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Verbesselt J, Walsh LK, Mitchel MW, Taylor CM, Finucane BM, Breckpot J, Zink I, Swillen A. Association of behavioural and social-communicative profiles in children with 16p11.2 copy number variants: a multi-site study. JOURNAL OF INTELLECTUAL DISABILITY RESEARCH : JIDR 2024; 68:969-984. [PMID: 38657658 DOI: 10.1111/jir.13141] [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: 09/22/2023] [Revised: 02/29/2024] [Accepted: 03/29/2024] [Indexed: 04/26/2024]
Abstract
BACKGROUND Despite the established knowledge that recurrent copy number variants (CNVs) at the 16p11.2 locus BP4-BP5 confer risk for behavioural and language difficulties, limited research has been conducted on the association between behavioural and social-communicative profiles. The current study aims to further delineate the prevalence, nature and severity of, and the association between, behavioural and social-communicative features of school-aged children with 16p11.2 deletion syndrome (16p11.2DS) and 16p11.2 duplication (16p11.2Dup). METHODS A total of 68 individuals (n = 47 16p11.2DS and n = 21 16p11.2Dup) aged 6-17 years participated. Standardised intelligence tests were administered, and behavioural and social-communicative skills were assessed by standardised questionnaires. Scores of both groups were compared with population norms and across CNVs. The influence of confounding factors was investigated, and correlation analyses were performed. RESULTS Compared with the normative sample, children with 16p11.2DS showed high rates of social responsiveness (67%) and communicative problems (69%), while approximately half (52%) of the patients displayed behavioural problems. Children with 16p11.2Dup demonstrated even higher rates of social-communicative problems (80-90%) with statistically significantly more externalising and overall behavioural challenges (89%). In both CNV groups, there was a strong positive correlation between behavioural and social-communicative skills. CONCLUSIONS School-aged children with 16p11.2 CNVs show high rates of behavioural, social responsiveness and communicative problems compared with the normative sample. These findings point to the high prevalence of autistic traits and diagnoses in these CNV populations. Moreover, there is a high comorbidity between behavioural and social-communicative problems. Patients with difficulties in both domains are vulnerable and need closer clinical follow-up and care.
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Affiliation(s)
- J Verbesselt
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Research Group Experimental Oto-Rhino-Laryngology (ExpORL), Department of Neurosciences, Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - L K Walsh
- Autism & Developmental Medicine Institute, Geisinger, Lewisburg, PA, USA
| | - M W Mitchel
- Autism & Developmental Medicine Institute, Geisinger, Lewisburg, PA, USA
| | - C M Taylor
- Autism & Developmental Medicine Institute, Geisinger, Lewisburg, PA, USA
| | - B M Finucane
- Autism & Developmental Medicine Institute, Geisinger, Lewisburg, PA, USA
| | - J Breckpot
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Centre for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - I Zink
- Research Group Experimental Oto-Rhino-Laryngology (ExpORL), Department of Neurosciences, Leuven Brain Institute, KU Leuven, Leuven, Belgium
- MUCLA, Department of Otorhinolaryngology, Head and Neck Surgery, University Hospitals Leuven, Leuven, Belgium
| | - A Swillen
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Centre for Human Genetics, University Hospitals Leuven, Leuven, Belgium
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2
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Hudac CM, Dommer K, Mahony M, DesChamps TD, Cairney B, Earl R, Kurtz-Nelson EC, Bradshaw J, Bernier RA, Eichler EE, Neuhaus E, Webb SJ, Shic F. Visual and auditory attention in individuals with DYRK1A and SCN2A disruptive variants. Autism Res 2024. [PMID: 39080977 DOI: 10.1002/aur.3202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 07/17/2024] [Indexed: 08/02/2024]
Abstract
This preliminary study sought to assess biomarkers of attention using electroencephalography (EEG) and eye tracking in two ultra-rare monogenic populations associated with autism spectrum disorder (ASD). Relative to idiopathic ASD (n = 12) and neurotypical comparison (n = 49) groups, divergent attention profiles were observed for the monogenic groups, such that individuals with DYRK1A (n = 9) exhibited diminished auditory attention condition differences during an oddball EEG paradigm whereas individuals with SCN2A (n = 5) exhibited diminished visual attention condition differences noted by eye gaze tracking when viewing social interactions. Findings provide initial support for alignment of auditory and visual attention markers in idiopathic ASD and neurotypical development but not monogenic groups. These results support ongoing efforts to develop translational ASD biomarkers within the attention domain.
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Affiliation(s)
- Caitlin M Hudac
- Department of Psychology, University of South Carolina, Columbia, South Carolina, USA
- Center for Autism and Neurodevelopment (CAN) Research Center, University of South Carolina, Columbia, South Carolina, USA
- Institute for Mind and Brain, University of South Carolina, Columbia, South Carolina, USA
| | - Kelsey Dommer
- Center for Child Health, Behavior and Development, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Monique Mahony
- Center for Child Health, Behavior and Development, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Trent D DesChamps
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, Washington, USA
| | - Brianna Cairney
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, Washington, USA
| | - Rachel Earl
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, Washington, USA
| | | | - Jessica Bradshaw
- Department of Psychology, University of South Carolina, Columbia, South Carolina, USA
- Center for Autism and Neurodevelopment (CAN) Research Center, University of South Carolina, Columbia, South Carolina, USA
- Institute for Mind and Brain, University of South Carolina, Columbia, South Carolina, USA
| | - Raphael A Bernier
- 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, University of Washington, Seattle, Washington, USA
| | - Emily Neuhaus
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, Washington, USA
| | - Sara Jane Webb
- Center for Child Health, Behavior and Development, Seattle Children's Research Institute, Seattle, Washington, USA
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, Washington, USA
| | - Frederick Shic
- Center for Child Health, Behavior and Development, Seattle Children's Research Institute, Seattle, Washington, USA
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
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3
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Kundu S, Sair H, Sherr EH, Mukherjee P, Rohde GK. Discovering the gene-brain-behavior link in autism via generative machine learning. SCIENCE ADVANCES 2024; 10:eadl5307. [PMID: 38865470 PMCID: PMC11168471 DOI: 10.1126/sciadv.adl5307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 05/08/2024] [Indexed: 06/14/2024]
Abstract
Autism is traditionally diagnosed behaviorally but has a strong genetic basis. A genetics-first approach could transform understanding and treatment of autism. However, isolating the gene-brain-behavior relationship from confounding sources of variability is a challenge. We demonstrate a novel technique, 3D transport-based morphometry (TBM), to extract the structural brain changes linked to genetic copy number variation (CNV) at the 16p11.2 region. We identified two distinct endophenotypes. In data from the Simons Variation in Individuals Project, detection of these endophenotypes enabled 89 to 95% test accuracy in predicting 16p11.2 CNV from brain images alone. Then, TBM enabled direct visualization of the endophenotypes driving accurate prediction, revealing dose-dependent brain changes among deletion and duplication carriers. These endophenotypes are sensitive to articulation disorders and explain a portion of the intelligence quotient variability. Genetic stratification combined with TBM could reveal new brain endophenotypes in many neurodevelopmental disorders, accelerating precision medicine, and understanding of human neurodiversity.
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Affiliation(s)
- Shinjini Kundu
- Department of Radiology, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Haris Sair
- Department of Radiology, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Elliott H. Sherr
- Department of Neurology, University of California San Francisco, San Francisco, USA
| | - Pratik Mukherjee
- Department of Radiology, University of California San Francisco, San Francisco, USA
| | - Gustavo K. Rohde
- Department of Biomedical Engineering, University of Virginia, Charlottesville, USA
- Department of Electrical and Computer Engineering, University of Virginia, Charlottesville, USA
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4
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McCluskey KE, Stovell KM, Law K, Kostyanovskaya E, Schmidt J, Exner CRT, Dea J, Brimble E, State MW, Willsey AJ, Willsey HR. Autism gene variants disrupt enteric neuron migration and cause gastrointestinal dysmotility. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.28.593642. [PMID: 38854068 PMCID: PMC11160671 DOI: 10.1101/2024.05.28.593642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
The comorbidity of autism spectrum disorders and severe gastrointestinal symptoms is well-established, yet the molecular underpinnings remain unknown. The identification of high-confidence large-effect autism risk genes offers the opportunity to identify convergent, underlying biology by studying these genes in the context of the gastrointestinal system. Here we show that the expression of these genes is enriched in human prenatal gut neurons as well as their migratory progenitors, suggesting that the development and/or function of these neurons may be disrupted by autism-associated pathogenic variants, leading to gastrointestinal dysfunction. Here we document the prevalence of gastrointestinal issues in patients with large-effect variants in sixteen of these genes, highlighting dysmotility, consistent with potential enteric neuron dysfunction. Using the high-throughput diploid frog Xenopus tropicalis , we individually target five of these genes ( SYNGAP1, CHD8, SCN2A, CHD2 , and DYRK1A ) and observe disrupted enteric neuronal progenitor migration for each. More extensive analysis of DYRK1A reveals that perturbation causes gut dysmotility in vivo , which can be ameliorated by treatment with a selective serotonin reuptake inhibitor (escitalopram) or a serotonin receptor 6 agonist, identified by in vivo drug screening. This work suggests that atypical development of enteric neurons contributes to the gastrointestinal distress commonly seen in individuals with autism and that increasing serotonin signaling may be a productive therapeutic avenue.
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5
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Jutla A, Harvey L, Veenstra-VanderWeele J, Chung WK. Motor difficulties in 16p11.2 copy number variation. Autism Res 2024; 17:906-916. [PMID: 38660979 DOI: 10.1002/aur.3132] [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] [Received: 12/15/2022] [Accepted: 02/17/2024] [Indexed: 04/26/2024]
Abstract
The rare genetic variants 16p11.2 duplication and 16p11.2 deletion have opposing effects on brain structure and function, yet are associated with broadly similar clinical phenotypes that include autism, intellectual impairment, psychiatric illness, and motor difficulties. In recent years, studies have identified subtle distinctions between the phenotypic effects of 16p11.2 duplication and 16p11.2 deletion with respect to patterns of autism, intellectual impairment, and psychiatric illness. However, although divergent phenotypic findings in some motor domains have been reported, no study has yet made a comprehensive comparison of motor difficulties between 16p11.2 deletion and 16p11.2 duplication carriers to elucidate points of convergence and divergence. We sought to make such a comparison in a group of 133 16p11.2 deletion carriers, 122 duplication carriers, and 388 familial controls, hypothesizing that motor impairment would overall be greater in deletion than duplication carriers. In a series of regression models, we found that 16p11.2 deletion status tended to predict greater impairment along indices of gross motor function, but less impairment along indices of fine motor function. These findings point to a potential pattern of performance difficulties that could be investigated in future studies. Elucidating motor differences between 16p11.2 duplication and 16p11.2 deletion carriers may help in understanding the complex effect of 16p11.2 copy number variation and other rare genetic causes of autism.
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Affiliation(s)
- Amandeep Jutla
- Department of Psychiatry, Columbia University, New York, New York, USA
- New York State Psychiatric Institute, New York, New York, USA
| | - Loraine Harvey
- City University of New York School of Medicine, New York, New York, USA
| | - Jeremy Veenstra-VanderWeele
- Department of Psychiatry, Columbia University, New York, New York, USA
- New York State Psychiatric Institute, New York, New York, USA
| | - Wendy K Chung
- Department of Pediatrics and Medicine, Columbia University, New York, New York, USA
- Simons Foundation, New York, New York, USA
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6
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Vos N, Kleinendorst L, van der Laan L, van Uhm J, Jansen PR, van Eeghen AM, Maas SM, Mannens MMAM, van Haelst MM. Evaluation of 100 Dutch cases with 16p11.2 deletion and duplication syndromes; from clinical manifestations towards personalized treatment options. Eur J Hum Genet 2024:10.1038/s41431-024-01601-2. [PMID: 38605127 DOI: 10.1038/s41431-024-01601-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 03/03/2024] [Accepted: 03/20/2024] [Indexed: 04/13/2024] Open
Abstract
The 16p11.2 deletion syndrome is a clinically heterogeneous disorder, characterized by developmental delay, intellectual disability, hyperphagia, obesity, macrocephaly and psychiatric problems. Cases with 16p11.2 duplication syndrome have similar neurodevelopmental problems, but typically show a partial 'mirror phenotype' with underweight and microcephaly. Various copy number variants (CNVs) of the chromosomal 16p11.2 region have been described. Most is known about the 'typical' 16p11.2 BP4-BP5 (29.6-30.2 Mb; ~600 kb) deletions and duplications, but there are also several published cohorts with more distal 16p11.2 BP2-BP3 CNVs (28.8-29.0 Mb; ~220 kb), who exhibit clinical overlap. We assessed 100 cases with various pathogenic 16p11.2 CNVs and compared their clinical characteristics to provide more clear genotype-phenotype correlations and raise awareness of the different 16p11.2 CNVs. Neurodevelopmental and weight issues were reported in the majority of cases. Cases with distal 16p11.2 BP2-BP3 deletion showed the most severe obesity phenotype (73.7% obesity, mean BMI SDS 3.2). In addition to the more well defined typical 16p11.2 BP4-BP5 and distal 16p11.2 BP2-BP3 CNVs, we describe the clinical features of five cases with other, overlapping, 16p11.2 CNVs in more detail. Interestingly, four cases had a second genetic diagnosis and 18 cases an additional gene variant of uncertain significance, that could potentially help explain the cases' phenotypes. In conclusion, we provide an overview of our Dutch cohort of cases with various pathogenic 16p11.2 CNVs and relevant second genetic findings, that can aid in adequately recognizing, diagnosing and counseling of individuals with 16p11.2 CNVs, and describe the personalized medicine for cases with these conditions.
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Affiliation(s)
- Niels Vos
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Reproduction and Development research institute, Amsterdam, The Netherlands
| | - Lotte Kleinendorst
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Reproduction and Development research institute, Amsterdam, The Netherlands
- Amsterdam UMC, University of Amsterdam, Emma Center for Personalized Medicine, Meibergdreef 9, Amsterdam, The Netherlands
| | - Liselot van der Laan
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Reproduction and Development research institute, Amsterdam, The Netherlands
| | - Jorrit van Uhm
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Reproduction and Development research institute, Amsterdam, The Netherlands
| | - Philip R Jansen
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Reproduction and Development research institute, Amsterdam, The Netherlands
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, VU University, Amsterdam, the Netherlands
| | - Agnies M van Eeghen
- Emma Children's Hospital, University of Amsterdam, Amsterdam, The Netherlands
| | - Saskia M Maas
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Reproduction and Development research institute, Amsterdam, The Netherlands
| | - Marcel M A M Mannens
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Reproduction and Development research institute, Amsterdam, The Netherlands
| | - Mieke M van Haelst
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Meibergdreef 9, Amsterdam, The Netherlands.
- Amsterdam Reproduction and Development research institute, Amsterdam, The Netherlands.
- Amsterdam UMC, University of Amsterdam, Emma Center for Personalized Medicine, Meibergdreef 9, Amsterdam, The Netherlands.
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7
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Prem S, Dev B, Peng C, Mehta M, Alibutud R, Connacher RJ, St Thomas M, Zhou X, Matteson P, Xing J, Millonig JH, DiCicco-Bloom E. Dysregulation of mTOR signaling mediates common neurite and migration defects in both idiopathic and 16p11.2 deletion autism neural precursor cells. eLife 2024; 13:e82809. [PMID: 38525876 PMCID: PMC11003747 DOI: 10.7554/elife.82809] [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] [Received: 08/18/2022] [Accepted: 03/04/2024] [Indexed: 03/26/2024] Open
Abstract
Autism spectrum disorder (ASD) is defined by common behavioral characteristics, raising the possibility of shared pathogenic mechanisms. Yet, vast clinical and etiological heterogeneity suggests personalized phenotypes. Surprisingly, our iPSC studies find that six individuals from two distinct ASD subtypes, idiopathic and 16p11.2 deletion, have common reductions in neural precursor cell (NPC) neurite outgrowth and migration even though whole genome sequencing demonstrates no genetic overlap between the datasets. To identify signaling differences that may contribute to these developmental defects, an unbiased phospho-(p)-proteome screen was performed. Surprisingly despite the genetic heterogeneity, hundreds of shared p-peptides were identified between autism subtypes including the mTOR pathway. mTOR signaling alterations were confirmed in all NPCs across both ASD subtypes, and mTOR modulation rescued ASD phenotypes and reproduced autism NPC-associated phenotypes in control NPCs. Thus, our studies demonstrate that genetically distinct ASD subtypes have common defects in neurite outgrowth and migration which are driven by the shared pathogenic mechanism of mTOR signaling dysregulation.
