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Zhang J, Weissenkampen JD, Kember RL, Grove J, Børglum AD, Robinson EB, Brodkin ES, Almasy L, Bucan M, Sebro R. Phenotypic and ancestry-related assortative mating in autism. Mol Autism 2024; 15:27. [PMID: 38877467 PMCID: PMC11177537 DOI: 10.1186/s13229-024-00605-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 05/30/2024] [Indexed: 06/16/2024] Open
Abstract
BACKGROUND Positive assortative mating (AM) in several neuropsychiatric traits, including autism, has been noted. However, it is unknown whether the pattern of AM is different in phenotypically defined autism subgroups [e.g., autism with and without intellectually disability (ID)]. It is also unclear what proportion of the phenotypic AM can be explained by the genetic similarity between parents of children with an autism diagnosis, and the consequences of AM on the genetic structure of the population. METHODS To address these questions, we analyzed two family-based autism collections: the Simons Foundation Powering Autism Research for Knowledge (SPARK) (1575 families) and the Simons Simplex Collection (SSC) (2283 families). RESULTS We found a similar degree of phenotypic and ancestry-related AM in parents of children with an autism diagnosis regardless of the presence of ID. We did not find evidence of AM for autism based on autism polygenic scores (PGS) (at a threshold of |r|> 0.1). The adjustment of ancestry-related AM or autism PGS accounted for only 0.3-4% of the fractional change in the estimate of the phenotypic AM. The ancestry-related AM introduced higher long-range linkage disequilibrium (LD) between single nucleotide polymorphisms (SNPs) on different chromosomes that are highly ancestry-informative compared to SNPs that are less ancestry-informative (D2 on the order of 1 × 10-5). LIMITATIONS We only analyzed participants of European ancestry, limiting the generalizability of our results to individuals of non-European ancestry. SPARK and SSC were both multicenter studies. Therefore, there could be ancestry-related AM in SPARK and SSC due to geographic stratification. The study participants from each site were unknown, so we were unable to evaluate for geographic stratification. CONCLUSIONS This study showed similar patterns of AM in autism with and without ID, and demonstrated that the common genetic influences of autism are likely relevant to both autism groups. The adjustment of ancestry-related AM and autism PGS accounted for < 5% of the fractional change in the estimate of the phenotypic AM. Future studies are needed to evaluate if the small increase of long-range LD induced by ancestry-related AM has impact on the downstream analysis.
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Affiliation(s)
- Jing Zhang
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - Rachel L Kember
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
| | - Jakob Grove
- Center for Genomics and Personalized Medicine, Aarhus University, Aarhus, Denmark
- Department of Biomedicine (Human Genetics) and iSEQ Center, Aarhus University, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
| | - Anders D Børglum
- Center for Genomics and Personalized Medicine, Aarhus University, Aarhus, Denmark
- Department of Biomedicine (Human Genetics) and iSEQ Center, Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
| | - Elise B Robinson
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Edward S Brodkin
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
| | - Laura Almasy
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Maja Bucan
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
| | - Ronnie Sebro
- Department of Radiology, Mayo Clinic, Jacksonville, FL, USA.
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Hegemann L, Corfield EC, Askelund AD, Allegrini AG, Askeland RB, Ronald A, Ask H, St Pourcain B, Andreassen OA, Hannigan LJ, Havdahl A. Genetic and phenotypic heterogeneity in early neurodevelopmental traits in the Norwegian Mother, Father and Child Cohort Study. Mol Autism 2024; 15:25. [PMID: 38849897 PMCID: PMC11161964 DOI: 10.1186/s13229-024-00599-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 04/18/2024] [Indexed: 06/09/2024] Open
Abstract
BACKGROUND Autism and different neurodevelopmental conditions frequently co-occur, as do their symptoms at sub-diagnostic threshold levels. Overlapping traits and shared genetic liability are potential explanations. METHODS In the population-based Norwegian Mother, Father, and Child Cohort study (MoBa), we leverage item-level data to explore the phenotypic factor structure and genetic architecture underlying neurodevelopmental traits at age 3 years (N = 41,708-58,630) using maternal reports on 76 items assessing children's motor and language development, social functioning, communication, attention, activity regulation, and flexibility of behaviors and interests. RESULTS We identified 11 latent factors at the phenotypic level. These factors showed associations with diagnoses of autism and other neurodevelopmental conditions. Most shared genetic liabilities with autism, ADHD, and/or schizophrenia. Item-level GWAS revealed trait-specific genetic correlations with autism (items rg range = - 0.27-0.78), ADHD (items rg range = - 0.40-1), and schizophrenia (items rg range = - 0.24-0.34). We find little evidence of common genetic liability across all neurodevelopmental traits but more so for several genetic factors across more specific areas of neurodevelopment, particularly social and communication traits. Some of these factors, such as one capturing prosocial behavior, overlap with factors found in the phenotypic analyses. Other areas, such as motor development, seemed to have more heterogenous etiology, with specific traits showing a less consistent pattern of genetic correlations with each other. CONCLUSIONS These exploratory findings emphasize the etiological complexity of neurodevelopmental traits at this early age. In particular, diverse associations with neurodevelopmental conditions and genetic heterogeneity could inform follow-up work to identify shared and differentiating factors in the early manifestations of neurodevelopmental traits and their relation to autism and other neurodevelopmental conditions. This in turn could have implications for clinical screening tools and programs.
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Affiliation(s)
- Laura Hegemann
- PsychGen Centre for Genetic Epidemiology and Mental Health, Norwegian Institute of Public Health, Oslo, Norway.
- Nic Waals Institute, Lovisenberg Diaconal Hospital, Oslo, Norway.
- Department of Psychology, University of Oslo, Oslo, Norway.
| | - Elizabeth C Corfield
- PsychGen Centre for Genetic Epidemiology and Mental Health, Norwegian Institute of Public Health, Oslo, Norway
- Nic Waals Institute, Lovisenberg Diaconal Hospital, Oslo, Norway
| | - Adrian Dahl Askelund
- PsychGen Centre for Genetic Epidemiology and Mental Health, Norwegian Institute of Public Health, Oslo, Norway
- Nic Waals Institute, Lovisenberg Diaconal Hospital, Oslo, Norway
- Department of Psychology, University of Oslo, Oslo, Norway
| | - Andrea G Allegrini
- Division of Psychology & Language Sciences, Department of Clinical, Educational & Health Psychology, Faculty of Brain Sciences, University College London, London, UK
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Ragna Bugge Askeland
- PsychGen Centre for Genetic Epidemiology and Mental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Angelica Ronald
- School of Psychology, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Helga Ask
- PsychGen Centre for Genetic Epidemiology and Mental Health, Norwegian Institute of Public Health, Oslo, Norway
- PROMENTA Research Centre,Department of Psychology, University of Oslo, Oslo, Norway
| | - Beate St Pourcain
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Ole A Andreassen
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Laurie J Hannigan
- PsychGen Centre for Genetic Epidemiology and Mental Health, Norwegian Institute of Public Health, Oslo, Norway
- Nic Waals Institute, Lovisenberg Diaconal Hospital, Oslo, Norway
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK
| | - Alexandra Havdahl
- PsychGen Centre for Genetic Epidemiology and Mental Health, Norwegian Institute of Public Health, Oslo, Norway
- Nic Waals Institute, Lovisenberg Diaconal Hospital, Oslo, Norway
- PROMENTA Research Centre,Department of Psychology, University of Oslo, Oslo, Norway
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3
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Bicks LK, Geschwind DH. Functional neurogenomics in autism spectrum disorders: A decade of progress. Curr Opin Neurobiol 2024; 86:102858. [PMID: 38547564 DOI: 10.1016/j.conb.2024.102858] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 02/29/2024] [Accepted: 02/29/2024] [Indexed: 06/11/2024]
Abstract
Advances in autism spectrum disorder (ASD) genetics have identified many genetic causes, reflecting remarkable progress while at the same time identifying challenges such as heterogeneity and pleiotropy, which complicate attempts to connect genetic risk to mechanisms. High-throughput functional genomic approaches have yielded progress by defining a molecular pathology in the brain of individuals with ASD and in identifying convergent biological pathways through which risk genes are predicted to act. These studies indicate that ASD genetic risk converges in early brain development, primarily during the period of cortical neurogenesis. Over development, genetic perturbations in turn lead to broad neuronal signaling dysregulation, most prominent in glutamatergic cortical-cortical projecting neurons and somatostatin positive interneurons, which is accompanied by glial dyshomeostasis throughout the cerebral cortex. Connecting these developmental perturbations to disrupted neuronal and glial function in the postnatal brain is an important direction in current research. Coupling functional genomic approaches with advances in induced pluripotent stem cell-derived neural organoid development provides a promising avenue for connecting brain pathology to developmental mechanisms.
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Affiliation(s)
- Lucy K Bicks
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095, USA. https://twitter.com/Bickslucy
| | - D H Geschwind
- Program in Neurobehavioral Genetics, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095, USA; Department of Psychiatry, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA.
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4
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Nóbrega IDS, Teles e Silva AL, Yokota-Moreno BY, Sertié AL. The Importance of Large-Scale Genomic Studies to Unravel Genetic Risk Factors for Autism. Int J Mol Sci 2024; 25:5816. [PMID: 38892002 PMCID: PMC11172008 DOI: 10.3390/ijms25115816] [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: 04/17/2024] [Revised: 05/17/2024] [Accepted: 05/21/2024] [Indexed: 06/21/2024] Open
Abstract
Autism spectrum disorder (ASD) is a common and highly heritable neurodevelopmental disorder. During the last 15 years, advances in genomic technologies and the availability of increasingly large patient cohorts have greatly expanded our knowledge of the genetic architecture of ASD and its neurobiological mechanisms. Over two hundred risk regions and genes carrying rare de novo and transmitted high-impact variants have been identified. Additionally, common variants with small individual effect size are also important, and a number of loci are now being uncovered. At the same time, these new insights have highlighted ongoing challenges. In this perspective article, we summarize developments in ASD genetic research and address the enormous impact of large-scale genomic initiatives on ASD gene discovery.
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Affiliation(s)
| | | | | | - Andréa Laurato Sertié
- Faculdade Israelita de Ciências da Saúde Albert Einstein, Hospital Israelita Albert Einstein, Rua Comendador Elias Jafet, 755. Morumbi, São Paulo 05653-000, Brazil; (I.d.S.N.); (A.L.T.e.S.); (B.Y.Y.-M.)
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5
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Schmilovich Z, Bourque VR, Douard E, Huguet G, Poulain C, Ross JP, Alipour P, Castonguay CÉ, Younis N, Jean-Louis M, Saci Z, Pausova Z, Paus T, Schuman G, Porteous D, Davies G, Redmond P, Harris SE, Deary IJ, Whalley H, Hayward C, Dion PA, Jacquemont S, Rouleau GA. Copy-number variants and polygenic risk for intelligence confer risk for autism spectrum disorder irrespective of their effects on cognitive ability. Front Psychiatry 2024; 15:1369767. [PMID: 38751416 PMCID: PMC11094536 DOI: 10.3389/fpsyt.2024.1369767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 04/05/2024] [Indexed: 05/18/2024] Open
Abstract
Introduction Rare copy number variants (CNVs) and polygenic risk for intelligence (PRS-IQ) both confer susceptibility for autism spectrum disorder (ASD) but have opposing effects on cognitive ability. The field has struggled to disentangle the effects of these two classes of genomic variants on cognitive ability from their effects on ASD susceptibility, in part because previous studies did not include controls with cognitive measures. We aim to investigate the impact of these genomic variants on ASD risk while adjusting for their known effects on cognitive ability. Methods In a cohort of 8,426 subjects with ASD and 169,804 controls with cognitive assessments, we found that rare coding CNVs and PRS-IQ increased ASD risk, even after adjusting for their effects on cognitive ability. Results Bottom decile PRS-IQ and CNVs both decreased cognitive ability but had opposing effects on ASD risk. Models combining both classes of variants showed that the effects of rare CNVs and PRS-IQ on ASD risk and cognitive ability were largely additive, further suggesting that susceptibility for ASD is conferred independently from its effects on cognitive ability. Despite imparting mostly additive effects on ASD risk, rare CNVs and PRS-IQ showed opposing effects on core and associated features and developmental history among subjects with ASD. Discussion Our findings suggest that cognitive ability itself may not be the factor driving the underlying liability for ASD conferred by these two classes of genomic variants. In other words, ASD risk and cognitive ability may be two distinct manifestations of CNVs and PRS-IQ. This study also highlights the challenge of understanding how genetic risk for ASD maps onto its dimensional traits.
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Affiliation(s)
- Zoe Schmilovich
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Montreal Neurological Institute-Hospital, McGill University, Montréal, QC, Canada
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
| | - Vincent-Raphaël Bourque
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
- Département de Pédiatrie, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Elise Douard
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
- Département de Pédiatrie, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Guillaume Huguet
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
| | - Cécile Poulain
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
- Département de Pédiatrie, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Jay P. Ross
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Montreal Neurological Institute-Hospital, McGill University, Montréal, QC, Canada
| | - Paria Alipour
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Montreal Neurological Institute-Hospital, McGill University, Montréal, QC, Canada
| | - Charles-Étienne Castonguay
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Montreal Neurological Institute-Hospital, McGill University, Montréal, QC, Canada
| | - Nadine Younis
- Département de Pédiatrie, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Martineau Jean-Louis
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
| | - Zohra Saci
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
| | - Zdenka Pausova
- The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
- Departments of Physiology and Nutritional Sciences, University of Toronto, Toronto, ON, Canada
| | - Tomas Paus
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
- Departments of Psychiatry of Neuroscience, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
- Departments of Psychology and Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Gunter Schuman
- Institute of Psychiatry, Psychology, and Neuroscience, King’s College London, London, United Kingdom
| | - David Porteous
- Lothian Birth Cohorts Group, Department of Psychology, School of Philosophy, Psychology and Language Sciences, The University of Edinburgh, Edinburgh, United Kingdom
- Generation Scotland, Centre for Genomic and Experimental Medicine, Institute of Genetics & Cancer, The University of Edinburgh, Edinburgh, United Kingdom
| | - Gail Davies
- Lothian Birth Cohorts Group, Department of Psychology, School of Philosophy, Psychology and Language Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Paul Redmond
- Lothian Birth Cohorts Group, Department of Psychology, School of Philosophy, Psychology and Language Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Sarah E. Harris
- Lothian Birth Cohorts Group, Department of Psychology, School of Philosophy, Psychology and Language Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Ian J. Deary
- Lothian Birth Cohorts Group, Department of Psychology, School of Philosophy, Psychology and Language Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Heather Whalley
- Generation Scotland, Centre for Genomic and Experimental Medicine, Institute of Genetics & Cancer, The University of Edinburgh, Edinburgh, United Kingdom
| | - Caroline Hayward
- Generation Scotland, Centre for Genomic and Experimental Medicine, Institute of Genetics & Cancer, The University of Edinburgh, Edinburgh, United Kingdom
| | - Patrick A. Dion
- Montreal Neurological Institute-Hospital, McGill University, Montréal, QC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada
| | - Sébastien Jacquemont
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
- Département de Pédiatrie, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Guy A. Rouleau
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Montreal Neurological Institute-Hospital, McGill University, Montréal, QC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada
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6
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Gu Y, Maria-Stauffer E, Bedford SA, Romero-Garcia R, Grove J, Børglum AD, Martin H, Baron-Cohen S, Bethlehem RA, Warrier V. Polygenic scores for autism are associated with neurite density in adults and children from the general population. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.04.10.24305539. [PMID: 38645251 PMCID: PMC11030520 DOI: 10.1101/2024.04.10.24305539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Genetic variants linked to autism are thought to change cognition and behaviour by altering the structure and function of the brain. Although a substantial body of literature has identified structural brain differences in autism, it is unknown whether autism-associated common genetic variants are linked to changes in cortical macro- and micro-structure. We investigated this using neuroimaging and genetic data from adults (UK Biobank, N = 31,748) and children (ABCD, N = 4,928). Using polygenic scores and genetic correlations we observe a robust negative association between common variants for autism and a magnetic resonance imaging derived phenotype for neurite density (intracellular volume fraction) in the general population. This result is consistent across both children and adults, in both the cortex and in white matter tracts, and confirmed using polygenic scores and genetic correlations. There were no sex differences in this association. Mendelian randomisation analyses provide no evidence for a causal relationship between autism and intracellular volume fraction, although this should be revisited using better powered instruments. Overall, this study provides evidence for shared common variant genetics between autism and cortical neurite density.
