, Washington, USA
| | - Rachel K Earl
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, Washington, USA.
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17
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Arnett AB, Beighley JS, Kurtz-Nelson EC, Hoekzema K, Wang T, Bernier RA, Eichler EE. Developmental Predictors of Cognitive and Adaptive Outcomes in Genetic Subtypes of Autism Spectrum Disorder. Autism Res 2020; 13:1659-1669. [PMID: 32918531 PMCID: PMC7861657 DOI: 10.1002/aur.2385] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 08/12/2020] [Accepted: 08/16/2020] [Indexed: 12/19/2022]
Abstract
Approximately one-fourth of autism spectrum disorder (ASD) cases are associated with a disruptive genetic variant. Many of these ASD genotypes have been described previously, and are characterized by unique constellations of medical, psychiatric, developmental, and behavioral features. Development of precision medicine care for affected individuals has been challenging due to the phenotypic heterogeneity that exists even within each genetic subtype. In the present study, we identify developmental milestones that predict cognitive and adaptive outcomes for five of the most common ASD genotypes. Sixty-five youth with a known pathogenic variant involving ADNP, CHD8, DYRK1A, GRIN2B, or SCN2A genes participated in cognitive and adaptive testing. Exploratory linear regressions were used to identify developmental milestones that predicted cognitive and adaptive outcomes within each gene group. We hypothesized that the earliest and most predictive milestones would vary across gene groups, but would be consistent across outcomes within each genetic subtype. Within the ADNP group, age of walking predicted cognitive outcomes, while age of first words predicted adaptive behaviors. Age of phrases predicted adaptive functioning in the CHD8 group, but cognitive outcomes were not clearly associated with early developmental milestones. Verbal milestones were the strongest predictors of cognitive and adaptive outcomes for individuals with mutations to DYRK1A, GRIN2B, or SCN2A. These trends inform decisions about treatment planning and long-term expectations for affected individuals, and they add to the growing body of research linking molecular genetic function to brain development and phenotypic outcomes. LAY SUMMARY: Researchers have found many genetic causes of autism including mutations to ADNP, CHD8, DYRK1A, GRIN2B, and SCN2A genes. We found that each genetic cause had different early developmental milestones that explained the overall functioning of the children when they were older. Depending on the genetic cause, the age that a child first starts walking and/or talking may help to better understand and support a child's development who has a mutation to one of the above genes. Autism Res 2020, 13: 1659-1669. © 2020 International Society for Autism Research and Wiley Periodicals LLC.
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Affiliation(s)
- Anne B Arnett
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, Washington, USA
- Center on Human Development and Disability, University of Washington, Seattle, Washington, USA
| | - Jennifer S Beighley
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, Washington, USA
- Center on Human Development and Disability, University of Washington, Seattle, Washington, USA
| | - Evangeline C Kurtz-Nelson
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, Washington, USA
- Center on Human Development and Disability, University of Washington, Seattle, Washington, USA
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
| | - Tianyun Wang
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
| | - Raphe A Bernier
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, Washington, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, Washington, USA
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18
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Courchesne E, Gazestani VH, Lewis NE. Prenatal Origins of ASD: The When, What, and How of ASD Development. Trends Neurosci 2020; 43:326-342. [PMID: 32353336 PMCID: PMC7373219 DOI: 10.1016/j.tins.2020.03.005] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 01/28/2020] [Accepted: 03/04/2020] [Indexed: 02/08/2023]
Abstract
Autism spectrum disorder (ASD) is a largely heritable, multistage prenatal disorder that impacts a child's ability to perceive and react to social information. Most ASD risk genes are expressed prenatally in many ASD-relevant brain regions and fall into two categories: broadly expressed regulatory genes that are expressed in the brain and other organs, and brain-specific genes. In trimesters one to three (Epoch-1), one set of broadly expressed (the majority) and brain-specific risk genes disrupts cell proliferation, neurogenesis, migration, and cell fate, while in trimester three and early postnatally (Epoch-2) another set (the majority being brain specific) disrupts neurite outgrowth, synaptogenesis, and the 'wiring' of the cortex. A proposed model is that upstream, highly interconnected regulatory ASD gene mutations disrupt transcriptional programs or signaling pathways resulting in dysregulation of downstream processes such as proliferation, neurogenesis, synaptogenesis, and neural activity. Dysregulation of signaling pathways is correlated with ASD social symptom severity. Since the majority of ASD risk genes are broadly expressed, many ASD individuals may benefit by being treated as having a broader medical disorder. An important future direction is the noninvasive study of ASD cell biology.