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Affiliation(s)
- Smrithi Prem
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical SchoolPiscatawayUnited States
- Graduate Program in Neuroscience, Rutgers UniversityPiscatawayUnited States
| | - Bharati Dev
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical SchoolPiscatawayUnited States
| | - Cynthia Peng
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical SchoolPiscatawayUnited States
| | - Monal Mehta
- Graduate Program in Neuroscience, Rutgers UniversityPiscatawayUnited States
- Center for Advanced Biotechnology and Medicine, Rutgers UniversityPiscatawayUnited States
| | - Rohan Alibutud
- Department of Genetics, Rutgers UniversityPiscatawayUnited States
| | - Robert J Connacher
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical SchoolPiscatawayUnited States
- Graduate Program in Neuroscience, Rutgers UniversityPiscatawayUnited States
| | - Madeline St Thomas
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical SchoolPiscatawayUnited States
- Graduate Program in Neuroscience, Rutgers UniversityPiscatawayUnited States
| | - Xiaofeng Zhou
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical SchoolPiscatawayUnited States
| | - Paul Matteson
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical SchoolPiscatawayUnited States
- Center for Advanced Biotechnology and Medicine, Rutgers UniversityPiscatawayUnited States
| | - Jinchuan Xing
- Department of Genetics, Rutgers UniversityPiscatawayUnited States
| | - James H Millonig
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical SchoolPiscatawayUnited States
- Center for Advanced Biotechnology and Medicine, Rutgers UniversityPiscatawayUnited States
| | - Emanuel DiCicco-Bloom
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical SchoolPiscatawayUnited States
- Department of Pediatrics, Rutgers Robert Wood Johnson Medical SchoolNew BrunswickUnited States
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8
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Maillard AM, Romascano D, Villalón-Reina JE, Moreau CA, Almeida Osório JM, Richetin S, Junod V, Yu P, Misic B, Thompson PM, Fornari E, Gygax MJ, Jacquemont S, Chabane N, Rodríguez-Herreros B. Pervasive alterations of intra-axonal volume and network organization in young children with a 16p11.2 deletion. Transl Psychiatry 2024; 14:95. [PMID: 38355713 PMCID: PMC10866898 DOI: 10.1038/s41398-024-02810-5] [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: 06/21/2023] [Revised: 12/04/2023] [Accepted: 01/29/2024] [Indexed: 02/16/2024] Open
Abstract
Reciprocal Copy Number Variants (CNVs) at the 16p11.2 locus confer high risk for autism spectrum disorder (ASD) and other neurodevelopmental disorders (NDDs). Morphometric MRI studies have revealed large and pervasive volumetric alterations in carriers of a 16p11.2 deletion. However, the specific neuroanatomical mechanisms underlying such alterations, as well as their developmental trajectory, are still poorly understood. Here we explored differences in microstructural brain connectivity between 24 children carrying a 16p11.2 deletion and 66 typically developing (TD) children between 2 and 8 years of age. We found a large pervasive increase of intra-axonal volume widespread over a high number of white matter tracts. Such microstructural alterations in 16p11.2 deletion children were already present at an early age, and led to significant changes in the global efficiency and integration of brain networks mainly associated to language, motricity and socio-emotional behavior, although the widespread pattern made it unlikely to represent direct functional correlates. Our results shed light on the neuroanatomical basis of the previously reported increase of white matter volume, and align well with analogous evidence of altered axonal diameter and synaptic function in 16p11.2 mice models. We provide evidence of a prevalent mechanistic deviation from typical maturation of brain structural connectivity associated with a specific biological risk to develop ASD. Future work is warranted to determine how this deviation contributes to the emergence of symptoms observed in young children diagnosed with ASD and other NDDs.
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Affiliation(s)
- Anne M Maillard
- Service des Troubles du Spectre de l'Autisme et apparentés, Département de psychiatrie, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - David Romascano
- Service des Troubles du Spectre de l'Autisme et apparentés, Département de psychiatrie, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Julio E Villalón-Reina
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California (USC), Marina del Rey, CA, USA
| | - Clara A Moreau
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California (USC), Marina del Rey, CA, USA
| | - Joana M Almeida Osório
- Service des Troubles du Spectre de l'Autisme et apparentés, Département de psychiatrie, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Sonia Richetin
- Service des Troubles du Spectre de l'Autisme et apparentés, Département de psychiatrie, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Vincent Junod
- Unité de Neurologie et neuroréhabilitation pédiatrique, Département femme-mère-enfant, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Paola Yu
- Service des Troubles du Spectre de l'Autisme et apparentés, Département de psychiatrie, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Bratislav Misic
- Department of Neurology and Neurosurgery, Montréal Neurological Institute, Montréal, QC, H3A 2B4, Canada
- McConnell Brain Imaging Center, McGill University, Montréal, QC, H3A 2B4, Canada
| | - Paul M Thompson
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California (USC), Marina del Rey, CA, USA
| | - Eleonora Fornari
- Biomedical Imaging Center (CIBM), Department of Radiology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Marine Jequier Gygax
- Service des Troubles du Spectre de l'Autisme et apparentés, Département de psychiatrie, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Sébastien Jacquemont
- Sainte Justine Hospital Research Center, Montréal, QC, Canada
- Department of Pediatrics, University of Montréal, Montreal, QC, Canada
| | - Nadia Chabane
- Service des Troubles du Spectre de l'Autisme et apparentés, Département de psychiatrie, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Borja Rodríguez-Herreros
- Service des Troubles du Spectre de l'Autisme et apparentés, Département de psychiatrie, Lausanne University Hospital (CHUV), Lausanne, Switzerland.
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9
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Washington P, Wall DP. A Review of and Roadmap for Data Science and Machine Learning for the Neuropsychiatric Phenotype of Autism. Annu Rev Biomed Data Sci 2023; 6:211-228. [PMID: 37137169 PMCID: PMC11093217 DOI: 10.1146/annurev-biodatasci-020722-125454] [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: 05/05/2023]
Abstract
Autism spectrum disorder (autism) is a neurodevelopmental delay that affects at least 1 in 44 children. Like many neurological disorder phenotypes, the diagnostic features are observable, can be tracked over time, and can be managed or even eliminated through proper therapy and treatments. However, there are major bottlenecks in the diagnostic, therapeutic, and longitudinal tracking pipelines for autism and related neurodevelopmental delays, creating an opportunity for novel data science solutions to augment and transform existing workflows and provide increased access to services for affected families. Several efforts previously conducted by a multitude of research labs have spawned great progress toward improved digital diagnostics and digital therapies for children with autism. We review the literature on digital health methods for autism behavior quantification and beneficial therapies using data science. We describe both case-control studies and classification systems for digital phenotyping. We then discuss digital diagnostics and therapeutics that integrate machine learning models of autism-related behaviors, including the factors that must be addressed for translational use. Finally, we describe ongoing challenges and potential opportunities for the field of autism data science. Given the heterogeneous nature of autism and the complexities of the relevant behaviors, this review contains insights that are relevant to neurological behavior analysis and digital psychiatry more broadly.
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Affiliation(s)
- Peter Washington
- Department of Information and Computer Sciences, University of Hawai'i at Mānoa, Honolulu, Hawai'i, USA
| | - Dennis P Wall
- Departments of Pediatrics (Systems Medicine), Biomedical Data Science, and Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, California, USA;
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10
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Moreau CA, Kumar K, Harvey A, Huguet G, Urchs SGW, Schultz LM, Sharmarke H, Jizi K, Martin CO, Younis N, Tamer P, Martineau JL, Orban P, Silva AI, Hall J, van den Bree MBM, Owen MJ, Linden DEJ, Lippé S, Bearden CE, Almasy L, Glahn DC, Thompson PM, Bourgeron T, Bellec P, Jacquemont S. Brain functional connectivity mirrors genetic pleiotropy in psychiatric conditions. Brain 2023; 146:1686-1696. [PMID: 36059063 PMCID: PMC10319760 DOI: 10.1093/brain/awac315] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/13/2022] [Accepted: 08/11/2022] [Indexed: 02/03/2023] Open
Abstract
Pleiotropy occurs when a genetic variant influences more than one trait. This is a key property of the genomic architecture of psychiatric disorders and has been observed for rare and common genomic variants. It is reasonable to hypothesize that the microscale genetic overlap (pleiotropy) across psychiatric conditions and cognitive traits may lead to similar overlaps at the macroscale brain level such as large-scale brain functional networks. We took advantage of brain connectivity, measured by resting-state functional MRI to measure the effects of pleiotropy on large-scale brain networks, a putative step from genes to behaviour. We processed nine resting-state functional MRI datasets including 32 726 individuals and computed connectome-wide profiles of seven neuropsychiatric copy-number-variants, five polygenic scores, neuroticism and fluid intelligence as well as four idiopathic psychiatric conditions. Nine out of 19 pairs of conditions and traits showed significant functional connectivity correlations (rFunctional connectivity), which could be explained by previously published levels of genomic (rGenetic) and transcriptomic (rTranscriptomic) correlations with moderate to high concordance: rGenetic-rFunctional connectivity = 0.71 [0.40-0.87] and rTranscriptomic-rFunctional connectivity = 0.83 [0.52; 0.94]. Extending this analysis to functional connectivity profiles associated with rare and common genetic risk showed that 30 out of 136 pairs of connectivity profiles were correlated above chance. These similarities between genetic risks and psychiatric disorders at the connectivity level were mainly driven by the overconnectivity of the thalamus and the somatomotor networks. Our findings suggest a substantial genetic component for shared connectivity profiles across conditions and traits, opening avenues to delineate general mechanisms-amenable to intervention-across psychiatric conditions and genetic risks.
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Affiliation(s)
- Clara A Moreau
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, Université Paris Cité, Paris, France
- Sainte Justine Research Center, University of Montréal, Montréal, QC H3T 1C5, Canada
- Centre de Recherche de l’Institut Universitaire de Gériatrie de Montréal, UdeM, Montreal, QC H3W 1W5, Canada
| | - Kuldeep Kumar
- Sainte Justine Research Center, University of Montréal, Montréal, QC H3T 1C5, Canada
| | - Annabelle Harvey
- Sainte Justine Research Center, University of Montréal, Montréal, QC H3T 1C5, Canada
- Centre de Recherche de l’Institut Universitaire de Gériatrie de Montréal, UdeM, Montreal, QC H3W 1W5, Canada
| | - Guillaume Huguet
- Sainte Justine Research Center, University of Montréal, Montréal, QC H3T 1C5, Canada
| | - Sebastian G W Urchs
- Centre de Recherche de l’Institut Universitaire de Gériatrie de Montréal, UdeM, Montreal, QC H3W 1W5, Canada
- Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
| | - Laura M Schultz
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Hanad Sharmarke
- Centre de Recherche de l’Institut Universitaire de Gériatrie de Montréal, UdeM, Montreal, QC H3W 1W5, Canada
| | - Khadije Jizi
- Sainte Justine Research Center, University of Montréal, Montréal, QC H3T 1C5, Canada
| | | | - Nadine Younis
- Sainte Justine Research Center, University of Montréal, Montréal, QC H3T 1C5, Canada
| | - Petra Tamer
- Sainte Justine Research Center, University of Montréal, Montréal, QC H3T 1C5, Canada
| | - Jean-Louis Martineau
- Sainte Justine Research Center, University of Montréal, Montréal, QC H3T 1C5, Canada
| | - Pierre Orban
- Centre de Recherche de l’Institut Universitaire en Santé Mentale de Montréal, UdeM, Montréal, QC H1N 3V2, Canada
- Département de Psychiatrie et d’Addictologie, Université de Montréal, Pavillon Roger-Gaudry, C.P. 6128, Succursale Centre-ville, Montréal, QC H3C 3J7, Canada
| | - Ana Isabel Silva
- Neuroscience and Mental Health Research Institute, Cardiff University, Cardiff, UK
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
- School for Mental Health and Neuroscience, Maastricht University, Maastricht, The Netherlands
| | - Jeremy Hall
- Neuroscience and Mental Health Research Institute, Cardiff University, Cardiff, UK
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Marianne B M van den Bree
- Neuroscience and Mental Health Research Institute, Cardiff University, Cardiff, UK
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Michael J Owen
- Neuroscience and Mental Health Research Institute, Cardiff University, Cardiff, UK
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - David E J Linden
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
- School for Mental Health and Neuroscience, Maastricht University, Maastricht, The Netherlands
| | - Sarah Lippé
- Sainte Justine Research Center, University of Montréal, Montréal, QC H3T 1C5, Canada
| | - Carrie E Bearden
- Integrative Center for Neurogenetics, Semel Institute for Neuroscience and Human Behavior, Los Angeles, CA 90095, USA
- Department of Psychiatry, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Biobehavioral Sciences and Psychology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Laura Almasy
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Lifespan Brain Institute, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - David C Glahn
- Department of Psychiatry, Harvard Medical School, Cambridge, MA 02115, USA
- Boston Children’s Hospital, Tommy Fuss Center for Neuropsychiatric Disease Research, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Paul M Thompson
- Imaging Genetics Center, Stevens Institute for Neuroimaging and Informatics, Keck USC School of Medicine, Marina del Rey, CA, USA
| | - Thomas Bourgeron
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, Université Paris Cité, Paris, France
| | - Pierre Bellec
- Centre de Recherche de l’Institut Universitaire de Gériatrie de Montréal, UdeM, Montreal, QC H3W 1W5, Canada
| | - Sebastien Jacquemont
- Sainte Justine Research Center, University of Montréal, Montréal, QC H3T 1C5, Canada
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11
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Taylor CM, Finucane BM, Moreno-De-Luca A, Walsh LK, Martin CL, Ledbetter DH. Phenotypic shift in copy number variants: Evidence in 16p11.2 duplication syndrome. Genet Med 2023; 25:151-154. [PMID: 36609147 PMCID: PMC10068678 DOI: 10.1016/j.gim.2022.09.011] [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] [Received: 07/12/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 11/07/2022] Open
Abstract
PURPOSE Recurrent 16p11.2 duplications produce a wide range of clinical outcomes with varying effects on cognition and social functioning. Family-based studies of copy number variants (CNVs) have revealed significant contributions of genomic background on variable expressivity. In this study, we measured the phenotypic effect of 16p11.2 duplications and quantified the modulating effect of familial background on cognitive and social outcomes. METHODS Genomic and clinical data were ascertained from 41 probands with a 16p11.2 duplication and their first-degree relatives. Paired comparisons were completed to determine the duplication's effect on expected vs actual performance on standardized tests of intelligence (IQ) and social functioning (Social Responsiveness Scale-2). Intraclass correlations between relatives and probands were also calculated. RESULTS Cognitive and social functioning were significantly lower among individuals with 16p11.2 duplications than their CNV-negative relatives, whereas intraclass correlations between the groups remained high for full-scale IQ and Social Responsiveness Scale-2 scores. CONCLUSION The 16p11.2 duplication confers deleterious effects on cognition and social functioning, whereas familial background significantly influences phenotypic expression of these traits. Understanding variable expressivity in CNV disorders has implications for anticipatory clinical care, particularly for individuals who receive a genetic diagnosis at an early age, long before the full scope of manifestations becomes evident.