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Affiliation(s)
- Yuanjun Gu
- Department of Psychiatry, University of Cambridge, Cambridge, CB2 8AH
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, CB2 8AH, UK
| | | | - Saashi A. Bedford
- Department of Psychiatry, University of Cambridge, Cambridge, CB2 8AH
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, CB2 8AH, UK
| | | | | | - Rafael Romero-Garcia
- Department of Psychiatry, University of Cambridge, Cambridge, CB2 8AH
- Department of Medical Physiology and Biophysics, Instituto de Biomedicina de Sevilla (IBiS), HUVR/CSIC/Universidad de Sevilla/CIBERSAM, ISCIII, 41013, Sevilla, Spain, 41013
| | - Jakob Grove
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, 8210, Denmark
- Center for Genomics and Personalized Medicine (CGPM), Aarhus University, Aarhus, 8000, Denmark
- Department of Biomedicine (Human Genetics) and iSEQ Center, Aarhus University, Aarhus, 8000, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark, 8000
| | - Anders D. Børglum
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, 8210, Denmark
- Center for Genomics and Personalized Medicine (CGPM), Aarhus University, Aarhus, 8000, Denmark
- Department of Biomedicine (Human Genetics) and iSEQ Center, Aarhus University, Aarhus, 8000, Denmark
| | - Hilary Martin
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Simon Baron-Cohen
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, CB2 8AH, UK
- Department of Psychology, University of Cambridge, Cambridge, CB2 3EB, UK
| | | | - Varun Warrier
- Department of Psychiatry, University of Cambridge, Cambridge, CB2 8AH
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Department of Psychology, University of Cambridge, Cambridge, CB2 3EB, UK
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7
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Veller C, Coop GM. Interpreting population- and family-based genome-wide association studies in the presence of confounding. PLoS Biol 2024; 22:e3002511. [PMID: 38603516 PMCID: PMC11008796 DOI: 10.1371/journal.pbio.3002511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 01/19/2024] [Indexed: 04/13/2024] Open
Abstract
A central aim of genome-wide association studies (GWASs) is to estimate direct genetic effects: the causal effects on an individual's phenotype of the alleles that they carry. However, estimates of direct effects can be subject to genetic and environmental confounding and can also absorb the "indirect" genetic effects of relatives' genotypes. Recently, an important development in controlling for these confounds has been the use of within-family GWASs, which, because of the randomness of mendelian segregation within pedigrees, are often interpreted as producing unbiased estimates of direct effects. Here, we present a general theoretical analysis of the influence of confounding in standard population-based and within-family GWASs. We show that, contrary to common interpretation, family-based estimates of direct effects can be biased by genetic confounding. In humans, such biases will often be small per-locus, but can be compounded when effect-size estimates are used in polygenic scores (PGSs). We illustrate the influence of genetic confounding on population- and family-based estimates of direct effects using models of assortative mating, population stratification, and stabilizing selection on GWAS traits. We further show how family-based estimates of indirect genetic effects, based on comparisons of parentally transmitted and untransmitted alleles, can suffer substantial genetic confounding. We conclude that, while family-based studies have placed GWAS estimation on a more rigorous footing, they carry subtle issues of interpretation that arise from confounding.
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Affiliation(s)
- Carl Veller
- Department of Ecology & Evolution, University of Chicago, Chicago, Illinois, United States of America
| | - Graham M. Coop
- Department of Evolution and Ecology, and Center for Population Biology, University of California, Davis, California, United States of America
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8
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Reisi-Vanani V, Lorigooini Z, Bijad E, Amini-Khoei H. Maternal separation stress through triggering of the neuro-immune response in the hippocampus induces autistic-like behaviors in male mice. Int J Dev Neurosci 2024; 84:87-98. [PMID: 38110192 DOI: 10.1002/jdn.10310] [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: 09/09/2023] [Revised: 10/28/2023] [Accepted: 12/01/2023] [Indexed: 12/20/2023] Open
Abstract
Autism spectrum disorder (ASD) is the fastest-growing neurodevelopmental disease throughout the world. Neuro-immune responses from prenatal to adulthood stages of life induce developmental defects in synaptic signaling, neurotransmitter imbalance, and even structural changes in the brain. In this study, we aimed to focus on the possible role of neuroinflammatory response in the hippocampus in development of the autistic-like behaviors following maternal separation (MS) stress in mice. To do this, mice neonates daily separated from their mothers from postnatal day (PND) 2 to PND 14 for 3 h. During PND45-60, behavioral tests related to autistic-like behaviors including three-chamber sociability, Morris water maze (MWM), shuttle box, resident-intruder, and marble burying tests were performed. Then, hippocampi were dissected out, and the gene expression of inflammatory mediators including TNF-α, IL-1β, TLR4, HMGB1, and NLRP3 was assessed in the hippocampus using RT-PCR. Results showed that MS mice exerted impaired sociability preference, repetitive behaviors, impaired passive avoidance, and spatial memories. The gene expression of inflammatory mediators significantly increased in the hippocampi of MS mice. We concluded that MS stress probably via activating of the HMGB1/TLR4 signaling cascade in the hippocampus induced autistic-like behaviors in mice.
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Affiliation(s)
- Vahid Reisi-Vanani
- Student Research Committee, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Zahra Lorigooini
- Medical Plants Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Elham Bijad
- Medical Plants Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Hossein Amini-Khoei
- Medical Plants Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
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9
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Viggiano M, Ceroni F, Visconti P, Posar A, Scaduto MC, Sandoni L, Baravelli I, Cameli C, Rochat MJ, Maresca A, Vaisfeld A, Gentilini D, Calzari L, Carelli V, Zody MC, Maestrini E, Bacchelli E. Genomic analysis of 116 autism families strengthens known risk genes and highlights promising candidates. NPJ Genom Med 2024; 9:21. [PMID: 38519481 PMCID: PMC10959942 DOI: 10.1038/s41525-024-00411-1] [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: 10/20/2023] [Accepted: 02/27/2024] [Indexed: 03/25/2024] Open
Abstract
Autism spectrum disorder (ASD) is a complex neurodevelopmental condition with a strong genetic component in which rare variants contribute significantly to risk. We performed whole genome and/or exome sequencing (WGS and WES) and SNP-array analysis to identify both rare sequence and copy number variants (SNVs and CNVs) in 435 individuals from 116 ASD families. We identified 37 rare potentially damaging de novo SNVs (pdSNVs) in the cases (n = 144). Interestingly, two of them (one stop-gain and one missense variant) occurred in the same gene, BRSK2. Moreover, the identification of 8 severe de novo pdSNVs in genes not previously implicated in ASD (AGPAT3, IRX5, MGAT5B, RAB8B, RAP1A, RASAL2, SLC9A1, YME1L1) highlighted promising candidates. Potentially damaging CNVs (pdCNVs) provided support to the involvement of inherited variants in PHF3, NEGR1, TIAM1 and HOMER1 in neurodevelopmental disorders (NDD), although mostly acting as susceptibility factors with incomplete penetrance. Interpretation of identified pdSNVs/pdCNVs according to the ACMG guidelines led to a molecular diagnosis in 19/144 cases, although this figure represents a lower limit and is expected to increase thanks to further clarification of the role of likely pathogenic variants in ASD/NDD candidate genes not yet established. In conclusion, our study highlights promising ASD candidate genes and contributes to characterize the allelic diversity, mode of inheritance and phenotypic impact of de novo and inherited risk variants in ASD/NDD genes.
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Affiliation(s)
- Marta Viggiano
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Fabiola Ceroni
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
- Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
| | - Paola Visconti
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOSI Disturbi dello Spettro Autistico, Bologna, Italy
| | - Annio Posar
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOSI Disturbi dello Spettro Autistico, Bologna, Italy
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Maria Cristina Scaduto
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOSI Disturbi dello Spettro Autistico, Bologna, Italy
| | - Laura Sandoni
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Irene Baravelli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Cinzia Cameli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Magali J Rochat
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Functional and Molecular Neuroimaging Unit, Bologna, Italy
| | - Alessandra Maresca
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| | - Alessandro Vaisfeld
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Davide Gentilini
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
- Bioinformatics and Statistical Genomic Unit, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Luciano Calzari
- Bioinformatics and Statistical Genomic Unit, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Valerio Carelli
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| | | | - Elena Maestrini
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.
| | - Elena Bacchelli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.
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10
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Xie Y, Wu R, Li H, Dong W, Zhou G, Zhao H. Statistical methods for assessing the effects of de novo variants on birth defects. Hum Genomics 2024; 18:25. [PMID: 38486307 PMCID: PMC10938830 DOI: 10.1186/s40246-024-00590-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 02/26/2024] [Indexed: 03/18/2024] Open
Abstract
With the development of next-generation sequencing technology, de novo variants (DNVs) with deleterious effects can be identified and investigated for their effects on birth defects such as congenital heart disease (CHD). However, statistical power is still limited for such studies because of the small sample size due to the high cost of recruiting and sequencing samples and the low occurrence of DNVs. DNV analysis is further complicated by genetic heterogeneity across diseased individuals. Therefore, it is critical to jointly analyze DNVs with other types of genomic/biological information to improve statistical power to identify genes associated with birth defects. In this review, we discuss the general workflow, recent developments in statistical methods, and future directions for DNV analysis.
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Affiliation(s)
- Yuhan Xie
- Department of Biostatistics, Yale School of Public Health, 60 College Street, New Haven, CT, 06520, USA
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Ruoxuan Wu
- Department of Biostatistics, Yale School of Public Health, 60 College Street, New Haven, CT, 06520, USA
| | - Hongyu Li
- Department of Biostatistics, Yale School of Public Health, 60 College Street, New Haven, CT, 06520, USA
| | - Weilai Dong
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Geyu Zhou
- Department of Biostatistics, Yale School of Public Health, 60 College Street, New Haven, CT, 06520, USA
| | - Hongyu Zhao
- Department of Biostatistics, Yale School of Public Health, 60 College Street, New Haven, CT, 06520, USA.
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06520, USA.
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11
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Jeong JH, Lee H, Kim D, Park E, Woo J, Cho Y, Keum G, Lee A, Kang T, Kim J, Choo H, Lee S, Jeon B. Identification of an Antagonist Targeting G Protein and β-Arrestin Signaling Pathways of 5-HT 7R. ACS Chem Neurosci 2024; 15:1026-1041. [PMID: 38387042 DOI: 10.1021/acschemneuro.3c00738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024] Open
Abstract
In consideration of the limited number of FDA-approved drugs for autism spectrum disorder (ASD), significant efforts have been devoted to identifying novel drug candidates. Among these, 5-HT7R modulators have garnered considerable attention due to their potential in alleviating autism-like behaviors in ASD animal models. In this study, we designed and synthesized biphenyl-3-ylmethylpyrrolidines 3 and biphenyl-3-yl-dihydroimidazoles 4 as 5-HT7R modulators. Through extensive biological tests of 3 and 4 in G protein and β-arrestin signaling pathways of 5-HT7R, it was determined that 2-(2'-methoxy-[1,1'-biphenyl]-3-yl)-4,5-dihydro-1H-imidazole 4h acted as a 5-HT7R antagonist in both signaling pathways. In in vivo study with Shank3-/- transgenic (TG) mice, the self-grooming behavior test was performed with 4h, resulting in a significant reduction in the duration of self-grooming. In addition, an immunohistochemical experiment with 4h restored reduced neurogenesis in Shank3-/- TG mice, which is confirmed by the quantification of doublecortin (DCX) positive neurons, suggesting the promising therapeutic potential of 4h.
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Affiliation(s)
- Jeong Hyun Jeong
- Brain Science Institute, Korea Institute of Science and Technology, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Haeun Lee
- Brain Science Institute, Korea Institute of Science and Technology, Seongbuk-gu, Seoul 02792, Republic of Korea
- Division of Bio-Medical Science and Technology, KIST School, University of Science and Technology, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Doyoung Kim
- Brain Science Institute, Korea Institute of Science and Technology, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Eunseo Park
- Brain Science Institute, Korea Institute of Science and Technology, Seongbuk-gu, Seoul 02792, Republic of Korea
- Division of Bio-Medical Science and Technology, KIST School, University of Science and Technology, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Jiwan Woo
- Research Animal Resource Center, Korea Institute of Science and Technology, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Yakdol Cho
- Research Animal Resource Center, Korea Institute of Science and Technology, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Gyochang Keum
- Brain Science Institute, Korea Institute of Science and Technology, Seongbuk-gu, Seoul 02792, Republic of Korea
- Division of Bio-Medical Science and Technology, KIST School, University of Science and Technology, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Ansoo Lee
- Brain Science Institute, Korea Institute of Science and Technology, Seongbuk-gu, Seoul 02792, Republic of Korea
- Division of Bio-Medical Science and Technology, KIST School, University of Science and Technology, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Taek Kang
- Brain Science Institute, Korea Institute of Science and Technology, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Jeongjin Kim
- Brain Science Institute, Korea Institute of Science and Technology, Seongbuk-gu, Seoul 02792, Republic of Korea
- Division of Bio-Medical Science and Technology, KIST School, University of Science and Technology, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Hyunah Choo
- Brain Science Institute, Korea Institute of Science and Technology, Seongbuk-gu, Seoul 02792, Republic of Korea
- Division of Bio-Medical Science and Technology, KIST School, University of Science and Technology, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Sanghee Lee
- Brain Science Institute, Korea Institute of Science and Technology, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Byungsun Jeon
- Brain Science Institute, Korea Institute of Science and Technology, Seongbuk-gu, Seoul 02792, Republic of Korea
- Division of Bio-Medical Science and Technology, KIST School, University of Science and Technology, Seongbuk-gu, Seoul 02792, Republic of Korea
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12
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Pugsley K, Namipashaki A, Bellgrove MA, Hawi Z. Evaluating the regulatory function of non-coding autism-associated single nucleotide polymorphisms on gene expression in human brain tissue. Autism Res 2024; 17:467-481. [PMID: 38323502 DOI: 10.1002/aur.3101] [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: 09/11/2023] [Accepted: 01/18/2024] [Indexed: 02/08/2024]
Abstract
Common variants account for most of the estimated heritability associated with autism spectrum disorder (autism). Although several replicable single nucleotide polymorphisms (SNPs) for the condition have been detected using genome-wide association study (GWAS) methodologies, their pathophysiological relevance remains elusive. Examining this is complicated, however, as all detected loci are situated within non-coding regions of the genome. It is therefore likely that they possess roles of regulatory function as opposed to directly affecting gene coding sequences. To bridge the gap between SNP discovery and mechanistic insight, we applied a comprehensive bioinformatic pipeline to functionally annotate autism-associated polymorphisms and their non-coding linkage disequilibrium (i.e., non-randomly associated) partners. We identified 82 DNA variants of probable regulatory function that may contribute to autism pathogenesis. To validate these predictions, we measured the impact of 11 high-confidence candidates and their GWAS linkage disequilibrium partners on gene expression in human brain tissue from Autistic and non-Autistic donors. Although a small number of the surveyed variants exhibited measurable influence on gene expression as determined via quantitative polymerase chain reaction, these did not survive correction for multiple comparisons. Additionally, no significant genotype-by-diagnosis effects were observed for any of the SNP-gene associations. We contend that this may reflect an inability to effectively capture the modest, neurodevelopmental-specific impact of individual variants on biological dysregulation in available post-mortem tissue samples, as well as limitations in the existing autism GWAS data.
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Affiliation(s)
- Kealan Pugsley
- Turner Institute for Brain and Mental Health and School of Psychological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Atefeh Namipashaki
- Turner Institute for Brain and Mental Health and School of Psychological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Mark A Bellgrove
- Turner Institute for Brain and Mental Health and School of Psychological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Ziarih Hawi
- Turner Institute for Brain and Mental Health and School of Psychological Sciences, Monash University, Melbourne, Victoria, Australia
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13
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Tarr I, Hesselson S, Troup M, Young P, Thompson JL, McGrath-Cadell L, Fatkin D, Dunwoodie SL, Muller DWM, Iismaa SE, Kovacic JC, Graham RM, Giannoulatou E. Polygenic Risk in Families With Spontaneous Coronary Artery Dissection. JAMA Cardiol 2024; 9:254-261. [PMID: 38265806 PMCID: PMC10809133 DOI: 10.1001/jamacardio.2023.5194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 11/06/2023] [Indexed: 01/25/2024]
Abstract
Importance Spontaneous coronary artery dissection (SCAD) is a poorly understood cause of acute coronary syndrome that predominantly affects women. Evidence to date suggests a complex genetic architecture, while a family history is reported for a minority of cases. Objective To determine the contribution of rare and common genetic variants to SCAD risk in familial cases, the latter via the comparison of a polygenic risk score (PRS) with those with sporadic SCAD and healthy controls. Design, Setting, and Participants This genetic association study analyzed families with SCAD, individuals with sporadic SCAD, and healthy controls. Genotyping was undertaken for all participants. Participants were recruited between 2017 and 2021. A PRS for SCAD was calculated for all participants. The presence of rare variants in genes associated with connective tissue disorders (CTD) was also assessed. Individuals with SCAD were recruited via social media or from a single medical center. A previously published control database of older healthy individuals was used. Data were analyzed from January 2022 to October 2023. Exposures PRS for SCAD comprised of 7 single-nucleotide variants. Main Outcomes and Measures Disease status (familial SCAD, sporadic SCAD, or healthy control) associated with PRS. Results A total of 13 families with SCAD (27 affected and 12 unaffected individuals), 173 individuals with sporadic SCAD, and 1127 healthy controls were included. A total of 188 individuals with SCAD (94.0%) were female, including 25 of 27 with familial SCAD and 163 of 173 with sporadic SCAD; of 12 unaffected individuals from families with SCAD, 6 (50%) were female; and of 1127 healthy controls, 672 (59.6%) were female. Compared with healthy controls, the odds of being an affected family member or having sporadic SCAD was significantly associated with a SCAD PRS (where the odds ratio [OR] represents an increase in odds per 1-SD increase in PRS) (affected family member: OR, 2.14; 95% CI, 1.78-2.50; adjusted P = 1.96 × 10-4; sporadic SCAD: OR, 1.63; 95% CI, 1.37-1.89; adjusted P = 5.69 × 10-4). This association was not seen for unaffected family members (OR, 1.03; 95% CI, 0.46-1.61; adjusted P = .91) compared with controls. Further, those with familial SCAD were overrepresented in the top quintile of the control PRS distribution (OR, 3.70; 95% CI, 2.93-4.47; adjusted P = .001); those with sporadic SCAD showed a similar pattern (OR, 2.51; 95% CI, 1.98-3.04; adjusted P = .001). Affected individuals within a family did not share any rare deleterious variants in CTD-associated genes. Conclusions and Relevance Extreme aggregation of common genetic risk appears to play a significant role in familial clustering of SCAD as well as in sporadic case predisposition, although further study is required.