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Affiliation(s)
- Eric Courchesne
- Department of Neuroscience, University of California, San Diego, San Diego, CA 92093, USA; Autism Center of Excellence, University of California, San Diego, San Diego, CA 92037, USA.
| | - Vahid H Gazestani
- Department of Neuroscience, University of California, San Diego, San Diego, CA 92093, USA; Autism Center of Excellence, University of California, San Diego, San Diego, CA 92037, USA; Department of Pediatrics, University of California, San Diego, San Diego, CA 92093, USA
| | - Nathan E Lewis
- Department of Pediatrics, University of California, San Diego, San Diego, CA 92093, USA; Department of Bioengineering, University of California, San Diego, San Diego, CA 92093, USA
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19
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Kurtz-Nelson EC, Beighley JS, Hudac CM, Gerdts J, Wallace AS, Hoekzema K, Eichler EE, Bernier RA. Co-occurring medical conditions among individuals with ASD-associated disruptive mutations. CHILDRENS HEALTH CARE 2020; 49:361-384. [PMID: 33727758 DOI: 10.1080/02739615.2020.1741361] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Children with autism spectrum disorder (ASD) are at risk for co-occurring medical conditions, many of which have also been reported among individuals with mutations in ASD-associated genes. This study examined rates of co-occurring medical conditions across 301 individuals with disruptive mutations to 1 of 18 ASD-risk genes in comparison to rates of conditions in an idiopathic ASD sample. Rates of gastrointestinal problems, seizures, physical anomalies, and immune problems were generally elevated, with significant differences in rates observed between groups. Results may inform medical care of individuals with ASD-associated mutations and research into mechanisms of co-occurring medical conditions in ASD.
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Affiliation(s)
| | - Jennifer S Beighley
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98195, USA
| | - Caitlin M Hudac
- Center for Youth Development and Interventions, Department of Psychology, University of Alabama, Tuscaloosa, AL 35401
| | - Jennifer Gerdts
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98195, USA
| | - Arianne S Wallace
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98195, USA
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.,Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Raphael A Bernier
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98195, USA
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20
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McDiarmid TA, Belmadani M, Liang J, Meili F, Mathews EA, Mullen GP, Hendi A, Wong WR, Rand JB, Mizumoto K, Haas K, Pavlidis P, Rankin CH. Systematic phenomics analysis of autism-associated genes reveals parallel networks underlying reversible impairments in habituation. Proc Natl Acad Sci U S A 2020; 117:656-667. [PMID: 31754030 PMCID: PMC6968627 DOI: 10.1073/pnas.1912049116] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A major challenge facing the genetics of autism spectrum disorders (ASDs) is the large and growing number of candidate risk genes and gene variants of unknown functional significance. Here, we used Caenorhabditis elegans to systematically functionally characterize ASD-associated genes in vivo. Using our custom machine vision system, we quantified 26 phenotypes spanning morphology, locomotion, tactile sensitivity, and habituation learning in 135 strains each carrying a mutation in an ortholog of an ASD-associated gene. We identified hundreds of genotype-phenotype relationships ranging from severe developmental delays and uncoordinated movement to subtle deficits in sensory and learning behaviors. We clustered genes by similarity in phenomic profiles and used epistasis analysis to discover parallel networks centered on CHD8•chd-7 and NLGN3•nlg-1 that underlie mechanosensory hyperresponsivity and impaired habituation learning. We then leveraged our data for in vivo functional assays to gauge missense variant effect. Expression of wild-type NLG-1 in nlg-1 mutant C. elegans rescued their sensory and learning impairments. Testing the rescuing ability of conserved ASD-associated neuroligin variants revealed varied partial loss of function despite proper subcellular localization. Finally, we used CRISPR-Cas9 auxin-inducible degradation to determine that phenotypic abnormalities caused by developmental loss of NLG-1 can be reversed by adult expression. This work charts the phenotypic landscape of ASD-associated genes, offers in vivo variant functional assays, and potential therapeutic targets for ASD.
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Affiliation(s)
- Troy A McDiarmid
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Manuel Belmadani
- Department of Psychiatry, University of British Columbia, Vancouver, BC V6T 2A1, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Joseph Liang
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Fabian Meili
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Eleanor A Mathews
- Genetic Models of Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104
| | - Gregory P Mullen
- Biology Program, Oklahoma City University, Oklahoma City, OK 73106
| | - Ardalan Hendi
- Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Wan-Rong Wong
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - James B Rand
- Genetic Models of Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104
- Oklahoma Center for Neuroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
| | - Kota Mizumoto
- Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Kurt Haas
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Paul Pavlidis
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC V6T 2B5, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, BC V6T 2A1, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Catharine H Rankin
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC V6T 2B5, Canada;
- Department of Psychology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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