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Affiliation(s)
- Cora M Taylor
- Autism & Developmental Medicine Institute, Geisinger, Lewisburg, PA.
| | | | | | - Lauren K Walsh
- Autism & Developmental Medicine Institute, Geisinger, Lewisburg, PA
| | | | - David H Ledbetter
- Department of Psychiatry, College of Medicine, University of Florida, Gainesville, FL
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12
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Aglinskas A, Anzellotti S. Precision psychiatry requires disentangling disorder-specific variation: The case of ASD. Clin Transl Med 2022; 12:e1079. [PMID: 36214746 PMCID: PMC9549877 DOI: 10.1002/ctm2.1079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 09/27/2022] [Indexed: 01/28/2023] Open
Affiliation(s)
- Aidas Aglinskas
- Department of Psychology and NeuroscienceBoston CollegeBostonMassachusettsUSA
| | - Stefano Anzellotti
- Department of Psychology and NeuroscienceBoston CollegeBostonMassachusettsUSA
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13
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Moufawad El Achkar C, Rosen A, Kessler SK, Steinman KJ, Spence SJ, Ramocki M, Marco EJ, Green Snyder L, Spiro JE, Chung WK, Annapurna P, Sherr EH. Clinical Characteristics of Seizures and Epilepsy in Individuals With Recurrent Deletions and Duplications in the 16p11.2 Region. Neurol Genet 2022; 8:e200018. [PMID: 36531974 PMCID: PMC9756306 DOI: 10.1212/nxg.0000000000200018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 07/01/2022] [Indexed: 11/15/2022]
Abstract
Background and Objectives Deletions and duplications at 16p11.2 (BP4 to BP5; 29.5-30.1 Mb) have been associated with several neurodevelopmental and neuropsychiatric disorders including autism spectrum disorder, intellectual disability (ID), and schizophrenia. Seizures have also been reported in individuals with these particular copy number variants, but the epilepsy phenotypes have not been well-delineated. We aimed to systematically characterize the seizure types, epilepsy syndromes, and epilepsy severity in a large cohort of individuals with these 16p11.2 deletions and duplications. Methods The cohort of ascertained participants with the recurrent 16p11.2 copy number variant was assembled through the multicenter Simons Variation in Individuals Project. Detailed data on individuals identified as having a history of seizures were obtained using a semistructured phone interview and review of medical records, EEG, and MRI studies obtained clinically or as part of the Simons Variation in Individuals Project. Results Among 129 individuals with the 16p11.2 deletion, 31 (24%) had at least one seizure, including 23 (18%) who met criteria for epilepsy; 42% of them fit the phenotype of classic or atypical Self-limited (Familial) Infantile Epilepsy (Se(F)IE). Among 106 individuals with 16p11.2 duplications, 16 (15%) had at least one seizure, including 11 (10%) who met criteria for epilepsy. The seizure types and epilepsy syndromes were heterogeneous in this group. Most of the individuals in both the deletion and duplication groups had well-controlled seizures with subsequent remission. Pharmacoresistant epilepsy was uncommon. Seizures responded favorably to phenobarbital, carbamazepine, and oxcarbazepine in the deletion group, specifically in the Se(F)IE, and to various antiseizure medications in the duplication group. Discussion These findings delineate the spectrum of seizures and epilepsies in the recurrent 16p11.2 deletions and duplications and provide potential diagnostic, therapeutic, and prognostic information.
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14
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Escher J, Yan W, Rissman EF, Wang HLV, Hernandez A, Corces VG. Beyond Genes: Germline Disruption in the Etiology of Autism Spectrum Disorders. J Autism Dev Disord 2022; 52:4608-4624. [PMID: 34596807 PMCID: PMC9035896 DOI: 10.1007/s10803-021-05304-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/21/2021] [Indexed: 01/31/2023]
Abstract
Investigations into the etiology of autism spectrum disorders have been largely confined to two realms: variations in DNA sequence and somatic developmental exposures. Here we suggest a third route-disruption of the germline epigenome induced by exogenous toxicants during a parent's gamete development. Similar to cases of germline mutation, these molecular perturbations may produce dysregulated transcription of brain-related genes during fetal and early development, resulting in abnormal neurobehavioral phenotypes in offspring. Many types of exposures may have these impacts, and here we discuss examples of anesthetic gases, tobacco components, synthetic steroids, and valproic acid. Alterations in parental germline could help explain some unsolved phenomena of autism, including increased prevalence, missing heritability, skewed sex ratio, and heterogeneity of neurobiology and behavior.
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Affiliation(s)
- Jill Escher
- Escher Fund for Autism, 1590 Calaveras Avenue, San Jose, CA, USA.
| | - Wei Yan
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Emilie F Rissman
- Center for Human Health and the Environment and Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Hsiao-Lin V Wang
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Arturo Hernandez
- Maine Medical Center Research Institute, MaineHealth, Scarborough, ME, USA
- Tufts University School of Medicine, Boston, MA, USA
| | - Victor G Corces
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
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15
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Thurm A, Srivastava S. On Terms: What's in a Name? Intellectual Disability and "Condition," "Disorder," "Syndrome," "Disease," and "Disability". AMERICAN JOURNAL ON INTELLECTUAL AND DEVELOPMENTAL DISABILITIES 2022; 127:349-354. [PMID: 36018763 DOI: 10.1352/1944-7558-127.5.349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 04/05/2022] [Indexed: 06/15/2023]
Abstract
Individuals living with intellectual disability can have multiple co-occurring medical conditions including associated genetic diagnoses. The number of genetic etiologies associated with ID is growing, with some quite new and rare, and others more common and associated with what is often considered a syndrome. In the context of genetic etiologies and associated medical comorbidities, appropriate use of descriptive terminology warrants clarification. Using accurate nomenclature is essential for descriptions, especially as terms are used across both research and clinical reports. Here we discuss several terms that may be confused with each other, including "condition," "disorder," "syndrome," "disease," and "disability." Our goal is to shed light on the meanings of the five descriptors and their appropriate use in the ID population, especially in relation to those who have a genetic diagnosis.
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Affiliation(s)
- Audrey Thurm
- Audrey Thurm, National Institute of Mental Health
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16
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Fu JM, Satterstrom FK, Peng M, Brand H, Collins RL, Dong S, Wamsley B, Klei L, Wang L, Hao SP, Stevens CR, Cusick C, Babadi M, Banks E, Collins B, Dodge S, Gabriel SB, Gauthier L, Lee SK, Liang L, Ljungdahl A, Mahjani B, Sloofman L, Smirnov AN, Barbosa M, Betancur C, Brusco A, Chung BHY, Cook EH, Cuccaro ML, Domenici E, Ferrero GB, Gargus JJ, Herman GE, Hertz-Picciotto I, Maciel P, Manoach DS, Passos-Bueno MR, Persico AM, Renieri A, Sutcliffe JS, Tassone F, Trabetti E, Campos G, Cardaropoli S, Carli D, Chan MCY, Fallerini C, Giorgio E, Girardi AC, Hansen-Kiss E, Lee SL, Lintas C, Ludena Y, Nguyen R, Pavinato L, Pericak-Vance M, Pessah IN, Schmidt RJ, Smith M, Costa CIS, Trajkova S, Wang JYT, Yu MHC, Cutler DJ, De Rubeis S, Buxbaum JD, Daly MJ, Devlin B, Roeder K, Sanders SJ, Talkowski ME. Rare coding variation provides insight into the genetic architecture and phenotypic context of autism. Nat Genet 2022; 54:1320-1331. [PMID: 35982160 PMCID: PMC9653013 DOI: 10.1038/s41588-022-01104-0] [Citation(s) in RCA: 168] [Impact Index Per Article: 84.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 05/24/2022] [Indexed: 01/11/2023]
Abstract
Some individuals with autism spectrum disorder (ASD) carry functional mutations rarely observed in the general population. We explored the genes disrupted by these variants from joint analysis of protein-truncating variants (PTVs), missense variants and copy number variants (CNVs) in a cohort of 63,237 individuals. We discovered 72 genes associated with ASD at false discovery rate (FDR) ≤ 0.001 (185 at FDR ≤ 0.05). De novo PTVs, damaging missense variants and CNVs represented 57.5%, 21.1% and 8.44% of association evidence, while CNVs conferred greatest relative risk. Meta-analysis with cohorts ascertained for developmental delay (DD) (n = 91,605) yielded 373 genes associated with ASD/DD at FDR ≤ 0.001 (664 at FDR ≤ 0.05), some of which differed in relative frequency of mutation between ASD and DD cohorts. The DD-associated genes were enriched in transcriptomes of progenitor and immature neuronal cells, whereas genes showing stronger evidence in ASD were more enriched in maturing neurons and overlapped with schizophrenia-associated genes, emphasizing that these neuropsychiatric disorders may share common pathways to risk.
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Affiliation(s)
- Jack M Fu
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - F Kyle Satterstrom
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Minshi Peng
- Department of Statistics and Data Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Harrison Brand
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Pediatric Surgical Research Laboratories, Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Ryan L Collins
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Program in Bioinformatics and Integrative Genomics, Harvard Medical School, Boston, MA, USA
| | - Shan Dong
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Brie Wamsley
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Lambertus Klei
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Lily Wang
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Bioinformatics and Integrative Genomics, Harvard Medical School, Boston, MA, USA
| | - Stephanie P Hao
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Pediatric Surgical Research Laboratories, Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Christine R Stevens
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Caroline Cusick
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mehrtash Babadi
- Data Sciences Platform, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eric Banks
- Data Sciences Platform, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Brett Collins
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sheila Dodge
- Genomics Platform, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stacey B Gabriel
- Genomics Platform, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Laura Gauthier
- Data Sciences Platform, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Samuel K Lee
- Data Sciences Platform, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lindsay Liang
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Alicia Ljungdahl
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Behrang Mahjani
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Laura Sloofman
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Andrey N Smirnov
- Data Sciences Platform, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mafalda Barbosa
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Catalina Betancur
- Sorbonne Université, INSERM, CNRS, Neuroscience Paris Seine, Institut de Biologie Paris Seine, Paris, France
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, Turin, Italy
- Medical Genetics Unit, 'Città della Salute e della Scienza' University Hospital, Turin, Italy
| | - Brian H Y Chung
- Department of Pediatrics and Adolescent Medicine, Duchess of Kent Children's Hospital, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Edwin H Cook
- Institute for Juvenile Research, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA
| | - Michael L Cuccaro
- The John P Hussman Institute for Human Genomics, The University of Miami Miller School of Medicine, Miami, FL, USA
| | - Enrico Domenici
- Department of Cellular, Computational and Integrative Biology, , University of Trento, Trento, Italy
| | | | - J Jay Gargus
- Center for Autism Research and Translation, University of California Irvine, Irvine, CA, USA
| | - Gail E Herman
- The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Irva Hertz-Picciotto
- MIND (Medical Investigation of Neurodevelopmental Disorders) Institute, University of California Davis, Davis, CA, USA
| | - Patricia Maciel
- Life and Health Sciences Research Institute, School of Medicine, University of Minho, Braga, Portugal
| | - Dara S Manoach
- Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Maria Rita Passos-Bueno
- Centro de Pesquisas sobre o Genoma Humano e Células tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Antonio M Persico
- Interdepartmental Program 'Autism 0-90', 'Gaetano Martino' University Hospital, University of Messina, Messina, Italy
| | - Alessandra Renieri
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
- Medical Genetics, , University of Siena, Siena, Italy
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - James S Sutcliffe
- Department of Molecular Physiology & Biophysics and Psychiatry, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Flora Tassone
- MIND (Medical Investigation of Neurodevelopmental Disorders) Institute, University of California Davis, Davis, CA, USA
- Department of Biochemistry and Molecular Medicine, University of California Davis, School of Medicine, Sacramento, CA, USA
| | - Elisabetta Trabetti
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biology and Genetics, University of Verona, Verona, Italy
| | - Gabriele Campos
- Centro de Pesquisas sobre o Genoma Humano e Células tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Simona Cardaropoli
- Department of Public Health and Pediatrics, University of Torino, Turin, Italy
| | - Diana Carli
- Department of Public Health and Pediatrics, University of Torino, Turin, Italy
| | - Marcus C Y Chan
- Department of Pediatrics and Adolescent Medicine, Duchess of Kent Children's Hospital, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Chiara Fallerini
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
- Medical Genetics, , University of Siena, Siena, Italy
| | - Elisa Giorgio
- Department of Medical Sciences, University of Torino, Turin, Italy
| | - Ana Cristina Girardi
- Centro de Pesquisas sobre o Genoma Humano e Células tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Emily Hansen-Kiss
- Department of Diagnostic and Biomedical Sciences, University of Texas Health Science Center at Houston, School of Dentistry, Houston, TX, USA
| | - So Lun Lee
- Department of Pediatrics and Adolescent Medicine, Duchess of Kent Children's Hospital, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Carla Lintas
- Service for Neurodevelopmental Disorders, University Campus Bio-medico of Rome, Rome, Italy
| | - Yunin Ludena
- MIND (Medical Investigation of Neurodevelopmental Disorders) Institute, University of California Davis, Davis, CA, USA
| | - Rachel Nguyen
- Center for Autism Research and Translation, University of California Irvine, Irvine, CA, USA
| | - Lisa Pavinato
- Department of Medical Sciences, University of Torino, Turin, Italy
| | - Margaret Pericak-Vance
- The John P Hussman Institute for Human Genomics, The University of Miami Miller School of Medicine, Miami, FL, USA
| | - Isaac N Pessah
- MIND (Medical Investigation of Neurodevelopmental Disorders) Institute, University of California Davis, Davis, CA, USA
- Department of Molecular Biosciences, University of California Davis, School of Veterinary Medicine, Davis, CA, USA
| | - Rebecca J Schmidt
- MIND (Medical Investigation of Neurodevelopmental Disorders) Institute, University of California Davis, Davis, CA, USA
| | - Moyra Smith
- Center for Autism Research and Translation, University of California Irvine, Irvine, CA, USA
| | - Claudia I S Costa
- Centro de Pesquisas sobre o Genoma Humano e Células tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Slavica Trajkova
- Department of Medical Sciences, University of Torino, Turin, Italy
| | - Jaqueline Y T Wang
- Centro de Pesquisas sobre o Genoma Humano e Células tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Mullin H C Yu
- Department of Pediatrics and Adolescent Medicine, Duchess of Kent Children's Hospital, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - David J Cutler
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Silvia De Rubeis
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joseph D Buxbaum
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Mark J Daly
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
| | - Kathryn Roeder
- Department of Statistics and Data Science, Carnegie Mellon University, Pittsburgh, PA, USA.
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA.
| | - Stephan J Sanders
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA.
| | - Michael E Talkowski
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Program in Bioinformatics and Integrative Genomics, Harvard Medical School, Boston, MA, USA.
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17
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Bain JM, Snyder LG, Helbig KL, Cooper DD, Chung WK, Goodspeed K. Consistency of parent-report SLC6A1 data in Simons Searchlight with Provider-Based Publications. J Neurodev Disord 2022; 14:40. [PMID: 35761184 PMCID: PMC9238190 DOI: 10.1186/s11689-022-09449-7] [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: 01/02/2022] [Accepted: 06/17/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND SLC6A1-related disorder is a recently identified, rare, genetic neurodevelopmental disorder that is associated with loss-of-function variants in SLC6A1. This gene encodes GABA transporter type I that is responsible for re-uptake of GABA from the synapse into the pre-synaptic terminal or circulating neuroglia. Based upon retrospective review of published cases and available research databases including Epi25 collective and SLC6A1 Connect patient database, the phenotypic spectrum is broad and includes developmental delay, epilepsy, and autism or autistic traits. SLC6A1 is one of the genes included in the Simons Searchlight registry, which includes standardized data collection across genetically identified neurodevelopmental conditions. METHODS In this study, we compare parent-report measures of phenotypic features in the Simons Searchlight registry to previously published, provider-reported cases to assess if parent-report measures are consistent with what has been reported in the literature. RESULTS There were 116 participants in the provider-reported dataset compared to 43 individuals in the caregiver-reported dataset. Carriers in Searchlight had 83 unique pathogenic or likely pathogenic variants in SLC6A1, which were predominantly missense or nonsense variants. There was no significant difference between groups for the prevalence of developmental delay, ASD, or ADHD. Caregivers more often reported hypotonia, while epilepsy was slightly more frequently reported by providers. CONCLUSIONS We propose that standardized parent-report data collection methods are consistent with provider reports on many core features of SLC6A1-related disorder. The availability of patient registries and standardized natural history studies may fill an important need in clinical trial readiness programs, with larger sample sizes than smaller published case series.