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Affiliation(s)
- Ingrid Tarr
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia
| | | | - Michael Troup
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia
| | - Paul Young
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia
| | | | - Lucy McGrath-Cadell
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia
- University of New South Wales Sydney, Kensington, Australia
| | - Diane Fatkin
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia
- University of New South Wales Sydney, Kensington, Australia
- Cardiology Department, St Vincent’s Hospital, Darlinghurst, Australia
| | - Sally L. Dunwoodie
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia
- University of New South Wales Sydney, Kensington, Australia
| | - David W. M. Muller
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia
- University of New South Wales Sydney, Kensington, Australia
- Cardiology Department, St Vincent’s Hospital, Darlinghurst, Australia
| | - Siiri E. Iismaa
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia
- University of New South Wales Sydney, Kensington, Australia
| | - Jason C. Kovacic
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia
- University of New South Wales Sydney, Kensington, Australia
- Cardiology Department, St Vincent’s Hospital, Darlinghurst, Australia
- Cardiovascular Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Robert M. Graham
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia
- University of New South Wales Sydney, Kensington, Australia
- Cardiology Department, St Vincent’s Hospital, Darlinghurst, Australia
| | - Eleni Giannoulatou
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia
- University of New South Wales Sydney, Kensington, Australia
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14
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Li Q, Li W, Hu K, Wang Y, Li Y, Xu J. A de novo variant in RERE causes autistic behavior by disrupting related genes and signaling pathway. Clin Genet 2024; 105:273-282. [PMID: 38018232 DOI: 10.1111/cge.14461] [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: 09/07/2023] [Revised: 11/10/2023] [Accepted: 11/15/2023] [Indexed: 11/30/2023]
Abstract
Autism spectrum disorder (ASD) is a highly variable neurodevelopmental disorder that typically manifests childhood, characterized by a triad of symptoms: impaired social interaction, communication difficulties, and restricted interests with repetitive behaviors. De novo variants in related genes can cause ASD. We present the case of a 6-year-old Chinese boy with autistic behavior, including language communication impairments, intellectual disabilities, stunted development, and irritability in social interactions. Using Sanger sequencing, we confirmed a pathogenic in the RERE gene (NM_012102.4) (c.3732delC, p.Tyr1245Thrfs*12; EX21; Het). Subsequently, we generated an RERE point mutation cell line (ReMut) using CRISPR/Cas9 Targeted Genome Editing. Immunofluorescence was conducted to determine the location of the mutant RERE. RNA-sequencing and mass spectrometry analyses were performed to elucidate the ASD-related genes and signaling pathways disrupted by this variant in RERE. We identified 3790 differentially expressed genes and 684 differentially expressed proteins. The SHH signaling pathway was found to be downregulated, and the Hippo pathway was upregulated in ReMut. Genes implicated in autism, such as CNTNAP2, STX1A, FARP2, and GPC1, were significantly downregulated. Simultaneously, we noted alterations in HDAC1 and HDAC2, which are members of the WHHERE complex, suggesting their role in the pathogenesis of this patient. In conclusion, we report a de novo variant in RERE associated with autistic behavior. The finding that ASD is associated with RERE variants underscore the role of genetic factors in ASD and provides insights regarding the mechanisms underlying RERE variants in disease onset.
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Affiliation(s)
- Qian Li
- The First Affiliated Hospital of Zhengzhou University & Institute of Reproductive Health, Henan Academy of Innovations in Medical Science, Zhengzhou, Henan, China
- NHC Key Laboratory of Birth Defects Prevention, Zhengzhou, Henan, China
- Jining No. 1 People's Hospital, Jining, Shandong, China
| | - Wenbo Li
- The First Affiliated Hospital of Zhengzhou University & Institute of Reproductive Health, Henan Academy of Innovations in Medical Science, Zhengzhou, Henan, China
- NHC Key Laboratory of Birth Defects Prevention, Zhengzhou, Henan, China
| | - Kaiyue Hu
- The First Affiliated Hospital of Zhengzhou University & Institute of Reproductive Health, Henan Academy of Innovations in Medical Science, Zhengzhou, Henan, China
- NHC Key Laboratory of Birth Defects Prevention, Zhengzhou, Henan, China
| | - Yaqian Wang
- The First Affiliated Hospital of Zhengzhou University & Institute of Reproductive Health, Henan Academy of Innovations in Medical Science, Zhengzhou, Henan, China
- NHC Key Laboratory of Birth Defects Prevention, Zhengzhou, Henan, China
| | - Yang Li
- The First Affiliated Hospital of Zhengzhou University & Institute of Reproductive Health, Henan Academy of Innovations in Medical Science, Zhengzhou, Henan, China
- NHC Key Laboratory of Birth Defects Prevention, Zhengzhou, Henan, China
| | - Jiawei Xu
- The First Affiliated Hospital of Zhengzhou University & Institute of Reproductive Health, Henan Academy of Innovations in Medical Science, Zhengzhou, Henan, China
- NHC Key Laboratory of Birth Defects Prevention, Zhengzhou, Henan, China
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15
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de Hoyos L, Barendse MT, Schlag F, van Donkelaar MMJ, Verhoef E, Shapland CY, Klassmann A, Buitelaar J, Verhulst B, Fisher SE, Rai D, St Pourcain B. Structural models of genome-wide covariance identify multiple common dimensions in autism. Nat Commun 2024; 15:1770. [PMID: 38413609 PMCID: PMC10899248 DOI: 10.1038/s41467-024-46128-8] [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: 11/04/2022] [Accepted: 02/12/2024] [Indexed: 02/29/2024] Open
Abstract
Common genetic variation has been associated with multiple phenotypic features in Autism Spectrum Disorder (ASD). However, our knowledge of shared genetic factor structures contributing to this highly heterogeneous phenotypic spectrum is limited. Here, we developed and implemented a structural equation modelling framework to directly model genomic covariance across core and non-core ASD phenotypes, studying autistic individuals of European descent with a case-only design. We identified three independent genetic factors most strongly linked to language performance, behaviour and developmental motor delay, respectively, studying an autism community sample (N = 5331). The three-factorial structure was largely confirmed in independent ASD-simplex families (N = 1946), although we uncovered, in addition, simplex-specific genetic overlap between behaviour and language phenotypes. Multivariate models across cohorts revealed novel associations, including links between language and early mastering of self-feeding. Thus, the common genetic architecture in ASD is multi-dimensional with overarching genetic factors contributing, in combination with ascertainment-specific patterns, to phenotypic heterogeneity.
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Affiliation(s)
- Lucía de Hoyos
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
| | - Maria T Barendse
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
- Department of Social Dentistry and Behavioural Sciences, Academic Centre for Dentistry Amsterdam (ACTA), Amsterdam, The Netherlands
| | - Fenja Schlag
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
| | | | - Ellen Verhoef
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
| | - Chin Yang Shapland
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, University of Bristol, Bristol, UK
| | | | - Jan Buitelaar
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
- Karakter Child and Adolescent Psychiatry University Centre, Nijmegen, The Netherlands
- Department of Cognitive Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Simon E Fisher
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Dheeraj Rai
- Population Health Sciences, University of Bristol, Bristol, UK
- Avon and Wiltshire Partnership NHS Mental Health Trust, Bristol, UK
- NIHR Biomedical Research Centre, University of Bristol, Bristol, UK
| | - Beate St Pourcain
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands.
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands.
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16
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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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17
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Yahia A, Li D, Lejerkrans S, Rajagopalan S, Kalnak N, Tammimies K. Whole exome sequencing and polygenic assessment of a Swedish cohort with severe developmental language disorder. Hum Genet 2024; 143:169-183. [PMID: 38300321 PMCID: PMC10881898 DOI: 10.1007/s00439-023-02636-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 12/25/2023] [Indexed: 02/02/2024]
Abstract
Developmental language disorder (DLD) overlaps clinically, genetically, and pathologically with other neurodevelopmental disorders (NDD), corroborating the concept of the NDD continuum. There is a lack of studies to understand the whole genetic spectrum in individuals with DLD. Previously, we recruited 61 probands with severe DLD from 59 families and examined 59 of them and their families using microarray genotyping with a 6.8% diagnostic yield. Herein, we investigated 53 of those probands using whole exome sequencing (WES). Additionally, we used polygenic risk scores (PRS) to understand the within family enrichment of neurodevelopmental difficulties and examine the associations between the results of language-related tests in the probands and language-related PRS. We identified clinically significant variants in four probands, resulting in a 7.5% (4/53) molecular diagnostic yield. Those variants were in PAK2, MED13, PLCB4, and TNRC6B. We also prioritized additional variants for future studies for their role in DLD, including high-impact variants in PARD3 and DIP2C. PRS did not explain the aggregation of neurodevelopmental difficulties in these families. We did not detect significant associations between the language-related tests and language-related PRS. Our results support using WES as the first-tier genetic test for DLD as it can identify monogenic DLD forms. Large-scale sequencing studies for DLD are needed to identify new genes and investigate the polygenic contribution to the condition.
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Affiliation(s)
- Ashraf Yahia
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet, Region Stockholm, Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, Stockholm, Sweden
| | - Danyang Li
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet, Region Stockholm, Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, Stockholm, Sweden
- Social, Genetic and Developmental Psychiatry Centre, King's College London, London, UK
| | - Sanna Lejerkrans
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet, Region Stockholm, Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, Stockholm, Sweden
| | - Shyam Rajagopalan
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet, Region Stockholm, Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, Stockholm, Sweden
- Institute of Bioinformatics and Applied Biotechnology, Bengaluru, India
| | - Nelli Kalnak
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet, Region Stockholm, Stockholm, Sweden
- Department of Speech-Language Pathology, Helsingborg Hospital, Helsingborg, Sweden
| | - Kristiina Tammimies
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet, Region Stockholm, Stockholm, Sweden.
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, Stockholm, Sweden.
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18
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Iannuccelli M, Vitriolo A, Licata L, Lo Surdo P, Contino S, Cheroni C, Capocefalo D, Castagnoli L, Testa G, Cesareni G, Perfetto L. Curation of causal interactions mediated by genes associated with autism accelerates the understanding of gene-phenotype relationships underlying neurodevelopmental disorders. Mol Psychiatry 2024; 29:186-196. [PMID: 38102483 PMCID: PMC11078740 DOI: 10.1038/s41380-023-02317-3] [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: 02/20/2023] [Revised: 10/14/2023] [Accepted: 10/31/2023] [Indexed: 12/17/2023]
Abstract
Autism spectrum disorder (ASD) comprises a large group of neurodevelopmental conditions featuring, over a wide range of severity and combinations, a core set of manifestations (restricted sociality, stereotyped behavior and language impairment) alongside various comorbidities. Common and rare variants in several hundreds of genes and regulatory regions have been implicated in the molecular pathogenesis of ASD along a range of causation evidence strength. Despite significant progress in elucidating the impact of few paradigmatic individual loci, such sheer complexity in the genetic architecture underlying ASD as a whole has hampered the identification of convergent actionable hubs hypothesized to relay between the vastness of risk alleles and the core phenotypes. In turn this has limited the development of strategies that can revert or ameliorate this condition, calling for a systems-level approach to probe the cross-talk of cooperating genes in terms of causal interaction networks in order to make convergences experimentally tractable and reveal their clinical actionability. As a first step in this direction, we have captured from the scientific literature information on the causal links between the genes whose variants have been associated with ASD and the whole human proteome. This information has been annotated in a computer readable format in the SIGNOR database and is made freely available in the resource website. To link this information to cell functions and phenotypes, we have developed graph algorithms that estimate the functional distance of any protein in the SIGNOR causal interactome to phenotypes and pathways. The main novelty of our approach resides in the possibility to explore the mechanistic links connecting the suggested gene-phenotype relations.
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Affiliation(s)
- Marta Iannuccelli
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica, 00133, Rome, Italy
| | - Alessandro Vitriolo
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157, Milan, Italy
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Via Santa Sofia 9, 20122, Milan, Italy
| | - Luana Licata
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica, 00133, Rome, Italy
- Computational Biology Research Centre, Human Technopole, Viale Rita Levi-Montalcini 1, 20157, Milan, Italy
| | - Prisca Lo Surdo
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica, 00133, Rome, Italy
- Computational Biology Research Centre, Human Technopole, Viale Rita Levi-Montalcini 1, 20157, Milan, Italy
| | - Silvia Contino
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica, 00133, Rome, Italy
| | - Cristina Cheroni
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Via Santa Sofia 9, 20122, Milan, Italy
| | - Daniele Capocefalo
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Via Santa Sofia 9, 20122, Milan, Italy
| | - Luisa Castagnoli
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica, 00133, Rome, Italy
| | - Giuseppe Testa
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157, Milan, Italy.
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139, Milan, Italy.
- Department of Oncology and Hemato-Oncology, University of Milan, Via Santa Sofia 9, 20122, Milan, Italy.
| | - Gianni Cesareni
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica, 00133, Rome, Italy.
| | - Livia Perfetto
- Computational Biology Research Centre, Human Technopole, Viale Rita Levi-Montalcini 1, 20157, Milan, Italy.
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy.
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19
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Wang S, Wang B, Drury V, Drake S, Sun N, Alkhairo H, Arbelaez J, Duhn C, Bal VH, Langley K, Martin J, Hoekstra PJ, Dietrich A, Xing J, Heiman GA, Tischfield JA, Fernandez TV, Owen MJ, O'Donovan MC, Thapar A, State MW, Willsey AJ. Rare X-linked variants carry predominantly male risk in autism, Tourette syndrome, and ADHD. Nat Commun 2023; 14:8077. [PMID: 38057346 PMCID: PMC10700338 DOI: 10.1038/s41467-023-43776-0] [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: 09/29/2022] [Accepted: 11/18/2023] [Indexed: 12/08/2023] Open
Abstract
Autism spectrum disorder (ASD), Tourette syndrome (TS), and attention-deficit/hyperactivity disorder (ADHD) display strong male sex bias, due to a combination of genetic and biological factors, as well as selective ascertainment. While the hemizygous nature of chromosome X (Chr X) in males has long been postulated as a key point of "male vulnerability", rare genetic variation on this chromosome has not been systematically characterized in large-scale whole exome sequencing studies of "idiopathic" ASD, TS, and ADHD. Here, we take advantage of informative recombinations in simplex ASD families to pinpoint risk-enriched regions on Chr X, within which rare maternally-inherited damaging variants carry substantial risk in males with ASD. We then apply a modified transmission disequilibrium test to 13,052 ASD probands and identify a novel high confidence ASD risk gene at exome-wide significance (MAGEC3). Finally, we observe that rare damaging variants within these risk regions carry similar effect sizes in males with TS or ADHD, further clarifying genetic mechanisms underlying male vulnerability in multiple neurodevelopmental disorders that can be exploited for systematic gene discovery.
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Affiliation(s)
- Sheng Wang
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Belinda Wang
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Vanessa Drury
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Sam Drake
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Nawei Sun
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Hasan Alkhairo
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Juan Arbelaez
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Clif Duhn
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Vanessa H Bal
- Graduate School of Applied and Professional Psychology, Rutgers University, New Brunswick, NJ, USA
| | - Kate Langley
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University School of Medicine, Cardiff, Wales, UK
- School of Psychology, Cardiff University School of Medicine, Cardiff, Wales, UK
| | - Joanna Martin
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University School of Medicine, Cardiff, Wales, UK
| | - Pieter J Hoekstra
- University of Groningen, University Medical Center Groningen, Department of Child and Adolescent Psychiatry, Groningen, The Netherlands
- Accare Child Study Center, Groningen, The Netherlands
| | - Andrea Dietrich
- University of Groningen, University Medical Center Groningen, Department of Child and Adolescent Psychiatry, Groningen, The Netherlands
- Accare Child Study Center, Groningen, The Netherlands
| | - Jinchuan Xing
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Gary A Heiman
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Jay A Tischfield
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Thomas V Fernandez
- Yale Child Study Center and Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Michael J Owen
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University School of Medicine, Cardiff, Wales, UK
| | - Michael C O'Donovan
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University School of Medicine, Cardiff, Wales, UK
| | - Anita Thapar
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University School of Medicine, Cardiff, Wales, UK
| | - Matthew W State
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - A Jeremy Willsey
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94143, USA.
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, 94143, USA.
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20
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Pua EPK, Desai T, Green C, Trevis K, Brown N, Delatycki M, Scheffer I, Wilson S. Endophenotyping social cognition in the broader autism phenotype. Autism Res 2023. [PMID: 38037242 DOI: 10.1002/aur.3057] [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: 07/13/2023] [Accepted: 10/30/2023] [Indexed: 12/02/2023]
Abstract
Relatives of individuals with autism spectrum disorder (ASD) may display milder social traits of the broader autism phenotype (BAP) providing potential endophenotypic markers of genetic risk for ASD. We performed a case-control comparison to quantify social cognition and pragmatic language difficulties in the BAP (n = 25 cases; n = 33 controls) using the Faux Pas test (FPT) and the Goldman-Eisler Cartoon task. Using deep phenotyping we then examined patterns of inheritance of social cognition in two large multiplex families and the spectrum of performance in 32 additional families (159 members; n = 51 ASD, n = 87 BAP, n = 21 unaffected). BAP individuals showed significantly poorer FPT performance and reduced verbal fluency with the absence of a compression effect in social discourse compared to controls. In multiplex families, we observed reduced FPT performance in 89% of autistic family members, 63% of BAP relatives and 50% of unaffected relatives. Across all affected families, there was a graded spectrum of difficulties, with ASD individuals showing the most severe FPT difficulties, followed by the BAP and unaffected relatives compared to community controls. We conclude that relatives of probands show an inherited pattern of graded difficulties in social cognition with atypical faux pas detection in social discourse providing a novel candidate endophenotype for ASD.
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Affiliation(s)
- Emmanuel Peng Kiat Pua
- Department of Medicine and Radiology, Austin Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Tarishi Desai
- Melbourne School of Psychological Sciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Cherie Green
- Department of Psychology, Counselling & Therapy, School of Psychology and Public Health, La Trobe University, Melbourne, Victoria, Australia
| | - Krysta Trevis
- Melbourne School of Psychological Sciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Natasha Brown
- Victorian Clinical Genetics Service, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Martin Delatycki
- Victorian Clinical Genetics Service, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Ingrid Scheffer
- Department of Medicine and Radiology, Austin Health, The University of Melbourne, Melbourne, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
- The Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia
| | - Sarah Wilson
- Department of Medicine and Radiology, Austin Health, The University of Melbourne, Melbourne, Victoria, Australia
- Melbourne School of Psychological Sciences, The University of Melbourne, Melbourne, Victoria, Australia
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21
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Schmilovich Z, Bourque VR, Douard E, Huguet G, Poulain C, Ross JP, Alipour P, Castonguay CÉ, Younis N, Jean-Louis M, Saci Z, Pausova Z, Paus T, Schuman G, Porteous D, Davies G, Redmond P, Harris SE, Deary IJ, Whalley H, Hayward C, Dion PA, Jacquemont S, Rouleau GA. Copy-number variants and polygenic risk for intelligence confer risk for autism spectrum disorder irrespective of their effects on cognitive ability. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.11.29.23299190. [PMID: 38076919 PMCID: PMC10705642 DOI: 10.1101/2023.11.29.23299190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Rare copy number variants (CNVs) and polygenic risk for intelligence (PRS-IQ) both confer risk for autism spectrum disorder (ASD) but have opposing effects on cognitive ability. The field has struggled to disentangle the effects of these two classes of genomic variants on cognitive ability from their effects on ASD risk, in part because previous studies did not include controls with cognitive measures. We aim to investigate the impact of these genomic variants on ASD risk while adjusting for their known effects on cognitive ability. In a cohort of 8,426 subjects with ASD and 169,804 controls with cognitive assessments, we found that rare coding CNVs and PRS-IQ increased ASD risk, even after adjusting for their effects on cognitive ability. Bottom decile PRS-IQ and CNVs both decreased cognitive ability but had opposing effects on ASD risk. Models combining both classes of variants showed that the effects of rare CNVs and PRS-IQ on ASD risk and cognitive ability were largely additive, further suggesting that risk for ASD is conferred independently from its effects on cognitive ability. Despite imparting mostly additive effects on ASD risk, rare CNVs and PRS-IQ showed opposing effects on core and associated features and developmental history among subjects with ASD. Our findings suggest that cognitive ability itself may not be the factor driving the underlying risk for ASD conferred by these two classes of genomic variants. In other words, ASD risk and cognitive ability may be two distinct manifestations of CNVs and PRS-IQ. This study also highlights the challenge of understanding how genetic risk for ASD maps onto its dimensional traits.
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Affiliation(s)
- Zoe Schmilovich
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Montreal Neurological Institute-Hospital, McGill University, Montréal, QC, Canada
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
| | - Vincent-Raphaël Bourque
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
- Département de Pédiatrie, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Elise Douard
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
- Département de Pédiatrie, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Guillaume Huguet
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
| | - Cécile Poulain
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
- Département de Pédiatrie, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Jay P. Ross
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Montreal Neurological Institute-Hospital, McGill University, Montréal, QC, Canada
| | - Paria Alipour
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Montreal Neurological Institute-Hospital, McGill University, Montréal, QC, Canada
| | - Charles-Étienne Castonguay
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Montreal Neurological Institute-Hospital, McGill University, Montréal, QC, Canada
| | - Nadine Younis
- Département de Pédiatrie, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Martineau Jean-Louis
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
| | - Zohra Saci
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
| | - Zdenka Pausova
- The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
- Departments of Physiology and Nutritional Sciences, University of Toronto, Toronto, ON, Canada
| | - Tomas Paus
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
- Departments of Psychiatry of Neuroscience, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
- Departments of Psychology and Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Gunter Schuman
- Institute of Psychiatry, Psychology, and Neuroscience, King’s College London, London, England
| | - David Porteous
- Lothian Birth Cohorts group, Department of Psychology, School of Philosophy, Psychology and Language Sciences, The University of Edinburgh, Edinburgh, UK
- Generation Scotland, Centre for Genomic and Experimental Medicine, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, UK
| | - Gail Davies
- Lothian Birth Cohorts group, Department of Psychology, School of Philosophy, Psychology and Language Sciences, The University of Edinburgh, Edinburgh, UK
| | - Paul Redmond
- Lothian Birth Cohorts group, Department of Psychology, School of Philosophy, Psychology and Language Sciences, The University of Edinburgh, Edinburgh, UK
| | - Sarah E. Harris
- Lothian Birth Cohorts group, Department of Psychology, School of Philosophy, Psychology and Language Sciences, The University of Edinburgh, Edinburgh, UK
| | - Ian J. Deary
- Lothian Birth Cohorts group, Department of Psychology, School of Philosophy, Psychology and Language Sciences, The University of Edinburgh, Edinburgh, UK
| | - Heather Whalley
- Generation Scotland, Centre for Genomic and Experimental Medicine, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, UK
| | - Caroline Hayward
- Generation Scotland, Centre for Genomic and Experimental Medicine, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, UK
| | - Patrick A. Dion
- Montreal Neurological Institute-Hospital, McGill University, Montréal, QC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montréal, Canada
| | - Sébastien Jacquemont
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
- Département de Pédiatrie, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Guy A. Rouleau
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Montreal Neurological Institute-Hospital, McGill University, Montréal, QC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montréal, Canada
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22
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Tang D, Freudenberg J, Dahl A. Factorizing polygenic epistasis improves prediction and uncovers biological pathways in complex traits. Am J Hum Genet 2023; 110:1875-1887. [PMID: 37922884 PMCID: PMC10645564 DOI: 10.1016/j.ajhg.2023.10.002] [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: 06/05/2023] [Revised: 10/04/2023] [Accepted: 10/05/2023] [Indexed: 11/07/2023] Open
Abstract
Epistasis is central in many domains of biology, but it has not yet been proven useful for understanding the etiology of complex traits. This is partly because complex-trait epistasis involves polygenic interactions that are poorly captured in current models. To address this gap, we developed a model called Epistasis Factor Analysis (EFA). EFA assumes that polygenic epistasis can be factorized into interactions between a few epistasis factors (EFs), which represent latent polygenic components of the observed complex trait. The statistical goals of EFA are to improve polygenic prediction and to increase power to detect epistasis, while the biological goal is to unravel genetic effects into more-homogeneous units. We mathematically characterize EFA and use simulations to show that EFA outperforms current epistasis models when its assumptions approximately hold. Applied to predicting yeast growth rates, EFA outperforms the additive model for several traits with large epistasis heritability and uniformly outperforms the standard epistasis model. We replicate these prediction improvements in a second dataset. We then apply EFA to four previously characterized traits in the UK Biobank and find statistically significant epistasis in all four, including two that are robust to scale transformation. Moreover, we find that the inferred EFs partly recover pre-defined biological pathways for two of the traits. Our results demonstrate that more realistic models can identify biologically and statistically meaningful epistasis in complex traits, indicating that epistasis has potential for precision medicine and characterizing the biology underlying GWAS results.
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Affiliation(s)
- David Tang
- Section of Genetic Medicine, University of Chicago, Chicago, IL, USA; Program in Bioinformatics and Integrative Genomics, Harvard Medical School, Boston, MA, USA.
| | - Jerome Freudenberg
- Section of Genetic Medicine, University of Chicago, Chicago, IL, USA; Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA
| | - Andy Dahl
- Section of Genetic Medicine, University of Chicago, Chicago, IL, USA.
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23
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Bacchelli E, Viggiano M, Ceroni F, Visconti P, Posar A, Scaduto M, Sandoni L, Baravelli I, Cameli C, Rochat M, Maresca A, Vaisfeld A, Gentilini D, Calzari L, Carelli V, Zody M, Maestrini E. Whole genome analysis of rare deleterious variants adds further evidence to BRSK2 and other risk genes in Autism Spectrum Disorder. RESEARCH SQUARE 2023:rs.3.rs-3468592. [PMID: 37961520 PMCID: PMC10635364 DOI: 10.21203/rs.3.rs-3468592/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Autism spectrum disorder (ASD) is a complex neurodevelopmental condition with a strong genetic component in which rare variants contribute significantly to risk. We have performed whole genome and/or exome sequencing (WGS and WES) and SNP-array analysis to identify both rare sequence and copy number variants (SNVs and CNVs) in 435 individuals from 116 ASD families. We identified 37 rare potentially damaging de novo SNVs (pdSNVs) in cases (n = 144). Interestingly, two of them (one stop-gain and one missense variant) occurred in the same gene, BRSK2. Moreover, the identification of 9 severe de novo pdSNVs in genes not previously implicated in ASD (RASAL2, RAP1A, IRX5, SLC9A1, AGPAT3, MGAT3, RAB8B, MGAT5B, YME1L1), highlighted novel candidates. Potentially damaging CNVs (pdCNVs) provided support to the involvement of inherited variants in PHF3, NEGR1, TIAM1 and HOMER1 in neurodevelopmental disorders (NDD), although mostly acting as susceptibility factors with incomplete penetrance. Interpretation of identified pdSNVs/pdCNVs according to the ACMG guidelines led to a molecular diagnosis in 19/144 cases, but this figure represents a lower limit and is expected to increase thanks to further clarification of the role of likely pathogenic variants in new ASD/NDD candidates. In conclusion, our study strengthens the role of BRSK2 and other neurodevelopmental genes in ASD risk, highlights novel candidates and contributes to characterize the allelic diversity, mode of inheritance and phenotypic impact of de novo and inherited risk variants in ASD/NDD genes.
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Affiliation(s)
| | | | | | | | - Annio Posar
- IRCCS Istituto delle Scienze Neurologiche di Bologna
| | - Maria Scaduto
- IRCCS Istituto delle Scienze Neurologiche di Bologna
| | | | | | | | - Magali Rochat
- IRCCS Istituto delle Scienze Neurologiche di Bologna
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Matsudaira I, Yamaguchi R, Taki Y. Transmit Radiant Individuality to Offspring (TRIO) study: investigating intergenerational transmission effects on brain development. Front Psychiatry 2023; 14:1150973. [PMID: 37840799 PMCID: PMC10568142 DOI: 10.3389/fpsyt.2023.1150973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 09/07/2023] [Indexed: 10/17/2023] Open
Abstract
Intergenerational transmission is a crucial aspect of human development. Although prior studies have demonstrated the continuity of psychopathology and maladaptive upbringing environments between parents and offspring, the underlying neurobiological mechanisms remain unclear. We have begun a novel neuroimaging research project, the Transmit Radiant Individuality to Offspring (TRIO) study, which focuses on biological parent-offspring trios. The participants of the TRIO study were Japanese parent-offspring trios consisting of offspring aged 10-40 and their biological mother and father. Structural and functional brain images of all participants were acquired using magnetic resonance imaging (MRI). Saliva samples were collected for DNA analysis. We obtained psychosocial information, such as intelligence, mental health problems, personality traits, and experiences during the developmental period from each parent and offspring in the same manner as much as possible. By April 2023, we completed data acquisition from 174 trios consisting of fathers, mothers, and offspring. The target sample size was 310 trios. However, we plan to conduct genetic and epigenetic analyses, and the sample size is expected to be expanded further while developing this project into a multi-site collaborative study in the future. The TRIO study can challenge the elucidation of the mechanism of intergenerational transmission effects on human development by collecting diverse information from parents and offspring at the molecular, neural, and behavioral levels. Our study provides interdisciplinary insights into how individuals' lives are involved in the construction of the lives of their descendants in the subsequent generation.
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Affiliation(s)
- Izumi Matsudaira
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Sendai, Japan
- Smart-Aging Research Center, Tohoku University, Sendai, Japan
| | - Ryo Yamaguchi
- Japan Society for the Promotion of Science, Tokyo, Japan
- Department of Medical Sciences, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Yasuyuki Taki
- Smart-Aging Research Center, Tohoku University, Sendai, Japan
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Kipkemoi P, Kim HA, Christ B, O'Heir E, Allen J, Austin-Tse C, Baxter S, Brand H, Bryant S, Buser N, de Menil V, Eastman E, Murugasen S, Galvin A, Kombe M, Ngombo A, Mkubwa B, Mwangi P, Kipkoech C, Lovgren A, MacArthur DG, Melly B, Mwangasha K, Martin A, Nkambule LL, Sanchis-Juan A, Singer-Berk M, Talkowski ME, VanNoy G, van der Merwe C, Newton C, O'Donnell-Luria A, Abubakar A, Donald KA, Robinson EB. Phenotype and genetic analysis of data collected within the first year of NeuroDev. Neuron 2023; 111:2800-2810.e5. [PMID: 37463579 DOI: 10.1016/j.neuron.2023.06.010] [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: 07/22/2022] [Revised: 01/13/2023] [Accepted: 06/16/2023] [Indexed: 07/20/2023]
Abstract
Genetic association studies have made significant contributions to our understanding of the etiology of neurodevelopmental disorders (NDDs). However, these studies rarely focused on the African continent. The NeuroDev Project aims to address this diversity gap through detailed phenotypic and genetic characterization of children with NDDs from Kenya and South Africa. We present results from NeuroDev's first year of data collection, including phenotype data from 206 cases and clinical genetic analyses of 99 parent-child trios. Most cases met criteria for global developmental delay/intellectual disability (GDD/ID, 80.3%). Approximately half of the children with GDD/ID also met criteria for autism. Analysis of exome-sequencing data identified a pathogenic or likely pathogenic variant in 13 (17%) of the 75 cases from South Africa and 9 (38%) of the 24 cases from Kenya. Data from the trio pilot are publicly available, and the NeuroDev Project will continue to develop resources for the global genetics community.
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Affiliation(s)
- Patricia Kipkemoi
- Neuroscience Unit, KEMRI-Wellcome Trust, Center for Geographic Medicine Research Coast, Kilifi, Kenya; Complex Trait Genetics Department, Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Heesu Ally Kim
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Bjorn Christ
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital and University of Cape Town, 4th Floor ICH Building, Rondebosch, South Africa
| | - Emily O'Heir
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jake Allen
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christina Austin-Tse
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - Harrison Brand
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Sam Bryant
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nick Buser
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Victoria de Menil
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Emma Eastman
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital and University of Cape Town, 4th Floor ICH Building, Rondebosch, South Africa
| | - Serini Murugasen
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital and University of Cape Town, 4th Floor ICH Building, Rondebosch, South Africa
| | - Alice Galvin
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Martha Kombe
- Neuroscience Unit, KEMRI-Wellcome Trust, Center for Geographic Medicine Research Coast, Kilifi, Kenya
| | - Alfred Ngombo
- Neuroscience Unit, KEMRI-Wellcome Trust, Center for Geographic Medicine Research Coast, Kilifi, Kenya
| | - Beatrice Mkubwa
- Neuroscience Unit, KEMRI-Wellcome Trust, Center for Geographic Medicine Research Coast, Kilifi, Kenya
| | - Paul Mwangi
- Neuroscience Unit, KEMRI-Wellcome Trust, Center for Geographic Medicine Research Coast, Kilifi, Kenya
| | - Collins Kipkoech
- Neuroscience Unit, KEMRI-Wellcome Trust, Center for Geographic Medicine Research Coast, Kilifi, Kenya
| | - Alysia Lovgren
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Brigitte Melly
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital and University of Cape Town, 4th Floor ICH Building, Rondebosch, South Africa
| | - Katini Mwangasha
- Neuroscience Unit, KEMRI-Wellcome Trust, Center for Geographic Medicine Research Coast, Kilifi, Kenya
| | - Alicia Martin
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Lethukuthula L Nkambule
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Alba Sanchis-Juan
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA
| | | | - Michael E Talkowski
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Grace VanNoy
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Charles Newton
- Neuroscience Unit, KEMRI-Wellcome Trust, Center for Geographic Medicine Research Coast, Kilifi, Kenya; Department of Psychiatry, University of Oxford, London, UK; Institute of Human Development, Aga Khan University, Nairobi, Kenya
| | - Anne O'Donnell-Luria
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Amina Abubakar
- Neuroscience Unit, KEMRI-Wellcome Trust, Center for Geographic Medicine Research Coast, Kilifi, Kenya; Department of Psychiatry, University of Oxford, London, UK; Institute of Human Development, Aga Khan University, Nairobi, Kenya.