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Affiliation(s)
- Jennifer M Bain
- Department of Neurology, Division of Child Neurology, Columbia University Irving Medical Center, New York, NY, USA.
| | | | - Katherine L Helbig
- Department of Pediatrics, Division of Neurology and Epilepsy NeuroGenetics Initiative, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Wendy K Chung
- Simons Foundation, New York, NY, USA.,Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Kimberly Goodspeed
- Department of Pediatrics, Division of Neurology, University of Texas Southwestern Medical Center, Dallas, TX, USA
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18
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Aglinskas A, Hartshorne JK, Anzellotti S. Contrastive machine learning reveals the structure of neuroanatomical variation within autism. Science 2022; 376:1070-1074. [PMID: 35653486 DOI: 10.1126/science.abm2461] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Autism spectrum disorder (ASD) is highly heterogeneous. Identifying systematic individual differences in neuroanatomy could inform diagnosis and personalized interventions. The challenge is that these differences are entangled with variation because of other causes: individual differences unrelated to ASD and measurement artifacts. We used contrastive deep learning to disentangle ASD-specific neuroanatomical variation from variation shared with typical control participants. ASD-specific variation correlated with individual differences in symptoms. The structure of this ASD-specific variation also addresses a long-standing debate about the nature of ASD: At least in terms of neuroanatomy, individuals do not cluster into distinct subtypes; instead, they are organized along continuous dimensions that affect distinct sets of regions.
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Affiliation(s)
- Aidas Aglinskas
- Department of Psychology and Neuroscience, Boston College, Boston, MA 02467, USA
| | - Joshua K Hartshorne
- Department of Psychology and Neuroscience, Boston College, Boston, MA 02467, USA
| | - Stefano Anzellotti
- Department of Psychology and Neuroscience, Boston College, Boston, MA 02467, USA
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19
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Aravamuthan BR, Shusterman M, Green Snyder L, Lemmon ME, Bain JM, Gross P. Diagnostic preferences include discussion of etiology for adults with cerebral palsy and their caregivers. Dev Med Child Neurol 2022; 64:723-733. [PMID: 35092695 PMCID: PMC10091392 DOI: 10.1111/dmcn.15164] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 12/20/2021] [Indexed: 12/12/2022]
Abstract
AIM To determine the views of individuals with cerebral palsy (CP) and their caregivers (CP community members) about carrying a CP diagnosis, an etiological diagnosis, or both diagnoses together. METHOD We surveyed CP community members across two registries querying their views on carrying a CP diagnosis, one type of etiological diagnosis (specifically, a genetic diagnosis), or both. Open-ended responses were analyzed using a conventional content analysis approach. RESULTS Of 197 respondents (108 adults with CP and 89 caregivers), most (75%) valued knowing the cause of their CP. Of those with a diagnostic preference, most preferred carrying both CP and etiological diagnoses together (68%). When compared with carrying an etiological diagnosis alone, significantly more respondents felt a CP diagnosis helped anticipate symptom evolution (84% vs 54%), explain symptoms to others (86% vs 48%), access services (86% vs 48%), and join support communities (78% vs 50%) (p < 0.01, χ2 test). INTERPRETATION Most CP community members surveyed want to know the cause of their CP and would prefer carrying both CP and etiological diagnoses together. Clinical practice should evolve to meet these community needs.
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Affiliation(s)
- Bhooma R Aravamuthan
- Department of Neurology, Washington University School of Medicine and St. Louis Children's Hospital, St. Louis, MO, USA
| | | | | | - Monica E Lemmon
- Department of Pediatrics, Department of Population Health Sciences, Duke University School of Medicine, Durham, NC, USA
| | - Jennifer M Bain
- Department of Neurology, Division of Child Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Paul Gross
- The Cerebral Palsy Research Network, Salt Lake City, UT, USA.,University of Utah, Salt Lake City, UT, USA
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- Simons Foundation, New York, NY, USA
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- The Cerebral Palsy Research Network, Salt Lake City, UT, USA
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20
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NISHIOKA MASAKI. The Current Progress of Psychiatric Genomics. JUNTENDO IJI ZASSHI = JUNTENDO MEDICAL JOURNAL 2022; 68:2-11. [PMID: 38911007 PMCID: PMC11189800 DOI: 10.14789/jmj.jmj21-0038-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 11/24/2021] [Indexed: 06/25/2024]
Abstract
Psychiatric disorders such as bipolar disorder and schizophrenia are highly heritable. While the genetic contribution to psychiatric disorders is quite sure, specific genetic factors contributing to particular conditions have long been a mystery. Empowered by the initial report of the Human Genome Project, the analysis of the comprehensive set of the human genome, called "genomics," became possible. Subsequent development of large-scale genomic technologies enabled us to elucidate various disease-related genetic information, accelerating our understanding of various diseases. Genomic research on psychiatric disorders is not an exception. In this Review, I introduce significant advancements in psychiatric genomics with a special focus on our investigation of bipolar disorder. International consortiums and advocacy groups accelerate psychiatric genomics, increasing the sample size and statistical power for robust findings. The genetic architecture of schizophrenia has been elucidated in both common and rare variant studies. The genetic architecture of autism spectrum disorder (ASD) has been elucidated mainly by rare variant analysis. As to bipolar disorder, common variant analysis precedes rare variant analysis, but we are struggling to elucidate relevant rare variants. While the genomic approach has explained specific genetic factors for particular disorders, overlapping risk genes or pleiotropy has been observed more than expected. The boundary in the current nosology of psychiatric disorders is more or less challenged. To understand the genotype-phenotype relation more deeply, an attempt to understand phenotypes based on genotypes, called the "genotype first" approach, has started. I discuss this new approach for better understanding and treatment of psychiatric disorders.
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Affiliation(s)
- MASAKI NISHIOKA
- Corresponding author: Masaki Nishioka, Department of Psychiatry, Faculty of Medicine, Juntendo University, Department of Molecular Pathology of Mood Disorders, Faculty of Medicine, Juntendo University, Hongo 2-1-1, Bunkyo-ku, Tokyo, 113-8421, Japan, TEL&FAX: +81-3-5802-1070 E-mail:
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21
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Tomasello DL, Kim JL, Khodour Y, McCammon JM, Mitalipova M, Jaenisch R, Futerman AH, Sive H. 16pdel lipid changes in iPSC-derived neurons and function of FAM57B in lipid metabolism and synaptogenesis. iScience 2022; 25:103551. [PMID: 34984324 PMCID: PMC8693007 DOI: 10.1016/j.isci.2021.103551] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 09/23/2021] [Accepted: 11/26/2021] [Indexed: 01/01/2023] Open
Abstract
The complex 16p11.2 deletion syndrome (16pdel) is accompanied by neurological disorders, including epilepsy, autism spectrum disorder, and intellectual disability. We demonstrated that 16pdel iPSC differentiated neurons from affected people show augmented local field potential activity and altered ceramide-related lipid species relative to unaffected. FAM57B, a poorly characterized gene in the 16p11.2 interval, has emerged as a candidate tied to symptomatology. We found that FAM57B modulates ceramide synthase (CerS) activity, but is not a CerS per se. In FAM57B mutant human neuronal cells and zebrafish brain, composition and levels of sphingolipids and glycerolipids associated with cellular membranes are disrupted. Consistently, we observed aberrant plasma membrane architecture and synaptic protein mislocalization, which were accompanied by depressed brain and behavioral activity. Together, these results suggest that haploinsufficiency of FAM57B contributes to changes in neuronal activity and function in 16pdel syndrome through a crucial role for the gene in lipid metabolism.
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Affiliation(s)
| | - Jiyoon L. Kim
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yara Khodour
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | | | - Maya Mitalipova
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Rudolf Jaenisch
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Anthony H. Futerman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Hazel Sive
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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22
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Crowd annotations can approximate clinical autism impressions from short home videos with privacy protections. INTELLIGENCE-BASED MEDICINE 2022; 6. [PMID: 35634270 PMCID: PMC9139408 DOI: 10.1016/j.ibmed.2022.100056] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Artificial Intelligence (A.I.) solutions are increasingly considered for telemedicine. For these methods to serve children and their families in home settings, it is crucial to ensure the privacy of the child and parent or caregiver. To address this challenge, we explore the potential for global image transformations to provide privacy while preserving the quality of behavioral annotations. Crowd workers have previously been shown to reliably annotate behavioral features in unstructured home videos, allowing machine learning classifiers to detect autism using the annotations as input. We evaluate this method with videos altered via pixelation, dense optical flow, and Gaussian blurring. On a balanced test set of 30 videos of children with autism and 30 neurotypical controls, we find that the visual privacy alterations do not drastically alter any individual behavioral annotation at the item level. The AUROC on the evaluation set was 90.0% ±7.5% for unaltered videos, 85.0% ±9.0% for pixelation, 85.0% ±9.0% for optical flow, and 83.3% ±9.3% for blurring, demonstrating that an aggregation of small changes across behavioral questions can collectively result in increased misdiagnosis rates. We also compare crowd answers against clinicians who provided the same annotations for the same videos as crowd workers, and we find that clinicians have higher sensitivity in their recognition of autism-related symptoms. We also find that there is a linear correlation (r = 0.75, p < 0.0001) between the mean Clinical Global Impression (CGI) score provided by professional clinicians and the corresponding score emitted by a previously validated autism classifier with crowd inputs, indicating that the classifier’s output probability is a reliable estimate of the clinical impression of autism. A significant correlation is maintained with privacy alterations, indicating that crowd annotations can approximate clinician-provided autism impression from home videos in a privacy-preserved manner.
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23
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Loureiro LO, Howe JL, Reuter MS, Iaboni A, Calli K, Roshandel D, Pritišanac I, Moses A, Forman-Kay JD, Trost B, Zarrei M, Rennie O, Lau LYS, Marshall CR, Srivastava S, Godlewski B, Buttermore ED, Sahin M, Hartley D, Frazier T, Vorstman J, Georgiades S, Lewis SME, Szatmari P, Bradley CAL, Tabet AC, Willems M, Lumbroso S, Piton A, Lespinasse J, Delorme R, Bourgeron T, Anagnostou E, Scherer SW. A recurrent SHANK3 frameshift variant in Autism Spectrum Disorder. NPJ Genom Med 2021; 6:91. [PMID: 34737294 PMCID: PMC8568906 DOI: 10.1038/s41525-021-00254-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 09/23/2021] [Indexed: 01/22/2023] Open
Abstract
Autism Spectrum Disorder (ASD) is genetically complex with ~100 copy number variants and genes involved. To try to establish more definitive genotype and phenotype correlations in ASD, we searched genome sequence data, and the literature, for recurrent predicted damaging sequence-level variants affecting single genes. We identified 18 individuals from 16 unrelated families carrying a heterozygous guanine duplication (c.3679dup; p.Ala1227Glyfs*69) occurring within a string of 8 guanines (genomic location [hg38]g.50,721,512dup) affecting SHANK3, a prototypical ASD gene (0.08% of ASD-affected individuals carried the predicted p.Ala1227Glyfs*69 frameshift variant). Most probands carried de novo mutations, but five individuals in three families inherited it through somatic mosaicism. We scrutinized the phenotype of p.Ala1227Glyfs*69 carriers, and while everyone (17/17) formally tested for ASD carried a diagnosis, there was the variable expression of core ASD features both within and between families. Defining such recurrent mutational mechanisms underlying an ASD outcome is important for genetic counseling and early intervention.
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Affiliation(s)
- Livia O Loureiro
- Genetics and Genome Biology and The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Jennifer L Howe
- Genetics and Genome Biology and The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Miriam S Reuter
- Canada's Genomics Enterprise (CGEn), The Hospital for Sick Children, Toronto, ON, Canada
| | - Alana Iaboni
- Holland Bloorview Kids Rehabilitation Hospital, Toronto, ON, Canada
| | - Kristina Calli
- Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Delnaz Roshandel
- Genetics and Genome Biology and The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Iva Pritišanac
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Alan Moses
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Julie D Forman-Kay
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Brett Trost
- Genetics and Genome Biology and The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Mehdi Zarrei
- Genetics and Genome Biology and The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Olivia Rennie
- Genetics and Genome Biology and The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Lynette Y S Lau
- Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Christian R Marshall
- Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Siddharth Srivastava
- Department of Neurology, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Brianna Godlewski
- Department of Neurology, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Elizabeth D Buttermore
- Department of Neurology, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Mustafa Sahin
- Department of Neurology, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Thomas Frazier
- Autism Speaks and Department of Psychology, John Carroll University, Cleveland, OH, USA
| | - Jacob Vorstman
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
- Department of Psychiatry, The Hospital for Sick Children, Toronto, ON, Canada
| | - Stelios Georgiades
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON, Canada
| | - Suzanne M E Lewis
- Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Peter Szatmari
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
- Department of Psychiatry, The Hospital for Sick Children, Toronto, ON, Canada
- Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Clarrisa A Lisa Bradley
- Genetics and Genome Biology and The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Anne-Claude Tabet
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, Université de Paris, F-75015, Paris, France
- Genetics Department, Cytogenetic Unit, Robert Debré Hospital, APHP, F-75019, Paris, France
| | | | - Serge Lumbroso
- Biochimie et Biologie Moléculaire, CHU Nimes, Univ. Montpellier, Nimes, France
| | - Amélie Piton
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique, UMR7104, Institut National de la Santé et de la Recherche Médicale, U964, Université de Strasbourg, Illkirch, France
- Unité de Génétique Moléculaire, IGMA, Hôpitaux Universitaire de Strasbourg, Strasbourg, France
- Institut Universitaire de France, Paris, France
| | | | - Richard Delorme
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, Université de Paris, F-75015, Paris, France
- Child and Adolescent Psychiatry Department, Robert Debré Hospital, APHP, F-75019, Paris, France
| | - Thomas Bourgeron
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, Université de Paris, F-75015, Paris, France
| | - Evdokia Anagnostou
- Holland Bloorview Kids Rehabilitation Hospital, Toronto, ON, Canada
- Department of Paediatrics, University of Toronto, Toronto, ON, Canada
| | - Stephen W Scherer
- Genetics and Genome Biology and The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada.
- Department of Molecular Genetics and the McLaughlin Centre, University of Toronto, Toronto, ON, Canada.
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24
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Wickstrom J, Farmer C, Snyder LG, Mitz AR, Sanders SJ, Bishop S, Thurm A. Patterns of delay in early gross motor and expressive language milestone attainment in probands with genetic conditions versus idiopathic ASD from SFARI registries. J Child Psychol Psychiatry 2021; 62:1297-1307. [PMID: 34382689 PMCID: PMC9939014 DOI: 10.1111/jcpp.13492] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/11/2021] [Indexed: 12/28/2022]
Abstract
BACKGROUND Recent large-scale initiatives have led to systematically collected phenotypic data for several rare genetic conditions implicated in autism spectrum disorder (ASD). The onset of developmentally expected skills (e.g. walking, talking) serve as readily quantifiable aspects of the behavioral phenotype. This study's aims were: (a) describe the distribution of ages of attainment of gross motor and expressive language milestones in several rare genetic conditions, and (b) characterize the likelihood of delays in these conditions compared with idiopathic ASD. METHODS Participants aged 3 years and older were drawn from two Simons Foundation Autism Research Initiative registries that employed consistent phenotyping protocols. Inclusion criteria were a confirmed genetic diagnosis of one of 16 genetic conditions (Simons Searchlight) or absence of known pathogenic genetic findings in individuals with ASD (SPARK). Parent-reported age of acquisition of three gross motor and two expressive language milestones was described and categorized as on-time or delayed, relative to normative expectations. RESULTS Developmental milestone profiles of probands with genetic conditions were marked by extensive delays (including nonattainment), with highest severity in single gene conditions and more delays than idiopathic ASD in motor skills. Compared with idiopathic ASD, the median odds of delay among the genetic groups were higher by 8.3 times (IQR 5.8-16.3) for sitting, 12.4 times (IQR 5.3-19.5) for crawling, 26.8 times (IQR 7.7-41.1) for walking, 2.7 times (IQR 1.7-5.5) for single words, and 5.7 times (IQR 2.7-18.3) for combined words. CONCLUSIONS Delays in developmental milestones, particularly in gross motor skills, are frequent and may be among the earliest indicators of differentially affected developmental processes in specific genetically defined conditions associated with ASD, as compared with those with clinical diagnoses of idiopathic ASD. The possibility of different developmental pathways leading to ASD-associated phenotypes should be considered when deciding how to employ specific genetic conditions as models for ASD.