| | - Kirsten A Donald
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital and University of Cape Town, 4th Floor ICH Building, Rondebosch, South Africa; Neuroscience Institute, University of Cape Town, Groote Schuur Hospital, Observatory, Cape Town, South Africa.
| | - Elise B Robinson
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
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26
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Gianferante DM, Moore A, Spector LG, Wheeler W, Yang T, Hubbard A, Gorlick R, Patiño-Garcia A, Lecanda F, Flanagan AM, Amary F, Andrulis IL, Wunder JS, Thomas DM, Ballinger ML, Serra M, Hattinger C, Demerath E, Johnson W, Birmann BM, De Vivo I, Giles G, Teras LR, Arslan A, Vermeulen R, Sample J, Freedman ND, Huang WY, Chanock SJ, Savage SA, Berndt SI, Mirabello L. Genetically inferred birthweight, height, and puberty timing and risk of osteosarcoma. Cancer Epidemiol 2023:102432. [PMID: 37596165 PMCID: PMC10869637 DOI: 10.1016/j.canep.2023.102432] [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: 05/04/2023] [Accepted: 07/14/2023] [Indexed: 08/20/2023]
Abstract
INTRODUCTION Several studies have linked increased risk of osteosarcoma with tall stature, high birthweight, and early puberty, although evidence is inconsistent. We used genetic risk scores (GRS) based on established genetic loci for these traits and evaluated associations between genetically inferred birthweight, height, and puberty timing with osteosarcoma. METHODS Using genotype data from two genome-wide association studies, totaling 1039 cases and 2923 controls of European ancestry, association analyses were conducted using logistic regression for each study and meta-analyzed to estimate pooled odds ratios (ORs) and 95% confidence intervals (CIs). Subgroup analyses were conducted by case diagnosis age, metastasis status, tumor location, tumor histology, and presence of a known pathogenic variant in a cancer susceptibility gene. RESULTS Genetically inferred higher birthweight was associated with an increased risk of osteosarcoma (OR =1.59, 95% CI 1.07-2.38, P = 0.02). This association was strongest in cases without metastatic disease (OR =2.46, 95% CI 1.44-4.19, P = 9.5 ×10-04). Although there was no overall association between osteosarcoma and genetically inferred taller stature (OR=1.06, 95% CI 0.96-1.17, P = 0.28), the GRS for taller stature was associated with an increased risk of osteosarcoma in 154 cases with a known pathogenic cancer susceptibility gene variant (OR=1.29, 95% CI 1.03-1.63, P = 0.03). There were no significant associations between the GRS for puberty timing and osteosarcoma. CONCLUSION A genetic propensity to higher birthweight was associated with increased osteosarcoma risk, suggesting that shared genetic factors or biological pathways that affect birthweight may contribute to osteosarcoma pathogenesis.
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Affiliation(s)
| | - Amy Moore
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Rockville, MD, USA
| | - Logan G Spector
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA
| | | | - Tianzhong Yang
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Aubrey Hubbard
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Rockville, MD, USA
| | - Richard Gorlick
- University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ana Patiño-Garcia
- Department of Pediatrics and Solid Tumor Division CIMA, IdiSNA, Clínica Universidad de Navarra, Pamplona, Spain
| | - Fernando Lecanda
- Center for Applied Medical Research (CIMA)-University of Navarra, IdiSNA, and CIBERONC, Pamplona, Spain
| | - Adrienne M Flanagan
- UCL Cancer Institute, Huntley Street, London WC1E 6BT, UK; Royal National Orthopaedic Hospital NHS Trust, Stanmore, Middlesex HA7 4LP, UK
| | - Fernanda Amary
- Royal National Orthopaedic Hospital NHS Trust, Stanmore, Middlesex HA7 4LP, UK
| | - Irene L Andrulis
- Litwin Centre for Cancer Genetics, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Jay S Wunder
- Litwin Centre for Cancer Genetics, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - David M Thomas
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia; St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Mandy L Ballinger
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia; St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Massimo Serra
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy; IRCCS Istituto Ortopedico Rizzoli, Osteoncology, Bone and Soft Tissue Sarcomas and Innovative Therapies, Pharmacogenomics and Pharmacogenetics Research Unit, Bologna, Italy
| | - Claudia Hattinger
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy; IRCCS Istituto Ortopedico Rizzoli, Osteoncology, Bone and Soft Tissue Sarcomas and Innovative Therapies, Pharmacogenomics and Pharmacogenetics Research Unit, Bologna, Italy
| | - Ellen Demerath
- Division of Epidemiology and Clinical Research, School of Public Health, UMN, USA
| | - Will Johnson
- School of Sport, Exercise, and Health Sciences, University of Loughborough, UK
| | - Brenda M Birmann
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Immaculata De Vivo
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Graham Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia; Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Lauren R Teras
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Alan Arslan
- Department of Obstetrics and Gynecology, New York School of Medicine, New York, NY, USA; Department of Population Health, New York University School of Medicine, New York, NY, USA
| | - Roel Vermeulen
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands; Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jeannette Sample
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Neal D Freedman
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Rockville, MD, USA
| | - Wen-Yi Huang
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Rockville, MD, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Rockville, MD, USA
| | - Sharon A Savage
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Rockville, MD, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Rockville, MD, USA
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Rockville, MD, USA.
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27
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Cirnigliaro M, Chang TS, Arteaga SA, Pérez-Cano L, Ruzzo EK, Gordon A, Bicks LK, Jung JY, Lowe JK, Wall DP, Geschwind DH. The contributions of rare inherited and polygenic risk to ASD in multiplex families. Proc Natl Acad Sci U S A 2023; 120:e2215632120. [PMID: 37506195 PMCID: PMC10400943 DOI: 10.1073/pnas.2215632120] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 06/13/2023] [Indexed: 07/30/2023] Open
Abstract
Autism spectrum disorder (ASD) has a complex genetic architecture involving contributions from both de novo and inherited variation. Few studies have been designed to address the role of rare inherited variation or its interaction with common polygenic risk in ASD. Here, we performed whole-genome sequencing of the largest cohort of multiplex families to date, consisting of 4,551 individuals in 1,004 families having two or more autistic children. Using this study design, we identify seven previously unrecognized ASD risk genes supported by a majority of rare inherited variants, finding support for a total of 74 genes in our cohort and a total of 152 genes after combined analysis with other studies. Autistic children from multiplex families demonstrate an increased burden of rare inherited protein-truncating variants in known ASD risk genes. We also find that ASD polygenic score (PGS) is overtransmitted from nonautistic parents to autistic children who also harbor rare inherited variants, consistent with combinatorial effects in the offspring, which may explain the reduced penetrance of these rare variants in parents. We also observe that in addition to social dysfunction, language delay is associated with ASD PGS overtransmission. These results are consistent with an additive complex genetic risk architecture of ASD involving rare and common variation and further suggest that language delay is a core biological feature of ASD.
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Affiliation(s)
- Matilde Cirnigliaro
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA90095
| | - Timothy S. Chang
- Movement Disorders Program, Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA90095
| | - Stephanie A. Arteaga
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA90095
| | - Laura Pérez-Cano
- STALICLA Discovery and Data Science Unit, World Trade Center, Barcelona08039, Spain
| | - Elizabeth K. Ruzzo
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA90095
- Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA90095
| | - Aaron Gordon
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA90095
| | - Lucy K. Bicks
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA90095
| | - Jae-Yoon Jung
- Department of Pediatrics, Division of Systems Medicine, Stanford University, Stanford, CA94304
- Department of Biomedical Data Science, Stanford University, Stanford, CA94305
| | - Jennifer K. Lowe
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA90095
- Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA90095
| | - Dennis P. Wall
- Department of Pediatrics, Division of Systems Medicine, Stanford University, Stanford, CA94304
- Department of Biomedical Data Science, Stanford University, Stanford, CA94305
| | - Daniel H. Geschwind
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA90095
- Movement Disorders Program, Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA90095
- Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA90095
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA90095
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28
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Rolland T, Cliquet F, Anney RJL, Moreau C, Traut N, Mathieu A, Huguet G, Duan J, Warrier V, Portalier S, Dry L, Leblond CS, Douard E, Amsellem F, Malesys S, Maruani A, Toro R, Børglum AD, Grove J, Baron-Cohen S, Packer A, Chung WK, Jacquemont S, Delorme R, Bourgeron T. Phenotypic effects of genetic variants associated with autism. Nat Med 2023; 29:1671-1680. [PMID: 37365347 PMCID: PMC10353945 DOI: 10.1038/s41591-023-02408-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 05/19/2023] [Indexed: 06/28/2023]
Abstract
While over 100 genes have been associated with autism, little is known about the prevalence of variants affecting them in individuals without a diagnosis of autism. Nor do we fully appreciate the phenotypic diversity beyond the formal autism diagnosis. Based on data from more than 13,000 individuals with autism and 210,000 undiagnosed individuals, we estimated the odds ratios for autism associated to rare loss-of-function (LoF) variants in 185 genes associated with autism, alongside 2,492 genes displaying intolerance to LoF variants. In contrast to autism-centric approaches, we investigated the correlates of these variants in individuals without a diagnosis of autism. We show that these variants are associated with a small but significant decrease in fluid intelligence, qualification level and income and an increase in metrics related to material deprivation. These effects were larger for autism-associated genes than in other LoF-intolerant genes. Using brain imaging data from 21,040 individuals from the UK Biobank, we could not detect significant differences in the overall brain anatomy between LoF carriers and non-carriers. Our results highlight the importance of studying the effect of the genetic variants beyond categorical diagnosis and the need for more research to understand the association between these variants and sociodemographic factors, to best support individuals carrying these variants.
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Affiliation(s)
- Thomas Rolland
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, IUF, Université Paris Cité, Paris, France.
| | - Freddy Cliquet
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, IUF, Université Paris Cité, Paris, France
| | - Richard J L Anney
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Clara Moreau
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, IUF, Université Paris Cité, Paris, France
| | - Nicolas Traut
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, IUF, Université Paris Cité, Paris, France
- Center for Research and Interdisciplinarity (CRI), Université Paris Descartes, Paris, France
| | - Alexandre Mathieu
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, IUF, Université Paris Cité, Paris, France
| | - Guillaume Huguet
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, Québec, Canada
| | - Jinjie Duan
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Department of Biomedicine and the iSEQ Centre, Aarhus University, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, Aarhus, Denmark
| | - Varun Warrier
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, UK
| | - Swan Portalier
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, IUF, Université Paris Cité, Paris, France
| | - Louise Dry
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, IUF, Université Paris Cité, Paris, France
| | - Claire S Leblond
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, IUF, Université Paris Cité, Paris, France
| | - Elise Douard
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, Québec, Canada
- Département de Pédiatrie, Université de Montréal, Montréal, Québec, Canada
| | - Frédérique Amsellem
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, IUF, Université Paris Cité, Paris, France
- Department of Child and Adolescent Psychiatry, Robert Debré Hospital, APHP, Paris, France
| | - Simon Malesys
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, IUF, Université Paris Cité, Paris, France
| | - Anna Maruani
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, IUF, Université Paris Cité, Paris, France
- Department of Child and Adolescent Psychiatry, Robert Debré Hospital, APHP, Paris, France
| | - Roberto Toro
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, IUF, Université Paris Cité, Paris, France
- Center for Research and Interdisciplinarity (CRI), Université Paris Descartes, Paris, France
| | - Anders D Børglum
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Department of Biomedicine and the iSEQ Centre, Aarhus University, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, Aarhus, Denmark
| | - Jakob Grove
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Department of Biomedicine and the iSEQ Centre, Aarhus University, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Simon Baron-Cohen
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, UK
| | | | - Wendy K Chung
- Simons Foundation, New York, NY, USA
- Department of Pediatrics, Columbia University Medical Center, New York, NY, USA
| | - Sébastien Jacquemont
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, Québec, Canada
- Département de Pédiatrie, Université de Montréal, Montréal, Québec, Canada
| | - Richard Delorme
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, IUF, Université Paris Cité, Paris, France
- Department of Child and Adolescent Psychiatry, Robert Debré Hospital, APHP, Paris, France
| | - Thomas Bourgeron
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, IUF, Université Paris Cité, Paris, France.
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LaPierre N, Fu B, Turnbull S, Eskin E, Sankararaman S. Leveraging family data to design Mendelian randomization that is provably robust to population stratification. Genome Res 2023; 33:1032-1041. [PMID: 37197991 PMCID: PMC10538495 DOI: 10.1101/gr.277664.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 04/16/2023] [Indexed: 05/19/2023]
Abstract
Mendelian randomization (MR) has emerged as a powerful approach to leverage genetic instruments to infer causality between pairs of traits in observational studies. However, the results of such studies are susceptible to biases owing to weak instruments, as well as the confounding effects of population stratification and horizontal pleiotropy. Here, we show that family data can be leveraged to design MR tests that are provably robust to confounding from population stratification, assortative mating, and dynastic effects. We show in simulations that our approach, MR-Twin, is robust to confounding from population stratification and is not affected by weak instrument bias, whereas standard MR methods yield inflated false positive rates. We then conduct an exploratory analysis of MR-Twin and other MR methods applied to 121 trait pairs in the UK Biobank data set. Our results suggest that confounding from population stratification can lead to false positives for existing MR methods, whereas MR-Twin is immune to this type of confounding, and that MR-Twin can help assess whether traditional approaches may be inflated owing to confounding from population stratification.
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Affiliation(s)
- Nathan LaPierre
- Department of Computer Science, University of California Los Angeles, Los Angeles, California 90095, USA;
| | - Boyang Fu
- Department of Computer Science, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Steven Turnbull
- Department of Statistics, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Eleazar Eskin
- Department of Computer Science, University of California Los Angeles, Los Angeles, California 90095, USA
- Department of Computational Medicine, University of California Los Angeles, Los Angeles, California 90095, USA
- Department of Human Genetics, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Sriram Sankararaman
- Department of Computer Science, University of California Los Angeles, Los Angeles, California 90095, USA;
- Department of Computational Medicine, University of California Los Angeles, Los Angeles, California 90095, USA
- Department of Human Genetics, University of California Los Angeles, Los Angeles, California 90095, USA
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30
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Mpoulimari I, Zintzaras E. Analysis of convergence of linkage and association studies in autism spectrum disorders. Psychiatr Genet 2023; 33:113-124. [PMID: 37212558 DOI: 10.1097/ypg.0000000000000341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Autism spectrum disorder (ASD) is a clinically and genetically heterogeneous group of pervasive neurodevelopmental disorders with a strong hereditary component. Although genome-wide linkage studies (GWLS) and [genome-wide association studies (GWAS)] have previously identified hundreds of ASD risk gene loci, the results remain inconclusive. In this study, a genomic convergence approach of GWAS and GWLS for ASD was implemented for the first time in order to identify genomic loci supported by both methods. A database with 32 GWLS and five GWAS for ASD was created. Convergence was quantified as the proportion of significant GWAS markers located within linked regions. Convergence was not found to be significantly higher than expected by chance (z-test = 1,177, P = 0,239). Although convergence is supportive of genuine effects, the lack of agreement between GWLS and GWAS is also indicative that these studies are designed to answer different questions and are not equally well suited for deciphering the genetics of complex traits.
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Affiliation(s)
- Ioanna Mpoulimari
- Department of Biomathematics, Faculty of Medicine, University of Thessaly, Larissa, Greece
| | - Elias Zintzaras
- Department of Biomathematics, Faculty of Medicine, University of Thessaly, Larissa, Greece
- The Institute for Clinical Research and Health Policy Studies, Tufts Medical Center, Tufts University School of Medicine, Boston, Massachusetts, USA
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31
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Carbonell AU, Freire-Cobo C, Deyneko IV, Dobariya S, Erdjument-Bromage H, Clipperton-Allen AE, Page DT, Neubert TA, Jordan BA. Comparing synaptic proteomes across five mouse models for autism reveals converging molecular similarities including deficits in oxidative phosphorylation and Rho GTPase signaling. Front Aging Neurosci 2023; 15:1152562. [PMID: 37255534 PMCID: PMC10225639 DOI: 10.3389/fnagi.2023.1152562] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 04/17/2023] [Indexed: 06/01/2023] Open
Abstract
Specific and effective treatments for autism spectrum disorder (ASD) are lacking due to a poor understanding of disease mechanisms. Here we test the idea that similarities between diverse ASD mouse models are caused by deficits in common molecular pathways at neuronal synapses. To do this, we leverage the availability of multiple genetic models of ASD that exhibit shared synaptic and behavioral deficits and use quantitative mass spectrometry with isobaric tandem mass tagging (TMT) to compare their hippocampal synaptic proteomes. Comparative analyses of mouse models for Fragile X syndrome (Fmr1 knockout), cortical dysplasia focal epilepsy syndrome (Cntnap2 knockout), PTEN hamartoma tumor syndrome (Pten haploinsufficiency), ANKS1B syndrome (Anks1b haploinsufficiency), and idiopathic autism (BTBR+) revealed several common altered cellular and molecular pathways at the synapse, including changes in oxidative phosphorylation, and Rho family small GTPase signaling. Functional validation of one of these aberrant pathways, Rac1 signaling, confirms that the ANKS1B model displays altered Rac1 activity counter to that observed in other models, as predicted by the bioinformatic analyses. Overall similarity analyses reveal clusters of synaptic profiles, which may form the basis for molecular subtypes that explain genetic heterogeneity in ASD despite a common clinical diagnosis. Our results suggest that ASD-linked susceptibility genes ultimately converge on common signaling pathways regulating synaptic function and propose that these points of convergence are key to understanding the pathogenesis of this disorder.
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Affiliation(s)
- Abigail U. Carbonell
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Carmen Freire-Cobo
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Ilana V. Deyneko
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Saunil Dobariya
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Hediye Erdjument-Bromage
- Department of Neuroscience and Physiology, New York University Grossman School of Medicine, New York, NY, United States
| | - Amy E. Clipperton-Allen
- Department of Neuroscience, The Scripps Research Institute Florida, Jupiter, FL, United States
| | - Damon T. Page
- Department of Neuroscience, The Scripps Research Institute Florida, Jupiter, FL, United States
| | - Thomas A. Neubert
- Department of Neuroscience and Physiology, New York University Grossman School of Medicine, New York, NY, United States
| | - Bryen A. Jordan
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, United States
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, NY, United States
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32
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Rammos A, Kirov G, Hubbard L, Walters JTR, Holmans P, Owen MJ, O'Donovan MC, Rees E. Family-based analysis of the contribution of rare and common genetic variants to school performance in schizophrenia. Mol Psychiatry 2023; 28:2081-2087. [PMID: 36914811 PMCID: PMC10575776 DOI: 10.1038/s41380-023-02013-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 02/15/2023] [Accepted: 02/22/2023] [Indexed: 03/16/2023]
Abstract
Impaired cognition in schizophrenia is associated with worse functional outcomes. While genetic factors are known to contribute to variation in cognition in schizophrenia, few rare coding variants with strong effects have been identified, and the relative effects from de novo, inherited and non-transmitted alleles are unknown. We used array and exome sequencing data from 656 proband-parent trios to examine the contribution of common and rare variants to school performance, and by implication cognitive function, in schizophrenia. Parental transmission of common alleles contributing to higher educational attainment (p value = 0.00015; OR = 2.63) and intelligence (p value = 0.00009; OR = 2.80), but not to schizophrenia, were associated with higher proband school performance. No significant effects were seen for non-transmitted parental common alleles. Probands with lower school performance were enriched for damaging de novo coding variants in genes associated with developmental disorders (DD) (p value = 0.00026; OR = 11.6). Damaging, ultra-rare coding variants in DD genes that were transmitted or non-transmitted from parents, had no effects on school performance. Among probands with lower school performance, those with damaging de novo coding variants in DD genes had a higher rate of comorbid mild intellectual disability (p value = 0.0002; OR = 15.6). Overall, we provide evidence for rare and common genetic contributions to school performance in schizophrenia. The strong effects for damaging de novo coding variants in DD genes provide further evidence that cognitive impairment in schizophrenia has a shared aetiology with developmental disorders. Furthermore, we report no evidence in this sample that non-transmitted parental common alleles for cognitive traits contributed to school performance in schizophrenia via indirect effects on the environment.
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Affiliation(s)
- Alexandros Rammos
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK.
| | - George Kirov
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Leon Hubbard
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - James T R Walters
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Peter Holmans
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Michael J Owen
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Michael C O'Donovan
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Elliott Rees
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK.
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More RP, Warrier V, Brunel H, Buckingham C, Smith P, Allison C, Holt R, Bradshaw CR, Baron-Cohen S. Identifying rare genetic variants in 21 highly multiplex autism families: the role of diagnosis and autistic traits. Mol Psychiatry 2023; 28:2148-2157. [PMID: 36702863 PMCID: PMC10575770 DOI: 10.1038/s41380-022-01938-4] [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: 05/18/2022] [Revised: 12/15/2022] [Accepted: 12/19/2022] [Indexed: 01/27/2023]
Abstract
Autism is a highly heritable, heterogeneous, neurodevelopmental condition. Large-scale genetic studies, predominantly focussing on simplex families and clinical diagnoses of autism have identified hundreds of genes associated with autism. Yet, the contribution of these classes of genes to multiplex families and autistic traits still warrants investigation. Here, we conducted whole-genome sequencing of 21 highly multiplex autism families, with at least three autistic individuals in each family, to prioritise genes associated with autism. Using a combination of both autistic traits and clinical diagnosis of autism, we identify rare variants in genes associated with autism, and related neurodevelopmental conditions in multiple families. We identify a modest excess of these variants in autistic individuals compared to individuals without an autism diagnosis. Finally, we identify a convergence of the genes identified in molecular pathways related to development and neurogenesis. In sum, our analysis provides initial evidence to demonstrate the value of integrating autism diagnosis and autistic traits to prioritise genes.
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Affiliation(s)
- Ravi Prabhakar More
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom.
| | - Varun Warrier
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom
| | - Helena Brunel
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom
| | - Clara Buckingham
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom
| | - Paula Smith
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom
| | - Carrie Allison
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom
| | - Rosemary Holt
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom
| | | | - Simon Baron-Cohen
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom.
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34
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Kaminski VDL, Michita RT, Ellwanger JH, Veit TD, Schuch JB, Riesgo RDS, Roman T, Chies JAB. Exploring potential impacts of pregnancy-related maternal immune activation and extracellular vesicles on immune alterations observed in autism spectrum disorder. Heliyon 2023; 9:e15593. [PMID: 37305482 PMCID: PMC10256833 DOI: 10.1016/j.heliyon.2023.e15593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 04/03/2023] [Accepted: 04/14/2023] [Indexed: 06/13/2023] Open
Abstract
Autism Spectrum Disorder (ASD) is a set of neurodevelopmental disorders usually observed in early life, with impacts on behavioral and social skills. Incidence of ASD has been dramatically increasing worldwide, possibly due to increase in awareness/diagnosis as well as to genetic and environmental triggers. Currently, it is estimated that ∼1% of the world population presents ASD symptoms. In addition to its genetic background, environmental and immune-related factors also influence the ASD etiology. In this context, maternal immune activation (MIA) has recently been suggested as a component potentially involved in ASD development. In addition, extracellular vesicles (EVs) are abundant at the maternal-fetal interface and are actively involved in the immunoregulation required for a healthy pregnancy. Considering that alterations in concentration and content of EVs have also been associated with ASD, this article raises a debate about the potential roles of EVs in the processes surrounding MIA. This represents the major differential of the present review compared to other ASD studies. To support the suggested correlations and hypotheses, findings regarding the roles of EVs during pregnancy and potential influences on ASD are discussed, along with a review and update concerning the participation of infections, cytokine unbalances, overweight and obesity, maternal anti-fetal brain antibodies, maternal fever, gestational diabetes, preeclampsia, labor type and microbiota unbalances in MIA and ASD.
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Affiliation(s)
- Valéria de Lima Kaminski
- Laboratório de Imunobiologia e Imunogenética, Departamento de Genética, Universidade Federal do Rio Grande do Sul – UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul – UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
- Programa de Pós-Graduação em Biotecnologia, Laboratório de Imunologia Aplicada, Instituto de Ciência e Tecnologia - ICT, Universidade Federal de São Paulo - UNIFESP, São José dos Campos, São Paulo, Brazil
| | - Rafael Tomoya Michita
- Laboratório de Genética Molecular Humana, Universidade Luterana do Brasil - ULBRA, Canoas, Rio Grande do Sul, Brazil
| | - Joel Henrique Ellwanger
- Laboratório de Imunobiologia e Imunogenética, Departamento de Genética, Universidade Federal do Rio Grande do Sul – UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul – UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
| | - Tiago Degani Veit
- Instituto de Ciências Básicas da Saúde, Departmento de Microbiologia, Imunologia e Parasitologia, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
| | - Jaqueline Bohrer Schuch
- Centro de Pesquisa em Álcool e Drogas, Hospital de Clínicas de Porto Alegre, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
- Programa de Pós-Graduação em Psiquiatria e Ciências do Comportamento, Universidade Federal do Rio Grande do Sul – UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
| | - Rudimar dos Santos Riesgo
- Child Neurology Unit, Hospital de Clínicas de Porto Alegre, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
| | - Tatiana Roman
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul – UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
| | - José Artur Bogo Chies
- Laboratório de Imunobiologia e Imunogenética, Departamento de Genética, Universidade Federal do Rio Grande do Sul – UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul – UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
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35
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Brito A, Franco F, Brentani H, Beltrão-Braga PCB. Assessment of vulnerability dimensions considering Family History and environmental interplay in Autism Spectrum Disorder. BMC Psychiatry 2023; 23:254. [PMID: 37059985 PMCID: PMC10105456 DOI: 10.1186/s12888-023-04747-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 04/03/2023] [Indexed: 04/16/2023] Open
Abstract
BACKGROUND Despite previous studies have recently shown Autism Spectrum Disorders (ASD) as having a strong genetics background, over a minimum environmental background, no study up to date has investigated the interplay between genetics and environment. METHODS We have collected data regarding Family History (FH) and Environmental Factors (EF) from 2,141 individuals with ASD and their caretakers throughout Brazil, based on an online questionnaire. Most of the ASD individuals were males (81%) and the average age was 02 years minimum for males and females, and the maximum age was 41 years for males and 54 for females. People from all states in Brazil have answered the questionnaire. Genetic inheritance was obtained based on the declared FH of Psychiatric and Neurological diagnosis. As for EF, exposure to risk factors during pregnancy was considered, like infections, diabetes, drugs/chemicals exposure, socioeconomic, and psychological factors. Respondents were invited to answer the questionnaire in lectures given throughout Brazil, and by the social networks of the NGO "The Tooth Fairy Project". A Multiple Correspondence Analysis (MCA) was conducted to search vulnerability dimensions, and a Cluster Analysis was conducted to classify and identify the subgroups. RESULTS Regarding EF, social and psychological exposures contributed to the first two dimensions. Concerning FH, the first dimension represented psychiatric FH, while the second represented neurological FH. When analyzed together, EF and FH contributed to two new dimensions: 1. psychiatric FH, and 2. a psychosocial component. Using Cluster Analysis, it was not possible to isolate subgroups by genetic vulnerability or environmental exposure. Instead, a gradient of psychiatric FH with similar contributions of EF was observed. CONCLUSION In this study, it was not possible to isolate groups of patients that correspond to only one component, but rather a continuum with different compositions of genetic and environmental interplay.
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Affiliation(s)
- Anita Brito
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
- Scientific Platform Pasteur-USP, São Paulo, SP, Brazil
| | - Felipe Franco
- Psychiatry Institute, University of São Paulo's Faculty of Medicine (IPq-FMUSP), São Paulo, SP, Brazil
- Interunit Postgraduate Program On Bioinformatics, Institute of Mathematics and Statistics (IME), University of São Paulo, São Paulo, SP, Brazil
| | - Helena Brentani
- Psychiatry Institute, University of São Paulo's Faculty of Medicine (IPq-FMUSP), São Paulo, SP, Brazil
| | - Patrícia Cristina Baleeiro Beltrão-Braga
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil.
- Scientific Platform Pasteur-USP, São Paulo, SP, Brazil.
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36
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Perini S, Filosi M, Domenici E. Candidate biomarkers from the integration of methylation and gene expression in discordant autistic sibling pairs. Transl Psychiatry 2023; 13:109. [PMID: 37012247 PMCID: PMC10070641 DOI: 10.1038/s41398-023-02407-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 03/18/2023] [Accepted: 03/21/2023] [Indexed: 04/05/2023] Open
Abstract
While the genetics of autism spectrum disorders (ASD) has been intensively studied, resulting in the identification of over 100 putative risk genes, the epigenetics of ASD has received less attention, and results have been inconsistent across studies. We aimed to investigate the contribution of DNA methylation (DNAm) to the risk of ASD and identify candidate biomarkers arising from the interaction of epigenetic mechanisms with genotype, gene expression, and cellular proportions. We performed DNAm differential analysis using whole blood samples from 75 discordant sibling pairs of the Italian Autism Network collection and estimated their cellular composition. We studied the correlation between DNAm and gene expression accounting for the potential effects of different genotypes on DNAm. We showed that the proportion of NK cells was significantly reduced in ASD siblings suggesting an imbalance in their immune system. We identified differentially methylated regions (DMRs) involved in neurogenesis and synaptic organization. Among candidate loci for ASD, we detected a DMR mapping to CLEC11A (neighboring SHANK1) where DNAm and gene expression were significantly and negatively correlated, independently from genotype effects. As reported in previous studies, we confirmed the involvement of immune functions in the pathophysiology of ASD. Notwithstanding the complexity of the disorder, suitable biomarkers such as CLEC11A and its neighbor SHANK1 can be discovered using integrative analyses even with peripheral tissues.
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Affiliation(s)
- Samuel Perini
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento (TN), Italy
| | - Michele Filosi
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento (TN), Italy
- EURAC Research, Bolzano, Italy
| | - Enrico Domenici
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento (TN), Italy.
- Fondazione The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto (TN), Italy.
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37
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Mollon J, Almasy L, Jacquemont S, Glahn DC. The contribution of copy number variants to psychiatric symptoms and cognitive ability. Mol Psychiatry 2023; 28:1480-1493. [PMID: 36737482 PMCID: PMC10213133 DOI: 10.1038/s41380-023-01978-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 01/18/2023] [Accepted: 01/20/2023] [Indexed: 02/05/2023]
Abstract
Copy number variants (CNVs) are deletions and duplications of DNA sequence. The most frequently studied CNVs, which are described in this review, are recurrent CNVs that occur in the same locations on the genome. These CNVs have been strongly implicated in neurodevelopmental disorders, namely autism spectrum disorder (ASD), intellectual disability (ID), and developmental delay (DD), but also in schizophrenia. More recent work has also shown that CNVs increase risk for other psychiatric disorders, namely, depression, bipolar disorder, and post-traumatic stress disorder. Many of the same CNVs are implicated across all of these disorders, and these neuropsychiatric CNVs are also associated with cognitive ability in the general population, as well as with structural and functional brain alterations. Neuropsychiatric CNVs also show incomplete penetrance, such that carriers do not always develop any psychiatric disorder, and may show only mild symptoms, if any. Variable expressivity, whereby the same CNVs are associated with many different phenotypes of varied severity, also points to highly complex mechanisms underlying disease risk in CNV carriers. Comprehensive and longitudinal phenotyping studies of individual CNVs have provided initial insights into these mechanisms. However, more work is needed to estimate and predict the effect of non-recurrent, ultra-rare CNVs, which also contribute to psychiatric and cognitive outcomes. Moreover, delineating the broader phenotypic landscape of neuropsychiatric CNVs in both clinical and general population cohorts may also offer important mechanistic insights.
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Affiliation(s)
- Josephine Mollon
- Department of Psychiatry, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Laura Almasy
- Department of Genetics, Perelman School of Medicine, Penn-CHOP Lifespan Brain Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Sebastien Jacquemont
- Department of Pediatrics, Université de Montréal, Montreal, QC, Canada
- Center Hospitalier Universitaire Sainte-Justine Research Center, Montreal, QC, Canada
| | - David C Glahn
- Department of Psychiatry, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Olin Neuropsychiatry Research Center, Institute of Living, Hartford, CT, USA
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38
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Li H, Mazumder R, Lin X. Accurate and Efficient Estimation of Local Heritability using Summary Statistics and LD Matrix. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.08.527759. [PMID: 36798290 PMCID: PMC9934676 DOI: 10.1101/2023.02.08.527759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Existing SNP-heritability estimation methods that leverage GWAS summary statistics produce estimators that are less efficient than the restricted maximum likelihood (REML) estimator using individual-level data under linear mixed models (LMMs). Increasing the precision of a heritability estimator is particularly important for regional analyses, as local genetic variances tend to be small. We introduce a new estimator for local heritability, "HEELS", which attains comparable statistical efficiency as REML (\emph{i.e.} relative efficiency greater than 92%) but only requires summary-level statistics -- Z-scores from the marginal association tests plus the empirical LD matrix. HEELS significantly improves the statistical efficiency of the existing summary-statistics-based heritability estimators-- for instance, HEELS produces heritability estimates that are more than 3-fold and 7-times less variable than GRE and LDSC, respectively. Moreover, we introduce a unified framework to evaluate and compare the performance of different LD approximation strategies. We propose representing the empirical LD as the sum of a low-rank matrix and a banded matrix. This approximation not only reduces the storage and memory cost of using the LD matrix, but also improves the computational efficiency of the HEELS estimation. We demonstrate the statistical efficiency of HEELS and the advantages of our proposed LD approximation strategies both in simulations and through empirical analyses of the UK Biobank data.
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39
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Stella C, Díaz-Caneja CM, Penzol MJ, García-Alcón A, Solís A, Andreu-Bernabeu Á, Gurriarán X, Arango C, Parellada M, González-Peñas J. Analysis of common genetic variation across targets of microRNAs dysregulated both in ASD and epilepsy reveals negative correlation. Front Genet 2023; 14:1072563. [PMID: 36968597 PMCID: PMC10034058 DOI: 10.3389/fgene.2023.1072563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 02/20/2023] [Indexed: 03/11/2023] Open
Abstract
Genetic overlap involving rare disrupting mutations may contribute to high comorbidity rates between autism spectrum disorders and epilepsy. Despite their polygenic nature, genome-wide association studies have not reported a significant contribution of common genetic variation to comorbidity between both conditions. Analysis of common genetic variation affecting specific shared pathways such as miRNA dysregulation could help to elucidate the polygenic mechanisms underlying comorbidity between autism spectrum disorders and epilepsy. We evaluated here the role of common predisposing variation to autism spectrum disorders and epilepsy across target genes of 14 miRNAs selected through bibliographic research as being dysregulated in both disorders. We considered 4,581 target genes from various in silico sources. We described negative genetic correlation between autism spectrum disorders and epilepsy across variants located within target genes of the 14 miRNAs selected (p = 0.0228). Moreover, polygenic transmission disequilibrium test on an independent cohort of autism spectrum disorders trios (N = 233) revealed an under-transmission of autism spectrum disorders predisposing alleles within miRNAs’ target genes across autism spectrum disorders trios without comorbid epilepsy, thus reinforcing the negative relationship at the common genetic variation between both traits. Our study provides evidence of a negative relationship between autism spectrum disorders and epilepsy at the common genetic variation level that becomes more evident when focusing on the miRNA regulatory networks, which contrasts with observed clinical comorbidity and results from rare variation studies. Our findings may help to conceptualize the genetic heterogeneity and the comorbidity with epilepsy in autism spectrum disorders.