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Affiliation(s)
- Jordan Wickstrom
- Neurodevelopmental and Behavioral Phenotyping Service, National Institutes of Health, Bethesda, MD, USA
| | - Cristan Farmer
- Neurodevelopmental and Behavioral Phenotyping Service, National Institutes of Health, Bethesda, MD, USA
| | | | - Andrew R. Mitz
- Laboratory of Neuropsychology, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Stephan J. Sanders
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Somer Bishop
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Audrey Thurm
- Neurodevelopmental and Behavioral Phenotyping Service, National Institutes of Health, Bethesda, MD, USA
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25
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Characterizing Sleep Problems in 16p11.2 Deletion and Duplication. J Autism Dev Disord 2021; 53:1462-1475. [PMID: 34633643 DOI: 10.1007/s10803-021-05311-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/24/2021] [Indexed: 10/20/2022]
Abstract
Studies of 16p11.2 copy number variants (CNVs) provide an avenue to identify mechanisms of impairment and develop targeted treatments for individuals with neurodevelopmental disorders. 16p11.2 deletion and duplication phenotypes are currently being ascertained; however, sleep disturbances are minimally described. In this study, we examine sleep disturbance in a well-characterized national sample of 16p11.2 CNVs, the Simons Foundation Autism Research Initiative (SFARI) database of youth and adults (n = 692). Factor analyses and multilevel models of derived sleep questionnaires for youth (n = 345) and adults (n = 347) indicate that 16p11.2 carriers show elevated sleep disturbance relative to community controls. Non-carrier family members also show elevated sleep disturbance. However, sleep duration does not differ between carriers and controls. Further studies of sleep in 16p11.2 are needed.
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26
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Dinneen TJ, Ghrálaigh FN, Walsh R, Lopez LM, Gallagher L. How does genetic variation modify ND-CNV phenotypes? Trends Genet 2021; 38:140-151. [PMID: 34364706 DOI: 10.1016/j.tig.2021.07.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/30/2021] [Accepted: 07/06/2021] [Indexed: 02/05/2023]
Abstract
Rare copy-number variants (CNVs) associated with neurodevelopmental disorders (NDDs), i.e., ND-CNVs, provide an insight into the neurobiology of NDDs and, potentially, a link between biology and clinical outcomes. However, ND-CNVs are characterised by incomplete penetrance resulting in heterogeneous carrier phenotypes, ranging from non-affected to multimorbid psychiatric, neurological, and physical phenotypes. Recent evidence indicates that other variants in the genome, or 'other hits', may partially explain the variable expressivity of ND-CNVs. These may be other rare variants or the aggregated effects of common variants that modify NDD risk. Here we discuss the recent findings, current questions, and future challenges relating to other hits research in the context of ND-CNVs and their potential for improved clinical diagnostics and therapeutics for ND-CNV carriers.
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Affiliation(s)
- Thomas J Dinneen
- Department of Psychiatry, Trinity College Dublin, Dublin, Ireland.
| | - Fiana Ní Ghrálaigh
- Department of Psychiatry, Trinity College Dublin, Dublin, Ireland; Department of Biology, National University of Ireland Maynooth, Maynooth, Ireland
| | - Ruth Walsh
- Department of Psychiatry, Trinity College Dublin, Dublin, Ireland
| | - Lorna M Lopez
- Department of Psychiatry, Trinity College Dublin, Dublin, Ireland; Department of Biology, National University of Ireland Maynooth, Maynooth, Ireland
| | - Louise Gallagher
- Department of Psychiatry, Trinity College Dublin, Dublin, Ireland.
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27
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Kowanda M, Cartner L, Kentros C, Geltzeiler AR, Singer KE, Weaver WC, Lehman CD, Smith S, Smith RS, Walsh LK, Diehl K, Nagpal N, Brooks E, Mebane CM, Wilson AL, Marvin AR, White LC, Law JK, Jensen W, Daniels AM, Tjernagel J, Snyder LG, Taylor CM, Chung WK. Availability of Services and Caregiver Burden: Supporting Individuals With Neurogenetic Conditions During the COVID-19 Pandemic. J Child Neurol 2021; 36:760-767. [PMID: 33829918 PMCID: PMC8033176 DOI: 10.1177/08830738211001209] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Because of the COVID-19 pandemic, in-person services for individuals with neurodevelopmental disabilities were disrupted globally, resulting in a transition to remote delivery of services and therapies. For individuals with neurogenetic conditions, reliance on nonclinical caregivers to facilitate all therapies and care was unprecedented. The study aimed to (1) describe caregivers' reported impact on their dependent's services, therapies, medical needs, and impact on themselves as a result of the COVID-19 pandemic and (2) assess the relationship between the extent of disruption of services and the degree of self-reported caregiver burden. Two online questionnaires were completed by caregivers participating in Simons Searchlight in April and May 2020. Surveys were completed by caregivers of children or dependent adults with neurodevelopmental genetic conditions in Simons Searchlight. Caregivers reported that the impact of the COVID-19 pandemic moderately or severely disrupted services, therapies, or medical supports. The majority of caregivers were responsible for providing some aspect of therapy. Caregivers reported "feeling stressed but able to deal with problems as they arise," and reported lower anxiety at follow-up. Caregivers reported that telehealth services were not meeting the needs of those with complex medical needs. Future surveys will assess if and how medical systems, educational programs, therapists, and caregivers adapt to the challenges arising during the COVID-19 pandemic.
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Affiliation(s)
| | | | - Catherine Kentros
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Alexa R. Geltzeiler
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Kaitlyn E. Singer
- Geisinger Autism & Developmental Medicine Institute, Lewisburg, PA, USA
| | - W. Curtis Weaver
- Geisinger Autism & Developmental Medicine Institute, Lewisburg, PA, USA
| | | | - Simone Smith
- Geisinger Autism & Developmental Medicine Institute, Lewisburg, PA, USA
| | | | | | | | | | | | - Caroline M. Mebane
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Ashley L. Wilson
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Alison R. Marvin
- Maryland Center for Developmental Disabilities, Kennedy Krieger Institute, Baltimore, MD, USA
| | | | - J. Kiely Law
- Maryland Center for Developmental Disabilities, Kennedy Krieger Institute, Baltimore, MD, USA
| | | | | | | | | | - Cora M. Taylor
- Geisinger Autism & Developmental Medicine Institute, Lewisburg, PA, USA
| | - Wendy K. Chung
- Simons Foundation, New York, NY, USA,Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA,Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA,Wendy K. Chung, MD, PhD, Simons Foundation, New York, NY 10010, USA.
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28
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Chung WK, Roberts TP, Sherr EH, Snyder LG, Spiro JE. 16p11.2 deletion syndrome. Curr Opin Genet Dev 2021; 68:49-56. [PMID: 33667823 DOI: 10.1016/j.gde.2021.01.011] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 01/09/2021] [Accepted: 01/29/2021] [Indexed: 10/22/2022]
Abstract
The 16p11.2 BP4 and BP5 region, is a recurrent ∼600kb copy number variant (CNV), and deletions are one of the most frequent etiologies of neurodevelopmental disorders and autism spectrum disorder with an incidence of approximately 1/2000. Deletion carriers have delays in early neurodevelopment that most specifically impair speech, phonology and language in 70%. Intelligence quotient is shifted 1.8 standard deviations lower than family controls without the deletion. Other common neurobehavioral conditions include motor coordination difficulties (60%) and autism (20-25%). Unprovoked seizures are common (24%) and readily treated and resolve with age in many. Obesity evolves throughout childhood and by adulthood 75% are obese. Congenital anomalies are more common than the general population. The deletion is associated with an increase in brain volumes across all areas of the brain, changes in the white matter microstructural properties, and early electrophysiological cortical responses from auditory cortex. Studies of genetically defined conditions, particularly CNVs that are not associated with profound disabilities, provide homogeneity to study genetic impact on brain development, structure, and function to better understand complex neurobehavioral phenotypes such as autism.
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Affiliation(s)
- Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY, Simons Foundation, New York, NY, United States.
| | - Timothy Pl Roberts
- Lurie Family Foundations MEG Imaging Center, Dept. of Radiology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, United States
| | - Elliott H Sherr
- Department of Neurology, Weill Institute of Neurosciences, University of California, San Francisco, United States
| | | | - John E Spiro
- Simons Foundation, 160 Fifth Avenue, New York, NY 10010, United States
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29
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Moreau CA, Ching CR, Kumar K, Jacquemont S, Bearden CE. Structural and functional brain alterations revealed by neuroimaging in CNV carriers. Curr Opin Genet Dev 2021; 68:88-98. [PMID: 33812299 PMCID: PMC8205978 DOI: 10.1016/j.gde.2021.03.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 02/01/2021] [Accepted: 03/09/2021] [Indexed: 01/21/2023]
Abstract
Copy Number Variants (CNVs) are associated with elevated rates of neuropsychiatric disorders. A 'genetics-first' approach, involving the CNV effects on the brain, irrespective of clinical symptomatology, allows investigation of mechanisms underlying neuropsychiatric disorders in the general population. Recent years have seen an increasing number of larger multisite neuroimaging studies investigating the effect of CNVs on structural and functional brain endophenotypes. Alterations overlap with those found in idiopathic psychiatric conditions but effect sizes are twofold to fivefold larger. Here we review new CNV-associated structural and functional brain alterations and outline the future of neuroimaging genomics research, with particular emphasis on developing new resources for the study of high-risk CNVs and rare genomic variants.
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Affiliation(s)
- Clara A Moreau
- Sainte-Justine Hospital Research Center, Montreal, Canada; Department of Pediatrics, University of Montreal, Montreal, Canada; Centre de Recherche de l'Institut Universitaire de Gériatrie de Montréal, Montréal, Canada; Human Genetics and Cognitive Functions, CNRS UMR 3571, Université de Paris, Institut Pasteur, Paris, France
| | - Christopher Rk Ching
- Imaging Genetics Center, USC Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of the University of Southern California, USA
| | - Kuldeep Kumar
- Sainte-Justine Hospital Research Center, Montreal, Canada
| | - Sebastien Jacquemont
- Sainte-Justine Hospital Research Center, Montreal, Canada; Department of Pediatrics, University of Montreal, Montreal, Canada.
| | - Carrie E Bearden
- Semel Institute for Neuroscience and Human Behavior, Departments of Psychiatry and Biobehavioral Sciences and Psychology, University of California, Los Angeles, USA.
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30
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Rasile M, Lauranzano E, Mirabella F, Matteoli M. Neurological consequences of neurovascular unit and brain vasculature damages: potential risks for pregnancy infections and COVID-19-babies. FEBS J 2021; 289:3374-3392. [PMID: 33998773 PMCID: PMC8237015 DOI: 10.1111/febs.16020] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 01/08/2023]
Abstract
Intragravidic and perinatal infections, acting through either direct viral effect or immune-mediated responses, are recognized causes of liability for neurodevelopmental disorders in the progeny. The large amounts of epidemiological data and the wealth of information deriving from animal models of gestational infections have contributed to delineate, in the last years, possible underpinning mechanisms for this phenomenon, including defects in neuronal migration, impaired spine and synaptic development, and altered activation of microglia. Recently, dysfunctions of the neurovascular unit and anomalies of the brain vasculature have unexpectedly emerged as potential causes at the origin of behavioral abnormalities and psychiatric disorders consequent to prenatal and perinatal infections. This review aims to discuss the up-to-date literature evidence pointing to the neurovascular unit and brain vasculature damages as the etiological mechanisms in neurodevelopmental syndromes. We focus on the inflammatory events consequent to intragravidic viral infections as well as on the direct viral effects as the potential primary triggers. These authors hope that a timely review of the literature will help to envision promising research directions, also relevant for the present and future COVID-19 longitudinal studies.
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Affiliation(s)
- Marco Rasile
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Italy.,IRCCS Humanitas Clinical and Research Center, Rozzano, Italy
| | | | - Filippo Mirabella
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Italy
| | - Michela Matteoli
- IRCCS Humanitas Clinical and Research Center, Rozzano, Italy.,CNR Institute of Neuroscience, Milano, Italy
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31
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Chiang AH, Chang J, Wang J, Vitkup D. Exons as units of phenotypic impact for truncating mutations in autism. Mol Psychiatry 2021; 26:1685-1695. [PMID: 33110259 DOI: 10.1038/s41380-020-00876-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 08/07/2020] [Accepted: 08/21/2020] [Indexed: 11/09/2022]
Abstract
Autism spectrum disorders (ASD) are a group of related neurodevelopmental diseases displaying significant genetic and phenotypic heterogeneity. Despite recent progress in understanding ASD genetics, the nature of phenotypic heterogeneity across probands remains unclear. Notably, likely gene-disrupting (LGD) de novo mutations affecting the same gene often result in substantially different ASD phenotypes. Nevertheless, we find that truncating mutations affecting the same exon frequently lead to strikingly similar intellectual phenotypes in unrelated ASD probands. Analogous patterns are observed for two independent proband cohorts and several other important ASD-associated phenotypes. We find that exons biased toward prenatal and postnatal expression preferentially contribute to ASD cases with lower and higher IQ phenotypes, respectively. These results suggest that exons, rather than genes, often represent a unit of effective phenotypic impact for truncating mutations in autism. The observed phenotypic patterns are likely mediated by nonsense-mediated decay (NMD) of splicing isoforms, with autism phenotypes usually triggered by relatively mild (15-30%) decreases in overall gene dosage. We find that each ASD gene with recurrent mutations can be characterized by a parameter, phenotype dosage sensitivity (PDS), which quantifies the relationship between changes in a gene's dosage and changes in a given disease phenotype. We further demonstrate analogous relationships between exon LGDs and gene expression changes in multiple human tissues. Therefore, similar phenotypic patterns may be also observed in other human genetic disorders.
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Affiliation(s)
- Andrew H Chiang
- Department of Biomedical Informatics, Columbia University, New York, NY, USA.,Department of Systems Biology, Center for Computational Biology and Bioinformatics, Columbia University, New York, NY, USA
| | - Jonathan Chang
- Department of Biomedical Informatics, Columbia University, New York, NY, USA.,Department of Systems Biology, Center for Computational Biology and Bioinformatics, Columbia University, New York, NY, USA
| | - Jiayao Wang
- Department of Biomedical Informatics, Columbia University, New York, NY, USA.,Department of Systems Biology, Center for Computational Biology and Bioinformatics, Columbia University, New York, NY, USA
| | - Dennis Vitkup
- Department of Biomedical Informatics, Columbia University, New York, NY, USA. .,Department of Systems Biology, Center for Computational Biology and Bioinformatics, Columbia University, New York, NY, USA.