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Affiliation(s)
- Carol Stella
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- CIBERSAM, Centro Investigación Biomédica en Red Salud Mental, Instituto de Salud Carlos III, Madrid, Spain
| | - Covadonga M. Díaz-Caneja
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- CIBERSAM, Centro Investigación Biomédica en Red Salud Mental, Instituto de Salud Carlos III, Madrid, Spain
- School of Medicine, Universidad Complutense, Madrid, Spain
| | - Maria Jose Penzol
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- CIBERSAM, Centro Investigación Biomédica en Red Salud Mental, Instituto de Salud Carlos III, Madrid, Spain
| | - Alicia García-Alcón
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- CIBERSAM, Centro Investigación Biomédica en Red Salud Mental, Instituto de Salud Carlos III, Madrid, Spain
| | - Andrea Solís
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- CIBERSAM, Centro Investigación Biomédica en Red Salud Mental, Instituto de Salud Carlos III, Madrid, Spain
| | - Álvaro Andreu-Bernabeu
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- CIBERSAM, Centro Investigación Biomédica en Red Salud Mental, Instituto de Salud Carlos III, Madrid, Spain
| | - Xaquín Gurriarán
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- CIBERSAM, Centro Investigación Biomédica en Red Salud Mental, Instituto de Salud Carlos III, Madrid, Spain
| | - Celso Arango
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- CIBERSAM, Centro Investigación Biomédica en Red Salud Mental, Instituto de Salud Carlos III, Madrid, Spain
- School of Medicine, Universidad Complutense, Madrid, Spain
| | - Mara Parellada
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- CIBERSAM, Centro Investigación Biomédica en Red Salud Mental, Instituto de Salud Carlos III, Madrid, Spain
- School of Medicine, Universidad Complutense, Madrid, Spain
| | - Javier González-Peñas
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- CIBERSAM, Centro Investigación Biomédica en Red Salud Mental, Instituto de Salud Carlos III, Madrid, Spain
- *Correspondence: Javier González-Peñas,
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Pintacuda G, Hsu YHH, Tsafou K, Li KW, Martín JM, Riseman J, Biagini JC, Ching JK, Mena D, Gonzalez-Lozano MA, Egri SB, Jaffe J, Smit AB, Fornelos N, Eggan KC, Lage K. Protein interaction studies in human induced neurons indicate convergent biology underlying autism spectrum disorders. CELL GENOMICS 2023; 3:100250. [PMID: 36950384 PMCID: PMC10025425 DOI: 10.1016/j.xgen.2022.100250] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 10/18/2022] [Accepted: 12/28/2022] [Indexed: 01/26/2023]
Abstract
Autism spectrum disorders (ASDs) have been linked to genes with enriched expression in the brain, but it is unclear how these genes converge into cell-type-specific networks. We built a protein-protein interaction network for 13 ASD-associated genes in human excitatory neurons derived from induced pluripotent stem cells (iPSCs). The network contains newly reported interactions and is enriched for genetic and transcriptional perturbations observed in individuals with ASDs. We leveraged the network data to show that the ASD-linked brain-specific isoform of ANK2 is important for its interactions with synaptic proteins and to characterize a PTEN-AKAP8L interaction that influences neuronal growth. The IGF2BP1-3 complex emerged as a convergent point in the network that may regulate a transcriptional circuit of ASD-associated genes. Our findings showcase cell-type-specific interactomes as a framework to complement genetic and transcriptomic data and illustrate how both individual and convergent interactions can lead to biological insights into ASDs.
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Affiliation(s)
- Greta Pintacuda
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Stem Cell Institute and Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Yu-Han H. Hsu
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Surgery, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Kalliopi Tsafou
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Surgery, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Ka Wan Li
- Department of Molecular and Cellular Neurobiology, CNCR, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Jacqueline M. Martín
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Stem Cell Institute and Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Jackson Riseman
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Stem Cell Institute and Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Julia C. Biagini
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Joshua K.T. Ching
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Daya Mena
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Miguel A. Gonzalez-Lozano
- Department of Molecular and Cellular Neurobiology, CNCR, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Shawn B. Egri
- Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jake Jaffe
- Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - August B. Smit
- Department of Molecular and Cellular Neurobiology, CNCR, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Nadine Fornelos
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Surgery, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Kevin C. Eggan
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Stem Cell Institute and Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Kasper Lage
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Surgery, Massachusetts General Hospital, Boston, MA 02114, USA
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Mental Health Services Copenhagen, 4000 Roskilde, Denmark
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41
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Nong Y, Stoppel DC, Johnson MA, Boillot M, Todorovic J, Shen J, Zhou X, Nadler MJ, Rodriguez C, Huo Y, Nagakura I, Kasper EM, Anderson MP. UBE3A and transsynaptic complex NRXN1-CBLN1-GluD1 in a hypothalamic VMHvl-arcuate feedback circuit regulates aggression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.28.530462. [PMID: 36909588 PMCID: PMC10002692 DOI: 10.1101/2023.02.28.530462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
Abstract
The circuit origins of aggression in autism spectrum disorder remain undefined. Here we report Tac1-expressing glutamatergic neurons in ventrolateral division of ventromedial hypothalamus (VMHvl) drive intermale aggression. Aggression is increased due to increases of Ube3a gene dosage in the VMHvl neurons when modeling autism due to maternal 15q11-13 triplication. Targeted deletion of increased Ube3a copies in VMHvl reverses the elevated aggression adult mice. VMHvl neurons form excitatory synapses onto hypothalamic arcuate nucleus AgRP/NPY neurons through a NRXN1-CBLN1-GluD1 transsynaptic complex and UBE3A impairs this synapse by decreasing Cbln1 gene expression. Exciting AgRP/NPY arcuate neurons leads to feedback inhibition of VMHvl neurons and inhibits aggression. Asymptomatic increases of UBE3A synergize with a heterozygous deficiency of presynaptic Nrxn1 or postsynaptic Grid1 (both ASD genes) to increase aggression. Targeted deletions of Grid1 in arcuate AgRP neurons impairs the VMHvl to AgRP/NPY neuron excitatory synapses while increasing aggression. Chemogenetic/optogenetic activation of arcuate AgRP/NPY neurons inhibits VMHvl neurons and represses aggression. These data reveal that multiple autism genes converge to regulate the VMHvl-arcuate AgRP/NPY glutamatergic synapse. The hypothalamic circuitry implicated by these data suggest impaired excitation of AgRP/NPY feedback inhibitory neurons may explain the increased aggression behavior found in genetic forms of autism.
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Affiliation(s)
- Yi Nong
- Department of Neurology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02115, USA
- Regeneron 777 Old Saw Mill River Road Tarrytown, NY 10591, USA
| | - David C. Stoppel
- Department of Neurology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02115, USA
- Program in Neuroscience, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Mark A. Johnson
- Department of Neurology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02115, USA
| | - Morgane Boillot
- Department of Neurology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02115, USA
| | - Jelena Todorovic
- Department of Neurology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02115, USA
| | - Jason Shen
- Department of Neurology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02115, USA
| | - Xinyu Zhou
- Department of Neurology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02115, USA
| | - Monica J.S. Nadler
- Department of Neurology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02115, USA
| | - Carrie Rodriguez
- Department of Neurology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02115, USA
| | - Yuda Huo
- Department of Neurology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02115, USA
- Regeneron 777 Old Saw Mill River Road Tarrytown, NY 10591, USA
| | - Ikue Nagakura
- Department of Neurology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02115, USA
| | - Ekkehard M. Kasper
- Department of Surgery, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02115, USA
| | - Matthew P. Anderson
- Department of Neurology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02115, USA
- Boston Children’s Hospital Intellectual and Developmental Disabilities Research Center, 300 Longwood Avenue, Boston, MA 02115, USA
- Program in Neuroscience, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
- Regeneron 777 Old Saw Mill River Road Tarrytown, NY 10591, USA
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42
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Pérez-Cano L, Azidane Chenlo S, Sabido-Vera R, Sirci F, Durham L, Guney E. Translating precision medicine for autism spectrum disorder: A pressing need. Drug Discov Today 2023; 28:103486. [PMID: 36623795 DOI: 10.1016/j.drudis.2023.103486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 12/01/2022] [Accepted: 01/03/2023] [Indexed: 01/09/2023]
Abstract
Autism spectrum disorder (ASD) is a heterogenous group of neurodevelopmental disorders (NDDs) with a high unmet medical need. Currently, ASD is diagnosed according to behavior-based criteria that overlook clinical and genomic heterogeneity, thus repeatedly resulting in failed clinical trials. Here, we summarize the scientific evidence pointing to the pressing need to create a precision medicine framework for ASD and other NDDs. We discuss the role of omics and systems biology to characterize more homogeneous disease subtypes with different underlying pathophysiological mechanisms and to determine corresponding tailored treatments. Finally, we provide recent initiatives towards tackling the complexity in NDDs for precision medicine and cost-effective drug discovery.
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Affiliation(s)
- Laura Pérez-Cano
- Discovery and Data Science (DDS) Unit, STALICLA SL, Moll de Barcelona, s/n, Edif Este, 08039 Barcelona, Spain
| | - Sara Azidane Chenlo
- Discovery and Data Science (DDS) Unit, STALICLA SL, Moll de Barcelona, s/n, Edif Este, 08039 Barcelona, Spain
| | - Rubén Sabido-Vera
- Discovery and Data Science (DDS) Unit, STALICLA SL, Moll de Barcelona, s/n, Edif Este, 08039 Barcelona, Spain
| | - Francesco Sirci
- Discovery and Data Science (DDS) Unit, STALICLA SL, Moll de Barcelona, s/n, Edif Este, 08039 Barcelona, Spain
| | - Lynn Durham
- Discovery and Data Science (DDS) Unit, STALICLA SL, Moll de Barcelona, s/n, Edif Este, 08039 Barcelona, Spain; Drug Development Unit (DDU), STALICLA SA, Avenue de Sécheron 15, 1202 Geneva, Switzerland.
| | - Emre Guney
- Discovery and Data Science (DDS) Unit, STALICLA SL, Moll de Barcelona, s/n, Edif Este, 08039 Barcelona, Spain.
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43
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Veller C, Coop G. Interpreting population and family-based genome-wide association studies in the presence of confounding. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.26.530052. [PMID: 36909521 PMCID: PMC10002712 DOI: 10.1101/2023.02.26.530052] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
A central aim of genome-wide association studies (GWASs) is to estimate direct genetic effects: the causal effects on an individual's phenotype of the alleles that they carry. However, estimates of direct effects can be subject to genetic and environmental confounding, and can also absorb the 'indirect' genetic effects of relatives' genotypes. Recently, an important development in controlling for these confounds has been the use of within-family GWASs, which, because of the randomness of Mendelian segregation within pedigrees, are often interpreted as producing unbiased estimates of direct effects. Here, we present a general theoretical analysis of the influence of confounding in standard population-based and within-family GWASs. We show that, contrary to common interpretation, family-based estimates of direct effects can be biased by genetic confounding. In humans, such biases will often be small per-locus, but can be compounded when effect size estimates are used in polygenic scores. We illustrate the influence of genetic confounding on population- and family-based estimates of direct effects using models of assortative mating, population stratification, and stabilizing selection on GWAS traits. We further show how family-based estimates of indirect genetic effects, based on comparisons of parentally transmitted and untransmitted alleles, can suffer substantial genetic confounding. In addition to known biases that can arise in family-based GWASs when interactions between family members are ignored, we show that biases can also arise from gene-by-environment (G×E) interactions when parental genotypes are not distributed identically across interacting environmental and genetic backgrounds. We conclude that, while family-based studies have placed GWAS estimation on a more rigorous footing, they carry subtle issues of interpretation that arise from confounding and interactions.
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Affiliation(s)
- Carl Veller
- Department of Evolution and Ecology, and Center for Population Biology, University of California, Davis, CA 95616
| | - Graham Coop
- Department of Evolution and Ecology, and Center for Population Biology, University of California, Davis, CA 95616
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44
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Tabbaa M, Knoll A, Levitt P. Mouse population genetics phenocopies heterogeneity of human Chd8 haploinsufficiency. Neuron 2023; 111:539-556.e5. [PMID: 36738737 PMCID: PMC9960295 DOI: 10.1016/j.neuron.2023.01.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 11/13/2022] [Accepted: 01/11/2023] [Indexed: 02/05/2023]
Abstract
Preclinical models of neurodevelopmental disorders typically use single inbred mouse strains, which fail to capture the genetic diversity and symptom heterogeneity that is common clinically. We tested whether modeling genetic background diversity in mouse genetic reference panels would recapitulate population and individual differences in responses to a syndromic mutation in the high-confidence autism risk gene, CHD8. We measured clinically relevant phenotypes in >1,000 mice from 33 strains, including brain and body weights and cognition, activity, anxiety, and social behaviors, using 5 behavioral assays: cued fear conditioning, open field tests in dark and bright light, direct social interaction, and social dominance. Trait disruptions mimicked those seen clinically, with robust strain and sex differences. Some strains exhibited large effect-size trait disruptions, sometimes in opposite directions, and-remarkably-others expressed resilience. Therefore, systematically introducing genetic diversity into models of neurodevelopmental disorders provides a better framework for discovering individual differences in symptom etiologies.
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Affiliation(s)
- Manal Tabbaa
- Children's Hospital Los Angeles, The Saban Research Institute, Los Angeles, CA 90027, USA; Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA
| | - Allison Knoll
- Children's Hospital Los Angeles, The Saban Research Institute, Los Angeles, CA 90027, USA; Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA
| | - Pat Levitt
- Children's Hospital Los Angeles, The Saban Research Institute, Los Angeles, CA 90027, USA; Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA.
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45
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Sex-Related Changes in the Clinical, Genetic, Electrophysiological, Connectivity, and Molecular Presentations of ASD: A Comparison between Human and Animal Models of ASD with Reference to Our Data. Int J Mol Sci 2023; 24:ijms24043287. [PMID: 36834699 PMCID: PMC9965966 DOI: 10.3390/ijms24043287] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/28/2023] [Accepted: 02/03/2023] [Indexed: 02/11/2023] Open
Abstract
The etiology of autism spectrum disorder (ASD) is genetic, environmental, and epigenetic. In addition to sex differences in the prevalence of ASD, which is 3-4 times more common in males, there are also distinct clinical, molecular, electrophysiological, and pathophysiological differences between sexes. In human, males with ASD have more externalizing problems (i.e., attention-deficit hyperactivity disorder), more severe communication and social problems, as well as repetitive movements. Females with ASD generally exhibit fewer severe communication problems, less repetitive and stereotyped behavior, but more internalizing problems, such as depression and anxiety. Females need a higher load of genetic changes related to ASD compared to males. There are also sex differences in brain structure, connectivity, and electrophysiology. Genetic or non-genetic experimental animal models of ASD-like behavior, when studied for sex differences, showed some neurobehavioral and electrophysiological differences between male and female animals depending on the specific model. We previously carried out studies on behavioral and molecular differences between male and female mice treated with valproic acid, either prenatally or early postnatally, that exhibited ASD-like behavior and found distinct differences between the sexes, the female mice performing better on tests measuring social interaction and undergoing changes in the expression of more genes in the brain compared to males. Interestingly, co-administration of S-adenosylmethionine alleviated the ASD-like behavioral symptoms and the gene-expression changes to the same extent in both sexes. The mechanisms underlying the sex differences are not yet fully understood.
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46
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Machipisa T, Chishala C, Shaboodien G, Zühlke LJ, Muhamed B, Pandie S, de Vries J, Laing N, Joachim A, Daniels R, Ntsekhe M, Hugo-Hamman CT, Gitura B, Ogendo S, Lwabi P, Okello E, Damasceno A, Novela C, Mocumbi AO, Madeira G, Musuku J, Mtaja A, ElSayed A, Alhassan HH, Bode-Thomas F, Yilgwan C, Amusa G, Nkereuwem E, Mulder N, Ramesar R, Lesosky M, Cordell HJ, Chong M, Keavney B, Paré G, Engel ME. Rationale, Design, and the Baseline Characteristics of the RHDGen (The Genetics of Rheumatic Heart Disease) Network Study†. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2023; 16:e003641. [PMID: 36548480 PMCID: PMC9946164 DOI: 10.1161/circgen.121.003641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 08/30/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND The genetics of rheumatic heart disease (RHDGen) Network was developed to assist the discovery and validation of genetic variations and biomarkers of risk for rheumatic heart disease (RHD) in continental Africans, as a part of the global fight to control and eradicate rheumatic fever/RHD. Thus, we describe the rationale and design of the RHDGen study, comprising participants from 8 African countries. METHODS RHDGen screened potential participants using echocardiography, thereafter enrolling RHD cases and ethnically-matched controls for whom case characteristics were documented. Biological samples were collected for conducting genetic analyses, including a discovery case-control genome-wide association study (GWAS) and a replication trio family study. Additional biological samples were also collected, and processed, for the measurement of biomarker analytes and the biomarker analyses are underway. RESULTS Participants were enrolled into RHDGen between December 2012 and March 2018. For GWAS, 2548 RHD cases and 2261 controls (3301 women [69%]; mean age [SD], 37 [16.3] years) were available. RHD cases were predominantly Black (66%), Admixed (24%), and other ethnicities (10%). Among RHD cases, 34% were asymptomatic, 26% had prior valve surgery, and 23% had atrial fibrillation. The trio family replication arm included 116 RHD trio probands and 232 parents. CONCLUSIONS RHDGen presents a rare opportunity to identify relevant patterns of genetic factors and biomarkers in Africans that may be associated with differential RHD risk. Furthermore, the RHDGen Network provides a platform for further work on fully elucidating the causes and mechanisms associated with RHD susceptibility and development.
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Affiliation(s)
- Tafadzwa Machipisa
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa (T.M., C.C., G.S., L.J.Z., B.M., S.P.; J.d.V., N.L., A.J., R.D., M.N., M.E.E.)
- Department of Medicine, Cape Heart Institute, University of Cape Town, Cape Town, South Africa (T.M., G.S., L.J.Z., B.M., M.E.E.)
- Population Health Research Institute, Hamilton, ON, Canada (T.M., B.M., M.C., G.P.)
- Thrombosis and Atherosclerosis Research Institute, David Braley Cardiac, Vascular and Stroke Research Institute, Hamilton, ON, Canada (T.M., B.M., M.C., G.P.)
- Department of Pathology and Molecular Medicine, Michael G. DeGroote School of Medicine, Hamilton, ON, Canada (T.M., B.M., M.C., G.P.)
| | - Chishala Chishala
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa (T.M., C.C., G.S., L.J.Z., B.M., S.P.; J.d.V., N.L., A.J., R.D., M.N., M.E.E.)
- Division of Cardiology, University of KwaZulu-Natal, Msunduzi, KwaZulu-Natal (C.C.)
| | - Gasnat Shaboodien
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa (T.M., C.C., G.S., L.J.Z., B.M., S.P.; J.d.V., N.L., A.J., R.D., M.N., M.E.E.)
- Department of Medicine, Cape Heart Institute, University of Cape Town, Cape Town, South Africa (T.M., G.S., L.J.Z., B.M., M.E.E.)
| | - Liesl J. Zühlke
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa (T.M., C.C., G.S., L.J.Z., B.M., S.P.; J.d.V., N.L., A.J., R.D., M.N., M.E.E.)
- Department of Medicine, Cape Heart Institute, University of Cape Town, Cape Town, South Africa (T.M., G.S., L.J.Z., B.M., M.E.E.)
- Division of Pediatric Cardiology, Department of Pediatrics and Child Health, Red Cross War Memorial Children’s Hospital, Cape Town, South Africa (L.J.Z.)
- South African Medical Research Council, Extramural Research and Internal Portfolio, Cape Town, South Africa (L.J.Z.)
| | - Babu Muhamed
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa (T.M., C.C., G.S., L.J.Z., B.M., S.P.; J.d.V., N.L., A.J., R.D., M.N., M.E.E.)
- Department of Medicine, Cape Heart Institute, University of Cape Town, Cape Town, South Africa (T.M., G.S., L.J.Z., B.M., M.E.E.)
- Population Health Research Institute, Hamilton, ON, Canada (T.M., B.M., M.C., G.P.)
- Thrombosis and Atherosclerosis Research Institute, David Braley Cardiac, Vascular and Stroke Research Institute, Hamilton, ON, Canada (T.M., B.M., M.C., G.P.)
- Department of Pathology and Molecular Medicine, Michael G. DeGroote School of Medicine, Hamilton, ON, Canada (T.M., B.M., M.C., G.P.)
| | - Shahiemah Pandie
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa (T.M., C.C., G.S., L.J.Z., B.M., S.P.; J.d.V., N.L., A.J., R.D., M.N., M.E.E.)
| | - Jantina de Vries
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa (T.M., C.C., G.S., L.J.Z., B.M., S.P.; J.d.V., N.L., A.J., R.D., M.N., M.E.E.)
| | - Nakita Laing
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa (T.M., C.C., G.S., L.J.Z., B.M., S.P.; J.d.V., N.L., A.J., R.D., M.N., M.E.E.)
| | - Alexia Joachim
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa (T.M., C.C., G.S., L.J.Z., B.M., S.P.; J.d.V., N.L., A.J., R.D., M.N., M.E.E.)
| | - Rezeen Daniels
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa (T.M., C.C., G.S., L.J.Z., B.M., S.P.; J.d.V., N.L., A.J., R.D., M.N., M.E.E.)
| | - Mpiko Ntsekhe
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa (T.M., C.C., G.S., L.J.Z., B.M., S.P.; J.d.V., N.L., A.J., R.D., M.N., M.E.E.)
| | - Christopher T. Hugo-Hamman
- Rheumatic Heart Disease Clinic, Windhoek Central Hospital, Ministry of Health and Social Services, Windhoek, Republic of Namibia (C.T.H.-H.)
| | - Bernard Gitura
- Cardiology Department of Medicine, Kenyatta National Hospital, University of Nairobi, Nairobi, Kenya (B.G.)
| | - Stephen Ogendo
- Uganda Heart Inst, Departments of Adult and Pediatric Cardiology, Kampala, Uganda (S.O.)
| | - Peter Lwabi
- School of Medicine, Maseno Univ, Kenya (P.L., E.O.)
| | - Emmy Okello
- School of Medicine, Maseno Univ, Kenya (P.L., E.O.)
| | - Albertino Damasceno
- Faculty of Medicine, Eduardo Mondlane Univ/Nucleo de Investigaçao, Departamento de Medicina, Hospital Central de Maputo, Maputo, Mozambique (A.D., C.N.)
| | - Celia Novela
- Faculty of Medicine, Eduardo Mondlane Univ/Nucleo de Investigaçao, Departamento de Medicina, Hospital Central de Maputo, Maputo, Mozambique (A.D., C.N.)
| | - Ana O. Mocumbi
- Instituto Nacional de Saúde Ministério da Saúde, Mozambique (A.O.M.)
| | | | - John Musuku
- University Teaching Hospital, Children’s Hospital, University of Zambia, Lusaka, Zambia (J.M., A.M.)
| | - Agnes Mtaja
- University Teaching Hospital, Children’s Hospital, University of Zambia, Lusaka, Zambia (J.M., A.M.)
| | - Ahmed ElSayed
- Department of Cardiothoracic Surgery, Alshaab Teaching Hospital, Alazhari Health Research Centre, Alzaiem Alazhari University, Khartoum, Sudan (A.E., H.H.M.A.)
| | - Huda H.M. Alhassan
- Department of Cardiothoracic Surgery, Alshaab Teaching Hospital, Alazhari Health Research Centre, Alzaiem Alazhari University, Khartoum, Sudan (A.E., H.H.M.A.)
| | - Fidelia Bode-Thomas
- Deptartments of Pediatrics and Medicine, Jos University Teaching Hospital and University of Jos, Jos, Plateau State, Nigeria (F.B.-T., C.Y., G.A., E.N.)
| | - Christopher Yilgwan
- Deptartments of Pediatrics and Medicine, Jos University Teaching Hospital and University of Jos, Jos, Plateau State, Nigeria (F.B.-T., C.Y., G.A., E.N.)
| | - Ganiyu Amusa
- Deptartments of Pediatrics and Medicine, Jos University Teaching Hospital and University of Jos, Jos, Plateau State, Nigeria (F.B.-T., C.Y., G.A., E.N.)
| | - Esin Nkereuwem
- Deptartments of Pediatrics and Medicine, Jos University Teaching Hospital and University of Jos, Jos, Plateau State, Nigeria (F.B.-T., C.Y., G.A., E.N.)
| | - Nicola Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences (N.M.), University of Cape Town, Cape Town, South Africa
| | - Raj Ramesar
- Department of Pathology (R.R.), University of Cape Town, Cape Town, South Africa
| | - Maia Lesosky
- Division of Epidemiology and Biostatistics, School of Public Health and Family Medicine (M.L.), University of Cape Town, Cape Town, South Africa
| | - Heather J. Cordell
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, International Centre for Life, Newcastle upon Tyne, UK (H.J.C.)
| | - Michael Chong
- Population Health Research Institute, Hamilton, ON, Canada (T.M., B.M., M.C., G.P.)
- Thrombosis and Atherosclerosis Research Institute, David Braley Cardiac, Vascular and Stroke Research Institute, Hamilton, ON, Canada (T.M., B.M., M.C., G.P.)
- Department of Pathology and Molecular Medicine, Michael G. DeGroote School of Medicine, Hamilton, ON, Canada (T.M., B.M., M.C., G.P.)
| | - Bernard Keavney
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, UK (B.K.)
- Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, UK (B.K.)
| | - Guillaume Paré
- Population Health Research Institute, Hamilton, ON, Canada (T.M., B.M., M.C., G.P.)
- Thrombosis and Atherosclerosis Research Institute, David Braley Cardiac, Vascular and Stroke Research Institute, Hamilton, ON, Canada (T.M., B.M., M.C., G.P.)
- Department of Pathology and Molecular Medicine, Michael G. DeGroote School of Medicine, Hamilton, ON, Canada (T.M., B.M., M.C., G.P.)
- Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, ON, Canada (G.P.)
| | - Mark E. Engel
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa (T.M., C.C., G.S., L.J.Z., B.M., S.P.; J.d.V., N.L., A.J., R.D., M.N., M.E.E.)
- Department of Medicine, Cape Heart Institute, University of Cape Town, Cape Town, South Africa (T.M., G.S., L.J.Z., B.M., M.E.E.)
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47
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Andreassen OA, Hindley GFL, Frei O, Smeland OB. New insights from the last decade of research in psychiatric genetics: discoveries, challenges and clinical implications. World Psychiatry 2023; 22:4-24. [PMID: 36640404 PMCID: PMC9840515 DOI: 10.1002/wps.21034] [Citation(s) in RCA: 40] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/07/2022] [Indexed: 01/15/2023] Open
Abstract
Psychiatric genetics has made substantial progress in the last decade, providing new insights into the genetic etiology of psychiatric disorders, and paving the way for precision psychiatry, in which individual genetic profiles may be used to personalize risk assessment and inform clinical decision-making. Long recognized to be heritable, recent evidence shows that psychiatric disorders are influenced by thousands of genetic variants acting together. Most of these variants are commonly occurring, meaning that every individual has a genetic risk to each psychiatric disorder, from low to high. A series of large-scale genetic studies have discovered an increasing number of common and rare genetic variants robustly associated with major psychiatric disorders. The most convincing biological interpretation of the genetic findings implicates altered synaptic function in autism spectrum disorder and schizophrenia. However, the mechanistic understanding is still incomplete. In line with their extensive clinical and epidemiological overlap, psychiatric disorders appear to exist on genetic continua and share a large degree of genetic risk with one another. This provides further support to the notion that current psychiatric diagnoses do not represent distinct pathogenic entities, which may inform ongoing attempts to reconceptualize psychiatric nosology. Psychiatric disorders also share genetic influences with a range of behavioral and somatic traits and diseases, including brain structures, cognitive function, immunological phenotypes and cardiovascular disease, suggesting shared genetic etiology of potential clinical importance. Current polygenic risk score tools, which predict individual genetic susceptibility to illness, do not yet provide clinically actionable information. However, their precision is likely to improve in the coming years, and they may eventually become part of clinical practice, stressing the need to educate clinicians and patients about their potential use and misuse. This review discusses key recent insights from psychiatric genetics and their possible clinical applications, and suggests future directions.
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Affiliation(s)
- Ole A Andreassen
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Guy F L Hindley
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Oleksandr Frei
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Centre for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Olav B Smeland
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
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48
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LaPierre N, Fu B, Turnbull S, Eskin E, Sankararaman S. Leveraging family data to design Mendelian Randomization that is provably robust to population stratification. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.05.522936. [PMID: 36711635 PMCID: PMC9881984 DOI: 10.1101/2023.01.05.522936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Mendelian Randomization (MR) has emerged as a powerful approach to leverage genetic instruments to infer causality between pairs of traits in observational studies. However, the results of such studies are susceptible to biases due to weak instruments as well as the confounding effects of population stratification and horizontal pleiotropy. Here, we show that family data can be leveraged to design MR tests that are provably robust to confounding from population stratification, assortative mating, and dynastic effects. We demonstrate in simulations that our approach, MR-Twin, is robust to confounding from population stratification and is not affected by weak instrument bias, while standard MR methods yield inflated false positive rates. We applied MR-Twin to 121 trait pairs in the UK Biobank dataset and found that MR-Twin identifies likely causal trait pairs and does not identify trait pairs that are unlikely to be causal. Our results suggest that confounding from population stratification can lead to false positives for existing MR methods, while MR-Twin is immune to this type of confounding.
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Affiliation(s)
| | - Boyang Fu
- Department of Computer Science, UCLA, Los Angeles CA
| | | | - Eleazar Eskin
- Department of Computer Science, UCLA, Los Angeles CA
- Department of Computational Medicine, UCLA, Los Angeles CA
- Department of Human Genetics, UCLA, Los Angeles CA
| | - Sriram Sankararaman
- Department of Computer Science, UCLA, Los Angeles CA
- Department of Computational Medicine, UCLA, Los Angeles CA
- Department of Human Genetics, UCLA, Los Angeles CA
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49
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Dong L, Wang Y, Wang X, Luo T, Zhou Q, Zhao G, Li B, Xia L, Xia K, Li J. Interactions of genetic risks for autism and the broad autism phenotypes. Front Psychiatry 2023; 14:1110080. [PMID: 37102084 PMCID: PMC10123509 DOI: 10.3389/fpsyt.2023.1110080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 03/07/2023] [Indexed: 04/28/2023] Open
Abstract
Background Common polygenic risk and de novo variants (DNVs) capture a small proportion of autism spectrum disorder (ASD) liability, and ASD phenotypic heterogeneity remains difficult to explain. Integrating multiple genetic factors contribute to clarifying the risk and clinical presentation of ASD. Methods In our study, we investigated the individual and combined effects of polygenic risk, damaging DNVs (including those in ASD risk genes), and sex among 2,591 ASD simplex families in the Simons Simplex Collection. We also explored the interactions among these factors, along with the broad autism phenotypes of ASD probands and their unaffected siblings. Finally, we combined the effects of polygenic risk, damaging DNVs in ASD risk genes, and sex to explain the total liability of ASD phenotypic spectrum. Results Our findings revealed that both polygenic risk and damaging DNVs contribute to an increased risk for ASD, with females exhibiting higher genetic burdens than males. ASD probands that carry damaging DNVs in ASD risk genes showed reduced polygenic risk. The effects of polygenic risk and damaging DNVs on autism broad phenotypes were inconsistent; probands with higher polygenic risk exhibited improvement in some behaviors, such as adaptive/cognitive behaviors, while those with damaging DNVs exhibited more severe phenotypes. Siblings with higher polygenic risk and damaging DNVs tended to have higher scores on broader autism phenotypes. Females exhibited more severe cognitive and behavioral problems compared to males among both ASD probands and siblings. The combination of polygenic risk, damaging DNVs in ASD risk genes, and sex explained 1-4% of the total liability of adaptive/cognitive behavior measurements. Conclusion Our study revealed that the risk for ASD and the autism broad phenotypes likely arises from a combination of common polygenic risk, damaging DNVs (including those in ASD risk genes), and sex.
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Affiliation(s)
- Lijie Dong
- Bioinformatics Center and National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Centre for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Yijing Wang
- Bioinformatics Center and National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Centre for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Xiaomeng Wang
- Bioinformatics Center and National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Centre for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Tengfei Luo
- Bioinformatics Center and National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Centre for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Qiao Zhou
- Bioinformatics Center and National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Guihu Zhao
- Bioinformatics Center and National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Bin Li
- Bioinformatics Center and National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Lu Xia
- Bioinformatics Center and National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Centre for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
- *Correspondence: Lu Xia,
| | - Kun Xia
- Bioinformatics Center and National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Kun Xia,
| | - Jinchen Li
- Bioinformatics Center and National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Centre for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Jinchen Li,
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50
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Oxytocin Exposure in Labor and its Relationship with Cognitive Impairment and the Genetic Architecture of Autism. J Autism Dev Disord 2023; 53:66-79. [PMID: 34982326 DOI: 10.1007/s10803-021-05409-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2021] [Indexed: 02/03/2023]
Abstract
Whether there is a relationship between oxytocin (OXT) use in labor and the risk of autism (ASD), and the nature of such relationship, is unclear. By integrating genetic and clinical data in a sample of 176 ASD participants, we tested the hypothesis that OXT is a marker for abnormal prenatal development which leads to impairments in the process of labor. OXT-exposed ASD had more obstetric complications (P = 0.031), earlier onset of symptoms (P = 0.027), poorer cognitive development (P = 0.011), higher mutation burden across neurodevelopment genes (P = 0.020; OR = 5.33) and lower transmission of polygenic risk for ASD (P = 0.0319), than non-exposed ASD. OXT seems to constitute a risk indicator rather than a risk factor for ASD, which is relevant for diagnostic and genetic counselling.
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