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32
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Al-Jawahiri R, Jones M, Milne E. Spontaneous neural activity relates to psychiatric traits in 16p11.2 CNV carriers: An analysis of EEG spectral power and multiscale entropy. J Psychiatr Res 2021; 136:610-618. [PMID: 33158556 DOI: 10.1016/j.jpsychires.2020.10.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 10/22/2020] [Accepted: 10/26/2020] [Indexed: 11/28/2022]
Abstract
Copy number variations (CNV) at the 16p11.2 chromosomal region are rare high-risk CNVs associated with various clinical features and psychiatric disorders including intellectual disability, developmental delays, and autism spectrum disorder. No study to date has investigated whether spontaneous neural activity is altered for 16p11.2 CNV carriers and whether this relates to psychiatric traits. The aim of this study is to examine the impact of 16p11.2 deletions (del) and duplications (dup) on spontaneous neural activity and its relationship to psychiatric problems. EEG was previously collected as part of the Simons Searchlight initiative. Using spectral power (delta, theta, alpha, and beta frequency bands), complexity index (CI), and multiscale entropy analysis techniques, we analyzed frontal resting-state EEG data collected from 22 16p11.2 del carriers, 14 dup carriers, and 13 controls. We then examined associations between neural activity and psychiatric traits, measured with the Child Behavior Checklist. Results indicated that EEG entropy was higher for del and dup compared to controls, respectively, at all timescales. CI was also higher for del and dup compared to controls. Theta power of 16p11.2 dup carriers was higher than controls. A strong association was found between entropy at higher timescales and anxiety problems. In addition, a strong correlation was found between theta power and pervasive developmental problems. Atypical spontaneous neural activity is implicated in 16p11.2 CNVs. With higher entropy or theta power, psychiatric traits increase in severity. Our findings provide evidence of the link between genotype, neural activity, and phenotypes in 16p11.2 CNVs.
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Affiliation(s)
- Reem Al-Jawahiri
- Department of Psychology, University of Sheffield, United Kingdom.
| | - Myles Jones
- Department of Psychology, University of Sheffield, United Kingdom
| | - Elizabeth Milne
- Department of Psychology, University of Sheffield, United Kingdom
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33
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Linden SC, Watson CJ, Smith J, Chawner SJRA, Lancaster TM, Evans F, Williams N, Skuse D, Raymond FL, Hall J, Owen MJ, Linden DEJ, Green-Snyder L, Chung WK, Maillard AM, Jacquemont S, van den Bree MBM. The psychiatric phenotypes of 1q21 distal deletion and duplication. Transl Psychiatry 2021; 11:105. [PMID: 33542195 PMCID: PMC7862693 DOI: 10.1038/s41398-021-01226-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 01/07/2021] [Accepted: 01/14/2021] [Indexed: 01/06/2023] Open
Abstract
Copy number variants are amongst the most highly penetrant risk factors for psychopathology and neurodevelopmental deficits, but little information about the detailed clinical phenotype associated with particular variants is available. We present the largest study of the microdeletion and -duplication at the distal 1q21 locus, which has been associated with schizophrenia and intellectual disability, in order to investigate the range of psychiatric phenotypes. Clinical and cognitive data from 68 deletion and 55 duplication carriers were analysed with logistic regression analysis to compare frequencies of mental disorders between carrier groups and controls, and linear mixed models to compare quantitative phenotypes. Both children and adults with copy number variants at 1q21 had high frequencies of psychopathology. In the children, neurodevelopmental disorders were most prominent (56% for deletion, 68% for duplication carriers). Adults had increased prevalence of mood (35% for deletion [OR = 6.6 (95% CI: 1.4-40.1)], 55% for duplication carriers [8.3 (1.4-55.5)]) and anxiety disorders (24% [1.8 (0.4-8.4)] and 55% [10.0 (1.9-71.2)]). The adult group, which included mainly genetically affected parents of probands, had an IQ in the normal range. These results confirm high prevalence of neurodevelopmental disorders associated with CNVs at 1q21 but also reveal high prevalence of mood and anxiety disorders in a high-functioning adult group with these CNVs. Because carriers of neurodevelopmental CNVs who show relevant psychopathology but no major cognitive impairment are not currently routinely receiving clinical genetic services widening of genetic testing in psychiatry may be considered.
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Affiliation(s)
- Stefanie C Linden
- Department of Health, Ethics and Society, Care and Public Health Research Institute (CAPHRI), Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
- Division of Psychological Medicine and Clinical Neurosciences, Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Cameron J Watson
- Division of Psychological Medicine and Clinical Neurosciences, Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
- Preventive Neurology Unit, Wolfson Institute of Preventive Medicine, Queen Mary University of London, London, UK
| | - Jacqueline Smith
- Division of Psychological Medicine and Clinical Neurosciences, Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Samuel J R A Chawner
- Division of Psychological Medicine and Clinical Neurosciences, Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Thomas M Lancaster
- Division of Psychological Medicine and Clinical Neurosciences, Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
- School of Psychology, University of Bath, Bath, UK
| | - Ffion Evans
- Division of Psychological Medicine and Clinical Neurosciences, Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Nigel Williams
- Division of Psychological Medicine and Clinical Neurosciences, Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - David Skuse
- Behavioural and Brain Sciences Unit Institute of Child Health, University College London, London, UK
| | - F Lucy Raymond
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Jeremy Hall
- Division of Psychological Medicine and Clinical Neurosciences, Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Michael J Owen
- Division of Psychological Medicine and Clinical Neurosciences, Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - David E J Linden
- Division of Psychological Medicine and Clinical Neurosciences, Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Faculty of Health, Medicine and Live Sciences, Maastricht University, Maastricht, The Netherlands
| | | | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY, USA
| | - Anne M Maillard
- Service des Troubles du Spectre de l'Autisme et apparentés, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
| | - Sébastien Jacquemont
- Service de Génétique Médicale, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Marianne B M van den Bree
- Division of Psychological Medicine and Clinical Neurosciences, Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK.
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34
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Gibbs W, Bell H, Ajith A, Sadtler K, Escuro K, Brooks D, Edwards S. Identification of 16p11.2 deletion syndrome on a child inpatient psychiatric unit: A case report and call for inpatient genetic testing. JOURNAL OF CHILD AND ADOLESCENT PSYCHIATRIC NURSING 2021; 34:133-138. [PMID: 33386643 DOI: 10.1111/jcap.12305] [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] [Received: 04/25/2020] [Revised: 11/28/2020] [Accepted: 12/07/2020] [Indexed: 01/15/2023]
Abstract
PURPOSE This case highlights the importance of nursing-directed interprofessional treatment and inpatient unit genetic testing to identify genetic syndromes that may potentiate psychiatric conditions. SOURCES USED A case study of a 10-year-old Caucasian male with a history of a congenital heart defect, hand malformation, and low academic functioning who was admitted to the child inpatient psychiatric unit for eloping from school, aggression, and possible psychotic symptoms. Data were collected using patient medical records and interprofessional evaluation from nursing, psychiatry, and occupational therapy. RESULTS The patient was treated with risperidone to manage psychotic symptoms. Dietary, occupational therapy, and scholastic plans were also implemented. After discharge, results of genetic microarray analysis revealed a Type 1 16p11.2 deletion. CONCLUSION The role of nursing, interprofessional collaboration, and access to consultation teams play a crucial role in patient care for early diagnosis and treatment. Inpatient genetic testing has the potential to quickly identify and diagnose previously unidentified symptom clusters, leading to early intervention, closer monitoring, and improved patient outcomes.
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Affiliation(s)
- William Gibbs
- Department of Psychiatry, Division of Child and Adolescent Psychiatry, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Harrison Bell
- Department of Psychiatry, Division of Child and Adolescent Psychiatry, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Aniruddh Ajith
- Department of Psychiatry, Division of Child and Adolescent Psychiatry, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Kim Sadtler
- Department of Psychiatry, Division of Child and Adolescent Psychiatry, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Katrina Escuro
- Department of Psychiatry, Division of Child and Adolescent Psychiatry, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Deborah Brooks
- Department of Psychiatry, Division of Child and Adolescent Psychiatry, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Sarah Edwards
- Department of Psychiatry, Division of Child and Adolescent Psychiatry, University of Maryland School of Medicine, Baltimore, Maryland, USA
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35
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Kimura H, Mori D, Aleksic B, Ozaki N. Elucidation of molecular pathogenesis and drug development for psychiatric disorders from rare disease-susceptibility variants. Neurosci Res 2020; 170:24-31. [PMID: 33316300 DOI: 10.1016/j.neures.2020.11.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/19/2020] [Accepted: 11/26/2020] [Indexed: 10/22/2022]
Abstract
Recent rapid progress in genome analysis and large-scale consortia has made it possible to discover variants with a variety of allele frequencies and effect sizes associated with psychiatric disorders. Among psychiatric disorder-susceptibility variants, rare variants with large effect sizes detected by sequencing analysis or array comparative genomic hybridization would be particularly useful for elucidating pathophysiology by developing disease models, such as genome-edited mouse or induced pluripotent stem cells. In the last decade, investigations of rare variants with large effect size have revealed an important role of neurodevelopment in the pathogenesis of psychiatric disorders. In future research, integration of recent evidence concerning the contribution of the immune system or gut microbiota will enhance our understanding of psychiatric disorders and facilitate novel drug development.
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Affiliation(s)
- Hiroki Kimura
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan.
| | - Daisuke Mori
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan; Brain & Mind Research Center, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Branko Aleksic
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Norio Ozaki
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan; Brain & Mind Research Center, Nagoya University Graduate School of Medicine, Nagoya, Japan; Medical Genomics Center, Nagoya University Hospital, Nagoya, Japan
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36
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Oliva-Teles N, de Stefano MC, Gallagher L, Rakic S, Jorge P, Cuturilo G, Markovska-Simoska S, Borg I, Wolstencroft J, Tümer Z, Harwood AJ, Kodra Y, Skuse D. Rare Pathogenic Copy Number Variation in the 16p11.2 (BP4-BP5) Region Associated with Neurodevelopmental and Neuropsychiatric Disorders: A Review of the Literature. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:E9253. [PMID: 33321999 PMCID: PMC7763014 DOI: 10.3390/ijerph17249253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/24/2020] [Accepted: 12/05/2020] [Indexed: 11/17/2022]
Abstract
Copy number variants (CNVs) play an important role in the genetic underpinnings of neuropsychiatric/neurodevelopmental disorders. The chromosomal region 16p11.2 (BP4-BP5) harbours both deletions and duplications that are associated in carriers with neurodevelopmental and neuropsychiatric conditions as well as several rare disorders including congenital malformation syndromes. The aim of this article is to provide a review of the current knowledge of the diverse neurodevelopmental disorders (NDD) associated with 16p11.2 deletions and duplications reported in published cohorts. A literature review was conducted using the PubMed/MEDLINE electronic database limited to papers published in English between 1 January 2010 and 31 July 2020, describing 16p11.2 deletions and duplications carriers' cohorts. Twelve articles meeting inclusion criteria were reviewed from the 75 articles identified by the search. Of these twelve papers, eight described both deletions and duplications, three described deletions only and one described duplications only. This study highlights the heterogeneity of NDD descriptions of the selected cohorts and inconsistencies concerning accuracy of data reporting.
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Affiliation(s)
- Natália Oliva-Teles
- Centro de Genética Médica Doutor Jacinto Magalhães/Centro Hospitalar Universitário do Porto, 4099-001 Porto, Portugal;
- Unit for Multidisciplinary Research in Biomedicine, Institute of Biomedical Sciences Abel Salazar, University of Porto (UMIB/ICBAS/UP), 4050-313 Porto, Portugal
| | - Maria Chiara de Stefano
- Italian National Transplant Center, Italian National Institute of Health, 00161 Rome, Italy;
| | - Louise Gallagher
- Trinity Institute of Neurosciences, Trinity College Dublin, University of Dublin, 152-160 Dublin, Ireland;
| | - Severin Rakic
- Public Health Institute of Republic of Srpska, 78000 Banja Luka, Bosnia and Herzegovina;
| | - Paula Jorge
- Centro de Genética Médica Doutor Jacinto Magalhães/Centro Hospitalar Universitário do Porto, 4099-001 Porto, Portugal;
- Unit for Multidisciplinary Research in Biomedicine, Institute of Biomedical Sciences Abel Salazar, University of Porto (UMIB/ICBAS/UP), 4050-313 Porto, Portugal
| | - Goran Cuturilo
- Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia;
- Department of Medical Genetics, University Children’s Hospital, Tirsova 10, 11000 Belgrade, Serbia
| | | | - Isabella Borg
- Department of Pathology, Faculty of Medicine and Surgery, University of Malta, MSD 2080 Msida, Malta;
- Medical Genetics Unit, Mater Dei Hospital, MSD 2090 L-Imsida, Malta
| | - Jeanne Wolstencroft
- UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; (J.W.); (D.S.)
| | - Zeynep Tümer
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, 2100 Copenhangen, Denmark;
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Adrian J. Harwood
- Neuroscience and Mental Health Research Institute (NMHRI), & School of Biosciences, Cardiff University, Cardiff CF24 4HQ, UK;
| | - Yllka Kodra
- National Centre for Rare Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy;
| | - David Skuse
- UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; (J.W.); (D.S.)
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37
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Leblanc E, Washington P, Varma M, Dunlap K, Penev Y, Kline A, Wall DP. Feature replacement methods enable reliable home video analysis for machine learning detection of autism. Sci Rep 2020; 10:21245. [PMID: 33277527 PMCID: PMC7719177 DOI: 10.1038/s41598-020-76874-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 11/02/2020] [Indexed: 12/15/2022] Open
Abstract
Autism Spectrum Disorder is a neuropsychiatric condition affecting 53 million children worldwide and for which early diagnosis is critical to the outcome of behavior therapies. Machine learning applied to features manually extracted from readily accessible videos (e.g., from smartphones) has the potential to scale this diagnostic process. However, nearly unavoidable variability in video quality can lead to missing features that degrade algorithm performance. To manage this uncertainty, we evaluated the impact of missing values and feature imputation methods on two previously published autism detection classifiers, trained on standard-of-care instrument scoresheets and tested on ratings of 140 children videos from YouTube. We compare the baseline method of listwise deletion to classic univariate and multivariate techniques. We also introduce a feature replacement method that, based on a score, selects a feature from an expanded dataset to fill-in the missing value. The replacement feature selected can be identical for all records (general) or automatically adjusted to the record considered (dynamic). Our results show that general and dynamic feature replacement methods achieve a higher performance than classic univariate and multivariate methods, supporting the hypothesis that algorithmic management can maintain the fidelity of video-based diagnostics in the face of missing values and variable video quality.
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Affiliation(s)
- Emilie Leblanc
- Department of Pediatrics, Stanford University, Palo Alto, CA, 94305, USA
| | - Peter Washington
- Department of Bioengineering, Stanford University, Palo Alto, CA, 94305, USA
| | - Maya Varma
- Department of Computer Science, Stanford University, Palo Alto, CA, 94305, USA
| | - Kaitlyn Dunlap
- Department of Pediatrics, Stanford University, Palo Alto, CA, 94305, USA
- Department of Biomedical Data Science, Stanford University, Palo Alto, CA, 94305, USA
| | - Yordan Penev
- Department of Pediatrics, Stanford University, Palo Alto, CA, 94305, USA
- Department of Biomedical Data Science, Stanford University, Palo Alto, CA, 94305, USA
| | - Aaron Kline
- Department of Pediatrics, Stanford University, Palo Alto, CA, 94305, USA
- Department of Biomedical Data Science, Stanford University, Palo Alto, CA, 94305, USA
| | - Dennis P Wall
- Department of Pediatrics, Stanford University, Palo Alto, CA, 94305, USA.
- Department of Biomedical Data Science, Stanford University, Palo Alto, CA, 94305, USA.
- Department of Psychiatry and Behavioral Sciences (by courtesy), Stanford University, Palo Alto, CA, 94305, USA.
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38
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Moreau CA, Urchs SGW, Kuldeep K, Orban P, Schramm C, Dumas G, Labbe A, Huguet G, Douard E, Quirion PO, Lin A, Kushan L, Grot S, Luck D, Mendrek A, Potvin S, Stip E, Bourgeron T, Evans AC, Bearden CE, Bellec P, Jacquemont S. Mutations associated with neuropsychiatric conditions delineate functional brain connectivity dimensions contributing to autism and schizophrenia. Nat Commun 2020; 11:5272. [PMID: 33077750 PMCID: PMC7573583 DOI: 10.1038/s41467-020-18997-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 09/21/2020] [Indexed: 12/13/2022] Open
Abstract
16p11.2 and 22q11.2 Copy Number Variants (CNVs) confer high risk for Autism Spectrum Disorder (ASD), schizophrenia (SZ), and Attention-Deficit-Hyperactivity-Disorder (ADHD), but their impact on functional connectivity (FC) remains unclear. Here we report an analysis of resting-state FC using magnetic resonance imaging data from 101 CNV carriers, 755 individuals with idiopathic ASD, SZ, or ADHD and 1,072 controls. We characterize CNV FC-signatures and use them to identify dimensions contributing to complex idiopathic conditions. CNVs have large mirror effects on FC at the global and regional level. Thalamus, somatomotor, and posterior insula regions play a critical role in dysconnectivity shared across deletions, duplications, idiopathic ASD, SZ but not ADHD. Individuals with higher similarity to deletion FC-signatures exhibit worse cognitive and behavioral symptoms. Deletion similarities identified at the connectivity level could be related to the redundant associations observed genome-wide between gene expression spatial patterns and FC-signatures. Results may explain why many CNVs affect a similar range of neuropsychiatric symptoms.
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Affiliation(s)
- Clara A Moreau
- Sainte Justine Hospital Research Center, University of Montreal, 3175 Chemin de la Côte-Sainte-Catherine, Montreal, QC, H3T 1C5, Canada.
- Centre de Recherche de l'Institut Universitaire de Gériatrie de Montréal, 4565 Queen Mary Rd, Montreal, QC, H3W 1W5, Canada.
| | - Sebastian G W Urchs
- Centre de Recherche de l'Institut Universitaire de Gériatrie de Montréal, 4565 Queen Mary Rd, Montreal, QC, H3W 1W5, Canada.
- Montreal Neurological Institute and Hospital, McGill University, 3801 Rue de l'Université, Montreal, QC, H3A 2B4, Canada.
| | - Kumar Kuldeep
- Sainte Justine Hospital Research Center, University of Montreal, 3175 Chemin de la Côte-Sainte-Catherine, Montreal, QC, H3T 1C5, Canada
| | - Pierre Orban
- Centre de Recherche de l'Institut Universitaire en Santé Mentale de Montréal, 7401 Rue Hochelaga, Montreal, QC, H1N 3M5, Canada
- Département de Psychiatrie et d'Addictologie, Université de Montréal, Pavillon Roger-Gaudry, C.P. 6128, succursale Centre-ville, Montreal, QC, H3C 3J7, Canada
| | - Catherine Schramm
- Sainte Justine Hospital Research Center, University of Montreal, 3175 Chemin de la Côte-Sainte-Catherine, Montreal, QC, H3T 1C5, Canada
- Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Chemin de la Côte-Sainte-Catherine, Montreal, QC, H3T 1E2, Canada
| | - Guillaume Dumas
- Sainte Justine Hospital Research Center, University of Montreal, 3175 Chemin de la Côte-Sainte-Catherine, Montreal, QC, H3T 1C5, Canada
- Human Genetics and Cognitive Functions, Institut Pasteur, Université de Paris, UMR3571 CNRS, Paris, France
| | - Aurélie Labbe
- Département des Sciences de la Décision, HEC, 3000, chemin de la Côte-Sainte-Catherine, Montreal, QC, H3T 2A7, Canada
| | - Guillaume Huguet
- Sainte Justine Hospital Research Center, University of Montreal, 3175 Chemin de la Côte-Sainte-Catherine, Montreal, QC, H3T 1C5, Canada
| | - Elise Douard
- Sainte Justine Hospital Research Center, University of Montreal, 3175 Chemin de la Côte-Sainte-Catherine, Montreal, QC, H3T 1C5, Canada
| | - Pierre-Olivier Quirion
- Centre de Recherche de l'Institut Universitaire de Gériatrie de Montréal, 4565 Queen Mary Rd, Montreal, QC, H3W 1W5, Canada
- Canadian Center for Computational Genomics, McGill University and Genome Quebec Innovation Center 740, Dr. Penfield Avenue, H3A 0G1, Montreal, Canada
| | - Amy Lin
- Semel Institute for Neuroscience and Human Behavior and Department of Psychology, University of California, Los Angeles, Semel Institute/NPI, 760 Westwood Plaza, Los Angeles, CA, 90024, USA
| | - Leila Kushan
- Semel Institute for Neuroscience and Human Behavior and Department of Psychology, University of California, Los Angeles, Semel Institute/NPI, 760 Westwood Plaza, Los Angeles, CA, 90024, USA
| | - Stephanie Grot
- Centre de Recherche de l'Institut Universitaire en Santé Mentale de Montréal, 7401 Rue Hochelaga, Montreal, QC, H1N 3M5, Canada
- Département de Psychiatrie et d'Addictologie, Université de Montréal, Pavillon Roger-Gaudry, C.P. 6128, succursale Centre-ville, Montreal, QC, H3C 3J7, Canada
| | - David Luck
- Sainte Justine Hospital Research Center, University of Montreal, 3175 Chemin de la Côte-Sainte-Catherine, Montreal, QC, H3T 1C5, Canada
| | - Adrianna Mendrek
- Department of Psychology, Bishop's University, 2600 College Street, Sherbrooke, QC, J1M IZ7, Canada
| | - Stephane Potvin
- Département de Psychiatrie et d'Addictologie, Université de Montréal, Pavillon Roger-Gaudry, C.P. 6128, succursale Centre-ville, Montreal, QC, H3C 3J7, Canada
| | - Emmanuel Stip
- Département de Psychiatrie et d'Addictologie, Université de Montréal, Pavillon Roger-Gaudry, C.P. 6128, succursale Centre-ville, Montreal, QC, H3C 3J7, Canada
- United Arab Emirates University, College of Medicine and health Sciences, PO 17666, Al Ain, QC, UAE
| | - Thomas Bourgeron
- Human Genetics and Cognitive Functions, Institut Pasteur, Université de Paris, UMR3571 CNRS, Paris, France
| | - Alan C Evans
- Montreal Neurological Institute and Hospital, McGill University, 3801 Rue de l'Université, Montreal, QC, H3A 2B4, Canada
| | - Carrie E Bearden
- Semel Institute for Neuroscience and Human Behavior and Department of Psychology, University of California, Los Angeles, Semel Institute/NPI, 760 Westwood Plaza, Los Angeles, CA, 90024, USA
| | - Pierre Bellec
- Centre de Recherche de l'Institut Universitaire de Gériatrie de Montréal, 4565 Queen Mary Rd, Montreal, QC, H3W 1W5, Canada
| | - Sebastien Jacquemont
- Sainte Justine Hospital Research Center, University of Montreal, 3175 Chemin de la Côte-Sainte-Catherine, Montreal, QC, H3T 1C5, Canada.
- Department of Pediatrics, University of Montreal, 3175 Chemin de la Côte-Sainte-Catherine, Montreal, QC, H3T 1C5, Canada.
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Kim SH, Green-Snyder L, Lord C, Bishop S, Steinman KJ, Bernier R, Hanson E, Goin-Kochel RP, Chung WK. Language characterization in 16p11.2 deletion and duplication syndromes. Am J Med Genet B Neuropsychiatr Genet 2020; 183:380-391. [PMID: 32652891 PMCID: PMC8939307 DOI: 10.1002/ajmg.b.32809] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/29/2020] [Accepted: 06/01/2020] [Indexed: 11/12/2022]
Abstract
Expressive language impairment is one of the most frequently associated clinical features of 16p11.2 copy number variations (CNV). However, our understanding of the language profiles of individuals with 16p11.2 CNVs is still limited. This study builds upon previous work in the Simons Variation in Individuals Project (VIP, now known as Simons Searchlight), to characterize language abilities in 16p11.2 deletion and duplication carriers using comprehensive assessments. Participants included 110 clinically ascertained children and family members (i.e., siblings and cousins) with 16p11.2 BP4-BP5 deletion and 58 with 16p11.2 BP4-BP5 duplication between the ages of 2-23 years, most of whom were verbal. Regression analyses were performed to quantify variation in language abilities in the presence of the 16p11.2 deletion and duplication, both with and without autism spectrum disorder (ASD) and cognitive deficit. Difficulties in pragmatic skills were equally prevalent in verbal individuals in both deletion and duplication groups. NVIQ had moderate quantifiable effects on language scores in syntax and semantics/pragmatics (a decrease of less than 1 SD) for both groups. Overall, language impairments persisted even after controlling for ASD diagnosis and cognitive deficit. Language impairment is one of the core clinical features of individuals with 16p11.2 CNVs even in the absence of ASD and cognitive deficit. Results highlight the need for more comprehensive and rigorous assessment of language impairments to maximize outcomes in carriers of 16p11.2 CNVs.
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Affiliation(s)
- So Hyun Kim
- Department of Psychiatry, Weill Cornell Medicine, White Plains, New York, USA
| | | | - Catherine Lord
- Semel Institute for Neuroscience and Behavior, University of California Los Angeles, California, Los Angeles, USA
| | - Somer Bishop
- Department of Psychiatry, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, California, USA
| | - Kyle J. Steinman
- Department of Neurology, Seattle Children’s Hospital, University of Washington, Seattle, Washington, USA,Department of Pediatrics, Seattle Children’s Hospital, University of Washington, Seattle, Washington, USA,Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, Washington, USA
| | - Raphael Bernier
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, Washington, USA
| | - Ellen Hanson
- Developmental Medicine, Boston Children’s Hospital/Harvard Medical School, Boston, Massachusetts, USA
| | | | - Wendy K. Chung
- Simons Foundation, New York, New York, USA,Department of Pediatrics, Columbia University, New York, New York, USA,Department of Medicine, Columbia University, New York, New York, USA
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40
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Lin A, Vajdi A, Kushan-Wells L, Helleman G, Hansen LP, Jonas RK, Jalbrzikowski M, Kingsbury L, Raznahan A, Bearden CE. Reciprocal Copy Number Variations at 22q11.2 Produce Distinct and Convergent Neurobehavioral Impairments Relevant for Schizophrenia and Autism Spectrum Disorder. Biol Psychiatry 2020; 88:260-272. [PMID: 32143830 PMCID: PMC7354903 DOI: 10.1016/j.biopsych.2019.12.028] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 12/12/2019] [Accepted: 12/30/2019] [Indexed: 01/09/2023]
Abstract
BACKGROUND 22q11.2 deletions and duplications are copy number variations (CNVs) that predispose to developmental neuropsychiatric disorders. Both CNVs are associated with autism spectrum disorder (ASD), while the deletion confers disproportionate risk for schizophrenia. Neurobehavioral profiles associated with these reciprocal CNVs in conjunction with brain imaging measures have not been reported. METHODS We profiled the impact of 22q11.2 CNVs on neurobehavioral measures relevant to ASD and psychosis in 106 22q11.2 deletion carriers, 38 22q11.2 duplication carriers, and 82 demographically matched healthy control subjects. To determine whether brain-behavior relationships were altered in CNV carriers, we further tested for interactions between group and regional brain structure on neurobehavioral domains. RESULTS Cognitive deficits were observed in both CNV groups, with the lowest IQs in deletion carriers. ASD and dimensionally measured ASD traits were elevated in both CNV groups; however, duplication carriers exhibited increased stereotypies compared to deletion carriers. Moreover, discriminant analysis using ASD subdomains distinguished between CNV cases with 76% accuracy. Both psychotic disorder diagnosis and dimensionally measured positive and negative symptoms were elevated in deletion carriers. Finally, healthy control subjects showed an inverse relationship between processing speed and cortical thickness in heteromodal association areas, which was absent in both CNV groups. CONCLUSIONS 22q11.2 CNVs differentially modulate intellectual functioning and psychosis-related symptomatology but converge on broad ASD-related symptomatology. However, subtle differences in ASD profiles distinguish CNV groups. Processing speed impairments, coupled with the lack of normative relationship between processing speed and cortical thickness in CNV carriers, implicate aberrant development of the cortical mantle in the pathology underlying impaired processing speed ability.
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Affiliation(s)
- Amy Lin
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, California
| | - Ariana Vajdi
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, California
| | - Leila Kushan-Wells
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, California
| | - Gerhard Helleman
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, California
| | - Laura Pacheco Hansen
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, California
| | - Rachel K Jonas
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, California
| | - Maria Jalbrzikowski
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Lyle Kingsbury
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, California; Department of Neurobiology, University of California, Los Angeles, Los Angeles, California
| | - Armin Raznahan
- Developmental Neurogenomics Unit, Human Genetics Branch, National Institute of Mental Health, Bethesda, Maryland
| | - Carrie E Bearden
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, California; Department of Psychology, University of California, Los Angeles, Los Angeles, California.
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41
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Hong SJ, Vogelstein JT, Gozzi A, Bernhardt BC, Yeo BTT, Milham MP, Di Martino A. Toward Neurosubtypes in Autism. Biol Psychiatry 2020; 88:111-128. [PMID: 32553193 DOI: 10.1016/j.biopsych.2020.03.022] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 03/25/2020] [Accepted: 03/28/2020] [Indexed: 12/22/2022]
Abstract
There is a consensus that substantial heterogeneity underlies the neurobiology of autism spectrum disorder (ASD). As such, it has become increasingly clear that a dissection of variation at the molecular, cellular, and brain network domains is a prerequisite for identifying biomarkers. Neuroimaging has been widely used to characterize atypical brain patterns in ASD, although findings have varied across studies. This is due, at least in part, to a failure to account for neurobiological heterogeneity. Here, we summarize emerging data-driven efforts to delineate more homogeneous ASD subgroups at the level of brain structure and function-that is, neurosubtyping. We break this pursuit into key methodological steps: the selection of diagnostic samples, neuroimaging features, algorithms, and validation approaches. Although preliminary and methodologically diverse, current studies generally agree that at least 2 to 4 distinct ASD neurosubtypes may exist. Their identification improved symptom prediction and diagnostic label accuracy above and beyond group average comparisons. Yet, this nascent literature has shed light onto challenges and gaps. These include 1) the need for wider and more deeply transdiagnostic samples collected while minimizing artifacts (e.g., head motion), 2) quantitative and unbiased methods for feature selection and multimodal fusion, 3) greater emphasis on algorithms' ability to capture hybrid dimensional and categorical models of ASD, and 4) systematic independent replications and validations that integrate different units of analyses across multiple scales. Solutions aimed to address these challenges and gaps are discussed for future avenues leading toward a comprehensive understanding of the mechanisms underlying ASD heterogeneity.
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Affiliation(s)
- Seok-Jun Hong
- Center for the Developing Brain, Child Mind Institute, New York
| | - Joshua T Vogelstein
- Department of Biomedical Engineering Institute for Computational Medicine, Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, Maryland
| | - Alessandro Gozzi
- Functional Neuroimaging Laboratory, Center for Neuroscience and Cognitive Systems, Istituto Italiano di Tecnologia, Rovereto, Italy
| | - Boris C Bernhardt
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada
| | - B T Thomas Yeo
- Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, Massachusetts; Department of Electrical and Computer Engineering, Center for Sleep and Cognition, Clinical Imaging Research Centre, N.1 Institute for Health, National University of Singapore; NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore; Centre for Cognitive Neuroscience, Duke-NUS Medical School, Singapore
| | - Michael P Milham
- Center for the Developing Brain, Child Mind Institute, New York; Center for Biomedical Imaging and Neuromodulation, Nathan Kline Institute, Orangeburg, New York
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42
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Hudac CM, Bove J, Barber S, Duyzend M, Wallace A, Martin CL, Ledbetter DH, Hanson E, Goin-Kochel RP, Green-Snyder L, Chung WK, Eichler EE, Bernier RA. Evaluating heterogeneity in ASD symptomatology, cognitive ability, and adaptive functioning among 16p11.2 CNV carriers. Autism Res 2020; 13:1300-1310. [PMID: 32597026 DOI: 10.1002/aur.2332] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 05/29/2020] [Accepted: 06/03/2020] [Indexed: 01/09/2023]
Abstract
Individuals with 16p11.2 copy number variant (CNV) show considerable phenotypic heterogeneity. Although autism spectrum disorder (ASD) is reported in approximately 20-23% of individuals with 16p11.2 CNVs, ASD-associated symptoms are observed in those without a clinical ASD diagnosis. Previous work has shown that genetic variation and prenatal and perinatal birth complications influence ASD risk and symptom severity. This study examined the impact of genetic and environmental risk factors on phenotypic heterogeneity among 16p11.2 CNV carriers. Participants included individuals with a 16p11.2 deletion (N = 96) or duplication (N = 77) with exome sequencing from the Simons VIP study. The presence of prenatal factors, perinatal events, additional genetic events, and gender was studied. Regression analyses examined the contribution of each risk factor on ASD symptomatology, cognitive functioning, and adaptive abilities. For deletion carriers, perinatal and additional genetic events were associated with increased ASD symptomatology and decrements in cognitive and adaptive functioning. For duplication carriers, secondary genetic events were associated with greater cognitive impairments. Being female sex was a protective factor for both deletion and duplication carriers. Our findings suggest that ASD-associated risk factors contribute to the variability in symptom presentation in individuals with 16p11.2 CNVs. LAY SUMMARY: There are a wide range of autism spectrum disorder (ASD) symptoms and abilities observed for individuals with genetic changes of the 16p11.2 region. Here, we found perinatal complications contributed to more severe ASD symptoms (deletion carriers) and additional genetic mutations contributed to decreased cognitive abilities (deletion and duplication carriers). A potential protective factor was also observed for females with 16p11.2 variations. Autism Res 2020, 13: 1300-1310. © 2020 International Society for Autism Research, Wiley Periodicals, Inc.
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Affiliation(s)
- Caitlin M Hudac
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, Washington, USA.,Center for Youth Development and Intervention and Department of Psychology at University of Alabama, Tuscaloosa, Alabama, USA
| | - Joanna Bove
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Shelley Barber
- Department of School Psychology, University of Washington, Seattle, Washington, USA
| | - Michael Duyzend
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Ari Wallace
- Department of School Psychology, University of Washington, Seattle, Washington, USA
| | - Christa Lese Martin
- Autism and Developmental Medicine Institute, Geisinger, Danville, Pennsylvania, USA
| | - David H Ledbetter
- Autism and Developmental Medicine Institute, Geisinger, Danville, Pennsylvania, USA
| | - Ellen Hanson
- Developmental Medicine, Children's Hospital Boston/Harvard Medical School, Boston, Massachusetts, USA
| | | | | | - Wendy K Chung
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA.,Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Raphael A Bernier
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, Washington, USA
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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 PMCID: PMC7958308 DOI: 10.1080/02739615.2020.1741361] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [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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Ernst C. A roadmap for neurodevelopmental disease modeling for non-stem cell biologists. Stem Cells Transl Med 2020; 9:567-574. [PMID: 32052596 PMCID: PMC7180294 DOI: 10.1002/sctm.19-0344] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 01/23/2020] [Indexed: 02/06/2023] Open
Abstract
Stem and derivative cells induced from somatic tissues are a critical tool for disease modeling but significant technical hurdles hamper their use. The purpose of this review is to provide an overview of pitfalls and mitigation strategies for the nonstem cell biologist using induced pluripotent stem cells and investigating neurodevelopmental disorders. What sample sizes are reasonable? What derivation and purification protocols should be used to make human neurons? In what way should gene editing technologies be used to support discoveries? What kinds of preclinical studies are the most feasible? It is hoped that this roadmap will provide the necessary details for experimental planning and execution for those less familiar in the area of stem cell disease modeling. High-quality human preclinical models will allow for the discovery of molecular and cellular phenotypes specific to different neurodevelopmental disorders, and may provide the assays to advance translational medicine for unmet medical needs.
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Affiliation(s)
- Carl Ernst
- Department of Human Genetics, McGill University and Douglas Hospital Research Institute, Montreal, Quebec, Canada.,Department of Psychiatry, McGill University and Douglas Hospital Research Institute, Montreal, Quebec, Canada.,Department of Neurology and Neurosurgery, McGill University and Douglas Hospital Research Institute, Montreal, Quebec, Canada
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45
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Abnormal Auditory Mismatch Fields in Children and Adolescents With 16p11.2 Deletion and 16p11.2 Duplication. BIOLOGICAL PSYCHIATRY: COGNITIVE NEUROSCIENCE AND NEUROIMAGING 2020; 5:942-950. [PMID: 32033921 DOI: 10.1016/j.bpsc.2019.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 11/02/2019] [Accepted: 11/04/2019] [Indexed: 11/23/2022]
Abstract
BACKGROUND Individuals with either deletion or duplication of the BP4-BP5 segment of chromosome 16p11.2 have varied behavioral phenotypes that may include autistic features, mild to moderate intellectual disability, and/or language impairment. However, the neurophysiological correlates of auditory language discrimination processing in individuals with 16p11.2 deletion and 16p11.2 duplication have not been investigated. METHODS Magnetoencephalography was used to measure magnetic mismatch fields (MMFs) arising from the left and right superior temporal gyrus during an auditory oddball paradigm with vowel stimuli (/a/ and /u/) in children and adolescents with 16p11.2 deletion or 16p11.2 duplication and in typically developing peers. One hundred twenty-eight participants ranging from 7 to 17 years of age were included in the final analysis (typically developing: n = 61, 12.08 ± 2.50 years of age; 16p11.2 deletion: n = 45, 11.28 ± 2.51 years of age; and 16p11.2 duplication: n = 22, 10.73 ± 2.49 years of age). RESULTS Delayed MMF latencies were found in both 16p11.2 deletion and 16p11.2 duplication groups compared with typically developing subjects. In addition, these delayed MMF latencies were associated with language and cognitive ability, with prolonged latency predicting greater impairment. CONCLUSIONS Our findings suggest that auditory MMF response delays are associated with clinical severity of language and cognitive impairment in individuals with either 16p11.2 deletion or 16p11.2 duplication, indicating a correlate of their shared/overlapping behavioral phenotype (and not a correlate of gene dosage).
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New Horizons for Molecular Genetics Diagnostic and Research in Autism Spectrum Disorder. ADVANCES IN NEUROBIOLOGY 2020; 24:43-81. [PMID: 32006356 DOI: 10.1007/978-3-030-30402-7_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Autism spectrum disorder (ASD) is a highly heritable, heterogeneous, and complex pervasive neurodevelopmental disorder (PND) characterized by distinctive abnormalities of human cognitive functions, social interaction, and speech development.Nowadays, several genetic changes including chromosome abnormalities, genetic variations, transcriptional epigenetics, and noncoding RNA have been identified in ASD. However, the association between these genetic modifications and ASDs has not been confirmed yet.The aim of this review is to summarize the key findings in ASD from genetic viewpoint that have been identified from the last few decades of genetic and molecular research.
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Escher J, Ford LD. General anesthesia, germ cells and the missing heritability of autism: an urgent need for research. ENVIRONMENTAL EPIGENETICS 2020; 6:dvaa007. [PMID: 32704384 PMCID: PMC7368377 DOI: 10.1093/eep/dvaa007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 03/31/2020] [Accepted: 04/14/2020] [Indexed: 05/08/2023]
Abstract
Agents of general anesthesia (GA) are commonly employed in surgical, dental and diagnostic procedures to effectuate global suppression of the nervous system, but in addition to somatic targets, the subject's germ cells-from the embryonic primordial stage to the mature gametes-may likewise be exposed. Although GA is generally considered safe for most patients, evidence has accumulated that various compounds, in particular the synthetic volatile anesthetic gases (SVAGs) such as sevoflurane, can exert neurotoxic, genotoxic and epigenotoxic effects, with adverse consequences for cellular and genomic function in both somatic and germline cells. The purpose of this paper is to review the evidence demonstrating that GA, and in particular, SVAGs, may in some circumstances adversely impact the molecular program of germ cells, resulting in brain and behavioral pathology in the progeny born of the exposed cells. Further, we exhort the medical and scientific communities to undertake comprehensive experimental and epidemiological research programs to address this critical gap in risk assessment.
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Affiliation(s)
- Jill Escher
- Correspondence address. Escher Fund for Autism, 1590 Calaveras Avenue, San Jose, CA 95126, USA. E-mail:
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Cárdenas-de-la-Parra A, Martin-Brevet S, Moreau C, Rodriguez-Herreros B, Fonov VS, Maillard AM, Zürcher NR, Hadjikhani N, Beckmann JS, Reymond A, Draganski B, Jacquemont S, Collins DL, Addor MC, Andrieux J, Arveiler B, Baujatm G, Sloan-Bénan F, Belfiore M, Bonneau D, Bouquillon S, Boute O, Brusco A, Busa T, Caberg JH, Campion D, Colombert V, Cordier MP, David A, Debray FG, Delrue MA, Doco-Fenzy M, Dunkhase-Heinl U, Edery P, Fagerberg C, Faivre L, Forzano F, Genevieve D, Gérard M, Giachino D, Guichet A, Guillin O, Héron D, Isidor B, Jacquette A, Jaillard S, Journel H, Keren B, Lacombe D, Lebon S, Le Caignec C, Lemaître MP, Lespinasse J, Mathieu-Dramart M, Mercier S, Mignot C, Missirian C, Petit F, Pilekær Sørensen K, Pinson L, Plessis G, Prieur F, Rooryck-Thambo C, Rossi M, Sanlaville D, Schlott Kristiansen B, Schluth-Bolard C, Till M, Van Haelst M, Van Maldergem L. Developmental trajectories of neuroanatomical alterations associated with the 16p11.2 Copy Number Variations. Neuroimage 2019; 203:116155. [DOI: 10.1016/j.neuroimage.2019.116155] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 08/23/2019] [Accepted: 09/02/2019] [Indexed: 01/18/2023] Open
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Jutla A, Turner JB, Green Snyder L, Chung WK, Veenstra-VanderWeele J. Psychotic symptoms in 16p11.2 copy-number variant carriers. Autism Res 2019; 13:187-198. [PMID: 31724820 DOI: 10.1002/aur.2232] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 09/09/2019] [Accepted: 09/26/2019] [Indexed: 01/26/2023]
Abstract
16p11.2 copy-number variation (CNV) is implicated in neurodevelopmental disorders, with the duplication and deletion associated with autism spectrum disorder (ASD) and the duplication associated with schizophrenia (SCZ). The 16p11.2 CNV may therefore provide insight into the relationship between ASD and SCZ, distinct disorders that co-occur at an elevated rate, and are difficult to distinguish from each other and from common co-occurring diagnoses such as obsessive compulsive disorder (OCD), itself a potential risk factor for SCZ. As psychotic symptoms are core to SCZ but distinct from ASD, we sought to examine their predictors in a population (n = 546) of 16p11.2 CNV carriers and their noncarrier siblings recruited by the Simons Variation in Individuals Project. We hypothesized that psychotic symptoms would be most common in duplication carriers followed by deletion carriers and noncarriers, that an ASD diagnosis would predict psychotic symptoms among CNV carriers, and that OCD symptoms would predict psychotic symptoms among all participants. Using data collected across multiple measures, we identified 19 participants with psychotic symptoms. Logistic regression models adjusting for biological sex, age, and IQ found that 16p11.2 duplication and ASD diagnosis predicted psychotic symptom presence. Our findings suggest that the association between 16p11.2 duplication and psychotic symptoms is independent of ASD diagnosis and that ASD diagnosis and psychotic symptoms may be associated in 16p11.2 CNV carriers. Autism Res 2020, 13: 187-198. © 2019 International Society for Autism Research, Wiley Periodicals, Inc. LAY SUMMARY: Either deletion or duplication at chromosome 16p11.2 raises the risk of autism spectrum disorder, and duplication, but not deletion, has been reported in schizophrenia (SCZ). In a sample of 16p11.2 deletion and duplication carriers, we found that having the duplication or having an autism diagnosis may increase the risk of psychosis, a key feature of SCZ.
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Affiliation(s)
- Amandeep Jutla
- Department of Psychiatry, Columbia University, New York, New York.,New York State Psychiatric Institute, New York, New York
| | - J Blake Turner
- Department of Psychiatry, Columbia University, New York, New York.,New York State Psychiatric Institute, New York, New York
| | | | - Wendy K Chung
- Department of Pediatrics and Department of Medicine, Columbia University, New York, New York
| | - Jeremy Veenstra-VanderWeele
- Department of Psychiatry, Columbia University, New York, New York.,New York State Psychiatric Institute, New York, New York.,Center for Autism and the Developing Brain, New York-Presbyterian Hospital, New York, New York
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Sanders SJ, Sahin M, Hostyk J, Thurm A, Jacquemont S, Avillach P, Douard E, Martin CL, Modi ME, Moreno-De-Luca A, Raznahan A, Anticevic A, Dolmetsch R, Feng G, Geschwind DH, Glahn DC, Goldstein DB, Ledbetter DH, Mulle JG, Pasca SP, Samaco R, Sebat J, Pariser A, Lehner T, Gur RE, Bearden CE. A framework for the investigation of rare genetic disorders in neuropsychiatry. Nat Med 2019; 25:1477-1487. [PMID: 31548702 PMCID: PMC8656349 DOI: 10.1038/s41591-019-0581-5] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Accepted: 07/31/2019] [Indexed: 02/07/2023]
Abstract
De novo and inherited rare genetic disorders (RGDs) are a major cause of human morbidity, frequently involving neuropsychiatric symptoms. Recent advances in genomic technologies and data sharing have revolutionized the identification and diagnosis of RGDs, presenting an opportunity to elucidate the mechanisms underlying neuropsychiatric disorders by investigating the pathophysiology of high-penetrance genetic risk factors. Here we seek out the best path forward for achieving these goals. We think future research will require consistent approaches across multiple RGDs and developmental stages, involving both the characterization of shared neuropsychiatric dimensions in humans and the identification of neurobiological commonalities in model systems. A coordinated and concerted effort across patients, families, researchers, clinicians and institutions, including rapid and broad sharing of data, is now needed to translate these discoveries into urgently needed therapies.
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Affiliation(s)
- Stephan J Sanders
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Mustafa Sahin
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Joseph Hostyk
- Institute for Genomic Medicine, Columbia University Medical Center, Hammer Health Sciences, New York, NY, USA
| | - Audrey Thurm
- National Institute of Mental Health, Bethesda, MD, USA
| | - Sebastien Jacquemont
- CHU Sainte-Justine Research Centre, University of Montreal, Montreal, Quebec, Canada
| | - Paul Avillach
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Elise Douard
- CHU Sainte-Justine Research Centre, University of Montreal, Montreal, Quebec, Canada
| | - Christa L Martin
- Geisinger Autism & Developmental Medicine Institute, Danville, PA, USA
| | - Meera E Modi
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | | | | | - Alan Anticevic
- Tommy Fuss Center for Neuropsychiatric Disease Research, Boston Children's Hospital, Boston, MA, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
| | - Ricardo Dolmetsch
- Department of Neuroscience, Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Guoping Feng
- McGovern Institute for Brain Research and Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daniel H Geschwind
- Center for Autism Research and Treatment, Semel Institute for Neuroscience and Human Behavior and Departments of Neurology and Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - David C Glahn
- Tommy Fuss Center for Neuropsychiatric Disease Research, Boston Children's Hospital, Boston, MA, USA
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University Medical Center, Hammer Health Sciences, New York, NY, USA
| | - David H Ledbetter
- Geisinger Autism & Developmental Medicine Institute, Danville, PA, USA
| | - Jennifer G Mulle
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Sergiu P Pasca
- Department of Psychiatry and Behavioral Sciences, Stanford University, Palo Alto, CA, USA
| | - Rodney Samaco
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jonathan Sebat
- Beyster Center for Genomics of Psychiatric Diseases, University of California, San Diego, La Jolla, CA, USA
| | - Anne Pariser
- National Center for Advancing Translational Sciences, Bethesda, MD, USA
| | - Thomas Lehner
- National Institute of Mental Health, Bethesda, MD, USA
| | - Raquel E Gur
- Department of Psychiatry, Neuropsychiatry Section, and the Lifespan Brain Institute, Perelman School of Medicine and Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA.
| | - Carrie E Bearden
- Semel Institute for Neuroscience and Human Behavior, Departments of Psychiatry and Biobehavioral Sciences and Psychology, University of California, Los Angeles, Los Angeles, CA, USA.
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